Pivoting

Introduction

This vignette describes the use of the new pivot_longer() and pivot_wider() functions. Their goal is to improve the usability of gather() and spread(), and incorporate state-of-the-art features found in other packages.

For some time, it’s been obvious that there is something fundamentally wrong with the design of spread() and gather(). Many people don’t find the names intuitive and find it hard to remember which direction corresponds to spreading and which to gathering. It also seems surprisingly hard to remember the arguments to these functions, meaning that many people (including me!) have to consult the documentation every time.

There are two important new features inspired by other R packages that have been advancing reshaping in R:

In this vignette, you’ll learn the key ideas behind pivot_longer() and pivot_wider() as you see them used to solve a variety of data reshaping challenges ranging from simple to complex.

To begin we’ll load some needed packages. In real analysis code, I’d imagine you’d do with the library(tidyverse), but I can’t do that here since this vignette is embedded in a package.

library(tidyr)
library(dplyr)
library(readr)

Longer

pivot_longer() makes datasets longer by increasing the number of rows and decreasing the number of columns. I don’t believe it makes sense to describe a dataset as being in “long form”. Length is a relative term, and you can only say (e.g.) that dataset A is longer than dataset B.

pivot_longer() is commonly needed to tidy wild-caught datasets as they often optimise for ease of data entry or ease of comparison rather than ease of analysis. The following sections show how to use pivot_longer() for a wide range of realistic datasets.

String data in column names

The relig_income dataset stores counts based on a survey which (among other things) asked people about their religion and annual income:

relig_income
#> # A tibble: 18 x 11
#>    religion `<$10k` `$10-20k` `$20-30k` `$30-40k` `$40-50k` `$50-75k`
#>    <chr>      <dbl>     <dbl>     <dbl>     <dbl>     <dbl>     <dbl>
#>  1 Agnostic      27        34        60        81        76       137
#>  2 Atheist       12        27        37        52        35        70
#>  3 Buddhist      27        21        30        34        33        58
#>  4 Catholic     418       617       732       670       638      1116
#>  5 Don’t k…      15        14        15        11        10        35
#>  6 Evangel…     575       869      1064       982       881      1486
#>  7 Hindu          1         9         7         9        11        34
#>  8 Histori…     228       244       236       238       197       223
#>  9 Jehovah…      20        27        24        24        21        30
#> 10 Jewish        19        19        25        25        30        95
#> # … with 8 more rows, and 4 more variables: `$75-100k` <dbl>,
#> #   `$100-150k` <dbl>, `>150k` <dbl>, `Don't know/refused` <dbl>

This dataset contains three variables:

To tidy it we use pivot_longer():

relig_income %>% 
  pivot_longer(-religion, names_to = "income", values_to = "count")
#> # A tibble: 180 x 3
#>    religion income             count
#>    <chr>    <chr>              <dbl>
#>  1 Agnostic <$10k                 27
#>  2 Agnostic $10-20k               34
#>  3 Agnostic $20-30k               60
#>  4 Agnostic $30-40k               81
#>  5 Agnostic $40-50k               76
#>  6 Agnostic $50-75k              137
#>  7 Agnostic $75-100k             122
#>  8 Agnostic $100-150k            109
#>  9 Agnostic >150k                 84
#> 10 Agnostic Don't know/refused    96
#> # … with 170 more rows

Neither the names_to nor the values_to column exists in relig_income, so we provide them as character strings surrounded in quotes.

Numeric data in column names

The billboard dataset records the billboard rank of songs in the year 2000. It has a form similar to the relig_income data, but the data encoded in the column names is really a number, not a string.

billboard
#> # A tibble: 317 x 79
#>    artist track date.entered   wk1   wk2   wk3   wk4   wk5   wk6   wk7
#>    <chr>  <chr> <date>       <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#>  1 2 Pac  Baby… 2000-02-26      87    82    72    77    87    94    99
#>  2 2Ge+h… The … 2000-09-02      91    87    92    NA    NA    NA    NA
#>  3 3 Doo… Kryp… 2000-04-08      81    70    68    67    66    57    54
#>  4 3 Doo… Loser 2000-10-21      76    76    72    69    67    65    55
#>  5 504 B… Wobb… 2000-04-15      57    34    25    17    17    31    36
#>  6 98^0   Give… 2000-08-19      51    39    34    26    26    19     2
#>  7 A*Tee… Danc… 2000-07-08      97    97    96    95   100    NA    NA
#>  8 Aaliy… I Do… 2000-01-29      84    62    51    41    38    35    35
#>  9 Aaliy… Try … 2000-03-18      59    53    38    28    21    18    16
#> 10 Adams… Open… 2000-08-26      76    76    74    69    68    67    61
#> # … with 307 more rows, and 69 more variables: wk8 <dbl>, wk9 <dbl>,
#> #   wk10 <dbl>, wk11 <dbl>, wk12 <dbl>, wk13 <dbl>, wk14 <dbl>,
#> #   wk15 <dbl>, wk16 <dbl>, wk17 <dbl>, wk18 <dbl>, wk19 <dbl>,
#> #   wk20 <dbl>, wk21 <dbl>, wk22 <dbl>, wk23 <dbl>, wk24 <dbl>,
#> #   wk25 <dbl>, wk26 <dbl>, wk27 <dbl>, wk28 <dbl>, wk29 <dbl>,
#> #   wk30 <dbl>, wk31 <dbl>, wk32 <dbl>, wk33 <dbl>, wk34 <dbl>,
#> #   wk35 <dbl>, wk36 <dbl>, wk37 <dbl>, wk38 <dbl>, wk39 <dbl>,
#> #   wk40 <dbl>, wk41 <dbl>, wk42 <dbl>, wk43 <dbl>, wk44 <dbl>,
#> #   wk45 <dbl>, wk46 <dbl>, wk47 <dbl>, wk48 <dbl>, wk49 <dbl>,
#> #   wk50 <dbl>, wk51 <dbl>, wk52 <dbl>, wk53 <dbl>, wk54 <dbl>,
#> #   wk55 <dbl>, wk56 <dbl>, wk57 <dbl>, wk58 <dbl>, wk59 <dbl>,
#> #   wk60 <dbl>, wk61 <dbl>, wk62 <dbl>, wk63 <dbl>, wk64 <dbl>,
#> #   wk65 <dbl>, wk66 <lgl>, wk67 <lgl>, wk68 <lgl>, wk69 <lgl>,
#> #   wk70 <lgl>, wk71 <lgl>, wk72 <lgl>, wk73 <lgl>, wk74 <lgl>,
#> #   wk75 <lgl>, wk76 <lgl>

We can start with the same basic specification as for the relig_income dataset. Here we want the names to become a variable called week, and the values to become a variable called rank. I also use values_drop_na to drop rows that correspond to missing values. Not every song stays in the charts for all 76 weeks, so the structure of the input data force the creation of unnessary explicit NAs.

billboard %>% 
  pivot_longer(
    cols = starts_with("wk"), 
    names_to = "week", 
    values_to = "rank",
    values_drop_na = TRUE
  )
#> # A tibble: 5,307 x 5
#>    artist  track                   date.entered week   rank
#>    <chr>   <chr>                   <date>       <chr> <dbl>
#>  1 2 Pac   Baby Don't Cry (Keep... 2000-02-26   wk1      87
#>  2 2 Pac   Baby Don't Cry (Keep... 2000-02-26   wk2      82
#>  3 2 Pac   Baby Don't Cry (Keep... 2000-02-26   wk3      72
#>  4 2 Pac   Baby Don't Cry (Keep... 2000-02-26   wk4      77
#>  5 2 Pac   Baby Don't Cry (Keep... 2000-02-26   wk5      87
#>  6 2 Pac   Baby Don't Cry (Keep... 2000-02-26   wk6      94
#>  7 2 Pac   Baby Don't Cry (Keep... 2000-02-26   wk7      99
#>  8 2Ge+her The Hardest Part Of ... 2000-09-02   wk1      91
#>  9 2Ge+her The Hardest Part Of ... 2000-09-02   wk2      87
#> 10 2Ge+her The Hardest Part Of ... 2000-09-02   wk3      92
#> # … with 5,297 more rows

It would be nice to easily determine how long each song stayed in the charts, but to do that, we’ll need to convert the week variable to an integer. We can do that by using two additional arguments: names_prefix strips off the wk prefix, and names_ptypes specifies that week should be an integer:

billboard %>% 
  pivot_longer(
    cols = starts_with("wk"), 
    names_to = "week", 
    names_prefix = "wk",
    names_ptypes = list(week = integer()),
    values_to = "rank",
    values_drop_na = TRUE,
  )
#> # A tibble: 5,307 x 5
#>    artist  track                   date.entered  week  rank
#>    <chr>   <chr>                   <date>       <int> <dbl>
#>  1 2 Pac   Baby Don't Cry (Keep... 2000-02-26       1    87
#>  2 2 Pac   Baby Don't Cry (Keep... 2000-02-26       2    82
#>  3 2 Pac   Baby Don't Cry (Keep... 2000-02-26       3    72
#>  4 2 Pac   Baby Don't Cry (Keep... 2000-02-26       4    77
#>  5 2 Pac   Baby Don't Cry (Keep... 2000-02-26       5    87
#>  6 2 Pac   Baby Don't Cry (Keep... 2000-02-26       6    94
#>  7 2 Pac   Baby Don't Cry (Keep... 2000-02-26       7    99
#>  8 2Ge+her The Hardest Part Of ... 2000-09-02       1    91
#>  9 2Ge+her The Hardest Part Of ... 2000-09-02       2    87
#> 10 2Ge+her The Hardest Part Of ... 2000-09-02       3    92
#> # … with 5,297 more rows

Many variables in column names

A more challenging situation occurs when you have multiple variables crammed into the column names. For example, take the who dataset:

who
#> # A tibble: 7,240 x 60
#>    country iso2  iso3   year new_sp_m014 new_sp_m1524 new_sp_m2534
#>    <chr>   <chr> <chr> <int>       <int>        <int>        <int>
#>  1 Afghan… AF    AFG    1980          NA           NA           NA
#>  2 Afghan… AF    AFG    1981          NA           NA           NA
#>  3 Afghan… AF    AFG    1982          NA           NA           NA
#>  4 Afghan… AF    AFG    1983          NA           NA           NA
#>  5 Afghan… AF    AFG    1984          NA           NA           NA
#>  6 Afghan… AF    AFG    1985          NA           NA           NA
#>  7 Afghan… AF    AFG    1986          NA           NA           NA
#>  8 Afghan… AF    AFG    1987          NA           NA           NA
#>  9 Afghan… AF    AFG    1988          NA           NA           NA
#> 10 Afghan… AF    AFG    1989          NA           NA           NA
#> # … with 7,230 more rows, and 53 more variables: new_sp_m3544 <int>,
#> #   new_sp_m4554 <int>, new_sp_m5564 <int>, new_sp_m65 <int>,
#> #   new_sp_f014 <int>, new_sp_f1524 <int>, new_sp_f2534 <int>,
#> #   new_sp_f3544 <int>, new_sp_f4554 <int>, new_sp_f5564 <int>,
#> #   new_sp_f65 <int>, new_sn_m014 <int>, new_sn_m1524 <int>,
#> #   new_sn_m2534 <int>, new_sn_m3544 <int>, new_sn_m4554 <int>,
#> #   new_sn_m5564 <int>, new_sn_m65 <int>, new_sn_f014 <int>,
#> #   new_sn_f1524 <int>, new_sn_f2534 <int>, new_sn_f3544 <int>,
#> #   new_sn_f4554 <int>, new_sn_f5564 <int>, new_sn_f65 <int>,
#> #   new_ep_m014 <int>, new_ep_m1524 <int>, new_ep_m2534 <int>,
#> #   new_ep_m3544 <int>, new_ep_m4554 <int>, new_ep_m5564 <int>,
#> #   new_ep_m65 <int>, new_ep_f014 <int>, new_ep_f1524 <int>,
#> #   new_ep_f2534 <int>, new_ep_f3544 <int>, new_ep_f4554 <int>,
#> #   new_ep_f5564 <int>, new_ep_f65 <int>, newrel_m014 <int>,
#> #   newrel_m1524 <int>, newrel_m2534 <int>, newrel_m3544 <int>,
#> #   newrel_m4554 <int>, newrel_m5564 <int>, newrel_m65 <int>,
#> #   newrel_f014 <int>, newrel_f1524 <int>, newrel_f2534 <int>,
#> #   newrel_f3544 <int>, newrel_f4554 <int>, newrel_f5564 <int>,
#> #   newrel_f65 <int>

country, iso2, iso3, and year are already variables, so they can be left as is. But the columns from new_sp_m014 to newrel_f65 encode four variables in their names:

We can break these variables up by specifying multiple column names in names_to, and then either providing names_sep or names_pattern. Here names_pattern is the most natural fit. It has a similar interface to extract: you give it a regular expression containing groups (defined by ()) and it puts each group in a column.

who %>% pivot_longer(
  cols = new_sp_m014:newrel_f65,
  names_to = c("diagnosis", "gender", "age"), 
  names_pattern = "new_?(.*)_(.)(.*)",
  values_to = "count"
)
#> # A tibble: 405,440 x 8
#>    country     iso2  iso3   year diagnosis gender age   count
#>    <chr>       <chr> <chr> <int> <chr>     <chr>  <chr> <int>
#>  1 Afghanistan AF    AFG    1980 sp        m      014      NA
#>  2 Afghanistan AF    AFG    1980 sp        m      1524     NA
#>  3 Afghanistan AF    AFG    1980 sp        m      2534     NA
#>  4 Afghanistan AF    AFG    1980 sp        m      3544     NA
#>  5 Afghanistan AF    AFG    1980 sp        m      4554     NA
#>  6 Afghanistan AF    AFG    1980 sp        m      5564     NA
#>  7 Afghanistan AF    AFG    1980 sp        m      65       NA
#>  8 Afghanistan AF    AFG    1980 sp        f      014      NA
#>  9 Afghanistan AF    AFG    1980 sp        f      1524     NA
#> 10 Afghanistan AF    AFG    1980 sp        f      2534     NA
#> # … with 405,430 more rows

We could go one step further and specify the types of the gender and age columns. I think this is good practice when you have categorical variables with a known set of values.

who %>% pivot_longer(
  cols = new_sp_m014:newrel_f65,
  names_to = c("diagnosis", "gender", "age"), 
  names_pattern = "new_?(.*)_(.)(.*)",
  names_ptypes = list(
    gender = factor(levels = c("f", "m")),
    age = factor(
      levels = c("014", "1524", "2534", "3544", "4554", "5564", "65"), 
      ordered = TRUE
    )
  ),
  values_to = "count",
)
#> # A tibble: 405,440 x 8
#>    country     iso2  iso3   year diagnosis gender age   count
#>    <chr>       <chr> <chr> <int> <chr>     <fct>  <ord> <int>
#>  1 Afghanistan AF    AFG    1980 sp        m      014      NA
#>  2 Afghanistan AF    AFG    1980 sp        m      1524     NA
#>  3 Afghanistan AF    AFG    1980 sp        m      2534     NA
#>  4 Afghanistan AF    AFG    1980 sp        m      3544     NA
#>  5 Afghanistan AF    AFG    1980 sp        m      4554     NA
#>  6 Afghanistan AF    AFG    1980 sp        m      5564     NA
#>  7 Afghanistan AF    AFG    1980 sp        m      65       NA
#>  8 Afghanistan AF    AFG    1980 sp        f      014      NA
#>  9 Afghanistan AF    AFG    1980 sp        f      1524     NA
#> 10 Afghanistan AF    AFG    1980 sp        f      2534     NA
#> # … with 405,430 more rows

Multiple observations per row

So far, we have been working with data frames that have one observation per row, but many important pivotting problems involve multiple observations per row. You can usually recognise this case because name of the column that you want to appear in the output is part of the column name in the input. In this section, you’ll learn how to pivot this sort of data.

The following example is adapted from the data.table vignette, as inspiration for tidyr’s solution to this problem.

family <- tribble(
  ~family,  ~dob_child1,  ~dob_child2, ~gender_child1, ~gender_child2,
       1L, "1998-11-26", "2000-01-29",             1L,             2L,
       2L, "1996-06-22",           NA,             2L,             NA,
       3L, "2002-07-11", "2004-04-05",             2L,             2L,
       4L, "2004-10-10", "2009-08-27",             1L,             1L,
       5L, "2000-12-05", "2005-02-28",             2L,             1L,
)
family <- family %>% mutate_at(vars(starts_with("dob")), parse_date)
family
#> # A tibble: 5 x 5
#>   family dob_child1 dob_child2 gender_child1 gender_child2
#>    <int> <date>     <date>             <int>         <int>
#> 1      1 1998-11-26 2000-01-29             1             2
#> 2      2 1996-06-22 NA                     2            NA
#> 3      3 2002-07-11 2004-04-05             2             2
#> 4      4 2004-10-10 2009-08-27             1             1
#> 5      5 2000-12-05 2005-02-28             2             1

Note that we have two pieces of information (or values) for each child: their gender and their dob (date of birth). These need to go into separate columns in the result. Again we supply multiple variables to names_to, using names_sep to split up each variable name. Note the special name .value: this tells pivot_longer() that that part of the column name specifies the “value” being measured (which will become a variable in the output).

family %>% 
  pivot_longer(
    -family, 
    names_to = c(".value", "child"), 
    names_sep = "_", 
    values_drop_na = TRUE
  )
#> # A tibble: 9 x 4
#>   family child  dob        gender
#>    <int> <chr>  <date>      <int>
#> 1      1 child1 1998-11-26      1
#> 2      1 child2 2000-01-29      2
#> 3      2 child1 1996-06-22      2
#> 4      3 child1 2002-07-11      2
#> 5      3 child2 2004-04-05      2
#> 6      4 child1 2004-10-10      1
#> 7      4 child2 2009-08-27      1
#> 8      5 child1 2000-12-05      2
#> 9      5 child2 2005-02-28      1

Note the use of values_drop_na = TRUE: the input shape forces the creation of explicit missing variables for observations that don’t exist.

This problem also exists in the anscombe dataset built in to base R:

anscombe
#>    x1 x2 x3 x4    y1   y2    y3    y4
#> 1  10 10 10  8  8.04 9.14  7.46  6.58
#> 2   8  8  8  8  6.95 8.14  6.77  5.76
#> 3  13 13 13  8  7.58 8.74 12.74  7.71
#> 4   9  9  9  8  8.81 8.77  7.11  8.84
#> 5  11 11 11  8  8.33 9.26  7.81  8.47
#> 6  14 14 14  8  9.96 8.10  8.84  7.04
#> 7   6  6  6  8  7.24 6.13  6.08  5.25
#> 8   4  4  4 19  4.26 3.10  5.39 12.50
#> 9  12 12 12  8 10.84 9.13  8.15  5.56
#> 10  7  7  7  8  4.82 7.26  6.42  7.91
#> 11  5  5  5  8  5.68 4.74  5.73  6.89

This dataset contains four pairs of variables (x1 and y1, x2 and y2, etc) that underlie Anscombe’s quartet, a collection of four datasets that have the same summary statistics (mean, sd, correlation etc), but have quite different data. We want to produce a dataset with columns set, x and y.

anscombe %>% 
  pivot_longer(everything(), 
    names_to = c(".value", "set"), 
    names_pattern = "(.)(.)"
  ) %>% 
  arrange(set)
#> # A tibble: 44 x 3
#>    set       x     y
#>    <chr> <dbl> <dbl>
#>  1 1        10  8.04
#>  2 1         8  6.95
#>  3 1        13  7.58
#>  4 1         9  8.81
#>  5 1        11  8.33
#>  6 1        14  9.96
#>  7 1         6  7.24
#>  8 1         4  4.26
#>  9 1        12 10.8 
#> 10 1         7  4.82
#> # … with 34 more rows

A similar situation can arise with panel data. For example, take this example dataset provided by Thomas Leeper. We can tidy it using the same approach as for anscombe:

pnl <- tibble(
  x = 1:4,
  a = c(1, 1,0, 0),
  b = c(0, 1, 1, 1),
  y1 = rnorm(4),
  y2 = rnorm(4),
  z1 = rep(3, 4),
  z2 = rep(-2, 4),
)

pnl %>% 
  pivot_longer(
    -c(x, a, b), 
    names_to = c(".value", "time"), 
    names_pattern = "(.)(.)"
  )
#> # A tibble: 8 x 6
#>       x     a     b time        y     z
#>   <int> <dbl> <dbl> <chr>   <dbl> <dbl>
#> 1     1     1     0 1      0.289      3
#> 2     1     1     0 2     -0.367     -2
#> 3     2     1     1 1     -1.37       3
#> 4     2     1     1 2     -0.138     -2
#> 5     3     0     1 1     -1.37       3
#> 6     3     0     1 2      0.0651    -2
#> 7     4     0     1 1      0.124      3
#> 8     4     0     1 2      1.60      -2

Duplicated column names

Occassionally you will come across datasets that have duplicated column names. Generally, such datasets are hard to work with in R, because when you refer to a column by name it only finds the first match. To create a tibble with duplicated names, you have to explicitly opt out of the name repair that usually prevents you from creating such a dataset:

df <- tibble(x = 1:3, y = 4:6, y = 5:7, y = 7:9, .name_repair = "minimal")
df
#> # A tibble: 3 x 4
#>       x     y     y     y
#>   <int> <int> <int> <int>
#> 1     1     4     5     7
#> 2     2     5     6     8
#> 3     3     6     7     9

When pivot_longer() encounters such data, it automatically adds another column to the output:

df %>% pivot_longer(-x, names_to = "name", values_to = "value")
#> Warning: Duplicate column names detected, adding .copy variable
#> # A tibble: 9 x 4
#>       x name  .copy value
#>   <int> <chr> <int> <int>
#> 1     1 y         1     4
#> 2     1 y         2     5
#> 3     1 y         3     7
#> 4     2 y         1     5
#> 5     2 y         2     6
#> 6     2 y         3     8
#> 7     3 y         1     6
#> 8     3 y         2     7
#> 9     3 y         3     9

Wider

pivot_wider() is the opposite of pivot_longer(): it makes a dataset wider by increasing the number of columns and decreasing the number of rows. It’s relatively rare to need pivot_wider() to make tidy data, but it’s often useful for creating summary tables for presentation, or data in a format needed by other tools.

Capture-recapture data

The fish_encounters dataset, contributed by Myfanwy Johnston, describes when fish swimming down a river are detected by automatic monitoring stations:

fish_encounters
#> # A tibble: 114 x 3
#>    fish  station  seen
#>    <fct> <fct>   <int>
#>  1 4842  Release     1
#>  2 4842  I80_1       1
#>  3 4842  Lisbon      1
#>  4 4842  Rstr        1
#>  5 4842  Base_TD     1
#>  6 4842  BCE         1
#>  7 4842  BCW         1
#>  8 4842  BCE2        1
#>  9 4842  BCW2        1
#> 10 4842  MAE         1
#> # … with 104 more rows

Many tools used to analyse this data need it in a form where each station is a column:

fish_encounters %>% pivot_wider(names_from = station, values_from = seen)
#> # A tibble: 19 x 12
#>    fish  Release I80_1 Lisbon  Rstr Base_TD   BCE   BCW  BCE2  BCW2   MAE
#>    <fct>   <int> <int>  <int> <int>   <int> <int> <int> <int> <int> <int>
#>  1 4842        1     1      1     1       1     1     1     1     1     1
#>  2 4843        1     1      1     1       1     1     1     1     1     1
#>  3 4844        1     1      1     1       1     1     1     1     1     1
#>  4 4845        1     1      1     1       1    NA    NA    NA    NA    NA
#>  5 4847        1     1      1    NA      NA    NA    NA    NA    NA    NA
#>  6 4848        1     1      1     1      NA    NA    NA    NA    NA    NA
#>  7 4849        1     1     NA    NA      NA    NA    NA    NA    NA    NA
#>  8 4850        1     1     NA     1       1     1     1    NA    NA    NA
#>  9 4851        1     1     NA    NA      NA    NA    NA    NA    NA    NA
#> 10 4854        1     1     NA    NA      NA    NA    NA    NA    NA    NA
#> # … with 9 more rows, and 1 more variable: MAW <int>

This dataset only records when a fish was detected by the station - it doesn’t record when it wasn’t detected (this is common with this type of data). That means the output data is filled with NAs. However, in this case we know that the absence of a record means that the fish was not seen, so we can ask pivot_wider() to fill these missing values in with zeros:

fish_encounters %>% pivot_wider(
  names_from = station, 
  values_from = seen,
  values_fill = list(seen = 0)
)
#> # A tibble: 19 x 12
#>    fish  Release I80_1 Lisbon  Rstr Base_TD   BCE   BCW  BCE2  BCW2   MAE
#>    <fct>   <int> <int>  <int> <int>   <int> <int> <int> <int> <int> <int>
#>  1 4842        1     1      1     1       1     1     1     1     1     1
#>  2 4843        1     1      1     1       1     1     1     1     1     1
#>  3 4844        1     1      1     1       1     1     1     1     1     1
#>  4 4845        1     1      1     1       1     0     0     0     0     0
#>  5 4847        1     1      1     0       0     0     0     0     0     0
#>  6 4848        1     1      1     1       0     0     0     0     0     0
#>  7 4849        1     1      0     0       0     0     0     0     0     0
#>  8 4850        1     1      0     1       1     1     1     0     0     0
#>  9 4851        1     1      0     0       0     0     0     0     0     0
#> 10 4854        1     1      0     0       0     0     0     0     0     0
#> # … with 9 more rows, and 1 more variable: MAW <int>

Aggregation

You can also use pivot_wider() to perform simple aggregation. For example, take the warpbreaks dataset built in to base R (converted to a tibble for the better print method):

warpbreaks <- warpbreaks %>% as_tibble() %>% select(wool, tension, breaks)
warpbreaks
#> # A tibble: 54 x 3
#>    wool  tension breaks
#>    <fct> <fct>    <dbl>
#>  1 A     L           26
#>  2 A     L           30
#>  3 A     L           54
#>  4 A     L           25
#>  5 A     L           70
#>  6 A     L           52
#>  7 A     L           51
#>  8 A     L           26
#>  9 A     L           67
#> 10 A     M           18
#> # … with 44 more rows

This is a designed experiment with nine replicates for every combination of wool (A and B) and tension (L, M, H):

warpbreaks %>% count(wool, tension)
#> # A tibble: 6 x 3
#>   wool  tension     n
#>   <fct> <fct>   <int>
#> 1 A     L           9
#> 2 A     M           9
#> 3 A     H           9
#> 4 B     L           9
#> 5 B     M           9
#> 6 B     H           9

What happens if we attempt to pivot the levels of wool into the columns?

warpbreaks %>% pivot_wider(names_from = wool, values_from = breaks)
#> Warning: Values in `breaks` are not uniquely identified; output will contain list-cols.
#> * Use `values_fn = list(breaks = list)` to suppress this warning.
#> * Use `values_fn = list(breaks = length)` to identify where the duplicates arise
#> * Use `values_fn = list(breaks = summary_fun)` to summarise duplicates
#> # A tibble: 3 x 3
#>   tension           A           B
#>   <fct>   <list<dbl>> <list<dbl>>
#> 1 L               [9]         [9]
#> 2 M               [9]         [9]
#> 3 H               [9]         [9]

We get a warning that each cell in the output corresponds to multiple cells in the input. The default behaviour produces list-columns, which contain all the individual values. A more useful output would be summary statistics, e.g. mean breaks for each combination of wool and tension:

warpbreaks %>% 
  pivot_wider(
    names_from = wool, 
    values_from = breaks,
    values_fn = list(breaks = mean)
  )
#> # A tibble: 3 x 3
#>   tension     A     B
#>   <fct>   <dbl> <dbl>
#> 1 L        44.6  28.2
#> 2 M        24    28.8
#> 3 H        24.6  18.8

For more complex summary operations, I recommend summarising before reshaping, but for simple cases it’s often convenient to summarise within pivot_wider().

Generate column name from multiple variables

Imagine, as in https://stackoverflow.com/questions/24929954, that we have information containing the combination of product, country, and year. In tidy form it might look like this:

production <- expand_grid(
    product = c("A", "B"), 
    country = c("AI", "EI"), 
    year = 2000:2014
  ) %>%
  filter((product == "A" & country == "AI") | product == "B") %>% 
  mutate(production = rnorm(nrow(.)))
production
#> # A tibble: 45 x 4
#>    product country  year production
#>    <chr>   <chr>   <int>      <dbl>
#>  1 A       AI       2000     -0.408
#>  2 A       AI       2001      0.746
#>  3 A       AI       2002     -1.09 
#>  4 A       AI       2003      0.614
#>  5 A       AI       2004      2.63 
#>  6 A       AI       2005     -0.219
#>  7 A       AI       2006     -0.688
#>  8 A       AI       2007      0.490
#>  9 A       AI       2008     -0.444
#> 10 A       AI       2009     -0.718
#> # … with 35 more rows

We want to widen the data so we have one column for each combination of product and country. The key is to specify multiple variables for names_from:

production %>% pivot_wider(
  names_from = c(product, country), 
  values_from = production
)
#> # A tibble: 15 x 4
#>     year   A_AI     B_AI     B_EI
#>    <int>  <dbl>    <dbl>    <dbl>
#>  1  2000 -0.408 -0.340    0.546  
#>  2  2001  0.746  0.00822  0.00232
#>  3  2002 -1.09   0.0316  -0.908  
#>  4  2003  0.614 -1.46    -0.636  
#>  5  2004  2.63   0.698    0.672  
#>  6  2005 -0.219  0.745   -0.708  
#>  7  2006 -0.688 -0.501    0.458  
#>  8  2007  0.490  0.215   -0.250  
#>  9  2008 -0.444  0.285   -0.210  
#> 10  2009 -0.718  0.389    0.0947 
#> # … with 5 more rows

Tidy census

The us_rent_income dataset contains information about median income and rent for each state in the US for 2017 (from the American Community Survey, retrieved with the tidycensus package).

us_rent_income
#> # A tibble: 104 x 5
#>    GEOID NAME       variable estimate   moe
#>    <chr> <chr>      <chr>       <dbl> <dbl>
#>  1 01    Alabama    income      24476   136
#>  2 01    Alabama    rent          747     3
#>  3 02    Alaska     income      32940   508
#>  4 02    Alaska     rent         1200    13
#>  5 04    Arizona    income      27517   148
#>  6 04    Arizona    rent          972     4
#>  7 05    Arkansas   income      23789   165
#>  8 05    Arkansas   rent          709     5
#>  9 06    California income      29454   109
#> 10 06    California rent         1358     3
#> # … with 94 more rows

Here both estimate and moe are values columns, so we can supply them to values_from:

us_rent_income %>% 
  pivot_wider(names_from = variable, values_from = c(estimate, moe))
#> # A tibble: 52 x 6
#>    GEOID NAME             estimate_income estimate_rent moe_income moe_rent
#>    <chr> <chr>                      <dbl>         <dbl>      <dbl>    <dbl>
#>  1 01    Alabama                    24476           747        136        3
#>  2 02    Alaska                     32940          1200        508       13
#>  3 04    Arizona                    27517           972        148        4
#>  4 05    Arkansas                   23789           709        165        5
#>  5 06    California                 29454          1358        109        3
#>  6 08    Colorado                   32401          1125        109        5
#>  7 09    Connecticut                35326          1123        195        5
#>  8 10    Delaware                   31560          1076        247       10
#>  9 11    District of Col…           43198          1424        681       17
#> 10 12    Florida                    25952          1077         70        3
#> # … with 42 more rows

Note that the name of the variable is automatically appended to the output columns.

Contact list

A final challenge is inspired by Jiena Gu. Imagine you have a contact list that you’ve copied and pasted from a website:

contacts <- tribble(
  ~field, ~value,
  "name", "Jiena McLellan",
  "company", "Toyota", 
  "name", "John Smith", 
  "company", "google", 
  "email", "[email protected]",
  "name", "Huxley Ratcliffe"
)

This is challenging because there’s no variable that identifies which observations belong together. We can fix this by noting that every contact starts with a name, so we can create a unique id by counting every time we see “name” as the field:

contacts <- contacts %>% 
  mutate(
    person_id = cumsum(field == "name")
  )
contacts
#> # A tibble: 6 x 3
#>   field   value            person_id
#>   <chr>   <chr>                <int>
#> 1 name    Jiena McLellan           1
#> 2 company Toyota                   1
#> 3 name    John Smith               2
#> 4 company google                   2
#> 5 email   [email protected]          2
#> 6 name    Huxley Ratcliffe         3

Now that we have a unique identifier for each person, we can pivot field and value into the columns:

contacts %>% 
  pivot_wider(names_from = field, values_from = value)
#> # A tibble: 3 x 4
#>   person_id name             company email          
#>       <int> <chr>            <chr>   <chr>          
#> 1         1 Jiena McLellan   Toyota  <NA>           
#> 2         2 John Smith       google  [email protected]
#> 3         3 Huxley Ratcliffe <NA>    <NA>

Longer, then wider

Some problems can’t be solved by pivotting in a single direction. The examples in this section show how you might combine pivot_longer() and pivot_wider() to solve more complex problems.

World bank

world_bank_pop contains data from the World Bank about population per country from 2000 to 2018.

world_bank_pop
#> # A tibble: 1,056 x 20
#>    country indicator `2000` `2001` `2002` `2003`  `2004`  `2005`   `2006`
#>    <chr>   <chr>      <dbl>  <dbl>  <dbl>  <dbl>   <dbl>   <dbl>    <dbl>
#>  1 ABW     SP.URB.T… 4.24e4 4.30e4 4.37e4 4.42e4 4.47e+4 4.49e+4  4.49e+4
#>  2 ABW     SP.URB.G… 1.18e0 1.41e0 1.43e0 1.31e0 9.51e-1 4.91e-1 -1.78e-2
#>  3 ABW     SP.POP.T… 9.09e4 9.29e4 9.50e4 9.70e4 9.87e+4 1.00e+5  1.01e+5
#>  4 ABW     SP.POP.G… 2.06e0 2.23e0 2.23e0 2.11e0 1.76e+0 1.30e+0  7.98e-1
#>  5 AFG     SP.URB.T… 4.44e6 4.65e6 4.89e6 5.16e6 5.43e+6 5.69e+6  5.93e+6
#>  6 AFG     SP.URB.G… 3.91e0 4.66e0 5.13e0 5.23e0 5.12e+0 4.77e+0  4.12e+0
#>  7 AFG     SP.POP.T… 2.01e7 2.10e7 2.20e7 2.31e7 2.41e+7 2.51e+7  2.59e+7
#>  8 AFG     SP.POP.G… 3.49e0 4.25e0 4.72e0 4.82e0 4.47e+0 3.87e+0  3.23e+0
#>  9 AGO     SP.URB.T… 8.23e6 8.71e6 9.22e6 9.77e6 1.03e+7 1.09e+7  1.15e+7
#> 10 AGO     SP.URB.G… 5.44e0 5.59e0 5.70e0 5.76e0 5.75e+0 5.69e+0  4.92e+0
#> # … with 1,046 more rows, and 11 more variables: `2007` <dbl>,
#> #   `2008` <dbl>, `2009` <dbl>, `2010` <dbl>, `2011` <dbl>, `2012` <dbl>,
#> #   `2013` <dbl>, `2014` <dbl>, `2015` <dbl>, `2016` <dbl>, `2017` <dbl>

My goal is to produce a tidy dataset where each variable is in a column. It’s not obvious exactly what steps are needed yet, but I’ll start with the most obvious problem: year is spread across multiple columns.

pop2 <- world_bank_pop %>% 
  pivot_longer(`2000`:`2017`, names_to = "year", values_to = "value")
pop2
#> # A tibble: 19,008 x 4
#>    country indicator   year  value
#>    <chr>   <chr>       <chr> <dbl>
#>  1 ABW     SP.URB.TOTL 2000  42444
#>  2 ABW     SP.URB.TOTL 2001  43048
#>  3 ABW     SP.URB.TOTL 2002  43670
#>  4 ABW     SP.URB.TOTL 2003  44246
#>  5 ABW     SP.URB.TOTL 2004  44669
#>  6 ABW     SP.URB.TOTL 2005  44889
#>  7 ABW     SP.URB.TOTL 2006  44881
#>  8 ABW     SP.URB.TOTL 2007  44686
#>  9 ABW     SP.URB.TOTL 2008  44375
#> 10 ABW     SP.URB.TOTL 2009  44052
#> # … with 18,998 more rows

Next we need to consider the indicator variable:

pop2 %>% count(indicator)
#> # A tibble: 4 x 2
#>   indicator       n
#>   <chr>       <int>
#> 1 SP.POP.GROW  4752
#> 2 SP.POP.TOTL  4752
#> 3 SP.URB.GROW  4752
#> 4 SP.URB.TOTL  4752

Here SP.POP.GROW is population growth, SP.POP.TOTL is total population, and SP.URB.* are the same but only for urban areas. Let’s split this up into two variables: area (total or urban) and the actual variable (population or growth):

pop3 <- pop2 %>% 
  separate(indicator, c(NA, "area", "variable"))
pop3
#> # A tibble: 19,008 x 5
#>    country area  variable year  value
#>    <chr>   <chr> <chr>    <chr> <dbl>
#>  1 ABW     URB   TOTL     2000  42444
#>  2 ABW     URB   TOTL     2001  43048
#>  3 ABW     URB   TOTL     2002  43670
#>  4 ABW     URB   TOTL     2003  44246
#>  5 ABW     URB   TOTL     2004  44669
#>  6 ABW     URB   TOTL     2005  44889
#>  7 ABW     URB   TOTL     2006  44881
#>  8 ABW     URB   TOTL     2007  44686
#>  9 ABW     URB   TOTL     2008  44375
#> 10 ABW     URB   TOTL     2009  44052
#> # … with 18,998 more rows

Now we can complete the tidying by pivoting variable and value to make TOTL and GROW columns:

pop3 %>% 
  pivot_wider(names_from = variable, values_from = value)
#> # A tibble: 9,504 x 5
#>    country area  year   TOTL    GROW
#>    <chr>   <chr> <chr> <dbl>   <dbl>
#>  1 ABW     URB   2000  42444  1.18  
#>  2 ABW     URB   2001  43048  1.41  
#>  3 ABW     URB   2002  43670  1.43  
#>  4 ABW     URB   2003  44246  1.31  
#>  5 ABW     URB   2004  44669  0.951 
#>  6 ABW     URB   2005  44889  0.491 
#>  7 ABW     URB   2006  44881 -0.0178
#>  8 ABW     URB   2007  44686 -0.435 
#>  9 ABW     URB   2008  44375 -0.698 
#> 10 ABW     URB   2009  44052 -0.731 
#> # … with 9,494 more rows

Multi-choice

Based on a suggestion by Maxime Wack, https://github.com/tidyverse/tidyr/issues/384), the final example shows how to deal with a common way of recording multiple choice data. Often you will get such data as follows:

multi <- tribble(
  ~id, ~choice1, ~choice2, ~choice3,
  1, "A", "B", "C",
  2, "C", "B",  NA,
  3, "D",  NA,  NA,
  4, "B", "D",  NA
)

But the actual order isn’t important, and you’d prefer to have the individual questions in the columns. You can achieve the desired transformation in two steps. First, you make the data longer, eliminating the explcit NAs, and adding a column to indicate that this choice was chosen:

multi2 <- multi %>% 
  pivot_longer(-id, values_drop_na = TRUE) %>% 
  mutate(checked = TRUE)
multi2
#> # A tibble: 8 x 4
#>      id name    value checked
#>   <dbl> <chr>   <chr> <lgl>  
#> 1     1 choice1 A     TRUE   
#> 2     1 choice2 B     TRUE   
#> 3     1 choice3 C     TRUE   
#> 4     2 choice1 C     TRUE   
#> 5     2 choice2 B     TRUE   
#> 6     3 choice1 D     TRUE   
#> 7     4 choice1 B     TRUE   
#> 8     4 choice2 D     TRUE

Then you make the data wider, filling in the missing observations with FALSE:

multi2 %>% 
  pivot_wider(
    id_cols = id,
    names_from = value, 
    values_from = checked, 
    values_fill = list(checked = FALSE)
  )
#> # A tibble: 4 x 5
#>      id A     B     C     D    
#>   <dbl> <lgl> <lgl> <lgl> <lgl>
#> 1     1 TRUE  TRUE  TRUE  FALSE
#> 2     2 FALSE TRUE  TRUE  FALSE
#> 3     3 FALSE FALSE FALSE TRUE 
#> 4     4 FALSE TRUE  FALSE TRUE

Manual specs

The arguments to pivot_longer() and pivot_wider() allow you to pivot a wide range of datasets. But the creativity that people apply to their data structures is seemingly endless, so it’s quite possible that you will encounter a dataset that you can’t immediately see how to reshape with pivot_longer() and pivot_wider(). To gain more control over pivotting, you can instead create a “spec” data frame that describes exactly how data stored in the column names becomes variables (and vice versa). This section introduces you to the spec data structure, and show you how to use it when pivot_longer() and pivot_wider() are insufficient.

Longer

To see how this works, lets return to the simplest case of pivotting applied to the relig_income dataset. Now pivotting happens in two steps: we first create a spec object (using build_longer_spec()) then use that to describe the pivotting operation:

spec <- relig_income %>% build_longer_spec(
  cols = -religion, 
  names_to = "income",
  values_to = "count"
)
pivot_longer_spec(relig_income, spec)
#> # A tibble: 180 x 3
#>    religion income             count
#>    <chr>    <chr>              <dbl>
#>  1 Agnostic <$10k                 27
#>  2 Agnostic $10-20k               34
#>  3 Agnostic $20-30k               60
#>  4 Agnostic $30-40k               81
#>  5 Agnostic $40-50k               76
#>  6 Agnostic $50-75k              137
#>  7 Agnostic $75-100k             122
#>  8 Agnostic $100-150k            109
#>  9 Agnostic >150k                 84
#> 10 Agnostic Don't know/refused    96
#> # … with 170 more rows

(This gives the same result as before, just with more code. There’s no need to use it here, it is presented as a simple example for using spec.)

What does spec look like? It’s a data frame with one row for each column, and two special columns that start with .:

spec
#> # A tibble: 10 x 3
#>    .name              .value income            
#>    <chr>              <chr>  <chr>             
#>  1 <$10k              count  <$10k             
#>  2 $10-20k            count  $10-20k           
#>  3 $20-30k            count  $20-30k           
#>  4 $30-40k            count  $30-40k           
#>  5 $40-50k            count  $40-50k           
#>  6 $50-75k            count  $50-75k           
#>  7 $75-100k           count  $75-100k          
#>  8 $100-150k          count  $100-150k         
#>  9 >150k              count  >150k             
#> 10 Don't know/refused count  Don't know/refused

Wider

Below we widen us_rent_income with pivot_wider(). The result is ok, but I think it could be improved:

us_rent_income %>% 
  pivot_wider(names_from = variable, values_from = c(estimate, moe))
#> # A tibble: 52 x 6
#>    GEOID NAME             estimate_income estimate_rent moe_income moe_rent
#>    <chr> <chr>                      <dbl>         <dbl>      <dbl>    <dbl>
#>  1 01    Alabama                    24476           747        136        3
#>  2 02    Alaska                     32940          1200        508       13
#>  3 04    Arizona                    27517           972        148        4
#>  4 05    Arkansas                   23789           709        165        5
#>  5 06    California                 29454          1358        109        3
#>  6 08    Colorado                   32401          1125        109        5
#>  7 09    Connecticut                35326          1123        195        5
#>  8 10    Delaware                   31560          1076        247       10
#>  9 11    District of Col…           43198          1424        681       17
#> 10 12    Florida                    25952          1077         70        3
#> # … with 42 more rows

I think it would be better to have columns income, rent, income_moe, and rent_moe, which we can achieve with a manual spec. The current spec looks like this:

spec1 <- us_rent_income %>% 
  build_wider_spec(names_from = variable, values_from = c(estimate, moe))
spec1
#> # A tibble: 4 x 3
#>   .name           .value   variable
#>   <chr>           <chr>    <chr>   
#> 1 estimate_income estimate income  
#> 2 estimate_rent   estimate rent    
#> 3 moe_income      moe      income  
#> 4 moe_rent        moe      rent

For this case, we mutate spec to carefully construct the column names:

spec2 <- spec1 %>%
  mutate(.name = paste0(variable, ifelse(.value == "moe", "_moe", "")))
spec2
#> # A tibble: 4 x 3
#>   .name      .value   variable
#>   <chr>      <chr>    <chr>   
#> 1 income     estimate income  
#> 2 rent       estimate rent    
#> 3 income_moe moe      income  
#> 4 rent_moe   moe      rent

Supplying this spec to pivot_wider() gives us the result we’re looking for:

pivot_wider_spec(us_rent_income, spec2)
#> # A tibble: 52 x 6
#>    GEOID NAME                 income  rent income_moe rent_moe
#>    <chr> <chr>                 <dbl> <dbl>      <dbl>    <dbl>
#>  1 01    Alabama               24476   747        136        3
#>  2 02    Alaska                32940  1200        508       13
#>  3 04    Arizona               27517   972        148        4
#>  4 05    Arkansas              23789   709        165        5
#>  5 06    California            29454  1358        109        3
#>  6 08    Colorado              32401  1125        109        5
#>  7 09    Connecticut           35326  1123        195        5
#>  8 10    Delaware              31560  1076        247       10
#>  9 11    District of Columbia  43198  1424        681       17
#> 10 12    Florida               25952  1077         70        3
#> # … with 42 more rows

By hand

Sometimes it’s not possible (or not convenient) to compute the spec, and instead it’s more convenient to construct the spec “by hand”. For example, take this construction data, which is lightly modified from Table 5 “completions” found at https://www.census.gov/construction/nrc/index.html:

construction
#> # A tibble: 9 x 9
#>    Year Month `1 unit` `2 to 4 units` `5 units or mor… Northeast Midwest
#>   <dbl> <chr>    <dbl> <lgl>                     <dbl>     <dbl>   <dbl>
#> 1  2018 Janu…      859 NA                          348       114     169
#> 2  2018 Febr…      882 NA                          400       138     160
#> 3  2018 March      862 NA                          356       150     154
#> 4  2018 April      797 NA                          447       144     196
#> 5  2018 May        875 NA                          364        90     169
#> 6  2018 June       867 NA                          342        76     170
#> 7  2018 July       829 NA                          360       108     183
#> 8  2018 Augu…      939 NA                          286        90     205
#> 9  2018 Sept…      835 NA                          304       117     175
#> # … with 2 more variables: South <dbl>, West <dbl>

This sort of data is not uncommon from government agencies: the column names actually belong to different variables, and here we have summaries for number of units (1, 2-4, 5+) and regions of the country (NE, NW, midwest, S, W). We can most easily describe that with a tibble:

spec <- tribble(
  ~.name,            ~.value, ~units,  ~region,     
  "1 unit",          "n",     "1",     NA,          
  "2 to 4 units",    "n",     "2-4",   NA,          
  "5 units or more", "n",     "5+",    NA,          
  "Northeast",       "n",     NA,      "Northeast", 
  "Midwest",         "n",     NA,      "Midwest",   
  "South",           "n",     NA,      "South",     
  "West",            "n",     NA,      "West",      
)

Which yields the following longer form:

pivot_longer_spec(construction, spec)
#> # A tibble: 63 x 5
#>     Year Month    units region        n
#>    <dbl> <chr>    <chr> <chr>     <dbl>
#>  1  2018 January  1     <NA>        859
#>  2  2018 January  2-4   <NA>         NA
#>  3  2018 January  5+    <NA>        348
#>  4  2018 January  <NA>  Northeast   114
#>  5  2018 January  <NA>  Midwest     169
#>  6  2018 January  <NA>  South       596
#>  7  2018 January  <NA>  West        339
#>  8  2018 February 1     <NA>        882
#>  9  2018 February 2-4   <NA>         NA
#> 10  2018 February 5+    <NA>        400
#> # … with 53 more rows

Note that there is no overlap between the units and region variables; here the data would really be most naturally described in two independent tables.

Theory

One neat property of the spec is that you need the same spec for pivot_longer() and pivot_wider(). This makes it very clear that the two operations are symmetric:

construction %>% 
  pivot_longer_spec(spec) %>% 
  pivot_wider_spec(spec)
#> # A tibble: 9 x 9
#>    Year Month `1 unit` `2 to 4 units` `5 units or mor… Northeast Midwest
#>   <dbl> <chr>    <dbl>          <dbl>            <dbl>     <dbl>   <dbl>
#> 1  2018 Janu…      859             NA              348       114     169
#> 2  2018 Febr…      882             NA              400       138     160
#> 3  2018 March      862             NA              356       150     154
#> 4  2018 April      797             NA              447       144     196
#> 5  2018 May        875             NA              364        90     169
#> 6  2018 June       867             NA              342        76     170
#> 7  2018 July       829             NA              360       108     183
#> 8  2018 Augu…      939             NA              286        90     205
#> 9  2018 Sept…      835             NA              304       117     175
#> # … with 2 more variables: South <dbl>, West <dbl>

The pivotting spec allows us to be more precise about exactly how pivot_longer(df, spec = spec) changes the shape of df: it will have nrow(df) * nrow(spec) rows, and ncol(df) - nrow(spec) + ncol(spec) - 2 columns.