R6: Advanced data management

Data management

Data transformation

tabulation

aggregation

Large datasets

apply

Author

Modesto

Published

August 16, 2023

Modified

December 2, 2024

1 Transform dataframes

When you need to explore, present, analyze, or transform your data, it often requires subdividing, aggregating, or sorting a vector or data frame by one or more variables. The R environment primarily relies on two approaches: Base R and tidyverse libraries (dplyr() & tidyr()). Although these two methods are often viewed as distinct philosophies, they are designed to complement each other(see ref. 8 below).

This lesson provides examples and techniques from Base R because learning Base R offers a wider range of capabilities for different types of data and work environments in the future.

1.1 Sorting and subsetting data

How come? Numeric? Alphabetic? increasing or decreasing order?

There are two main functions in R to order your data, sort() and order(). Let’s see an example using the file coli_genomes_renamed.csv, that we used in the lesson R3.

#load the dataset
coli_genomes <- read.csv(file = "data/coli_genomes_renamed.csv", strip.white = TRUE)

#test sort() & order() in a vector
order(coli_genomes$Year)

 [1] 15  7  8  6  3  2  5 14 16 17 18 20 22  9 10 11 12 13 19 21  1  4

sort(coli_genomes$Year)

 [1] 2005 2006 2006 2007 2008 2010 2011 2011 2012 2012 2012 2012 2012 2013 2013
[16] 2013 2013 2013 2015 2016

sort(coli_genomes$Year, decreasing=TRUE)

 [1] 2016 2015 2013 2013 2013 2013 2013 2012 2012 2012 2012 2012 2011 2011 2010
[16] 2008 2007 2006 2006 2005

order(coli_genomes$Phylogroup)

 [1]  4  5  6  7  8 12 13 18 20 21  3 14 22  2 15 16 17 19  1  9 10 11

sort(coli_genomes$Phylogroup)

 [1] "A"  "A"  "A"  "A"  "A"  "A"  "A"  "A"  "A"  "A"  "B1" "B1" "B1" "C"  "C" 
[16] "C"  "C"  "C"  "D"  "D"  "D"  "D"

As you noticed, the R function order() returns a permutation of the order of the elements of a vector. The output is an index vector, not the vector itself. Also note that if the vector contains any NA values, they will be at the end of the index vector by default.

On the other hand, the function sort() returns returns the vector you pass as input sorted in ascending order by default.

Both functions order the data increasingly, and can be used for numeric or string variables. If you set the decreasing argument to TRUE in a sort() or order(), you will geet the vector of indices in descending order.

You can also use these functions to order a data frame according to a vector. Alternatively, you can also arrange or shuffle a data frame in reverse order.

#order the dataframe by one column, sort or order?
coli_genomes[order(coli_genomes$Year),]

    Strain    Biosample Year  Source Phylogroup Serotype  Clonotype
15 LREC255 SAMN14278630 2005   Avian          C  O78:H19     CH4-27
7  LREC244 SAMN14278619 2006 Porcine          A   O2:H32    CH11-23
8  LREC245 SAMN14278620 2006 Porcine          A  ONT:H45    C11-398
6  LREC243 SAMN14278618 2007 Porcine          A   O9:H37     CH7-31
3  LREC240 SAMN14278615 2008   Human         B1  O76:H30    CH29-38
2  LREC239 SAMN14278614 2010   Human          C O153:H19     CH4-25
5  LREC242 SAMN14278617 2011 Porcine          A  ONT:HNM     CH7-54
14 LREC254 SAMN14278629 2011   Avian         B1 O142:H30     C41-35
16 LREC256 SAMN14278631 2012   Human          C   O8:H19     CH4-54
17 LREC257 SAMN14278632 2012   Human          C   O9:H19     CH4-27
18 LREC258 SAMN14278633 2012   Human          A    O9:H4     CH7-34
20 LREC260 SAMN14278635 2012   Human          A  ONT:H33    CH11-54
22 LREC262 SAMN14278637 2012   Human         B1  O66:H10     CH4-32
9  LREC249 SAMN14278624 2013   Human          D O145:H28   CH23-331
10 LREC250 SAMN14278625 2013   Human          D O145:H28   CH23-331
11 LREC251 SAMN14278626 2013   Human          D O145:H28   CH23-331
12 LREC252 SAMN14278627 2013   Human          A  ONT:H37     C11-54
13 LREC253 SAMN14278628 2013   Avian          A  ONT:H19    CH94-23
19 LREC259 SAMN14278634 2015   Human          C   O9:H19 CH4like-27
21 LREC261 SAMN14278636 2016   Human          A  O98:H26    CH27-23
1  LREC237 SAMN14278613   NA   Human          D  ONT:H28   CH23-331
4  LREC241 SAMN14278616   NA   Human          A  O78:H11    CH11-41
   Sequence.Type VF Plasmids kmer Contigs    N50 longest.contig..bp.
15          ST88 11        4  113     108 405376             1190696
7           ST10  4        7  115     277  89185              281444
8        ST10888  2        7  115     203  94368              280268
6         ST3011  7        3   93     158 106897              369508
3          ST156 10        2   89     114 270767              738861
2           ST88 14        3  117     159 323172              760527
5          ST746  5        9   89     320  45936              128053
14         ST359  9        4  113     102 240847              460510
16          ST88 14        2  113     108 281822             1140163
17          ST88 14        4   91     224 140521              284241
18          ST46  8        4   85     204  86565              300086
20          ST10  2        5  117     120 228491              576949
22        ST1049  4        2  113      94 325747              822206
9           ST32 22        1  115     376 200150              424527
10         ST137 22        3  111     205 281589              617142
11          ST32 20        1  113     206 182651              412836
12          ST48  1        0  113     140 105396              272304
13         ST347  2        0  117     134 110661              497785
19       ST10890 13        3  113     171 326962              749412
21        ST8233  2        4   89     114 187945              537848
1          ST524 18        3  117     223 272287              662555
4           ST48  5        3  117     212 112160              285056
   Assembly_length contigs1kb average_contig
15         5196698         38       48117.57
7          5406295        155       19517.31
8          4796593        114       23628.54
6          4638334         93       29356.54
3          4875343         47       42766.17
2          5415613         57       34060.46
5          4858138        212       15181.68
14         4992565         42       48946.72
16         5252065         43       48630.23
17         5085107        110       22701.37
18         4915667        121       24096.41
20         4881205         48       40676.71
22         4839344         32       51482.38
9          5389075        131       14332.65
10         5340478         78       26051.11
11         5276782         95       25615.45
12         4507328         78       32195.20
13         4664768         77       34811.70
19         5200701         77       30413.46
21         4821342         53       42292.47
1          5341632         74       23953.51
4          5167401        101       24374.53

coli_genomes[sort(coli_genomes$Year),] #what happened?

      Strain Biosample Year Source Phylogroup Serotype Clonotype Sequence.Type
NA      <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.1    <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.2    <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.3    <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.4    <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.5    <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.6    <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.7    <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.8    <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.9    <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.10   <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.11   <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.12   <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.13   <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.14   <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.15   <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.16   <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.17   <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.18   <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
NA.19   <NA>      <NA>   NA   <NA>       <NA>     <NA>      <NA>          <NA>
      VF Plasmids kmer Contigs N50 longest.contig..bp. Assembly_length
NA    NA       NA   NA      NA  NA                  NA              NA
NA.1  NA       NA   NA      NA  NA                  NA              NA
NA.2  NA       NA   NA      NA  NA                  NA              NA
NA.3  NA       NA   NA      NA  NA                  NA              NA
NA.4  NA       NA   NA      NA  NA                  NA              NA
NA.5  NA       NA   NA      NA  NA                  NA              NA
NA.6  NA       NA   NA      NA  NA                  NA              NA
NA.7  NA       NA   NA      NA  NA                  NA              NA
NA.8  NA       NA   NA      NA  NA                  NA              NA
NA.9  NA       NA   NA      NA  NA                  NA              NA
NA.10 NA       NA   NA      NA  NA                  NA              NA
NA.11 NA       NA   NA      NA  NA                  NA              NA
NA.12 NA       NA   NA      NA  NA                  NA              NA
NA.13 NA       NA   NA      NA  NA                  NA              NA
NA.14 NA       NA   NA      NA  NA                  NA              NA
NA.15 NA       NA   NA      NA  NA                  NA              NA
NA.16 NA       NA   NA      NA  NA                  NA              NA
NA.17 NA       NA   NA      NA  NA                  NA              NA
NA.18 NA       NA   NA      NA  NA                  NA              NA
NA.19 NA       NA   NA      NA  NA                  NA              NA
      contigs1kb average_contig
NA            NA             NA
NA.1          NA             NA
NA.2          NA             NA
NA.3          NA             NA
NA.4          NA             NA
NA.5          NA             NA
NA.6          NA             NA
NA.7          NA             NA
NA.8          NA             NA
NA.9          NA             NA
NA.10         NA             NA
NA.11         NA             NA
NA.12         NA             NA
NA.13         NA             NA
NA.14         NA             NA
NA.15         NA             NA
NA.16         NA             NA
NA.17         NA             NA
NA.18         NA             NA
NA.19         NA             NA

# Random order of rows with sample 
coli_genomes[sample(nrow(coli_genomes), replace = FALSE), ]

    Strain    Biosample Year  Source Phylogroup Serotype  Clonotype
21 LREC261 SAMN14278636 2016   Human          A  O98:H26    CH27-23
2  LREC239 SAMN14278614 2010   Human          C O153:H19     CH4-25
22 LREC262 SAMN14278637 2012   Human         B1  O66:H10     CH4-32
12 LREC252 SAMN14278627 2013   Human          A  ONT:H37     C11-54
7  LREC244 SAMN14278619 2006 Porcine          A   O2:H32    CH11-23
14 LREC254 SAMN14278629 2011   Avian         B1 O142:H30     C41-35
15 LREC255 SAMN14278630 2005   Avian          C  O78:H19     CH4-27
18 LREC258 SAMN14278633 2012   Human          A    O9:H4     CH7-34
3  LREC240 SAMN14278615 2008   Human         B1  O76:H30    CH29-38
20 LREC260 SAMN14278635 2012   Human          A  ONT:H33    CH11-54
16 LREC256 SAMN14278631 2012   Human          C   O8:H19     CH4-54
1  LREC237 SAMN14278613   NA   Human          D  ONT:H28   CH23-331
11 LREC251 SAMN14278626 2013   Human          D O145:H28   CH23-331
6  LREC243 SAMN14278618 2007 Porcine          A   O9:H37     CH7-31
13 LREC253 SAMN14278628 2013   Avian          A  ONT:H19    CH94-23
4  LREC241 SAMN14278616   NA   Human          A  O78:H11    CH11-41
9  LREC249 SAMN14278624 2013   Human          D O145:H28   CH23-331
8  LREC245 SAMN14278620 2006 Porcine          A  ONT:H45    C11-398
19 LREC259 SAMN14278634 2015   Human          C   O9:H19 CH4like-27
17 LREC257 SAMN14278632 2012   Human          C   O9:H19     CH4-27
10 LREC250 SAMN14278625 2013   Human          D O145:H28   CH23-331
5  LREC242 SAMN14278617 2011 Porcine          A  ONT:HNM     CH7-54
   Sequence.Type VF Plasmids kmer Contigs    N50 longest.contig..bp.
21        ST8233  2        4   89     114 187945              537848
2           ST88 14        3  117     159 323172              760527
22        ST1049  4        2  113      94 325747              822206
12          ST48  1        0  113     140 105396              272304
7           ST10  4        7  115     277  89185              281444
14         ST359  9        4  113     102 240847              460510
15          ST88 11        4  113     108 405376             1190696
18          ST46  8        4   85     204  86565              300086
3          ST156 10        2   89     114 270767              738861
20          ST10  2        5  117     120 228491              576949
16          ST88 14        2  113     108 281822             1140163
1          ST524 18        3  117     223 272287              662555
11          ST32 20        1  113     206 182651              412836
6         ST3011  7        3   93     158 106897              369508
13         ST347  2        0  117     134 110661              497785
4           ST48  5        3  117     212 112160              285056
9           ST32 22        1  115     376 200150              424527
8        ST10888  2        7  115     203  94368              280268
19       ST10890 13        3  113     171 326962              749412
17          ST88 14        4   91     224 140521              284241
10         ST137 22        3  111     205 281589              617142
5          ST746  5        9   89     320  45936              128053
   Assembly_length contigs1kb average_contig
21         4821342         53       42292.47
2          5415613         57       34060.46
22         4839344         32       51482.38
12         4507328         78       32195.20
7          5406295        155       19517.31
14         4992565         42       48946.72
15         5196698         38       48117.57
18         4915667        121       24096.41
3          4875343         47       42766.17
20         4881205         48       40676.71
16         5252065         43       48630.23
1          5341632         74       23953.51
11         5276782         95       25615.45
6          4638334         93       29356.54
13         4664768         77       34811.70
4          5167401        101       24374.53
9          5389075        131       14332.65
8          4796593        114       23628.54
19         5200701         77       30413.46
17         5085107        110       22701.37
10         5340478         78       26051.11
5          4858138        212       15181.68

# Reverse order of rows
coli_genomes[nrow(coli_genomes):1, ]

    Strain    Biosample Year  Source Phylogroup Serotype  Clonotype
22 LREC262 SAMN14278637 2012   Human         B1  O66:H10     CH4-32
21 LREC261 SAMN14278636 2016   Human          A  O98:H26    CH27-23
20 LREC260 SAMN14278635 2012   Human          A  ONT:H33    CH11-54
19 LREC259 SAMN14278634 2015   Human          C   O9:H19 CH4like-27
18 LREC258 SAMN14278633 2012   Human          A    O9:H4     CH7-34
17 LREC257 SAMN14278632 2012   Human          C   O9:H19     CH4-27
16 LREC256 SAMN14278631 2012   Human          C   O8:H19     CH4-54
15 LREC255 SAMN14278630 2005   Avian          C  O78:H19     CH4-27
14 LREC254 SAMN14278629 2011   Avian         B1 O142:H30     C41-35
13 LREC253 SAMN14278628 2013   Avian          A  ONT:H19    CH94-23
12 LREC252 SAMN14278627 2013   Human          A  ONT:H37     C11-54
11 LREC251 SAMN14278626 2013   Human          D O145:H28   CH23-331
10 LREC250 SAMN14278625 2013   Human          D O145:H28   CH23-331
9  LREC249 SAMN14278624 2013   Human          D O145:H28   CH23-331
8  LREC245 SAMN14278620 2006 Porcine          A  ONT:H45    C11-398
7  LREC244 SAMN14278619 2006 Porcine          A   O2:H32    CH11-23
6  LREC243 SAMN14278618 2007 Porcine          A   O9:H37     CH7-31
5  LREC242 SAMN14278617 2011 Porcine          A  ONT:HNM     CH7-54
4  LREC241 SAMN14278616   NA   Human          A  O78:H11    CH11-41
3  LREC240 SAMN14278615 2008   Human         B1  O76:H30    CH29-38
2  LREC239 SAMN14278614 2010   Human          C O153:H19     CH4-25
1  LREC237 SAMN14278613   NA   Human          D  ONT:H28   CH23-331
   Sequence.Type VF Plasmids kmer Contigs    N50 longest.contig..bp.
22        ST1049  4        2  113      94 325747              822206
21        ST8233  2        4   89     114 187945              537848
20          ST10  2        5  117     120 228491              576949
19       ST10890 13        3  113     171 326962              749412
18          ST46  8        4   85     204  86565              300086
17          ST88 14        4   91     224 140521              284241
16          ST88 14        2  113     108 281822             1140163
15          ST88 11        4  113     108 405376             1190696
14         ST359  9        4  113     102 240847              460510
13         ST347  2        0  117     134 110661              497785
12          ST48  1        0  113     140 105396              272304
11          ST32 20        1  113     206 182651              412836
10         ST137 22        3  111     205 281589              617142
9           ST32 22        1  115     376 200150              424527
8        ST10888  2        7  115     203  94368              280268
7           ST10  4        7  115     277  89185              281444
6         ST3011  7        3   93     158 106897              369508
5          ST746  5        9   89     320  45936              128053
4           ST48  5        3  117     212 112160              285056
3          ST156 10        2   89     114 270767              738861
2           ST88 14        3  117     159 323172              760527
1          ST524 18        3  117     223 272287              662555
   Assembly_length contigs1kb average_contig
22         4839344         32       51482.38
21         4821342         53       42292.47
20         4881205         48       40676.71
19         5200701         77       30413.46
18         4915667        121       24096.41
17         5085107        110       22701.37
16         5252065         43       48630.23
15         5196698         38       48117.57
14         4992565         42       48946.72
13         4664768         77       34811.70
12         4507328         78       32195.20
11         5276782         95       25615.45
10         5340478         78       26051.11
9          5389075        131       14332.65
8          4796593        114       23628.54
7          5406295        155       19517.31
6          4638334         93       29356.54
5          4858138        212       15181.68
4          5167401        101       24374.53
3          4875343         47       42766.17
2          5415613         57       34060.46
1          5341632         74       23953.51

Now imagine you have a large data set and want to subdivide only some cases (=rows). You already know some ways to do this, but in the following example we will test the function subset(), which is very handy when you want to extract the cases that satisfy multiple conditions.

Imagine that for a new project we want to select the strains with better genome design quality or from a subset. We will keep strains from Phylogroup A, with an assembly N50 > 150,000 bp and less than 100 contigs >= 1 kb.

#option 1: multi-step
selection<-coli_genomes[coli_genomes$contigs1kb<100,]
selection<-selection[selection$N50>150000,]
selection<-selection[selection$Phylogroup=='A',]

#option 2:  which statements 
selection2<-coli_genomes[which(coli_genomes$contigs1kb<100 & coli_genomes$N50>150000 & coli_genomes$Phylogroup=='A'),]

#option 2b:with attach(dataframe) you avoid repeat the name of the dataframe
attach(coli_genomes)
selection2 <- coli_genomes[which(contigs1kb<100 & N50>150000 & Phylogroup=='A'),]
detach(coli_genomes) #detach dataframe

#option 3: subset() is a straightforward way to do that trick 
selection3<-subset(coli_genomes, subset= contigs1kb<100 & N50>150000 & Phylogroup=='A')

If you want to make sure that the three methods give the same output, you can check the data frame, or check the dimensions or structure with dim() or str(), but this is difficult with large data sets with hundreds or thousands of cases (see below). The function all.equal() does this task for you.

#Are they the same?
all.equal(selection,selection2)

[1] TRUE

all.equal(selection,selection3)

[1] TRUE

1.2 Combining dataframes

If you work with a lot of data or get different batches of related data frames, you may have multiple tables and want to combine them in different ways. An easy way is to use cbind() or rbind() if you have the same number of rows and columns. A more practical way is to use the merge() function. Look and test the following examples using the coli_genomes data frame and a new table named colis3.csv

colis <- read.csv2(file = 'data/colis3.csv')
#rbind() and cbind()
rbind(coli_genomes,colis) #did it work? why??

Error in rbind(deparse.level, ...): numbers of columns of arguments do not match

cbind(coli_genomes, colis)

Error in data.frame(..., check.names = FALSE): arguments imply differing number of rows: 22, 27

#merge()
merge<-merge(coli_genomes,colis) #inner join
str(merge)

'data.frame':   22 obs. of  24 variables:
 $ Strain             : chr  "LREC237" "LREC239" "LREC240" "LREC241" ...
 $ Year               : int  NA 2010 2008 NA 2011 2007 2006 2006 2013 2013 ...
 $ Biosample          : chr  "SAMN14278613" "SAMN14278614" "SAMN14278615" "SAMN14278616" ...
 $ Source             : chr  "Human" "Human" "Human" "Human" ...
 $ Phylogroup         : chr  "D" "C" "B1" "A" ...
 $ Serotype           : chr  "ONT:H28" "O153:H19" "O76:H30" "O78:H11" ...
 $ Clonotype          : chr  "CH23-331" "CH4-25" "CH29-38" "CH11-41" ...
 $ Sequence.Type      : chr  "ST524" "ST88" "ST156" "ST48" ...
 $ VF                 : int  18 14 10 5 5 7 4 2 22 22 ...
 $ Plasmids           : int  3 3 2 3 9 3 7 7 1 3 ...
 $ kmer               : int  117 117 89 117 89 93 115 115 115 111 ...
 $ Contigs            : int  223 159 114 212 320 158 277 203 376 205 ...
 $ N50                : int  272287 323172 270767 112160 45936 106897 89185 94368 200150 281589 ...
 $ longest.contig..bp.: int  662555 760527 738861 285056 128053 369508 281444 280268 424527 617142 ...
 $ Assembly_length    : int  5341632 5415613 4875343 5167401 4858138 4638334 5406295 4796593 5389075 5340478 ...
 $ contigs1kb         : int  74 57 47 101 212 93 155 114 131 78 ...
 $ average_contig     : num  23954 34060 42766 24375 15182 ...
 $ X                  : int  1 2 3 4 5 6 7 8 12 13 ...
 $ CRISPR             : int  9 12 5 9 9 10 7 10 7 7 ...
 $ Cas                : chr  "[CAS-TypeIE (n=1),]" "[CAS-TypeIE (n=1),]" "[CAS-TypeIE (n=1),]" "[CAS (n=1),, CAS (n=1),, CAS (n=1),, CAS-TypeIE (n=1),]" ...
 $ AMR                : int  2 2 5 2 4 2 2 4 2 2 ...
 $ Vir                : int  20 12 10 3 4 6 7 4 26 21 ...
 $ Integron           : int  0 0 0 0 0 0 0 0 0 0 ...
 $ seqs               : chr  "2020-07-24" "2019-02-27" "2018-03-08" "2020-10-12" ...

merge1<-merge(coli_genomes,colis, by="Strain")
str(merge1)

'data.frame':   22 obs. of  25 variables:
 $ Strain             : chr  "LREC237" "LREC239" "LREC240" "LREC241" ...
 $ Biosample          : chr  "SAMN14278613" "SAMN14278614" "SAMN14278615" "SAMN14278616" ...
 $ Year.x             : int  NA 2010 2008 NA 2011 2007 2006 2006 2013 2013 ...
 $ Source             : chr  "Human" "Human" "Human" "Human" ...
 $ Phylogroup         : chr  "D" "C" "B1" "A" ...
 $ Serotype           : chr  "ONT:H28" "O153:H19" "O76:H30" "O78:H11" ...
 $ Clonotype          : chr  "CH23-331" "CH4-25" "CH29-38" "CH11-41" ...
 $ Sequence.Type      : chr  "ST524" "ST88" "ST156" "ST48" ...
 $ VF                 : int  18 14 10 5 5 7 4 2 22 22 ...
 $ Plasmids           : int  3 3 2 3 9 3 7 7 1 3 ...
 $ kmer               : int  117 117 89 117 89 93 115 115 115 111 ...
 $ Contigs            : int  223 159 114 212 320 158 277 203 376 205 ...
 $ N50                : int  272287 323172 270767 112160 45936 106897 89185 94368 200150 281589 ...
 $ longest.contig..bp.: int  662555 760527 738861 285056 128053 369508 281444 280268 424527 617142 ...
 $ Assembly_length    : int  5341632 5415613 4875343 5167401 4858138 4638334 5406295 4796593 5389075 5340478 ...
 $ contigs1kb         : int  74 57 47 101 212 93 155 114 131 78 ...
 $ average_contig     : num  23954 34060 42766 24375 15182 ...
 $ X                  : int  1 2 3 4 5 6 7 8 12 13 ...
 $ Year.y             : int  NA 2010 2008 NA 2011 2007 2006 2006 2013 2013 ...
 $ CRISPR             : int  9 12 5 9 9 10 7 10 7 7 ...
 $ Cas                : chr  "[CAS-TypeIE (n=1),]" "[CAS-TypeIE (n=1),]" "[CAS-TypeIE (n=1),]" "[CAS (n=1),, CAS (n=1),, CAS (n=1),, CAS-TypeIE (n=1),]" ...
 $ AMR                : int  2 2 5 2 4 2 2 4 2 2 ...
 $ Vir                : int  20 12 10 3 4 6 7 4 26 21 ...
 $ Integron           : int  0 0 0 0 0 0 0 0 0 0 ...
 $ seqs               : chr  "2020-07-24" "2019-02-27" "2018-03-08" "2020-10-12" ...

merge2<-merge(coli_genomes,colis, by="Year")
str(merge2)

'data.frame':   81 obs. of  25 variables:
 $ Year               : int  2005 2006 2006 2006 2006 2007 2008 2010 2010 2011 ...
 $ Strain.x           : chr  "LREC255" "LREC244" "LREC244" "LREC245" ...
 $ Biosample          : chr  "SAMN14278630" "SAMN14278619" "SAMN14278619" "SAMN14278620" ...
 $ Source             : chr  "Avian" "Porcine" "Porcine" "Porcine" ...
 $ Phylogroup         : chr  "C" "A" "A" "A" ...
 $ Serotype           : chr  "O78:H19" "O2:H32" "O2:H32" "ONT:H45" ...
 $ Clonotype          : chr  "CH4-27" "CH11-23" "CH11-23" "C11-398" ...
 $ Sequence.Type      : chr  "ST88" "ST10" "ST10" "ST10888" ...
 $ VF                 : int  11 4 4 2 2 7 10 14 14 5 ...
 $ Plasmids           : int  4 7 7 7 7 3 2 3 3 9 ...
 $ kmer               : int  113 115 115 115 115 93 89 117 117 89 ...
 $ Contigs            : int  108 277 277 203 203 158 114 159 159 320 ...
 $ N50                : int  405376 89185 89185 94368 94368 106897 270767 323172 323172 45936 ...
 $ longest.contig..bp.: int  1190696 281444 281444 280268 280268 369508 738861 760527 760527 128053 ...
 $ Assembly_length    : int  5196698 5406295 5406295 4796593 4796593 4638334 4875343 5415613 5415613 4858138 ...
 $ contigs1kb         : int  38 155 155 114 114 93 47 57 57 212 ...
 $ average_contig     : num  48118 19517 19517 23629 23629 ...
 $ X                  : int  18 8 7 8 7 6 3 9 2 5 ...
 $ Strain.y           : chr  "LREC255" "LREC245" "LREC244" "LREC245" ...
 $ CRISPR             : int  10 10 7 10 7 10 5 6 12 9 ...
 $ Cas                : chr  "[CAS-TypeIE (n=1),, CAS-TypeID (n=1),]" "[CAS (n=1),, CAS (n=1),, CAS-TypeIE (n=1),, CAS (n=1),, CAS (n=1),]" "[CAS (n=1),, CAS (n=1),, CAS (n=1),]" "[CAS (n=1),, CAS (n=1),, CAS-TypeIE (n=1),, CAS (n=1),, CAS (n=1),]" ...
 $ AMR                : int  NA 4 2 4 2 2 5 4 2 4 ...
 $ Vir                : int  7 4 7 4 7 6 10 8 12 4 ...
 $ Integron           : int  0 0 0 0 0 0 0 0 0 0 ...
 $ seqs               : chr  "2020-08-03" "2019-12-30" "2018-08-14" "2019-12-30" ...

merge3<-merge(coli_genomes,colis, by=c("Strain","Year"))
str(merge3)

'data.frame':   22 obs. of  24 variables:
 $ Strain             : chr  "LREC237" "LREC239" "LREC240" "LREC241" ...
 $ Year               : int  NA 2010 2008 NA 2011 2007 2006 2006 2013 2013 ...
 $ Biosample          : chr  "SAMN14278613" "SAMN14278614" "SAMN14278615" "SAMN14278616" ...
 $ Source             : chr  "Human" "Human" "Human" "Human" ...
 $ Phylogroup         : chr  "D" "C" "B1" "A" ...
 $ Serotype           : chr  "ONT:H28" "O153:H19" "O76:H30" "O78:H11" ...
 $ Clonotype          : chr  "CH23-331" "CH4-25" "CH29-38" "CH11-41" ...
 $ Sequence.Type      : chr  "ST524" "ST88" "ST156" "ST48" ...
 $ VF                 : int  18 14 10 5 5 7 4 2 22 22 ...
 $ Plasmids           : int  3 3 2 3 9 3 7 7 1 3 ...
 $ kmer               : int  117 117 89 117 89 93 115 115 115 111 ...
 $ Contigs            : int  223 159 114 212 320 158 277 203 376 205 ...
 $ N50                : int  272287 323172 270767 112160 45936 106897 89185 94368 200150 281589 ...
 $ longest.contig..bp.: int  662555 760527 738861 285056 128053 369508 281444 280268 424527 617142 ...
 $ Assembly_length    : int  5341632 5415613 4875343 5167401 4858138 4638334 5406295 4796593 5389075 5340478 ...
 $ contigs1kb         : int  74 57 47 101 212 93 155 114 131 78 ...
 $ average_contig     : num  23954 34060 42766 24375 15182 ...
 $ X                  : int  1 2 3 4 5 6 7 8 12 13 ...
 $ CRISPR             : int  9 12 5 9 9 10 7 10 7 7 ...
 $ Cas                : chr  "[CAS-TypeIE (n=1),]" "[CAS-TypeIE (n=1),]" "[CAS-TypeIE (n=1),]" "[CAS (n=1),, CAS (n=1),, CAS (n=1),, CAS-TypeIE (n=1),]" ...
 $ AMR                : int  2 2 5 2 4 2 2 4 2 2 ...
 $ Vir                : int  20 12 10 3 4 6 7 4 26 21 ...
 $ Integron           : int  0 0 0 0 0 0 0 0 0 0 ...
 $ seqs               : chr  "2020-07-24" "2019-02-27" "2018-03-08" "2020-10-12" ...

merge4<-merge(coli_genomes,colis, all=TRUE) #outer join
str(merge4)

'data.frame':   27 obs. of  24 variables:
 $ Strain             : chr  "LREC237" "LREC239" "LREC240" "LREC241" ...
 $ Year               : int  NA 2010 2008 NA 2011 2007 2006 2006 2010 2013 ...
 $ Biosample          : chr  "SAMN14278613" "SAMN14278614" "SAMN14278615" "SAMN14278616" ...
 $ Source             : chr  "Human" "Human" "Human" "Human" ...
 $ Phylogroup         : chr  "D" "C" "B1" "A" ...
 $ Serotype           : chr  "ONT:H28" "O153:H19" "O76:H30" "O78:H11" ...
 $ Clonotype          : chr  "CH23-331" "CH4-25" "CH29-38" "CH11-41" ...
 $ Sequence.Type      : chr  "ST524" "ST88" "ST156" "ST48" ...
 $ VF                 : int  18 14 10 5 5 7 4 2 NA NA ...
 $ Plasmids           : int  3 3 2 3 9 3 7 7 NA NA ...
 $ kmer               : int  117 117 89 117 89 93 115 115 NA NA ...
 $ Contigs            : int  223 159 114 212 320 158 277 203 NA NA ...
 $ N50                : int  272287 323172 270767 112160 45936 106897 89185 94368 NA NA ...
 $ longest.contig..bp.: int  662555 760527 738861 285056 128053 369508 281444 280268 NA NA ...
 $ Assembly_length    : int  5341632 5415613 4875343 5167401 4858138 4638334 5406295 4796593 NA NA ...
 $ contigs1kb         : int  74 57 47 101 212 93 155 114 NA NA ...
 $ average_contig     : num  23954 34060 42766 24375 15182 ...
 $ X                  : int  1 2 3 4 5 6 7 8 9 10 ...
 $ CRISPR             : int  9 12 5 9 9 10 7 10 6 8 ...
 $ Cas                : chr  "[CAS-TypeIE (n=1),]" "[CAS-TypeIE (n=1),]" "[CAS-TypeIE (n=1),]" "[CAS (n=1),, CAS (n=1),, CAS (n=1),, CAS-TypeIE (n=1),]" ...
 $ AMR                : int  2 2 5 2 4 2 2 4 4 2 ...
 $ Vir                : int  20 12 10 3 4 6 7 4 8 23 ...
 $ Integron           : int  0 0 0 0 0 0 0 0 0 0 ...
 $ seqs               : chr  "2020-07-24" "2019-02-27" "2018-03-08" "2020-10-12" ...

merge5<-merge(coli_genomes,colis, all.x=TRUE)
str(merge5)

'data.frame':   22 obs. of  24 variables:
 $ Strain             : chr  "LREC237" "LREC239" "LREC240" "LREC241" ...
 $ Year               : int  NA 2010 2008 NA 2011 2007 2006 2006 2013 2013 ...
 $ Biosample          : chr  "SAMN14278613" "SAMN14278614" "SAMN14278615" "SAMN14278616" ...
 $ Source             : chr  "Human" "Human" "Human" "Human" ...
 $ Phylogroup         : chr  "D" "C" "B1" "A" ...
 $ Serotype           : chr  "ONT:H28" "O153:H19" "O76:H30" "O78:H11" ...
 $ Clonotype          : chr  "CH23-331" "CH4-25" "CH29-38" "CH11-41" ...
 $ Sequence.Type      : chr  "ST524" "ST88" "ST156" "ST48" ...
 $ VF                 : int  18 14 10 5 5 7 4 2 22 22 ...
 $ Plasmids           : int  3 3 2 3 9 3 7 7 1 3 ...
 $ kmer               : int  117 117 89 117 89 93 115 115 115 111 ...
 $ Contigs            : int  223 159 114 212 320 158 277 203 376 205 ...
 $ N50                : int  272287 323172 270767 112160 45936 106897 89185 94368 200150 281589 ...
 $ longest.contig..bp.: int  662555 760527 738861 285056 128053 369508 281444 280268 424527 617142 ...
 $ Assembly_length    : int  5341632 5415613 4875343 5167401 4858138 4638334 5406295 4796593 5389075 5340478 ...
 $ contigs1kb         : int  74 57 47 101 212 93 155 114 131 78 ...
 $ average_contig     : num  23954 34060 42766 24375 15182 ...
 $ X                  : int  1 2 3 4 5 6 7 8 12 13 ...
 $ CRISPR             : int  9 12 5 9 9 10 7 10 7 7 ...
 $ Cas                : chr  "[CAS-TypeIE (n=1),]" "[CAS-TypeIE (n=1),]" "[CAS-TypeIE (n=1),]" "[CAS (n=1),, CAS (n=1),, CAS (n=1),, CAS-TypeIE (n=1),]" ...
 $ AMR                : int  2 2 5 2 4 2 2 4 2 2 ...
 $ Vir                : int  20 12 10 3 4 6 7 4 26 21 ...
 $ Integron           : int  0 0 0 0 0 0 0 0 0 0 ...
 $ seqs               : chr  "2020-07-24" "2019-02-27" "2018-03-08" "2020-10-12" ...

merge6<-merge(coli_genomes,colis, all.y=TRUE)
str(merge6)

'data.frame':   27 obs. of  24 variables:
 $ Strain             : chr  "LREC237" "LREC239" "LREC240" "LREC241" ...
 $ Year               : int  NA 2010 2008 NA 2011 2007 2006 2006 2010 2013 ...
 $ Biosample          : chr  "SAMN14278613" "SAMN14278614" "SAMN14278615" "SAMN14278616" ...
 $ Source             : chr  "Human" "Human" "Human" "Human" ...
 $ Phylogroup         : chr  "D" "C" "B1" "A" ...
 $ Serotype           : chr  "ONT:H28" "O153:H19" "O76:H30" "O78:H11" ...
 $ Clonotype          : chr  "CH23-331" "CH4-25" "CH29-38" "CH11-41" ...
 $ Sequence.Type      : chr  "ST524" "ST88" "ST156" "ST48" ...
 $ VF                 : int  18 14 10 5 5 7 4 2 NA NA ...
 $ Plasmids           : int  3 3 2 3 9 3 7 7 NA NA ...
 $ kmer               : int  117 117 89 117 89 93 115 115 NA NA ...
 $ Contigs            : int  223 159 114 212 320 158 277 203 NA NA ...
 $ N50                : int  272287 323172 270767 112160 45936 106897 89185 94368 NA NA ...
 $ longest.contig..bp.: int  662555 760527 738861 285056 128053 369508 281444 280268 NA NA ...
 $ Assembly_length    : int  5341632 5415613 4875343 5167401 4858138 4638334 5406295 4796593 NA NA ...
 $ contigs1kb         : int  74 57 47 101 212 93 155 114 NA NA ...
 $ average_contig     : num  23954 34060 42766 24375 15182 ...
 $ X                  : int  1 2 3 4 5 6 7 8 9 10 ...
 $ CRISPR             : int  9 12 5 9 9 10 7 10 6 8 ...
 $ Cas                : chr  "[CAS-TypeIE (n=1),]" "[CAS-TypeIE (n=1),]" "[CAS-TypeIE (n=1),]" "[CAS (n=1),, CAS (n=1),, CAS (n=1),, CAS-TypeIE (n=1),]" ...
 $ AMR                : int  2 2 5 2 4 2 2 4 4 2 ...
 $ Vir                : int  20 12 10 3 4 6 7 4 8 23 ...
 $ Integron           : int  0 0 0 0 0 0 0 0 0 0 ...
 $ seqs               : chr  "2020-07-24" "2019-02-27" "2018-03-08" "2020-10-12" ...

merge7<-merge(coli_genomes,colis, by=NULL)
str(merge7)

'data.frame':   594 obs. of  26 variables:
 $ Strain.x           : chr  "LREC237" "LREC239" "LREC240" "LREC241" ...
 $ Biosample          : chr  "SAMN14278613" "SAMN14278614" "SAMN14278615" "SAMN14278616" ...
 $ Year.x             : int  NA 2010 2008 NA 2011 2007 2006 2006 2013 2013 ...
 $ Source             : chr  "Human" "Human" "Human" "Human" ...
 $ Phylogroup         : chr  "D" "C" "B1" "A" ...
 $ Serotype           : chr  "ONT:H28" "O153:H19" "O76:H30" "O78:H11" ...
 $ Clonotype          : chr  "CH23-331" "CH4-25" "CH29-38" "CH11-41" ...
 $ Sequence.Type      : chr  "ST524" "ST88" "ST156" "ST48" ...
 $ VF                 : int  18 14 10 5 5 7 4 2 22 22 ...
 $ Plasmids           : int  3 3 2 3 9 3 7 7 1 3 ...
 $ kmer               : int  117 117 89 117 89 93 115 115 115 111 ...
 $ Contigs            : int  223 159 114 212 320 158 277 203 376 205 ...
 $ N50                : int  272287 323172 270767 112160 45936 106897 89185 94368 200150 281589 ...
 $ longest.contig..bp.: int  662555 760527 738861 285056 128053 369508 281444 280268 424527 617142 ...
 $ Assembly_length    : int  5341632 5415613 4875343 5167401 4858138 4638334 5406295 4796593 5389075 5340478 ...
 $ contigs1kb         : int  74 57 47 101 212 93 155 114 131 78 ...
 $ average_contig     : num  23954 34060 42766 24375 15182 ...
 $ X                  : int  1 1 1 1 1 1 1 1 1 1 ...
 $ Strain.y           : chr  "LREC237" "LREC237" "LREC237" "LREC237" ...
 $ Year.y             : int  NA NA NA NA NA NA NA NA NA NA ...
 $ CRISPR             : int  9 9 9 9 9 9 9 9 9 9 ...
 $ Cas                : chr  "[CAS-TypeIE (n=1),]" "[CAS-TypeIE (n=1),]" "[CAS-TypeIE (n=1),]" "[CAS-TypeIE (n=1),]" ...
 $ AMR                : int  2 2 2 2 2 2 2 2 2 2 ...
 $ Vir                : int  20 20 20 20 20 20 20 20 20 20 ...
 $ Integron           : int  0 0 0 0 0 0 0 0 0 0 ...
 $ seqs               : chr  "2020-07-24" "2020-07-24" "2020-07-24" "2020-07-24" ...

As you noticed, the function merge() combines dataframes, however it is a generic function that can be also used with other objects (like vectors or matrices), but they will be coerced to data.frame class.

By default, merge() will do a natural join or inner join, merging two dataframes in one that contains only once the common elements of both. The arguments all = TRUE, all.x = TRUE and all.y = TRUE will force an outer join in which all elements of both, the first or the second dataframes are selected. In these cases, if not all rows in the first data frame match all the rows in the second, the output is filled with NA values in those cases.

Finally, the Cartesian product of both dataframes can be obtained in R setting as NULL the argument by of the merge() function.

Quick exercise (I)

Two students enrolled in different University courses: Rafa in A, B, D, E and G and Roger in B, C, D and F. Rafa got the following marks 8, 9, 9.5, 8.75 and 9 and Roger obtained 10, 9.7, 9 and 10. Write a R program to create merged dataframes with all the marks (outer join), all the Rafa’s marks (left outer), all the Roger’s marks (right outer), and the marks in the common courses (inner join).

#Create the dataframes
rafa <- data.frame(c("A","B","D","E","G"),c(8,9,9.5,8.75,9.5))
roger <- data.frame(c("B","C","D","F"),c(10,9.7,9,10))
names(rafa) <- c("Course","Rafa")
names(roger) <- c("Course","Roger")

How would you obtain a table containing the marks of both students only for their common courses?

merge(rafa, roger, by = “Student”) merge(rafa, roger, by = “Course”) merge(rafa, roger) merge(rafa, roger, by = “Course”, all=TRUE)

How would you obtain a table containing the marks of both students only for Rafa’s courses?

merge(rafa, roger, by = “Student”) merge(rafa, roger, all.y=TRUE) merge(rafa, roger, all.x=TRUE) merge(rafa, roger, by = “Course”, all=TRUE)

1.3 Data matrix format (wide vs. long table)

How should I arrange my data table?

A column per experimental condition or a column per variable? Is the same?

In the table Zebrafish_data.csv from the Lesson R5 we have the results of an experiment in which a collaborator scored the number of metastatic cancer cells upon the expression of different transcripts of the EFNA3 gene. Each transcript is cloned into a pLoC plasmid, and we have negative (empty plasmid) and positive controls (wt transcript). Let’s import and check the data.

ZFdata <- read.csv("data/Zebrafish_data.csv")
str(ZFdata)

'data.frame':   41 obs. of  6 variables:
 $ pLoC : int  36 32 10 26 15 23 17 14 44 12 ...
 $ EFNA3: int  35 33 17 25 89 36 40 36 35 37 ...
 $ NC1  : int  58 26 26 18 20 24 10 31 28 26 ...
 $ NC1s : int  11 11 19 12 12 20 7 104 116 11 ...
 $ NC2  : int  53 37 56 48 27 29 22 79 22 18 ...
 $ NC2s : int  40 43 19 18 33 29 29 25 28 47 ...

head(ZFdata)

  pLoC EFNA3 NC1 NC1s NC2 NC2s
1   36    35  58   11  53   40
2   32    33  26   11  37   43
3   10    17  26   19  56   19
4   26    25  18   12  48   18
5   15    89  20   12  27   33
6   23    36  24   20  29   29

How many columns has the table? How many variables are there?

Here we have one column per experimental condition. Thus, this table format does not agree with the standard way to introduce the data in a table, the data-matrix: Rows for cases and columns for variables.

Having the data, we transform it in a datamatrix (aka long table) using the function stack(). You can also do it the other way around with the function unstack().

ZF_stacked <- stack(ZFdata)
str(ZF_stacked)

'data.frame':   246 obs. of  2 variables:
 $ values: int  36 32 10 26 15 23 17 14 44 12 ...
 $ ind   : Factor w/ 6 levels "pLoC","EFNA3",..: 1 1 1 1 1 1 1 1 1 1 ...

head(ZF_stacked)

  values  ind
1     36 pLoC
2     32 pLoC
3     10 pLoC
4     26 pLoC
5     15 pLoC
6     23 pLoC

ZF_old <- unstack(ZF_stacked)
str(ZF_old)

'data.frame':   41 obs. of  6 variables:
 $ pLoC : int  36 32 10 26 15 23 17 14 44 12 ...
 $ EFNA3: int  35 33 17 25 89 36 40 36 35 37 ...
 $ NC1  : int  58 26 26 18 20 24 10 31 28 26 ...
 $ NC1s : int  11 11 19 12 12 20 7 104 116 11 ...
 $ NC2  : int  53 37 56 48 27 29 22 79 22 18 ...
 $ NC2s : int  40 43 19 18 33 29 29 25 28 47 ...

head(ZF_old)

  pLoC EFNA3 NC1 NC1s NC2 NC2s
1   36    35  58   11  53   40
2   32    33  26   11  37   43
3   10    17  26   19  56   19
4   26    25  18   12  48   18
5   15    89  20   12  27   33
6   23    36  24   20  29   29

However, some times the dataset is more complex and there are other variables that change the table structure, as in the table Zebrafish_full.csv. In this case, remember that stack is designed to transform tables of only two variables. Thus, you must stack only the desired two variables and then final construct the table by adding the rest of the information, for instance with cbind(), as in the example below.

ZF_full <- read.csv("data/Zebrafish_full.csv", row.names=1)
head(ZF_full)

  pLoC EFNA3 NC1 NC1s NC2 NC2s assay
1   36    35  58   11  53   40     2
2   32    33  26   11  37   43     2
3   10    17  26   19  56   19     2
4   26    25  18   12  48   18     1
5   15    89  20   12  27   33     1
6   23    36  24   20  29   29     1

#option 1:
#step1: stack two main variables (sample & number of cells)
ZF_full_some_stack <- stack(ZF_full[,1:6])
head(ZF_full_some_stack,15)

   values  ind
1      36 pLoC
2      32 pLoC
3      10 pLoC
4      26 pLoC
5      15 pLoC
6      23 pLoC
7      17 pLoC
8      14 pLoC
9      44 pLoC
10     12 pLoC
11      3 pLoC
12     21 pLoC
13     21 pLoC
14     39 pLoC
15     19 pLoC

#step2: reconstruct the table adding the third variable
ZF_full_stack <- cbind(ZF_full_some_stack,ZF_full[,7])
colnames(ZF_full_stack) <- c("Cells","Sample","Assay")
head(ZF_full_stack,15)

   Cells Sample Assay
1     36   pLoC     2
2     32   pLoC     2
3     10   pLoC     2
4     26   pLoC     1
5     15   pLoC     1
6     23   pLoC     1
7     17   pLoC     3
8     14   pLoC     2
9     44   pLoC     3
10    12   pLoC     1
11     3   pLoC     1
12    21   pLoC     1
13    21   pLoC     3
14    39   pLoC     2
15    19   pLoC     3

#option2: shorcut
ZF_full_stack2 <- cbind(stack(ZF_full[,1:6]),ZF_full[,7])
colnames(ZF_full_stack2) <- c("Cells","Sample","Assay")
head(ZF_full_stack2,15)

   Cells Sample Assay
1     36   pLoC     2
2     32   pLoC     2
3     10   pLoC     2
4     26   pLoC     1
5     15   pLoC     1
6     23   pLoC     1
7     17   pLoC     3
8     14   pLoC     2
9     44   pLoC     3
10    12   pLoC     1
11     3   pLoC     1
12    21   pLoC     1
13    21   pLoC     3
14    39   pLoC     2
15    19   pLoC     3

#the same result in both cases?
all.equal(ZF_full_stack,ZF_full_stack2)

[1] TRUE

Remember that datamatrix is not an R structure, but a general concept in data analysis. Also, for more complex dataframes, I suggest to use the function melt(). However, this function name refers to two different functions in two alternative packages: reshape2 and data.table, with slightly different behavior.

Quick exercise (II)

From the previous exercise with marks of two students, we have a table students with all the marks, in which each student is a column.

students <-  merge(rafa, roger, by = "Course", all = TRUE)
students

  Course Rafa Roger
1      A 8.00    NA
2      B 9.00  10.0
3      C   NA   9.7
4      D 9.50   9.0
5      E 8.75    NA
6      F   NA  10.0
7      G 9.50    NA

However, we need a table in which each column is a variable, as follows:

   Course  Mark Student
1       A  8.00    Rafa
2       B  9.00    Rafa
3       C    NA    Rafa
4       D  9.50    Rafa
5       E  8.75    Rafa
6       F    NA    Rafa
7       G  9.50    Rafa
8       A    NA   Roger
9       B 10.00   Roger
10      C  9.70   Roger
11      D  9.00   Roger
12      E    NA   Roger
13      F 10.00   Roger
14      G    NA   Roger

How would you obtain the second table?

#1. Create the table
students2 <- cbind(students[,1], stack(students[,2:3]))
#Note that we have used stack() for only two columns and bind the output with the column 1 in the previous table

#2. Rename variables
names(students2) <- c("Course","Mark","Student")

#3. Show table
students2

   Course  Mark Student
1       A  8.00    Rafa
2       B  9.00    Rafa
3       C    NA    Rafa
4       D  9.50    Rafa
5       E  8.75    Rafa
6       F    NA    Rafa
7       G  9.50    Rafa
8       A    NA   Roger
9       B 10.00   Roger
10      C  9.70   Roger
11      D  9.00   Roger
12      E    NA   Roger
13      F 10.00   Roger
14      G    NA   Roger

2 Working efficiently with large datasets

2.1 Fast loading of huge datasets and creation of contingency tables

We are going to make some examples with a huge dataset of Covid19 Vaccination data in EU. The data is publicly available at https://www.ecdc.europa.eu/en/publications-data/data-covid-19-vaccination-eu-eea. While you can download and open a file from internet in R, in order to use the same dataset, we have a file vaccines_EU_22oct2022.csv in our data folder.

Note

From this point on, in some examples we will show only some lines of the output of the code chunks (you will notice that the output ends with — Cropped output —). Otherwise, this document is very long and difficult to follow.

As always, it’s encouraged to run the code yourself to see and understand the full returned output.

#open directly from the ECDC
vaccines <- read.csv(file = "https://opendata.ecdc.europa.eu/covid19/vaccine_tracker/csv/data.csv", header=TRUE)

#explore the data
str(vaccines)

'data.frame':   813367 obs. of  18 variables:
 $ YearWeekISO        : chr  "2021-W02" "2023-W19" "2023-W19" "2023-W19" ...
 $ ReportingCountry   : chr  "AT" "AT" "AT" "AT" ...
 $ Denominator        : int  424628 431785 7427239 1551690 524214 741680 1086320 1392642 435176 3005708 ...
 $ NumberDosesReceived: int  0 0 0 0 0 0 0 0 0 0 ...
 $ NumberDosesExported: int  0 0 0 0 0 0 0 0 0 0 ...
 $ FirstDose          : int  0 0 1 0 0 0 0 0 0 0 ...
 $ FirstDoseRefused   : int  NA NA NA NA NA NA NA NA NA NA ...
 $ SecondDose         : int  0 0 0 0 0 0 0 0 0 0 ...
 $ DoseAdditional1    : int  0 0 1 0 0 0 0 0 0 1 ...
 $ DoseAdditional2    : int  0 0 9 0 1 1 3 1 0 3 ...
 $ DoseAdditional3    : int  0 0 13 0 3 4 2 3 0 1 ...
 $ DoseAdditional4    : int  0 0 0 0 0 0 0 0 0 0 ...
 $ DoseAdditional5    : int  0 0 0 0 0 0 0 0 0 0 ...
 $ UnknownDose        : int  0 0 0 0 0 0 0 0 0 0 ...
 $ Region             : chr  "AT" "AT" "AT" "AT" ...
 $ TargetGroup        : chr  "Age10_14" "Age0_4" "ALL" "Age<18" ...
 $ Vaccine            : chr  "COMBA.4-5" "MODBA.1" "MOD" "MOD" ...
 $ Population         : int  8932664 8978929 8978929 8978929 8978929 8978929 8978929 8978929 8978929 8978929 ...
NA
--- Cropped output ---

head(vaccines)

  YearWeekISO ReportingCountry Denominator NumberDosesReceived
1    2021-W02               AT      424628                   0
2    2023-W19               AT      431785                   0
3    2023-W19               AT     7427239                   0
4    2023-W19               AT     1551690                   0
5    2023-W19               AT      524214                   0
6    2023-W19               AT      741680                   0
  NumberDosesExported FirstDose FirstDoseRefused SecondDose DoseAdditional1
1                   0         0               NA          0               0
2                   0         0               NA          0               0
3                   0         1               NA          0               1
4                   0         0               NA          0               0
5                   0         0               NA          0               0
6                   0         0               NA          0               0
  DoseAdditional2 DoseAdditional3 DoseAdditional4 DoseAdditional5 UnknownDose
1               0               0               0               0           0
2               0               0               0               0           0
3               9              13               0               0           0
4               0               0               0               0           0
5               1               3               0               0           0
--- Cropped output ---

Even with large datasets, we can use table() or summary() functions, to overview data. But, sometimes we just doesn’t.

table(vaccines$Region)


     AT      BE      BG      CY      CZ      DE      DK      EE      EL      ES 
  17292    7330    6001    7098    6593     564    4821    7755   16413   12960 
     FI    FI19   FI193   FI194   FI195   FI197    FI1B   FI1B1    FI1C   FI1C1 
  16965   16965   16965   16965   16965   16965   16965   16965   16965   16965 
  FI1C2   FI1C3   FI1C4   FI1C5    FI1D   FI1D1   FI1D2   FI1D3   FI1D5   FI1D7 
  16965   16965   16965   16965   16965   16965   16965   16965   16965   16965 
  FI1D8   FI1D9    FI20   FI200      FR     FR1     FRB     FRC     FRD     FRE 
  16965   16965   16965   16965    2394    1064    1064    1064    1064    1064 
    FRF     FRG     FRH     FRI     FRJ     FRK     FRL     FRM    FRY1    FRY2 
   1064    1064    1064    1064    1064    1064    1064    1064    1064    1064 
   FRY3    FRY4    FRY5      HR      HU      IE      IS      IT    ITC1    ITC2 
   1064    1064    1064    9270    6712    6367    5215    7119     570     347 
   ITC3    ITC4    ITF1    ITF2    ITF3    ITF4    ITF5    ITF6    ITG1    ITG2 
    486     503     436     337     492     449     393     419     468     389 
   ITH1    ITH2    ITH3    ITH4    ITH5    ITI1    ITI2    ITI3    ITI4      LI 
    399     419     486     445     507     437     449     451     506    5070 
     LT    LT01    LT02      LU      LV      MT      NL      NO      PL    PL21 
   8502    1308    1308   10476    5454    5964   14355    4467    9425    9425 
   PL22    PL41    PL42    PL43    PL51    PL52    PL61    PL62    PL63    PL71 
   9425    9425    9425    9425    9425    9425    9425    9425    9425    9425 
   PL72    PL81    PL82    PL84   PL92X      PT PTCSR01 PTCSR02 PTCSR03 PTCSR04 
   9425    9425    9425    9425    9425    8136     750     756     403     953 
PTCSR05 PTCSR06 PTCSR07      RO      SE    SE11    SE12    SE21    SE22    SE23 
   1092     278    1048    5867    4673     580     580     580     580     580 
   SE31    SE32    SE33      SI      SK     UNK 
    580     580     580    3131    3710    1197

table(vaccines$Region, vaccines$NumberDosesReceived)

         
              0     1     2     3     4     5     6     7     8     9    10
  AT      17072     0     0     0     0     0     0     0     0     0     0
  BE        129     0     0     0     0     0     0     0     0     0     0
  BG        423     0     0     0     0     0     0     0     0     0     0
  CY       6957     0     0     0     0     0     0     0     0     0     0
  CZ        649     0     0     0     0     0     0     0     0     0     0
  DE         21     0     0     0     0     0     0     0     0     0     0
  DK       4756     0     0     0     0     0     0     0     0     0     0
  EE       7603     0     0     0     0     0     0     0     0     0     0
  EL        866     0     0     0     0     0     0     0     0     0     0
  ES        478     0     0     0     0     0     0     0     0     0     0
  FI          0     0     0     0     0     0     0     0     0     0     0
  FI19        0     0     0     0     0     0     0     0     0     0     0
  FI193       0     0     0     0     0     0     0     0     0     0     0
  FI194       0     0     0     0     0     0     0     0     0     0     0
  FI195       0     0     0     0     0     0     0     0     0     0     0
  FI197       0     0     0     0     0     0     0     0     0     0     0
  FI1B        0     0     0     0     0     0     0     0     0     0     0
  FI1B1       0     0     0     0     0     0     0     0     0     0     0
  FI1C        0     0     0     0     0     0     0     0     0     0     0
  FI1C1       0     0     0     0     0     0     0     0     0     0     0
  FI1C2       0     0     0     0     0     0     0     0     0     0     0
  FI1C3       0     0     0     0     0     0     0     0     0     0     0
  FI1C4       0     0     0     0     0     0     0     0     0     0     0
  FI1C5       0     0     0     0     0     0     0     0     0     0     0
  FI1D        0     0     0     0     0     0     0     0     0     0     0
  FI1D1       0     0     0     0     0     0     0     0     0     0     0
  FI1D2       0     0     0     0     0     0     0     0     0     0     0
  FI1D3       0     0     0     0     0     0     0     0     0     0     0
--- Cropped output ---

summary(vaccines[which(vaccines$Region=="ES"),][,6]) #see the data from Spain

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      0       0       0    6581       2 1512566

table(vaccines)

Error in table(vaccines): attempt to make a table with >= 2^31 elements

When exploring (very) large datasets as in the example above you can find that some functions don’t work because they can’t handle all that data (Error in table(vaccines) : attempt to make a table with >= 2^31 elements). Here, we are going to use alternative methods, more efficient and convenient for reading and handle these large datasets.

One of those tricks is the use of the package data.table, very handy for large datasets. In the following lines, we will compare reading/writting data with the function fread() and fwrite().

#load the package may require installing it before
if(!require(data.table)){
    install.packages("data.table")
}

Loading required package: data.table

# if that doesn't work try: install.packages("data.table", type = "source", repos = "https://Rdatatable.gitlab.io/data.table")

system.time(vaccines <- read.csv(file = 'data/vaccines_EU_22oct2022.csv', header=TRUE))

   user  system elapsed 
  2.587   0.092   2.682

system.time(vaccines<-fread('data/vaccines_EU_22oct2022.csv'))

   user  system elapsed 
  1.507   0.061   0.215

#we can also prevent loading of some columns  to save time
system.time(vaccines2 <-fread('data/vaccines_EU_22oct2022.csv',drop=c(3,5,7,9,10)))

   user  system elapsed 
  0.935   0.028   0.121

system.time(vaccines3 <-fread('data/vaccines_EU_22oct2022.csv',colClasses = "character")) #we can also select the variables by type

   user  system elapsed 
  3.683   0.089   0.474

2.2 Frequency tables: `table()` vs. `xtabs()`

Tabulating frequencies is a common and efficient way to explore data. While the table() function is versatile and can be used with various data structures (vectors, dataframes, lists…), it might become less convenient for complex cross-tabulations, especially with large datasets. Alternatively, as shown below, the xtabs() function offers a more streamlined approach, particularly for multi-dimensional tables. It leverages a formula-based syntax, allowing for easy specification of variables and automatic generation of row and column labels. Additionally, the data= argument in xtabs() simplifies the process by directly referencing variable names within the dataframe.

#compare table() and xtabs()
table(vaccines$ReportingCountry)


    AT     BE     BG     CY     CZ     DE     DK     EE     EL     ES     FI 
 17292   7330   6001   7098   6593    564   4821   7755  16413  12960 407160 
    FR     HR     HU     IE     IS     IT     LI     LT     LU     LV     MT 
 22743   9270   6712   6367   5215  16507   5070  11118  10476   5454   5964 
    NL     NO     PL     PT     RO     SE     SI     SK 
 14355   4467 160225  13416   5867   9313   3131   3710

str(table(vaccines$ReportingCountry))

 'table' int [1:30(1d)] 17292 7330 6001 7098 6593 564 4821 7755 16413 12960 ...
 - attr(*, "dimnames")=List of 1
  ..$ : chr [1:30] "AT" "BE" "BG" "CY" ...

xtabs(formula= ~ ReportingCountry  ,data=vaccines)

ReportingCountry
    AT     BE     BG     CY     CZ     DE     DK     EE     EL     ES     FI 
 17292   7330   6001   7098   6593    564   4821   7755  16413  12960 407160 
    FR     HR     HU     IE     IS     IT     LI     LT     LU     LV     MT 
 22743   9270   6712   6367   5215  16507   5070  11118  10476   5454   5964 
    NL     NO     PL     PT     RO     SE     SI     SK 
 14355   4467 160225  13416   5867   9313   3131   3710

str(xtabs(formula= ~ ReportingCountry  ,data=vaccines))

 'xtabs' int [1:30(1d)] 17292 7330 6001 7098 6593 564 4821 7755 16413 12960 ...
 - attr(*, "dimnames")=List of 1
  ..$ ReportingCountry: chr [1:30] "AT" "BE" "BG" "CY" ...
 - attr(*, "call")= language xtabs(formula = ~ReportingCountry, data = vaccines)

#Note: library(stats) if xtabs() does not work

So far, they seem very similar in terms of coding and obtained output. However, what about if you want to use to several variables?

#with 2 or more variables?
table(vaccines[,c(ReportingCountry,as.factor(Vaccine))]) #not really


     1     10     11     12     13     14     15     16     17     18     19 
108389 117037   8332   3003   2317  92285   1973   1385    681  74429  46812 
     2      3      4      5      6      7      8      9     AT     BE     BG 
  2342    344 124068  58714  59509   2533     83 109131  17292   7330   6001 
    CY     CZ     DE     DK     EE     EL     ES     FI     FR     HR     HU 
  7098   6593    564   4821   7755  16413  12960 407160  22743   9270   6712 
    IE     IS     IT     LI     LT     LU     LV     MT     NL     NO     PL 
  6367   5215  16507   5070  11118  10476   5454   5964  14355   4467 160225 
    PT     RO     SE     SI     SK 
 13416   5867   9313   3131   3710 
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
--- Cropped output ---

table(vaccines$ReportingCountry,vaccines$Vaccine) #yes!

    
        AZ BECNBG BHACOV   COM COMBA.1 COMBA.4-5 COMBIV COMXBB JANSS   MOD
  AT  1572      0      0  1572    1572      1572      0      0  1572  1572
  BE   920      0      0  1540     640       620      0      0  1160  1320
  BG  1500      0      0  1551       0         0      0      0  1400  1550
  CY  1130      0      0  1530     264       641      0      0  1153  1108
  CZ   581      0      0  1758     433       645      0     32   879  1364
  DE     0      0      0     0       0         0      0      0     0     0
  DK   600      0      0  1487     406       512      0      0   648  1118
  EE  1274      0      0  1351     504       477      0      0  1169  1306
  EL  2320      0      0  2413    2320      2372      0      0  2348  2320
  ES  2160      0      0  2160       0         0   2160      0  2160  2160
  FI 45240      0      0 45240   45240     45240      0      0 45240 45240
  FR   133      0      0   133       0       133      0      0   133   133
  HR  1410      0      0  2175       0         0      0      0  2025  1950
  HU   701   1130      0  1426     495         0      0      0  1266  1180
  IE   704      0      0  1794     533       711      0      0   550  1069
  IS   646      0      0  1736     492       411      0      0   877   809
  IT  1318      0      0  4176    1464      1591      0      0  1737  3079
  LI     0      0      0  1430     500         0      0      0  1040  1430
  LT  2346      0      0  2465       0         0      0      0  2176  2414
  LU  1668      0      0  1740     672       852      0     48  1560  1704
  LV   465      0      0  1275     415       434      0      0   854  1016
  MT  1524      0      0  1549       0         0      0      0  1396  1495
  NL  1595      0      0  1595    1595      1595      0      0  1595  1595
--- Cropped output ---

## you can also use "with", but not so intuitive to me
with(vaccines, table(ReportingCountry, as.factor(Vaccine)))

                
ReportingCountry    AZ BECNBG BHACOV   COM COMBA.1 COMBA.4-5 COMBIV COMXBB
              AT  1572      0      0  1572    1572      1572      0      0
              BE   920      0      0  1540     640       620      0      0
              BG  1500      0      0  1551       0         0      0      0
              CY  1130      0      0  1530     264       641      0      0
              CZ   581      0      0  1758     433       645      0     32
              DE     0      0      0     0       0         0      0      0
              DK   600      0      0  1487     406       512      0      0
              EE  1274      0      0  1351     504       477      0      0
              EL  2320      0      0  2413    2320      2372      0      0
              ES  2160      0      0  2160       0         0   2160      0
              FI 45240      0      0 45240   45240     45240      0      0
              FR   133      0      0   133       0       133      0      0
              HR  1410      0      0  2175       0         0      0      0
              HU   701   1130      0  1426     495         0      0      0
              IE   704      0      0  1794     533       711      0      0
              IS   646      0      0  1736     492       411      0      0
              IT  1318      0      0  4176    1464      1591      0      0
              LI     0      0      0  1430     500         0      0      0
              LT  2346      0      0  2465       0         0      0      0
              LU  1668      0      0  1740     672       852      0     48
              LV   465      0      0  1275     415       434      0      0
              MT  1524      0      0  1549       0         0      0      0
              NL  1595      0      0  1595    1595      1595      0      0
--- Cropped output ---

#more strightforward alternative with xtabs
(vaccines_split <- xtabs(formula= ~ ReportingCountry  + as.factor(Vaccine), data = vaccines))

                as.factor(Vaccine)
ReportingCountry    AZ BECNBG BHACOV   COM COMBA.1 COMBA.4-5 COMBIV COMXBB
              AT  1572      0      0  1572    1572      1572      0      0
              BE   920      0      0  1540     640       620      0      0
              BG  1500      0      0  1551       0         0      0      0
              CY  1130      0      0  1530     264       641      0      0
              CZ   581      0      0  1758     433       645      0     32
              DE     0      0      0     0       0         0      0      0
              DK   600      0      0  1487     406       512      0      0
              EE  1274      0      0  1351     504       477      0      0
              EL  2320      0      0  2413    2320      2372      0      0
              ES  2160      0      0  2160       0         0   2160      0
              FI 45240      0      0 45240   45240     45240      0      0
              FR   133      0      0   133       0       133      0      0
              HR  1410      0      0  2175       0         0      0      0
              HU   701   1130      0  1426     495         0      0      0
              IE   704      0      0  1794     533       711      0      0
              IS   646      0      0  1736     492       411      0      0
              IT  1318      0      0  4176    1464      1591      0      0
              LI     0      0      0  1430     500         0      0      0
              LT  2346      0      0  2465       0         0      0      0
              LU  1668      0      0  1740     672       852      0     48
              LV   465      0      0  1275     415       434      0      0
              MT  1524      0      0  1549       0         0      0      0
              NL  1595      0      0  1595    1595      1595      0      0
--- Cropped output ---

As mentioned above, xtabs() can be easily used with more than two variables. Moreover, you can create a cross-tabulated table using a numeric variable instead of frequencies. To do so, you just need to use the left side of the formula.

#also with several variables
(vaccines_split2 <- xtabs(NumberDosesReceived ~ ReportingCountry  + as.factor(Vaccine) + as.factor(TargetGroup), vaccines))

, , as.factor(TargetGroup) = 1_Age<60

                as.factor(Vaccine)
ReportingCountry        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5
              AT         0         0         0         0         0         0
              BE         0         0         0         0         0         0
              BG         0         0         0         0         0         0
              CY         0         0         0         0         0         0
              CZ         0         0         0         0         0         0
              DE         0         0         0         0         0         0
              DK         0         0         0         0         0         0
              EE         0         0         0         0         0         0
              EL                   0         0                              
              ES         0         0         0         0         0         0
              FI         0         0         0         0         0         0
              FR         0         0         0         0         0         0
              HR         0         0         0         0         0         0
              HU         0         0         0         0         0         0
              IE         0         0         0         0         0         0
              IS         0         0         0         0         0         0
              IT         0         0         0         0         0         0
              LI         0         0         0         0         0         0
              LT         0         0         0         0         0         0
              LU         0         0         0         0         0         0
              LV         0         0         0         0         0         0
              MT         0         0         0         0         0         0
              NL         0         0         0         0         0         0
              NO         0         0         0         0         0         0
              PL         0         0         0         0         0         0
              PT         0         0         0         0         0         0
              RO                   0         0                   0         0
              SE         0         0         0         0         0         0
              SI         0         0         0         0         0         0
              SK         0         0         0         0         0         0
                as.factor(Vaccine)
ReportingCountry    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5
              AT         0         0         0         0         0         0
              BE         0         0         0         0         0         0
              BG         0         0         0         0         0         0
              CY         0         0         0         0         0         0
              CZ         0         0         0         0         0         0
              DE         0         0         0         0         0         0
              DK         0         0         0         0         0         0
              EE         0         0         0         0         0         0
              EL         0         0                             0         0
              ES         0         0         0         0         0         0
              FI         0         0         0         0         0         0
              FR         0         0         0         0         0         0
              HR         0         0         0         0         0         0
              HU         0         0         0         0         0         0
--- Cropped output ---

That was a very long output to check! If you want to show your tabulated data in a more useful format, you can covert the cross-tabulated data into a flat table with ftable(). See the examples below and try to understand how the row.bars statement works.

ftable(vaccines_split, row.vars = 2)

                   ReportingCountry    AT    BE    BG    CY    CZ    DE    DK    EE    EL    ES    FI    FR    HR    HU    IE    IS    IT    LI    LT    LU    LV    MT    NL    NO    PL    PT    RO    SE    SI    SK
as.factor(Vaccine)                                                                                                                                                                                                     
AZ                                   1572   920  1500  1130   581     0   600  1274  2320  2160 45240   133  1410   701   704   646  1318     0  2346  1668   465  1524  1595   602 32045  1548  1417  2320   376   274
BECNBG                                  0     0     0     0     0     0     0     0     0     0     0     0     0  1130     0     0     0     0     0     0     0     0     0     0     0  1212     0     0     0     0
BHACOV                                  0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0   344     0     0     0     0
COM                                  1572  1540  1551  1530  1758     0  1487  1351  2413  2160 45240   133  2175  1426  1794  1736  4176  1430  2465  1740  1275  1549  1595  1248 32045  2480  1549  2320  1022  1308
COMBA.1                              1572   640     0   264   433     0   406   504  2320     0 45240     0     0   495   533   492  1464   500     0   672   415     0  1595   305     0   864     0     0     0     0
COMBA.4-5                            1572   620     0   641   645     0   512   477  2372     0 45240   133     0     0   711   411  1591     0     0   852   434     0  1595   436     0  1267     0     0     0     0
COMBIV                                  0     0     0     0     0     0     0     0     0  2160     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0   373     0
COMXBB                                  0     0     0     0    32     0     0     0     0     0     0     0     0     0     0     0     0     0     0    48     0     0     0     0     0     0     0     0     3     0
JANSS                                1572  1160  1400  1153   879     0   648  1169  2348  2160 45240   133  2025  1266   550   877  1737  1040  2176  1560   854  1396  1595   438 32045  1410  1362     0   328   610
MOD                                  1572  1320  1550  1108  1364     0  1118  1306  2320  2160 45240   133  1950  1180  1069   809  3079  1430  2414  1704  1016  1495  1595  1002 32045  1672  1539  2320   718   809
MODBA.1                              1572   460     0   264   350     0     0   504     0     0     0   133     0     0   363     4   850   510     0   672   318     0  1595   150     0   587     0     0     0     0
MODBA.4-5                               0     0     0   432    69     0     0   414     0     0     0   133     0     0   225    29   732     0     0   552     3     0     0   286     0   128     0     0     0     0
MODBIV                                  0     0     0     0     0     0     0     0     0  2160     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0   157     0
NVXD                                 1572   670     0   576   443     0     0   756  2320     0 45240   133   465     0   418    91  1415   160     0  1008   227     0  1595     0 32045   441     0  2320   151   239
SGSK                                 1572     0     0     0    39     0     0     0     0     0     0   133     0     0     0     0   145     0     0     0     3     0     0     0     0    78     0     0     3     0
SIN                                     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0  1385     0     0     0     0
SPU                                     0     0     0     0     0     0     0     0     0     0     0     0     0   514     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0   167
UNK                                  1572     0     0     0     0   564    50     0     0     0 45240 21546  1245     0     0   120     0     0  1717     0   444     0  1595     0     0     0     0    33     0   303
VLA                                  1572     0     0     0     0     0     0     0     0     0 45240     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0
NA
NA
NA
NA
--- Cropped output ---

ftable(vaccines_split2, row.vars = 2)

                   ReportingCountry              AT                                                                                                                                                                        BE                                                                                                                                                                        BG                                                                                                                                                                        CY                                                                                                                                                                        CZ                                                                                                                                                                        DE                                                                                                                                                                        DK                                                                                                                                                                        EE                                                                                                                                                                        EL                                                                                                                                                                        ES                                                                                                                                                                        FI                                                                                                                                                                        FR                                                                                                                                                                        HR                                                                                                                                                                        HU                                                                                                                                                                        IE                                                                                                                                                                        IS                                                                                                                                                                        IT                                                                                                                                                                        LI                                                                                                                                                                        LT                                                                                                                                                                        LU                                                                                                                                                                        LV                                                                                                                                                                        MT                                                                                                                                                                        NL                                                                                                                                                                        NO                                                                                                                                                                        PL                                                                                                                                                                        PT                                                                                                                                                                        RO                                                                                                                                                                        SE                                                                                                                                                                        SI                                                                                                                                                                        SK                                                                                                                                                                
                   as.factor(TargetGroup)  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF  1_Age<60  1_Age60+    Age<18    Age0_4  Age10_14  Age15_17  Age18_24  Age25_49    Age5_9  Age50_59  Age60_69  Age70_79    Age80+    AgeUNK       ALL       HCW      LTCF
as.factor(Vaccine)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
AZ                                                0         0         0         0         0         0         0         0         0         0         0         0         0         0   5519600         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA        NA        NA        NA         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0    432300         0         0         0         0        NA         0         0        NA        NA        NA         0        NA        NA        NA        NA         0   1628400        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    202920         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    818300         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA   4035800        NA         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0  10355500         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA   6513800        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0   1442700         0         0         0         0         0     97800     97800     97800     97800     97800     97800     97800     97800     97800     97800     97800    100880     97800     97800         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   1121594         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    186600         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   1273400         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0   4503400         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0    578400        NA         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0        NA        NA         0         0         0         0        NA        NA         0        NA        NA        NA        NA         0   2999600        NA        NA         0         0         0         0         0        NA        NA        NA         0        NA        NA        NA        NA         0        NA         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0   1123800        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   1612810         0         0
BECNBG                                            0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA   5187056        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
BHACOV                                            0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA        NA        NA        NA         0        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
COM                                               0         0         0         0         0         0         0         0         0         0         0         0         0         0  24394773         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA        NA        NA        NA         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA   7265580        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0   2033293         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0  21204560        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   7614360         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   2304060         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA  25348740        NA        NA         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA 100959011        NA        NA         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0 136804000         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA  13163840        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0  11135050         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA    794870        NA        NA         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0        NA        NA        NA         0         0         0         0         0         0       763         0         0         0         0         0         0         0     22650         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   6789378         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   1346640         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   3001755         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0  34003726         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0  11373105        NA         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0        NA        NA        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0  18276235        NA        NA         0         0         0         0         0        NA        NA        NA         0        NA        NA        NA        NA         0        NA         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0   3987390        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   7723560         0         0
COMBA.1                                           0         0         0         0         0         0         0         0         0         0         0         0         0         0   1512000         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0        NA        NA        NA        NA        NA        NA        NA        NA        NA         0   1321920        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    279360         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA    800640        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA    216000         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA    126720        NA        NA         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0        NA        NA        NA         0         0         0         0         0         0      1020         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     86400         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    460800         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   2871360         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0    889920        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
COMBA.4-5                                         0         0         0         0         0         0         0         0         0         0         0         0         0         0   5530560         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     37440         0         0         0         0        NA         0        NA        NA        NA        NA        NA        NA        NA        NA        NA         0   5135040        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    350400         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA   1428480        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0  23481600         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA    100800        NA        NA         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    168000         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   1088640         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   6325440         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0   2453760        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
COMBIV                                            0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0    800640        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
COMXBB                                            0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0        NA        NA        NA        NA         0        NA        NA        NA        NA         0     97920        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     18240         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     58560         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
JANSS                                             0         0         0         0         0         0         0         0         0         0         0         0         0         0   1292400         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA        NA        NA        NA         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0    190100         0         0         0         0        NA         0        NA        NA        NA        NA         0        NA        NA        NA        NA         0   1396200        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     42300         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    120800         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA   2401800        NA        NA         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   3732300         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA   4309200        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0    281500         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA     57500        NA        NA         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0       650         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    653097         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     80250         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   1259800         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0   2464800         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0    403900        NA         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0        NA        NA         0         0         0         0        NA        NA         0        NA        NA        NA        NA         0   2820300        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0    230400        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    475200         0         0
MOD                                               0         0         0         0         0         0         0         0         0         0         0         0         0         0   5963500         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA        NA        NA        NA         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0    155200         0         0         0         0        NA         0        NA        NA        NA        NA         0        NA        NA        NA        NA         0   3685100        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   1350690         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    270400         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA   1770000        NA         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0  54929280         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA   1736400        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0   3290500         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA    261720        NA        NA         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0        NA        NA        NA         0         0         0         0         0         0       680         0         0         0         0         0         0         0     44500         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    732830         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    302610         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   1171300         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0  11327200         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0   3982600        NA         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0        NA        NA        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0   2805700        NA        NA         0         0         0         0         0        NA        NA        NA         0        NA        NA        NA        NA         0        NA         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0    714400        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    871200         0         0
MODBA.1                                           0         0         0         0         0         0         0         0         0         0         0         0         0         0   2474610         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     24250         0         0         0         0        NA         0        NA        NA        NA        NA         0        NA        NA        NA        NA         0    199700        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    192750         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   8321200         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     65350         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0        NA        NA        NA         0         0         0         0         0         0      2505         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    303240         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    543980         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   6175700         0         0         0         0         0         0         0         0        NA        NA         0        NA        NA        NA        NA         0   1443150        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA        NA         0        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
MODBA.4-5                                         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0      9500         0         0         0         0         0         0         0         0        NA        NA         0        NA        NA        NA        NA         0     46750        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     98400         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   3315650         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     98350         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    243300         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    123600         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA         0        NA        NA        NA        NA         0   2271400        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA         0        NA        NA        NA         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
MODBIV                                            0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA         0        NA        NA        NA        NA         0    705400        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
NVXD                                              0         0         0         0         0         0         0         0         0         0         0         0         0         0   3192000         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     90000         0         0         0         0        NA         0        NA        NA        NA        NA         0        NA        NA        NA        NA         0    578000        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     60800         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA    396000        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0   2965000         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    198000         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA     42000        NA        NA         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    105000         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    189600         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    707000         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA         0        NA        NA        NA        NA         0        NA         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0     94000         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     93000         0         0
SGSK                                              0         0         0         0         0         0         0         0         0         0         0         0         0         0   2243300         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     64800         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0  16576400         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA         0        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    108000         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0         0         0    115200         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
SIN                                               0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
SPU                                               0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA   2000000        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0    200000         0         0
UNK                                               0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0 241419933         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0        NA         0         0         0        NA        NA         0        NA        NA        NA        NA        NA        NA         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     10162         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
VLA                                               0         0         0         0         0         0         0         0         0         0         0         0         0         0    151200         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
NA
NA
NA
--- Cropped output ---

ftable(vaccines_split2, row.vars = 3)

                       ReportingCountry          AT                                                                                                                                                                                            BE                                                                                                                                                                                            BG                                                                                                                                                                                            CY                                                                                                                                                                                            CZ                                                                                                                                                                                            DE                                                                                                                                                                                            DK                                                                                                                                                                                            EE                                                                                                                                                                                            EL                                                                                                                                                                                            ES                                                                                                                                                                                            FI                                                                                                                                                                                            FR                                                                                                                                                                                            HR                                                                                                                                                                                            HU                                                                                                                                                                                            IE                                                                                                                                                                                            IS                                                                                                                                                                                            IT                                                                                                                                                                                            LI                                                                                                                                                                                            LT                                                                                                                                                                                            LU                                                                                                                                                                                            LV                                                                                                                                                                                            MT                                                                                                                                                                                            NL                                                                                                                                                                                            NO                                                                                                                                                                                            PL                                                                                                                                                                                            PT                                                                                                                                                                                            RO                                                                                                                                                                                            SE                                                                                                                                                                                            SI                                                                                                                                                                                            SK                                                                                                                                                                                    
                       as.factor(Vaccine)        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA        AZ    BECNBG    BHACOV       COM   COMBA.1 COMBA.4-5    COMBIV    COMXBB     JANSS       MOD   MODBA.1 MODBA.4-5    MODBIV      NVXD      SGSK       SIN       SPU       UNK       VLA
as.factor(TargetGroup)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
1_Age<60                                          0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
1_Age60+                                          0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
Age<18                                            0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0        NA        NA        NA        NA         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0        NA         0        NA        NA         0        NA        NA         0         0         0        NA        NA         0         0         0         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA        NA         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
Age0_4                                            0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     97800         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA        NA        NA        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
Age10_14                                          0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA         0        NA        NA        NA        NA         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     97800         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA        NA        NA        NA        NA        NA         0         0        NA        NA        NA         0         0        NA         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
Age15_17                                          0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0        NA        NA        NA        NA         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     97800         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA        NA        NA        NA        NA        NA         0         0        NA        NA        NA         0         0        NA         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0         0        NA         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
Age18_24                                          0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0        NA        NA        NA        NA        NA         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0        NA         0        NA        NA         0        NA        NA         0         0         0        NA        NA         0         0         0         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     97800         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA        NA         0        NA        NA         0         0         0         0         0         0         0       763      1020         0         0         0         0       680      2505         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA        NA         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA        NA        NA        NA        NA        NA         0         0        NA        NA        NA        NA         0        NA        NA        NA         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0         0        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
Age25_49                                          0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0        NA        NA        NA        NA        NA         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0        NA         0        NA        NA         0        NA        NA         0         0         0        NA        NA         0         0         0         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     97800         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA        NA         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA        NA         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA        NA        NA        NA        NA        NA         0         0        NA        NA        NA        NA         0        NA        NA        NA         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0         0        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
Age5_9                                            0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     97800         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA        NA        NA        NA        NA        NA         0         0        NA        NA         0         0         0        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
Age50_59                                          0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0        NA        NA        NA        NA        NA         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0        NA         0        NA        NA         0        NA        NA         0         0         0        NA        NA         0         0         0         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     97800         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA        NA         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA        NA         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA        NA         0        NA        NA        NA         0         0        NA        NA        NA        NA         0        NA        NA        NA         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0         0        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
Age60_69                                          0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0        NA        NA        NA        NA        NA         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0        NA         0        NA        NA         0        NA        NA         0         0         0        NA        NA         0         0         0         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     97800         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA        NA         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA        NA         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA        NA        NA        NA        NA        NA         0         0        NA        NA        NA        NA         0        NA        NA        NA         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0         0        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
Age70_79                                          0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0        NA        NA        NA        NA        NA         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0        NA         0        NA        NA         0        NA        NA         0         0         0        NA        NA         0         0         0         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     97800         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA        NA         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA        NA         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA        NA        NA        NA        NA        NA         0         0        NA        NA        NA        NA         0        NA        NA        NA         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0         0        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
Age80+                                            0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0        NA        NA        NA        NA        NA         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0        NA         0        NA        NA         0        NA        NA         0         0         0        NA        NA         0         0         0         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     97800         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA        NA         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA        NA         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA        NA        NA        NA        NA        NA         0         0        NA        NA        NA         0         0        NA        NA        NA         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0         0        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
AgeUNK                                            0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0        NA         0        NA        NA         0        NA        NA         0         0         0        NA        NA         0         0         0         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     97800         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA        NA        NA        NA        NA        NA         0         0        NA        NA        NA         0         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
ALL                                         5519600         0         0  24394773   1512000   5530560         0         0   1292400   5963500   2474610         0         0   3192000   2243300         0         0         0    151200        NA         0         0        NA        NA        NA         0         0        NA        NA        NA         0         0        NA         0         0         0         0         0        NA         0         0   7265580         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0    432300         0         0   2033293         0     37440         0         0    190100    155200     24250      9500         0     90000         0         0         0         0         0   1628400         0         0  21204560   1321920   5135040         0     97920   1396200   3685100    199700     46750         0    578000     64800         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0 241419933         0    202920         0         0   7614360         0         0         0         0     42300   1350690         0         0         0         0         0         0         0         0         0    818300         0         0   2304060    279360    350400         0         0    120800    270400    192750     98400         0     60800         0         0         0         0         0   4035800         0         0  25348740    800640   1428480         0         0   2401800   1770000         0         0         0    396000         0         0         0         0         0        NA         0         0 100959011         0         0        NA         0        NA        NA         0         0        NA         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0        NA        NA  10355500         0         0 136804000         0  23481600         0         0   3732300  54929280   8321200   3315650         0   2965000  16576400         0         0        NA         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0        NA         0   6513800   5187056         0  13163840    216000         0         0         0   4309200   1736400         0         0         0         0         0         0   2000000         0         0   1442700         0         0  11135050         0         0         0         0    281500   3290500         0         0         0    198000         0         0         0         0         0    100880         0         0    794870    126720    100800         0         0     57500    261720     65350     98350         0     42000         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA        NA         0        NA        NA         0         0         0         0         0         0         0     22650         0         0         0         0       650     44500         0         0         0         0         0         0         0         0         0   1121594         0         0   6789378         0         0         0         0    653097    732830         0         0         0         0         0         0         0     10162         0    186600         0         0   1346640     86400    168000         0     18240     80250    302610    303240    243300         0    105000         0         0         0         0         0   1273400         0         0   3001755    460800   1088640         0         0   1259800   1171300    543980    123600         0    189600    108000         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0   4503400         0         0  34003726   2871360   6325440         0         0   2464800  11327200   6175700         0         0    707000         0         0         0         0         0    578400         0         0  11373105    889920   2453760         0         0    403900   3982600   1443150   2271400         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA        NA        NA        NA        NA        NA         0         0        NA        NA        NA        NA         0        NA        NA        NA         0         0         0   2999600         0         0  18276235         0         0         0         0   2820300   2805700         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0         0        NA         0         0         0        NA         0         0         0         0         0   1123800         0         0   3987390         0         0    800640     58560    230400    714400         0         0    705400     94000    115200         0         0         0         0   1612810         0         0   7723560         0         0         0         0    475200    871200         0         0         0     93000         0         0    200000         0         0
HCW                                               0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0        NA        NA        NA        NA        NA         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0        NA         0        NA        NA         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     97800         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA        NA         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA        NA         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
LTCF                                              0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA         0         0        NA         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA        NA        NA         0        NA        NA        NA        NA         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0        NA         0         0        NA         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0        NA         0        NA        NA         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0        NA         0         0         0        NA         0        NA        NA         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0     97800         0         0        NA        NA        NA         0         0        NA        NA         0         0         0        NA         0         0         0         0         0        NA         0         0        NA        NA        NA         0         0        NA        NA        NA        NA         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0        NA         0         0         0         0        NA        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        NA         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
NA
NA
NA
NA
NA
--- Cropped output ---

Quick exercise (III)

Sometimes, it is better to use a shorter table as an example… Let’s go back to the coli_genomes data that you already know.

Could you obtain a table like the following, with the number of Contigs by isolation source (Source) and phylogenetic group (Phylogroup)?

with(coli_genomes, table(Source, Phylogroup)) xtabs(Contigs ~ Source + Phylogroup, coli_genomes) xtabs( ~ Contigs + Source + Phylogroup, coli_genomes)

         Phylogroup
Source       A   B1    C    D
  Avian    134  102  108    0
  Human    790  208  662 1010
  Porcine  958    0    0    0

Now, let’s do it a little bit more complicated. If we split the previous table by the STs (aka. multilocus sequence typing), you obtain a very large table:

, , Sequence.Type = ST10

         Phylogroup
Source      A  B1   C   D
  Avian     0   0   0   0
  Human   120   0   0   0
  Porcine 277   0   0   0

, , Sequence.Type = ST1049

         Phylogroup
Source      A  B1   C   D
  Avian     0   0   0   0
  Human     0  94   0   0
  Porcine   0   0   0   0

, , Sequence.Type = ST10888

         Phylogroup
Source      A  B1   C   D
  Avian     0   0   0   0
  Human     0   0   0   0
  Porcine 203   0   0   0

, , Sequence.Type = ST10890

         Phylogroup
Source      A  B1   C   D
  Avian     0   0   0   0
  Human     0   0 171   0
  Porcine   0   0   0   0

, , Sequence.Type = ST137

         Phylogroup
Source      A  B1   C   D
  Avian     0   0   0   0
  Human     0   0   0 205
  Porcine   0   0   0   0

, , Sequence.Type = ST156

         Phylogroup
Source      A  B1   C   D
  Avian     0   0   0   0
  Human     0 114   0   0
  Porcine   0   0   0   0

, , Sequence.Type = ST3011

--- Cropped output ---

This is quite a long cross-table that we have cropped on the output, maybe you could find more convenient transforming it to a flat contingency table with ftable().

How would you generate a flat table using the previous cross-tabulated table?

ftable(coli_xgenomes) ftable(coli_xgenomes, col.vars=1 ftable(coli_xgenomes, row.vars=3 ftable(coli_xgenomes, col.vars=c(1,2)

If you test the different options, you will notice that the format of the table can be defined by the order of the variables and also using the arguments row.vars and col.vars to define which variables will be summarized as column or row.

Again, rather than concepts from R or RStudio, cross-tabulation and flat contingency tables are general concepts in data analysis.

3 Data aggregation and transformation

3.1 By() & aggregate()

While frequency tables can be very quickly generated with table() and xtable(), sometimes you may want other calculations than frequency, like basic statistics per group or other, even custom, calculations.

You have already tried the function by() as a very useful trick to make group-calculations. However, this function has some limitations when we have large datasets and when we try to use multiple factors that can be solved with aggregate(). In both cases, the function can be any function that suits your data, either from R packages or a custom function.

In the following example, we are using a smaller dataset named vacines2 that we can obtain by sampling (randomly extraction of a portion of data) with the R function sample().

vaccines2 <- vaccines[sample(x = 1:nrow(vaccines),size = 50000, replace=FALSE),]

#using by()
by(vaccines2$NumberDosesReceived, INDICES = vaccines2$Region, FUN=mean, na.rm=TRUE)

vaccines2$Region: AT
[1] 1820.799
------------------------------------------------------------ 
vaccines2$Region: BE
[1] 129075
------------------------------------------------------------ 
vaccines2$Region: BG
[1] 7526.923
------------------------------------------------------------ 
vaccines2$Region: CY
[1] 961.1449
------------------------------------------------------------ 
vaccines2$Region: CZ
[1] 42646.17
------------------------------------------------------------ 
vaccines2$Region: DE
[1] 1508313
------------------------------------------------------------ 
vaccines2$Region: DK
[1] 846.0469
------------------------------------------------------------ 
vaccines2$Region: EE
[1] 568.2353
------------------------------------------------------------ 
vaccines2$Region: EL
--- Cropped output ---

In the example above, we could calculate the mean by groups. Can we do it with more than one grouping factor? Let’s try some alternatives and see the output

by(vaccines2$NumberDosesReceived, INDICES = vaccines2$Region + vaccines2$Vaccine, FUN=mean, na.rm=TRUE)

Error in vaccines2$Region + vaccines2$Vaccine: non-numeric argument to binary operator

by(vaccines2$NumberDosesReceived, INDICES = c(vaccines2$Region,vaccines2$Vaccine), FUN=mean, na.rm=TRUE)

Error in tapply(seq_len(50000L), list(`c(vaccines2$Region, vaccines2$Vaccine)` = c("FI1D3", : arguments must have same length

by(vaccines2$NumberDosesReceived, INDICES = list(vaccines2$Region,vaccines2$Vaccine), FUN=mean, na.rm=TRUE)

: AT
: AZ
[1] 0
------------------------------------------------------------ 
: BE
: AZ
[1] 7200
------------------------------------------------------------ 
: BG
: AZ
[1] 15120
------------------------------------------------------------ 
: CY
: AZ
[1] 1293.151
------------------------------------------------------------ 
: CZ
: AZ
[1] 1000
------------------------------------------------------------ 
: DE
: AZ
[1] NA
------------------------------------------------------------ 
: DK
--- Cropped output ---

When you find difficult using by(), aggregate() is usually the best quick alternative

#aggregate is more convenient sometimes
aggregate(vaccines2$NumberDosesReceived ~ vaccines2$Region, FUN=mean)

   vaccines2$Region vaccines2$NumberDosesReceived
1                AT                  1.820799e+03
2                BE                  1.290750e+05
3                BG                  7.526923e+03
4                CY                  9.611449e+02
5                CZ                  4.264617e+04
6                DE                  1.508313e+06
7                DK                  8.460469e+02
8                EE                  5.682353e+02
9                EL                  2.371864e+04
10               ES                  3.382172e+05
11               FI                  1.116314e+05
12               FR                  1.957214e+05
13               HR                  8.688250e+04
14               HU                  6.722391e+04
--- Cropped output ---

aggregate(NumberDosesReceived ~ Region+Vaccine, data=vaccines2, FUN=mean)

    Region   Vaccine NumberDosesReceived
1       AT        AZ        0.000000e+00
2       BE        AZ        7.200000e+03
3       BG        AZ        1.512000e+04
4       CY        AZ        1.293151e+03
5       CZ        AZ        1.000000e+03
6       DK        AZ        1.824000e+03
7       EE        AZ        0.000000e+00
8       EL        AZ        3.296000e+04
9       ES        AZ        4.043429e+05
10      FR        AZ        0.000000e+00
11      HR        AZ        8.820000e+04
12      HU        AZ        1.478125e+05
13      IE        AZ        3.272727e+03
14      IS        AZ        2.492857e+03
--- Cropped output ---

aggregate(FirstDoseRefused ~ TargetGroup, data=vaccines2, FUN=median)

   TargetGroup FirstDoseRefused
1     1_Age<60                0
2     1_Age60+                0
3       Age<18                0
4     Age18_24                0
5     Age25_49                0
6     Age50_59                0
7     Age60_69                0
8     Age70_79                0
9       Age80+                0
10         ALL                0
11         HCW                0
12        LTCF                0
NA
NA
--- Cropped output ---

#note that by default NAs are disregarded
aggregate(FirstDoseRefused ~ TargetGroup, data=vaccines2, na.action = NULL, FUN=median)

   TargetGroup FirstDoseRefused
1     1_Age<60               NA
2     1_Age60+               NA
3       Age<18               NA
4       Age0_4               NA
5     Age10_14               NA
6     Age15_17               NA
7     Age18_24               NA
8     Age25_49               NA
9       Age5_9               NA
10    Age50_59               NA
11    Age60_69               NA
12    Age70_79               NA
13      Age80+               NA
14      AgeUNK               NA
--- Cropped output ---

#we can make it for several numeric variables at the same time
aggregate(cbind(NumberDosesReceived,FirstDose,SecondDose) ~ as.factor(TargetGroup), data=vaccines2, FUN=mean)

   as.factor(TargetGroup) NumberDosesReceived    FirstDose   SecondDose
1                  Age<18             0.00000   360.761905   207.704082
2                  Age0_4            37.50000     4.709091     4.540909
3                Age10_14            96.20419   226.910995    96.395288
4                Age15_17           142.01474   209.975430   158.481572
5                Age18_24           189.38614   216.421782    96.994059
6                Age25_49            40.58594   771.611328   702.041016
7                  Age5_9           269.50000    21.011765    13.173529
8                Age50_59           148.78193   836.726916   518.021611
9                Age60_69           117.41410   513.113924   252.345389
10               Age70_79            66.21771   296.022140   477.173432
11                 Age80+           141.37525   151.667976   189.634578
12                 AgeUNK           577.50000     1.515625     1.351562
13                    ALL         79578.49621 23380.368939 15199.045455
14                    HCW           451.43590    32.707692   120.261538
--- Cropped output ---

We can also add a custom function, using the short, usually with the inline notation:

#we can also use custom functions here
aggregate(cbind(FirstDose,SecondDose) ~ as.factor(TargetGroup), data=vaccines2, FUN=function(x) mean(x)*100/mean(vaccines2$NumberDosesReceived, na.rm=TRUE))

   as.factor(TargetGroup)    FirstDose   SecondDose
1                1_Age<60 1.413636e+02 1.114906e+02
2                1_Age60+ 2.662959e+01 7.600026e+01
3                  Age<18 4.873412e+00 3.680116e+00
4                  Age0_4 3.089616e-03 3.031055e-03
5                Age10_14 1.623797e+00 6.841251e-01
6                Age15_17 5.816713e-01 4.111577e-01
7                Age18_24 2.119778e+00 1.974510e+00
8                Age25_49 1.093650e+01 9.386779e+00
9                  Age5_9 1.315910e-01 1.318426e-01
10               Age50_59 4.691836e+00 4.204253e+00
11               Age60_69 3.992111e+00 3.348901e+00
12               Age70_79 4.032144e+00 3.293795e+00
13                 Age80+ 2.271214e+00 1.823335e+00
14                 AgeUNK 8.045944e-02 1.872705e-02
15                    ALL 4.650848e+01 3.291632e+01
16                    HCW 1.761317e+00 1.155694e+00
17                   LTCF 1.955176e+00 1.179603e+00

Quick exercise (IV)

We are using again the coli_genomes dataframe.

Can you obtain the following table displaying the mean (%) of virulece factors (VF) and plasmids per genome nucleotide (Assembly_length) grouped by Source

aggregate(cbind(VF,Plasmids) ~ Source, data=coli_genomes, FUN=mean) aggregate(cbind(VF,Plasmids) ~ Source, data=coli_genomes, FUN=function(x) mean(x) * 100 / mean(Assembly_length)) aggregate(cbind(VF,Plasmids) ~ Source, data=coli_genomes, FUN=function(x) mean(x) * 100 / mean(coli_genomes$Assembly_length))

   Source           VF     Plasmids
1   Avian 1.455256e-04 5.291842e-05
2   Human 2.235803e-04 5.291842e-05
3 Porcine 8.929983e-05 1.289886e-04

3.2 Apply family of functions

The functions of the Apply family are designed to apply a function to each element of a data structure. It includes various functions, designed for matrices, dataframes or lists. What is special about these functions is that their arguments are not only data but also functions. Using an apply function can sometimes seem complicated, but once you get used to it, it’s actually very handy and faster than other alternatives, such as loops. In this section, we look at the apply() function and its variants, including lapply(), sapply(), tapply(), rapply() & mapply(). In general, Apply is a very efficient tool to perform repetitive calculations.

Rather than describing in detail all the functions, in the following examples we test some of the possibilities of some applies. Try yourself and check the code comments.

#apply()
apply(vaccines[,4:12], MARGIN = 1, FUN = mean, na.rm=TRUE)

    [1] 0.000000e+00 0.000000e+00 3.000000e+00 0.000000e+00 5.000000e-01
    [6] 6.250000e-01 6.250000e-01 5.000000e-01 0.000000e+00 6.250000e-01
   [11] 1.250000e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
   [16] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
   [21] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
   [26] 0.000000e+00 8.887500e+01 3.750000e+00 1.325000e+01 1.862500e+01
--- Cropped output ---

apply(vaccines[,4:12], 2, mean, na.rm=TRUE) # 1 for row-wise operation, 2 for column-wise

NumberDosesReceived NumberDosesExported           FirstDose    FirstDoseRefused 
       1.400034e+04        8.621084e+02        1.147629e+03        4.015204e-01 
         SecondDose     DoseAdditional1     DoseAdditional2     DoseAdditional3 
       1.044477e+03        8.282688e+02        2.215100e+02        3.164597e+01 
    DoseAdditional4 
       4.815256e-01 
--- Cropped output ---

apply(vaccines, 2, is.numeric)

        YearWeekISO    ReportingCountry         Denominator NumberDosesReceived 
              FALSE               FALSE               FALSE               FALSE 
NumberDosesExported           FirstDose    FirstDoseRefused          SecondDose 
              FALSE               FALSE               FALSE               FALSE 
    DoseAdditional1     DoseAdditional2     DoseAdditional3     DoseAdditional4 
              FALSE               FALSE               FALSE               FALSE 
    DoseAdditional5         UnknownDose              Region         TargetGroup 
              FALSE               FALSE               FALSE               FALSE 
            Vaccine          Population 
              FALSE               FALSE

apply(vaccines[,3:6], 2, is.numeric)

        Denominator NumberDosesReceived NumberDosesExported           FirstDose 
               TRUE                TRUE                TRUE                TRUE

Note that you can use any function, although apply()is best suited for numeric calculations as it coerces your data to an array (via as.matrix()). Thus, when a dataframe cannot be transformed in a matrix your function may return fail. In the example above is.numeric() returns false for all columns within the apply when the dataframe contains character data, but if we use a subset that only contains numeric data the result makes sense. As you can see below, sapply() and lapply() are best suited for this kind of functions.

#lapply() and sapply() are very useful
lapply(by(vaccines$Population,vaccines$ReportingCountry,mean), log10)

$AT
[1] 6.952307

$BE
[1] 7.064378

$BG
[1] 6.836669

$CY
[1] 5.955408

$CZ
[1] 7.021618

$DE
[1] 7.920154

$DK
[1] 6.767897

$EE
[1] 6.124304

$EL
--- Cropped output ---

sapply(by(vaccines$Population,vaccines$ReportingCountry,mean), log10)

      AT       BE       BG       CY       CZ       DE       DK       EE 
6.952307 7.064378 6.836669 5.955408 7.021618 7.920154 6.767897 6.124304 
      EL       ES       FI       FR       HR       HU       IE       IS 
7.022918 7.675960 6.743725 7.831098 6.594992 6.987135 6.702566 5.571271 
      IT       LI       LT       LU       LV       MT       NL       NO 
7.771600 4.593620 6.447600 5.808232 6.274627 5.715350 7.244198 6.733418 
      PL       PT       RO       SE       SI       SK 
7.576630 7.014051 7.280790 7.018045 6.323863 6.736098

class(lapply(by(vaccines$Population,vaccines$ReportingCountry,mean), log10) )

[1] "list"

#lapply take a list (or object that can be coerced as one) and gives a list
class(sapply(by(vaccines$Population,vaccines$ReportingCountry,mean), log10) )

[1] "numeric"

#sapply is actually a 'wrapper' of lapply that returns a vector or matrix instead of a list


sapply(list(vaccines2$Population, vaccines2$FirstDose,vaccines2$SecondDose, vaccines2$NumberDosesReceived), median) # we can do it with several variables

[1] 5548241       0       0      NA

sapply(vaccines2,class) #again, you can use any function, not only numeric calculations

        YearWeekISO    ReportingCountry         Denominator NumberDosesReceived 
        "character"         "character"           "integer"           "integer" 
NumberDosesExported           FirstDose    FirstDoseRefused          SecondDose 
          "integer"           "integer"           "integer"           "integer" 
    DoseAdditional1     DoseAdditional2     DoseAdditional3     DoseAdditional4 
          "integer"           "integer"           "integer"           "integer" 
    DoseAdditional5         UnknownDose              Region         TargetGroup 
          "integer"           "integer"         "character"         "character" 
            Vaccine          Population 
        "character"           "integer"

sapply(vaccines2, is.numeric)

        YearWeekISO    ReportingCountry         Denominator NumberDosesReceived 
              FALSE               FALSE                TRUE                TRUE 
NumberDosesExported           FirstDose    FirstDoseRefused          SecondDose 
               TRUE                TRUE                TRUE                TRUE 
    DoseAdditional1     DoseAdditional2     DoseAdditional3     DoseAdditional4 
               TRUE                TRUE                TRUE                TRUE 
    DoseAdditional5         UnknownDose              Region         TargetGroup 
               TRUE                TRUE               FALSE               FALSE 
            Vaccine          Population 
              FALSE                TRUE

#other apply functions are more case-specific:

#mapply() is the matrix (or multivariable) version
mapply(sub,vaccines2[,4],vaccines2[,6],vaccines2[,7])

Warning in (function (pattern, replacement, x, ignore.case = FALSE, perl =
FALSE, : argument 'pattern' has length > 1 and only the first element will be
used

Warning in (function (pattern, replacement, x, ignore.case = FALSE, perl =
FALSE, : argument 'replacement' has length > 1 and only the first element will
be used

         NumberDosesReceived
    [1,] NA                 
    [2,] NA                 
    [3,] NA                 
    [4,] NA                 
    [5,] NA                 
    [6,] NA                 
    [7,] NA                 
    [8,] NA                 
    [9,] NA                 
--- Cropped output ---

mapply(rep, letters[1:4], 4:1)

$a
[1] "a" "a" "a" "a"

$b
[1] "b" "b" "b"

$c
[1] "c" "c"

$d
[1] "d"

#tapply() breaks a vector into pieces, can be used instead of aggregate
tapply(vaccines$NumberDosesReceived, vaccines$ReportingCountry, median,na.rm=TRUE)

    AT     BE     BG     CY     CZ     DE     DK     EE     EL     ES     FI 
     0      0      0      0      0 842400      0      0      0      0  91875 
    FR     HR     HU     IE     IS     IT     LI     LT     LU     LV     MT 
     0  34800      0      0      0      0      0      0      0      0     NA 
    NL     NO     PL     PT     RO     SE     SI     SK 
     0      0      0      0      0      0      0      0

tapply(coli_genomes$VF, coli_genomes$Source, mean, na.rm=TRUE)

    Avian     Human   Porcine 
 7.333333 11.266667  4.500000

#vapply() is similar to sapply(), but has a pre-specified type of return value
vapply(vaccines[,8:11],mean,numeric(1))

     SecondDose DoseAdditional1 DoseAdditional2 DoseAdditional3 
     1044.47747       828.26878       221.51000        31.64597

vapply(vaccines[,8:11],function(x) x^2,numeric(nrow(vaccines)))

            SecondDose DoseAdditional1 DoseAdditional2 DoseAdditional3
     [1,] 0.000000e+00    0.000000e+00    0.000000e+00               0
     [2,] 0.000000e+00    0.000000e+00    0.000000e+00               0
     [3,] 0.000000e+00    1.000000e+00    8.100000e+01             169
     [4,] 0.000000e+00    0.000000e+00    0.000000e+00               0
     [5,] 0.000000e+00    0.000000e+00    1.000000e+00               9
     [6,] 0.000000e+00    0.000000e+00    1.000000e+00              16
     [7,] 0.000000e+00    0.000000e+00    9.000000e+00               4
     [8,] 0.000000e+00    0.000000e+00    1.000000e+00               9
     [9,] 0.000000e+00    0.000000e+00    0.000000e+00               0
--- Cropped output ---

#rapply can be a handy trick for recursive calculations
rapply(vaccines, mean, class="integer")

        Denominator NumberDosesReceived NumberDosesExported           FirstDose 
                 NA                  NA                  NA        1.147629e+03 
   FirstDoseRefused          SecondDose     DoseAdditional1     DoseAdditional2 
                 NA        1.044477e+03        8.282688e+02        2.215100e+02 
    DoseAdditional3     DoseAdditional4     DoseAdditional5         UnknownDose 
       3.164597e+01        4.815256e-01        4.917829e-06        9.610626e+00 
         Population 
       1.584276e+07

rapply(vaccines, table, class="factor")

NULL

vaccines$ReportingCountry<-as.factor(vaccines$ReportingCountry)
vaccines$Vaccine<-as.factor(vaccines$Vaccine)
vaccines$TargetGroup<-as.factor(vaccines$TargetGroup)
vaccines$Region<-as.factor(vaccines$Region)
rapply(vaccines, table, class="factor") #factors need to be defined and now it gives the counts for each group of each factor

 ReportingCountry.AT  ReportingCountry.BE  ReportingCountry.BG 
               17292                 7330                 6001 
 ReportingCountry.CY  ReportingCountry.CZ  ReportingCountry.DE 
                7098                 6593                  564 
 ReportingCountry.DK  ReportingCountry.EE  ReportingCountry.EL 
                4821                 7755                16413 
 ReportingCountry.ES  ReportingCountry.FI  ReportingCountry.FR 
               12960               407160                22743 
 ReportingCountry.HR  ReportingCountry.HU  ReportingCountry.IE 
                9270                 6712                 6367 
--- Cropped output ---

rapply(vaccines, median, how="list", class="integer", na.rm=TRUE) #returns a list

$YearWeekISO
NULL

$ReportingCountry
NULL

$Denominator
[1] 272851

$NumberDosesReceived
--- Cropped output ---

rapply(vaccines, median,  how="unlist",class="integer", na.rm=TRUE) #gives a vector

        Denominator NumberDosesReceived NumberDosesExported           FirstDose 
             272851                   0                   0                   0 
   FirstDoseRefused          SecondDose     DoseAdditional1     DoseAdditional2 
                  0                   0                   0                   0 
    DoseAdditional3     DoseAdditional4     DoseAdditional5         UnknownDose 
                  0                   0                   0                   0 
         Population 
            5548241

#what do you mean by RECURSIVELY?
x <- list("a",list(24,443),434,list(54,list(6443,7234))) #this is a complex list with sublists

str(x)

List of 4
 $ : chr "a"
 $ :List of 2
  ..$ : num 24
  ..$ : num 443
 $ : num 434
 $ :List of 2
  ..$ : num 54
  ..$ :List of 2
  .. ..$ : num 6443
  .. ..$ : num 7234

rapply(x,log2,class=c("numeric"))

[1]  4.584963  8.791163  8.761551  5.754888 12.653517 12.820578

(r <- rapply(x,log2,class=c("numeric"), how="unlist"))

[1]  4.584963  8.791163  8.761551  5.754888 12.653517 12.820578

str(r)

 num [1:6] 4.58 8.79 8.76 5.75 12.65 ...

Note that tapply() and by() are very similar. Indeed, by() is a wrapper of tapply(). On the other hand, vapply() is similar to sapply, but has a pre-specified type of return value, so it can be safer (or faster) to use sometimes. Finally, rapply() is not very often used, but it can be the best option for complex datasets, like those including nested lists or complex lists with several dataframes and/or vectors.

The applications of apply functions are very wide, particularly the apply() and lapply(). You can use them to parse data with many different input and output structures and almost any kind of R functions, including plots (see Lesson R8).

4 References

Manipulación de datos en R: https://r-coder.com/manipulacion-datos-r/ [ES] & https://r-coder.com/r-data-manipulation/ [EN]
R in action. Robert I. Kabacoff. March 2022 ISBN 9781617296055
Working with tables in R: https://bookdown.org/kdonovan125/ibis_data_analysis_r4/working-with-tables-in-r.html
About flat tables in R: https://cran.r-project.org/web/packages/memisc/vignettes/ftable-matrix.html
data.table cheatsheet: https://raw.githubusercontent.com/rstudio/cheatsheets/main/datatable.pdf
Data aggregation: https://r-coder.com/aggregate-r/
About Applies: https://www.r-bloggers.com/2016/03/apply-lapply-rapply-sapply-functions-in-r-2/ & https://gist.github.com/lyndametref/4d137fcba1ec4d9af80ad53245b358ff
Efficient data management in R: https://www.mzes.uni-mannheim.de/socialsciencedatalab/article/efficient-data-r/

5 Review Exercises¹

We are using the Covid19 test data for exercises. You can download the updated csv file from https://opendata.ecdc.europa.eu/covid19/testing/csv/data.csv (see also https://www.ecdc.europa.eu/en/publications-data/covid-19-testing). Read and explore the data. I also suggest to save the table in your computer as covid_tests.csv.

1. Generate two contingency tables showing the number of tests done (1) by country per week and (2) by country per month.

Hint. For the second table, use the function ISOweek2date() from the package “ISOweek” to transform the ISO date_week to standard date format.

2. Remove all the character columns to create a subset dataframe named minitests. You can use `subset()` and `sapply()` here.

3. Use apply() to obtain the min, max, median and mean of each column.

4. Use `tapply()` to obtain the mean, median and min of new_cases per country and construct a dataframe with the result.

Hint. Consider how to handle NA’s.

6 Extra exercises

The topics in this lesson can be dense and bewildering the first time. I selected some sheets of exercises from great websites that can give you an extra practice.

7 Session Info

sessionInfo()

R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.6.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Madrid
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] data.table_1.16.2  webexercises_1.1.0 formatR_1.14       knitr_1.48        

loaded via a namespace (and not attached):
 [1] digest_0.6.37     fastmap_1.2.0     xfun_0.48         htmltools_0.5.8.1
 [5] rmarkdown_2.28    cli_3.6.3         compiler_4.4.1    rstudioapi_0.17.1
 [9] tools_4.4.1       evaluate_1.0.1    yaml_2.3.10       rlang_1.1.4      
[13] jsonlite_1.8.9    htmlwidgets_1.6.4

Footnotes

Check proposed answers in the repo: https://github.com/r4biochemists/r4biochemists.github.io/tree/main/answers2exercises ↩︎

1 Transform dataframes

1.1 Sorting and subsetting data

1.2 Combining dataframes

Quick exercise (I)

1.3 Data matrix format (wide vs. long table)

Quick exercise (II)

2 Working efficiently with large datasets

2.1 Fast loading of huge datasets and creation of contingency tables

2.2 Frequency tables: table() vs. xtabs()

Quick exercise (III)

3 Data aggregation and transformation

3.1 By() & aggregate()

Quick exercise (IV)

3.2 Apply family of functions

Quick exercise (V)

4 References

5 Review Exercises1

1. Generate two contingency tables showing the number of tests done (1) by country per week and (2) by country per month.

2. Remove all the character columns to create a subset dataframe named minitests. You can use subset() and sapply() here.

3. Use apply() to obtain the min, max, median and mean of each column.

4. Use tapply() to obtain the mean, median and min of new_cases per country and construct a dataframe with the result.

6 Extra exercises

7 Session Info

Footnotes

2.2 Frequency tables: `table()` vs. `xtabs()`

5 Review Exercises¹

2. Remove all the character columns to create a subset dataframe named minitests. You can use `subset()` and `sapply()` here.

4. Use `tapply()` to obtain the mean, median and min of new_cases per country and construct a dataframe with the result.