Introduction
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. There are three functions from tidyr that are particularly useful for 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. -
hoist()
is similar tounnest_wider()
but only plucks out selected components, and can reach down multiple levels.
(Alternative, for complex inputs where you need to rectangle a nested list according to a specification, see the tibblify package.)
A very large number of data rectangling problems can be solved by combining these functions with a splash of dplyr (largely eliminating prior approaches that combined mutate()
with multiple purrr::map()
s).
To illustrate these techniques, we’ll use the repurrrsive package, which provides a number deeply nested lists originally mostly captured from web APIs.
GitHub users
We’ll start with gh_users
, a list which contains information about six GitHub users. To begin, we put the gh_users
list into a data frame:
users <- tibble(user = gh_users)
This seems a bit counter-intuitive: why is the first step in making a list simpler to make it more complicated? But a data frame has a big advantage: it bundles together multiple vectors so that everything is tracked together in a single object.
Each user
is a named list, where each element represents a column.
names(users$user[[1]])
#> [1] "login" "id" "avatar_url"
#> [4] "gravatar_id" "url" "html_url"
#> [7] "followers_url" "following_url" "gists_url"
#> [10] "starred_url" "subscriptions_url" "organizations_url"
#> [13] "repos_url" "events_url" "received_events_url"
#> [16] "type" "site_admin" "name"
#> [19] "company" "blog" "location"
#> [22] "email" "hireable" "bio"
#> [25] "public_repos" "public_gists" "followers"
#> [28] "following" "created_at" "updated_at"
There are two ways to turn the list components into columns. unnest_wider()
takes every component and makes a new column:
users %>% unnest_wider(user)
#> # A tibble: 6 × 30
#> login id avatar_url gravatar_id url html_url followers_url
#> <chr> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 gaborcsardi 660288 https://a… "" http… https:/… https://api.…
#> 2 jennybc 599454 https://a… "" http… https:/… https://api.…
#> 3 jtleek 1571674 https://a… "" http… https:/… https://api.…
#> 4 juliasilge 12505835 https://a… "" http… https:/… https://api.…
#> 5 leeper 3505428 https://a… "" http… https:/… https://api.…
#> 6 masalmon 8360597 https://a… "" http… https:/… https://api.…
#> # … with 23 more variables: following_url <chr>, gists_url <chr>,
#> # starred_url <chr>, subscriptions_url <chr>, organizations_url <chr>,
#> # repos_url <chr>, events_url <chr>, received_events_url <chr>,
#> # type <chr>, site_admin <lgl>, name <chr>, company <chr>, blog <chr>,
#> # location <chr>, email <chr>, hireable <lgl>, bio <chr>,
#> # public_repos <int>, public_gists <int>, followers <int>,
#> # following <int>, created_at <chr>, updated_at <chr>
But in this case, there are many components and we don’t need most of them so we can instead use hoist()
. hoist()
allows us to pull out selected components using the same syntax as purrr::pluck()
:
users %>% hoist(user,
followers = "followers",
login = "login",
url = "html_url"
)
#> # A tibble: 6 × 4
#> followers login url user
#> <int> <chr> <chr> <list>
#> 1 303 gaborcsardi https://github.com/gaborcsardi <named list [27]>
#> 2 780 jennybc https://github.com/jennybc <named list [27]>
#> 3 3958 jtleek https://github.com/jtleek <named list [27]>
#> 4 115 juliasilge https://github.com/juliasilge <named list [27]>
#> 5 213 leeper https://github.com/leeper <named list [27]>
#> 6 34 masalmon https://github.com/masalmon <named list [27]>
hoist()
removes the named components from the user
list-column, so you can think of it as moving components out of the inner list into the top-level data frame.
GitHub repos
We start off gh_repos
similarly, by putting it in a tibble:
repos <- tibble(repo = gh_repos)
repos
#> # A tibble: 6 × 1
#> repo
#> <list>
#> 1 <list [30]>
#> 2 <list [30]>
#> 3 <list [30]>
#> 4 <list [26]>
#> 5 <list [30]>
#> 6 <list [30]>
This time the elements of user
are a list of repositories that belong to that user. These are observations, so should become new rows, so we use unnest_longer()
rather than unnest_wider()
:
repos <- repos %>% unnest_longer(repo)
repos
#> # A tibble: 176 × 1
#> repo
#> <list>
#> 1 <named list [68]>
#> 2 <named list [68]>
#> 3 <named list [68]>
#> 4 <named list [68]>
#> 5 <named list [68]>
#> 6 <named list [68]>
#> 7 <named list [68]>
#> 8 <named list [68]>
#> 9 <named list [68]>
#> 10 <named list [68]>
#> # … with 166 more rows
Then we can use unnest_wider()
or hoist()
:
repos %>% hoist(repo,
login = c("owner", "login"),
name = "name",
homepage = "homepage",
watchers = "watchers_count"
)
#> # A tibble: 176 × 5
#> login name homepage watchers repo
#> <chr> <chr> <chr> <int> <list>
#> 1 gaborcsardi after NA 5 <named list [65]>
#> 2 gaborcsardi argufy NA 19 <named list [65]>
#> 3 gaborcsardi ask NA 5 <named list [65]>
#> 4 gaborcsardi baseimports NA 0 <named list [65]>
#> 5 gaborcsardi citest NA 0 <named list [65]>
#> 6 gaborcsardi clisymbols "" 18 <named list [65]>
#> 7 gaborcsardi cmaker NA 0 <named list [65]>
#> 8 gaborcsardi cmark NA 0 <named list [65]>
#> 9 gaborcsardi conditions NA 0 <named list [65]>
#> 10 gaborcsardi crayon NA 52 <named list [65]>
#> # … with 166 more rows
Note the use of c("owner", "login")
: this allows us to reach two levels deep inside of a list. An alternative approach would be to pull out just owner
and then put each element of it in a column:
repos %>%
hoist(repo, owner = "owner") %>%
unnest_wider(owner)
#> # A tibble: 176 × 18
#> login id avatar_url gravatar_id url html_url followers_url
#> <chr> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 gaborcsardi 660288 https://av… "" http… https:/… https://api.…
#> 2 gaborcsardi 660288 https://av… "" http… https:/… https://api.…
#> 3 gaborcsardi 660288 https://av… "" http… https:/… https://api.…
#> 4 gaborcsardi 660288 https://av… "" http… https:/… https://api.…
#> 5 gaborcsardi 660288 https://av… "" http… https:/… https://api.…
#> 6 gaborcsardi 660288 https://av… "" http… https:/… https://api.…
#> 7 gaborcsardi 660288 https://av… "" http… https:/… https://api.…
#> 8 gaborcsardi 660288 https://av… "" http… https:/… https://api.…
#> 9 gaborcsardi 660288 https://av… "" http… https:/… https://api.…
#> 10 gaborcsardi 660288 https://av… "" http… https:/… https://api.…
#> # … with 166 more rows, and 11 more variables: following_url <chr>,
#> # gists_url <chr>, starred_url <chr>, subscriptions_url <chr>,
#> # organizations_url <chr>, repos_url <chr>, events_url <chr>,
#> # received_events_url <chr>, type <chr>, site_admin <lgl>, repo <list>
Game of Thrones characters
got_chars
has a similar structure to gh_users
: it’s a list of named lists, where each element of the inner list describes some attribute of a GoT character. We start in the same way, first by creating a data frame and then by unnesting each component into a column:
chars <- tibble(char = got_chars)
chars
#> # A tibble: 30 × 1
#> char
#> <list>
#> 1 <named list [18]>
#> 2 <named list [18]>
#> 3 <named list [18]>
#> 4 <named list [18]>
#> 5 <named list [18]>
#> 6 <named list [18]>
#> 7 <named list [18]>
#> 8 <named list [18]>
#> 9 <named list [18]>
#> 10 <named list [18]>
#> # … with 20 more rows
chars2 <- chars %>% unnest_wider(char)
chars2
#> # A tibble: 30 × 18
#> url id name gender culture born died alive titles aliases
#> <chr> <int> <chr> <chr> <chr> <chr> <chr> <lgl> <list> <list>
#> 1 https://ww… 1022 Theo… Male "Ironb… "In … "" TRUE <chr> <chr>
#> 2 https://ww… 1052 Tyri… Male "" "In … "" TRUE <chr> <chr>
#> 3 https://ww… 1074 Vict… Male "Ironb… "In … "" TRUE <chr> <chr>
#> 4 https://ww… 1109 Will Male "" "" "In … FALSE <chr> <chr>
#> 5 https://ww… 1166 Areo… Male "Norvo… "In … "" TRUE <chr> <chr>
#> 6 https://ww… 1267 Chett Male "" "At … "In … FALSE <chr> <chr>
#> 7 https://ww… 1295 Cres… Male "" "In … "In … FALSE <chr> <chr>
#> 8 https://ww… 130 Aria… Female "Dorni… "In … "" TRUE <chr> <chr>
#> 9 https://ww… 1303 Daen… Female "Valyr… "In … "" TRUE <chr> <chr>
#> 10 https://ww… 1319 Davo… Male "Weste… "In … "" TRUE <chr> <chr>
#> # … with 20 more rows, and 8 more variables: father <chr>, mother <chr>,
#> # spouse <chr>, allegiances <list>, books <list>, povBooks <list>,
#> # tvSeries <list>, playedBy <list>
This is more complex than gh_users
because some component of char
are themselves a list, giving us a collection of list-columns:
chars2 %>% select_if(is.list)
#> # A tibble: 30 × 7
#> titles aliases allegiances books povBooks tvSeries playedBy
#> <list> <list> <list> <list> <list> <list> <list>
#> 1 <chr [3]> <chr [4]> <chr [1]> <chr [3]> <chr [2]> <chr [6]> <chr>
#> 2 <chr [2]> <chr [11]> <chr [1]> <chr [2]> <chr [4]> <chr [6]> <chr>
#> 3 <chr [2]> <chr [1]> <chr [1]> <chr [3]> <chr [2]> <chr [1]> <chr>
#> 4 <chr [1]> <chr [1]> <NULL> <chr [1]> <chr [1]> <chr [1]> <chr>
#> 5 <chr [1]> <chr [1]> <chr [1]> <chr [3]> <chr [2]> <chr [2]> <chr>
#> 6 <chr [1]> <chr [1]> <NULL> <chr [2]> <chr [1]> <chr [1]> <chr>
#> 7 <chr [1]> <chr [1]> <NULL> <chr [2]> <chr [1]> <chr [1]> <chr>
#> 8 <chr [1]> <chr [1]> <chr [1]> <chr [4]> <chr [1]> <chr [1]> <chr>
#> 9 <chr [5]> <chr [11]> <chr [1]> <chr [1]> <chr [4]> <chr [6]> <chr>
#> 10 <chr [4]> <chr [5]> <chr [2]> <chr [1]> <chr [3]> <chr [5]> <chr>
#> # … with 20 more rows
What you do next will depend on the purposes of the analysis. Maybe you want a row for every book and TV series that the character appears in:
chars2 %>%
select(name, books, tvSeries) %>%
pivot_longer(c(books, tvSeries), names_to = "media", values_to = "value") %>%
unnest_longer(value)
#> # A tibble: 180 × 3
#> name media value
#> <chr> <chr> <chr>
#> 1 Theon Greyjoy books A Game of Thrones
#> 2 Theon Greyjoy books A Storm of Swords
#> 3 Theon Greyjoy books A Feast for Crows
#> 4 Theon Greyjoy tvSeries Season 1
#> 5 Theon Greyjoy tvSeries Season 2
#> 6 Theon Greyjoy tvSeries Season 3
#> 7 Theon Greyjoy tvSeries Season 4
#> 8 Theon Greyjoy tvSeries Season 5
#> 9 Theon Greyjoy tvSeries Season 6
#> 10 Tyrion Lannister books A Feast for Crows
#> # … with 170 more rows
Or maybe you want to build a table that lets you match title to name:
chars2 %>%
select(name, title = titles) %>%
unnest_longer(title)
#> # A tibble: 60 × 2
#> name title
#> <chr> <chr>
#> 1 Theon Greyjoy "Prince of Winterfell"
#> 2 Theon Greyjoy "Captain of Sea Bitch"
#> 3 Theon Greyjoy "Lord of the Iron Islands (by law of the green lands…
#> 4 Tyrion Lannister "Acting Hand of the King (former)"
#> 5 Tyrion Lannister "Master of Coin (former)"
#> 6 Victarion Greyjoy "Lord Captain of the Iron Fleet"
#> 7 Victarion Greyjoy "Master of the Iron Victory"
#> 8 Will ""
#> 9 Areo Hotah "Captain of the Guard at Sunspear"
#> 10 Chett ""
#> # … with 50 more rows
(Note that the empty titles (""
) are due to an infelicity in the input got_chars
: ideally people without titles would have a title vector of length 0, not a title vector of length 1 containing an empty string.)
Geocoding with google
Next we’ll tackle a more complex form of data that comes from Google’s geocoding service. It’s against the terms of service to cache this data, so I first write a very simple wrapper around the API. This relies on having an Google maps API key stored in an environment; if that’s not available these code chunks won’t be run.
has_key <- !identical(Sys.getenv("GOOGLE_MAPS_API_KEY"), "")
if (!has_key) {
message("No Google Maps API key found; code chunks will not be run")
}
#> No Google Maps API key found; code chunks will not be run
# https://developers.google.com/maps/documentation/geocoding
geocode <- function(address, api_key = Sys.getenv("GOOGLE_MAPS_API_KEY")) {
url <- "https://maps.googleapis.com/maps/api/geocode/json"
url <- paste0(url, "?address=", URLencode(address), "&key=", api_key)
jsonlite::read_json(url)
}
The list that this function returns is quite complex:
houston <- geocode("Houston TX")
str(houston)
Fortunately, we can attack the problem step by step with tidyr functions. To make the problem a bit harder (!) and more realistic, I’ll start by geocoding a few cities:
city <- c("Houston", "LA", "New York", "Chicago", "Springfield")
city_geo <- purrr::map(city, geocode)
I’ll put these results in a tibble, next to the original city name:
loc <- tibble(city = city, json = city_geo)
loc
The first level contains components status
and result
, which we can reveal with unnest_wider()
:
loc %>%
unnest_wider(json)
Notice that results
is a list of lists. Most of the cities have 1 element (representing a unique match from the geocoding API), but Springfield has two. We can pull these out into separate rows with unnest_longer()
:
loc %>%
unnest_wider(json) %>%
unnest_longer(results)
Now these all have the same components, as revealed by unnest_wider()
:
loc %>%
unnest_wider(json) %>%
unnest_longer(results) %>%
unnest_wider(results)
We can find the lat and lon coordinates by unnesting geometry
:
loc %>%
unnest_wider(json) %>%
unnest_longer(results) %>%
unnest_wider(results) %>%
unnest_wider(geometry)
And then location:
loc %>%
unnest_wider(json) %>%
unnest_longer(results) %>%
unnest_wider(results) %>%
unnest_wider(geometry) %>%
unnest_wider(location)
We could also just look at the first address for each city:
loc %>%
unnest_wider(json) %>%
hoist(results, first_result = 1) %>%
unnest_wider(first_result) %>%
unnest_wider(geometry) %>%
unnest_wider(location)
Or use hoist()
to dive deeply to get directly to lat
and lng
:
Sharla Gelfand’s discography
We’ll finish off with the most complex list, from Sharla Gelfand’s discography. We’ll start the usual way: putting the list into a single column data frame, and then widening so each component is a column. I also parse the date_added
column into a real date-time1.
discs <- tibble(disc = discog) %>%
unnest_wider(disc) %>%
mutate(date_added = as.POSIXct(strptime(date_added, "%Y-%m-%dT%H:%M:%S")))
discs
#> # A tibble: 155 × 5
#> instance_id date_added basic_information id rating
#> <int> <dttm> <list> <int> <int>
#> 1 354823933 2019-02-16 17:48:59 <named list [11]> 7496378 0
#> 2 354092601 2019-02-13 14:13:11 <named list [11]> 4490852 0
#> 3 354091476 2019-02-13 14:07:23 <named list [11]> 9827276 0
#> 4 351244906 2019-02-02 11:39:58 <named list [11]> 9769203 0
#> 5 351244801 2019-02-02 11:39:37 <named list [11]> 7237138 0
#> 6 351052065 2019-02-01 20:40:53 <named list [11]> 13117042 0
#> 7 350315345 2019-01-29 15:48:37 <named list [11]> 7113575 0
#> 8 350315103 2019-01-29 15:47:22 <named list [11]> 10540713 0
#> 9 350314507 2019-01-29 15:44:08 <named list [11]> 11260950 0
#> 10 350314047 2019-01-29 15:41:35 <named list [11]> 11726853 0
#> # … with 145 more rows
At this level, we see information about when each disc was added to Sharla’s discography, not any information about the disc itself. To do that we need to widen the basic_information
column:
discs %>% unnest_wider(basic_information)
#> Error in `unpack()`:
#> ! Names must be unique.
#> ✖ These names are duplicated:
#> * "id" at locations 7 and 14.
#> ℹ Use argument `names_repair` to specify repair strategy.
Unfortunately that fails because there’s an id
column inside basic_information
. We can quickly see what’s going on by setting names_repair = "unique"
:
discs %>% unnest_wider(basic_information, names_repair = "unique")
#> New names:
#> • `id` -> `id...7`
#> • `id` -> `id...14`
#> # A tibble: 155 × 15
#> instance_id date_added labels year master_url artists id...7
#> <int> <dttm> <list> <int> <chr> <list> <int>
#> 1 354823933 2019-02-16 17:48:59 <list> 2015 NA <list> 7.50e6
#> 2 354092601 2019-02-13 14:13:11 <list> 2013 https://ap… <list> 4.49e6
#> 3 354091476 2019-02-13 14:07:23 <list> 2017 https://ap… <list> 9.83e6
#> 4 351244906 2019-02-02 11:39:58 <list> 2017 https://ap… <list> 9.77e6
#> 5 351244801 2019-02-02 11:39:37 <list> 2015 https://ap… <list> 7.24e6
#> 6 351052065 2019-02-01 20:40:53 <list> 2019 https://ap… <list> 1.31e7
#> 7 350315345 2019-01-29 15:48:37 <list> 2014 https://ap… <list> 7.11e6
#> 8 350315103 2019-01-29 15:47:22 <list> 2015 https://ap… <list> 1.05e7
#> 9 350314507 2019-01-29 15:44:08 <list> 2017 https://ap… <list> 1.13e7
#> 10 350314047 2019-01-29 15:41:35 <list> 2017 NA <list> 1.17e7
#> # … with 145 more rows, and 8 more variables: thumb <chr>, title <chr>,
#> # formats <list>, cover_image <chr>, resource_url <chr>,
#> # master_id <int>, id...14 <int>, rating <int>
The problem is that basic_information
repeats the id
column that’s also stored at the top-level, so we can just drop that:
discs %>%
select(!id) %>%
unnest_wider(basic_information)
#> # A tibble: 155 × 14
#> instance_id date_added labels year master_url artists id
#> <int> <dttm> <list> <int> <chr> <list> <int>
#> 1 354823933 2019-02-16 17:48:59 <list> 2015 NA <list> 7.50e6
#> 2 354092601 2019-02-13 14:13:11 <list> 2013 https://ap… <list> 4.49e6
#> 3 354091476 2019-02-13 14:07:23 <list> 2017 https://ap… <list> 9.83e6
#> 4 351244906 2019-02-02 11:39:58 <list> 2017 https://ap… <list> 9.77e6
#> 5 351244801 2019-02-02 11:39:37 <list> 2015 https://ap… <list> 7.24e6
#> 6 351052065 2019-02-01 20:40:53 <list> 2019 https://ap… <list> 1.31e7
#> 7 350315345 2019-01-29 15:48:37 <list> 2014 https://ap… <list> 7.11e6
#> 8 350315103 2019-01-29 15:47:22 <list> 2015 https://ap… <list> 1.05e7
#> 9 350314507 2019-01-29 15:44:08 <list> 2017 https://ap… <list> 1.13e7
#> 10 350314047 2019-01-29 15:41:35 <list> 2017 NA <list> 1.17e7
#> # … with 145 more rows, and 7 more variables: thumb <chr>, title <chr>,
#> # formats <list>, cover_image <chr>, resource_url <chr>,
#> # master_id <int>, rating <int>
Alternatively, we could use hoist()
:
discs %>%
hoist(basic_information,
title = "title",
year = "year",
label = list("labels", 1, "name"),
artist = list("artists", 1, "name")
)
#> # A tibble: 155 × 9
#> instance_id date_added title year label artist
#> <int> <dttm> <chr> <int> <chr> <chr>
#> 1 354823933 2019-02-16 17:48:59 Demo 2015 Tobi… Mollot
#> 2 354092601 2019-02-13 14:13:11 Observant Com El Mo… 2013 La V… Una B…
#> 3 354091476 2019-02-13 14:07:23 I 2017 La V… S.H.I…
#> 4 351244906 2019-02-02 11:39:58 Oído Absoluto 2017 La V… Rata …
#> 5 351244801 2019-02-02 11:39:37 A Cat's Cause, No D… 2015 Kato… Ivy (…
#> 6 351052065 2019-02-01 20:40:53 Tashme 2019 High… Tashme
#> 7 350315345 2019-01-29 15:48:37 Demo 2014 Mind… Desgr…
#> 8 350315103 2019-01-29 15:47:22 Let The Miracles Be… 2015 Not … Phant…
#> 9 350314507 2019-01-29 15:44:08 Sub Space 2017 Not … Sub S…
#> 10 350314047 2019-01-29 15:41:35 Demo 2017 Pres… Small…
#> # … with 145 more rows, and 3 more variables: basic_information <list>,
#> # id <int>, rating <int>
Here I quickly extract the name of the first label and artist by indexing deeply into the nested list.
A more systematic approach would be to create separate tables for artist and label:
discs %>%
hoist(basic_information, artist = "artists") %>%
select(disc_id = id, artist) %>%
unnest_longer(artist) %>%
unnest_wider(artist)
#> # A tibble: 167 × 8
#> disc_id join name anv tracks role resource_url id
#> <int> <chr> <chr> <chr> <chr> <chr> <chr> <int>
#> 1 7496378 "" Mollot "" "" "" https://api… 4.62e6
#> 2 4490852 "" Una Bèstia Incon… "" "" "" https://api… 3.19e6
#> 3 9827276 "" S.H.I.T. (3) "" "" "" https://api… 2.77e6
#> 4 9769203 "" Rata Negra "" "" "" https://api… 4.28e6
#> 5 7237138 "" Ivy (18) "" "" "" https://api… 3.60e6
#> 6 13117042 "" Tashme "" "" "" https://api… 5.21e6
#> 7 7113575 "" Desgraciados "" "" "" https://api… 4.45e6
#> 8 10540713 "" Phantom Head "" "" "" https://api… 4.27e6
#> 9 11260950 "" Sub Space (2) "" "" "" https://api… 5.69e6
#> 10 11726853 "" Small Man (2) "" "" "" https://api… 6.37e6
#> # … with 157 more rows
discs %>%
hoist(basic_information, format = "formats") %>%
select(disc_id = id, format) %>%
unnest_longer(format) %>%
unnest_wider(format) %>%
unnest_longer(descriptions)
#> # A tibble: 281 × 5
#> disc_id descriptions text name qty
#> <int> <chr> <chr> <chr> <chr>
#> 1 7496378 "Numbered" Black Cassette 1
#> 2 4490852 "LP" NA Vinyl 1
#> 3 9827276 "7\"" NA Vinyl 1
#> 4 9827276 "45 RPM" NA Vinyl 1
#> 5 9827276 "EP" NA Vinyl 1
#> 6 9769203 "LP" NA Vinyl 1
#> 7 9769203 "Album" NA Vinyl 1
#> 8 7237138 "7\"" NA Vinyl 1
#> 9 7237138 "45 RPM" NA Vinyl 1
#> 10 13117042 "7\"" NA Vinyl 1
#> # … with 271 more rows
Then you could join these back on to the original dataset as needed.