tidyr 1.0.0

Photo by Victor Garcia

Hadley Wickham

I’m very excited to announce the release of tidyr 1.0.0! tidyr provides a set of tools for transforming data frames to and from tidy data, where each variable is a column and each observation is a row. Tidy data is a convention for matching the semantics and structure of your data that makes using the rest of the tidyverse (and many other R packages) much easier.

Install tidyr with:

install.packages("tidyr")

As you might guess from the version number, this is a major release, and the 1.0.0 moniker indicates that I’m finally happy with the overall interface of the package. This has been a long time coming: it’s five years since the first tidyr release, nine years since the first reshape2 release, and fourteen years since the first reshape release!

This blog post summarises the four major changes to the package:

  • New pivot_longer() and pivot_wider() provide improved tools for reshaping, superceding spread() and gather(). The new functions are substantially more powerful, thanks to ideas from the data.table and cdata packages, and I’m confident that you’ll find them easier to use and remember than their predecessors.

  • New unnest_auto(), unnest_longer(), unnest_wider(), and hoist() provide new tools for rectangling, converting deeply nested lists into tidy data frames.

  • nest() and unnest() have been changed to match an emerging principle for the design of ... interfaces. Four new functions (pack()/unpack(), and chop()/unchop()) reveal that nesting is the combination of two simpler steps.

  • New expand_grid(), a variant of base::expand.grid(). This is a useful function to know about, but also serves as a good reason to discuss the important role that vctrs plays behind the scenes. You shouldn’t ever have to learn about vctrs, but it brings improvements to consistency and performance.

As well as implementing the new features, I’ve spent considerable time on the documentation, including four major new vignettes:

You can see a list of all the other minor bug fixes and improvements in the release notes. I strongly recommend reading the complete release notes if you’re a package developer.

library(tidyr)
library(dplyr)

Pivoting

New pivot_longer() and pivot_wider() provide modern alternatives to spread() and gather(). They have been carefully redesigned to be easier to learn and remember, and include many new features. spread() and gather() won’t go away, but they’ve been retired which means that they’re no longer under active development.

The best place to learn about pivot_longer() and pivot_wider() is vignette("pivot"), or by watching my presentation to the Vienna R users group. Here I’ll quickly show off a few of the coolest new features:

  • pivot_longer() can now separate column names into multiple variables in a single step. For example, take the who dataset which has column names that look like new_{diagnosis}_{gender}{age}:

    names(who)
    #>  [1] "country"      "iso2"         "iso3"         "year"        
    #>  [5] "new_sp_m014"  "new_sp_m1524" "new_sp_m2534" "new_sp_m3544"
    #>  [9] "new_sp_m4554" "new_sp_m5564" "new_sp_m65"   "new_sp_f014" 
    #> [13] "new_sp_f1524" "new_sp_f2534" "new_sp_f3544" "new_sp_f4554"
    #> [17] "new_sp_f5564" "new_sp_f65"   "new_sn_m014"  "new_sn_m1524"
    #> [21] "new_sn_m2534" "new_sn_m3544" "new_sn_m4554" "new_sn_m5564"
    #> [25] "new_sn_m65"   "new_sn_f014"  "new_sn_f1524" "new_sn_f2534"
    #> [29] "new_sn_f3544" "new_sn_f4554" "new_sn_f5564" "new_sn_f65"  
    #> [33] "new_ep_m014"  "new_ep_m1524" "new_ep_m2534" "new_ep_m3544"
    #> [37] "new_ep_m4554" "new_ep_m5564" "new_ep_m65"   "new_ep_f014" 
    #> [41] "new_ep_f1524" "new_ep_f2534" "new_ep_f3544" "new_ep_f4554"
    #> [45] "new_ep_f5564" "new_ep_f65"   "newrel_m014"  "newrel_m1524"
    #> [49] "newrel_m2534" "newrel_m3544" "newrel_m4554" "newrel_m5564"
    #> [53] "newrel_m65"   "newrel_f014"  "newrel_f1524" "newrel_f2534"
    #> [57] "newrel_f3544" "newrel_f4554" "newrel_f5564" "newrel_f65"
    

    You can now tease apart the variable names in a single step (i.e. without separate())) by supplying a vector of variable names to names_to and a regular expression to names_pattern (simpler cases might only need names_sep):

    who %>% pivot_longer(
      cols = new_sp_m014:newrel_f65,
      names_to = c("diagnosis", "gender", "age"), 
      names_pattern = "new_?(.*)_(.)(.*)",
      values_to = "count",
      values_drop_na = TRUE
    )
    #> # A tibble: 76,046 x 8
    #>   country     iso2  iso3   year diagnosis gender age   count
    #>   <chr>       <chr> <chr> <int> <chr>     <chr>  <chr> <int>
    #> 1 Afghanistan AF    AFG    1997 sp        m      014       0
    #> 2 Afghanistan AF    AFG    1997 sp        m      1524     10
    #> 3 Afghanistan AF    AFG    1997 sp        m      2534      6
    #> 4 Afghanistan AF    AFG    1997 sp        m      3544      3
    #> 5 Afghanistan AF    AFG    1997 sp        m      4554      5
    #> 6 Afghanistan AF    AFG    1997 sp        m      5564      2
    #> # … with 7.604e+04 more rows
    
  • pivot_longer() can now work with rows that contain multiple observations (this feature was inspired by data.table’s dcast() method). For example, take the base anscombe dataset. Each row consists of four pairs of x and y measurements:

    head(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
    

    We can now tidy this in a single step by using the special .value variable name:

    anscombe %>% 
      pivot_longer(
        everything(),
        names_to = c(".value", "set"),
        names_pattern = "(.)(.)"
      ) %>% 
      as_tibble()
    #> # A tibble: 44 x 3
    #>   set       x     y
    #>   <chr> <dbl> <dbl>
    #> 1 1        10  8.04
    #> 2 2        10  9.14
    #> 3 3        10  7.46
    #> 4 4         8  6.58
    #> 5 1         8  6.95
    #> 6 2         8  8.14
    #> # … with 38 more rows
    
  • pivot_wider() can now do simple aggregations (reshape2::dcast() fans rejoice!). For example, take the base warpbreaks dataset (converted to a tibble to print more compactly):

    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
    #> # … with 48 more rows
    

    This is a designed experiment with nine replicates for every combination of wool (A and B) and tension (L, M, H). If we attempt to pivot the levels of wool into the columns, we get a warning and the output contains list-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]
    

    You can now summarise the duplicates with the values_fn argument:

    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
    

Learn the full details and see many more examples in vignette("pivot").

Rectangling

Rectangling is the art and craft of taking a deeply nested list (often sourced from wild-caught JSON or XML) and taming it into a tidy data set of rows and columns. tidyr 1.0.0 provides four new functions to aid rectangling:

  • unnest_longer() takes each element of a list-column and makes a new row.
  • unnest_wider() takes each element of a list-column and makes a new column.
  • unnest_auto() uses some heuristics to guess whether you want unnest_longer() or unnest_wider().
  • hoist() is similar to unnest_wider() but only plucks out selected components, and can reach down multiple levels.

To see them in action, take this small sample from repurrrsive::got_chars. It contains data about three characters from the Game of Thrones:

characters <- list(
  list(
    name = "Theon Greyjoy",
    aliases = c("Prince of Fools", "Theon Turncloak", "Theon Kinslayer"),
    alive = TRUE
  ),
  list(
    name = "Tyrion Lannister",
    aliases = c("The Imp", "Halfman", "Giant of Lannister"),
    alive = TRUE
  ),
  list(
    name = "Arys Oakheart",
    alive = FALSE
  )
)

To work with the new tidyr rectangling tools, we first put the list into a data frame, creating a list-column:

got <- tibble(character = characters)
got
#> # A tibble: 3 x 1
#>   character       
#>   <list>          
#> 1 <named list [3]>
#> 2 <named list [3]>
#> 3 <named list [2]>

We can then use unnest_wider() to make each element of that list into a column:

got %>% 
  unnest_wider(character)
#> # A tibble: 3 x 3
#>   name             aliases   alive
#>   <chr>            <list>    <lgl>
#> 1 Theon Greyjoy    <chr [3]> TRUE 
#> 2 Tyrion Lannister <chr [3]> TRUE 
#> 3 Arys Oakheart    <???>     FALSE

Followed by unnest_longer() to turn each alias into its own row:

got %>% 
  unnest_wider(character) %>% 
  unnest_longer(aliases)
#> # A tibble: 7 x 3
#>   name             aliases            alive
#>   <chr>            <chr>              <lgl>
#> 1 Theon Greyjoy    Prince of Fools    TRUE 
#> 2 Theon Greyjoy    Theon Turncloak    TRUE 
#> 3 Theon Greyjoy    Theon Kinslayer    TRUE 
#> 4 Tyrion Lannister The Imp            TRUE 
#> 5 Tyrion Lannister Halfman            TRUE 
#> 6 Tyrion Lannister Giant of Lannister TRUE 
#> 7 Arys Oakheart    <NA>               FALSE

Even more conveniently, you can use unnest_auto() to guess which direction a list column should be unnested in. Here it yields the same results as above, and the messages tell you why:

got %>% 
  unnest_auto(character) %>% 
  unnest_auto(aliases)
#> Using `unnest_wider(character)`; elements have 2 names in common
#> Using `unnest_longer(aliases)`; no element has names

Alternatively, you can use hoist() to reach deeply into a data structure and put out just the pieces you need:

got %>% hoist(character, 
  name = "name",
  alias = list("aliases", 1),
  alive = "alive"
)
#> # A tibble: 3 x 4
#>   name             alias           alive character       
#>   <chr>            <chr>           <lgl> <list>          
#> 1 Theon Greyjoy    Prince of Fools TRUE  <named list [1]>
#> 2 Tyrion Lannister The Imp         TRUE  <named list [1]>
#> 3 Arys Oakheart    <NA>            FALSE <named list [0]>

This syntax provides a more approachable alternative to using purrr::map() inside dplyr::mutate(), as we’d previously recommended:

got %>% mutate(
  name = purrr::map_chr(character, "name"),
  alias = purrr::map_chr(character, list("aliases", 1), .default = NA),
  alive = purrr::map_lgl(character, "alive")
)

Learn more in vignette("rectangle").

Nesting

nest() and unnest() have been updated with new interfaces that are more closely aligned to evolving tidyverse conventions. The biggest change is to their operation with multiple columns:

# old
df %>% nest(x, y, z)
# new
df %>% nest(data = c(x, y, z))

# old
df %>% unnest(x, y, z)
# new
df %>% unnest(c(x, y, z))

I’ve done my best to ensure that common uses of nest() and unnest() will continue to work, generating an informative warning telling you precisely how you need to update your code. If this doesn’t work, you can use nest_legacy() or unnest_legacy() to access the previous interfaces; see vignette("in-packages") for more advice on managing this transition.

Behind the scenes, I discovered that nesting (and unnesting) can be decomposed into the combination of two simpler operations:

  • pack() and unpack() multiple columns into and out of a data frame column.

  • chop() and unchop() chop up rows into and out of list-columns. It’s a bit like an explicit form of dplyr::group_by().

This is primarily of internal interest, but it considerably simplifies the implementation of nest(), and you may occasionally find the underlying functions useful when working with exotic data structures.

expand_grid()

expand_grid() completes the existing family of expand(), nesting(), and crossing() with a low-level function that works with vectors:

expand_grid(
  x = 1:3,
  y = letters[1:3],
  z = LETTERS[1:3]
)
#> # A tibble: 27 x 3
#>       x y     z    
#>   <int> <chr> <chr>
#> 1     1 a     A    
#> 2     1 a     B    
#> 3     1 a     C    
#> 4     1 b     A    
#> 5     1 b     B    
#> 6     1 b     C    
#> # … with 21 more rows

Compared to the existing base function expand.grid(), expand_grid():

  • Varies the first element most slowly (not most quickly).
  • Never converts strings to factors and doesn’t add any additional attributes.
  • Returns a tibble, not a data frame.
  • Can expand data frames.

The last feature is quite powerful, as it allows you to generate partial grids:

students <- tribble(
  ~ school, ~ student,
  "A",      "John",
  "A",      "Mary",
  "A",      "Susan",
  "B",      "John"
)
expand_grid(students, semester = 1:2)
#> # A tibble: 8 x 3
#>   school student semester
#>   <chr>  <chr>      <int>
#> 1 A      John           1
#> 2 A      John           2
#> 3 A      Mary           1
#> 4 A      Mary           2
#> 5 A      Susan          1
#> 6 A      Susan          2
#> 7 B      John           1
#> 8 B      John           2

This is made possible by the vctrs package. vctrs is primarily of interest to package developers but I want to talk about it briefly here because I’ve been having a lot of fun working with it. It’s hard to concisely describe vctrs, but one aspect is carefully defining what a “vector” is, and providing a set of useful functions that work on all types of vctrs, without any special cases. One interesting finding is that thinking of a data frame as a vector of rows (not columns, as R usually does) is suprisingly useful, and something you can expect to see in more places in the tidyverse in the future.

Note that when data frame inputs are unnamed, they’re automatically unpacked into individual columns in the output. It’s also possible to create a column that is itself a data frame, a df-column, if you name it:

expand_grid(student = students, semester = 1:2)
#> # A tibble: 8 x 2
#>   student$school $student semester
#>   <chr>          <chr>       <int>
#> 1 A              John            1
#> 2 A              John            2
#> 3 A              Mary            1
#> 4 A              Mary            2
#> 5 A              Susan           1
#> 6 A              Susan           2
#> 7 B              John            1
#> 8 B              John            2

Df-columns aren’t particularly useful yet, but they provide powerful building blocks for future extensions. For example, we expect a future version of dplyr will support df-columns as a way for mutate() and summarise() to create multiple new columns from a single function call.

Thanks

A big thanks to all 95 people who help to make this release possible! @abiyug, @AdvikS, @ahcyip, @alexpghayes, @aneisse, @apreshill, @atusy, @ax42, @banfai, @billdenney, @brentthorne, @brunj7, @coolbutuseless, @courtiol, @cwickham, @DanielReedOcean, @DavisVaughan, @dewittpe, @donboyd5, @earowang, @eElor, @enricoferrero, @fresques, @garrettgman, @gederajeg, @georgevbsantiago, @giocomai, @gireeshkbogu, @gorkang, @ha0ye, @hadley, @hplieninger, @iago-pssjd, @IndrajeetPatil, @jackdolgin, @japhir, @jayhesselberth, @jennybc, @jeroenjanssens, @jestarr, @jgendrinal, @Jim89, @jl5000, @jmcastagnetto, @justasmundeikis, @Kaz272, @KenatRSF, @koncina, @krlmlr, @kuriwaki, @lazappi, @leeper, @lionel-, @markdly, @martinjhnhadley, @MatthieuStigler, @mattwarkentin, @mehrgoltiv, @meriops, @mikemc, @mikmart, @mine-cetinkaya-rundel, @mitchelloharawild, @mixolydianpink, @mkapplebee, @moodymudskipper, @mpaulacaldas, @Myfanwy, @ogorodriguez, @onesandzeroes, @Overlytic, @paleolimbot, @PMassicotte, @psychometrician, @Rekyt, @romainfrancois, @romatik, @rubenarslan, @SchollJ, @seabbs, @sethmund, @sfirke, @SimonCoulombe, @Stephonomon, @stufield, @tdjames1, @thierrygosselin, @tklebel, @tmastny, @trannhatanh89, @TrentLobdell, @wcmbishop, @wulixin, @yutannihilation, and @zeehio.

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