../../../data/GHE/deployment/deployments/2021-10-18/vignettes/rectangle.Rmd
rectangle.RmdRectangling 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.unnest_auto() guesses 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.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.
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 following_url
#> <chr> <int> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 gaborcsardi 6.60e5 https://a… "" http… https:/… https://api.… https://api.…
#> 2 jennybc 5.99e5 https://a… "" http… https:/… https://api.… https://api.…
#> 3 jtleek 1.57e6 https://a… "" http… https:/… https://api.… https://api.…
#> 4 juliasilge 1.25e7 https://a… "" http… https:/… https://api.… https://api.…
#> 5 leeper 3.51e6 https://a… "" http… https:/… https://api.… https://api.…
#> 6 masalmon 8.36e6 https://a… "" http… https:/… https://api.… https://api.…
#> # … with 22 more variables: 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>,
#> # public_repos <int>, public_gists <int>, followers <int>, following <int>,
#> # created_at <chr>, updated_at <chr>, bio <chr>, hireable <lgl>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.
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 rowsThen 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 rowsNote 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://avat… "" https:… https://… https://api.g…
#> 2 gaborcsardi 660288 https://avat… "" https:… https://… https://api.g…
#> 3 gaborcsardi 660288 https://avat… "" https:… https://… https://api.g…
#> 4 gaborcsardi 660288 https://avat… "" https:… https://… https://api.g…
#> 5 gaborcsardi 660288 https://avat… "" https:… https://… https://api.g…
#> 6 gaborcsardi 660288 https://avat… "" https:… https://… https://api.g…
#> 7 gaborcsardi 660288 https://avat… "" https:… https://… https://api.g…
#> 8 gaborcsardi 660288 https://avat… "" https:… https://… https://api.g…
#> 9 gaborcsardi 660288 https://avat… "" https:… https://… https://api.g…
#> 10 gaborcsardi 660288 https://avat… "" https:… https://… https://api.g…
#> # … 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>Instead of looking at the list and carefully thinking about whether it needs to become rows or columns, you can use unnest_auto(). It uses a handful of heuristics to figure out whether unnest_longer() or unnest_wider() is appropriate, and tells you about its reasoning.
tibble(repo = gh_repos) %>%
unnest_auto(repo) %>%
unnest_auto(repo)
#> Using `unnest_longer(repo)`; no element has names
#> Using `unnest_wider(repo)`; elements have 68 names in common
#> # A tibble: 176 × 67
#> id name full_name owner private html_url description fork url
#> <int> <chr> <chr> <lis> <lgl> <chr> <chr> <lgl> <chr>
#> 1 61160198 after gaborcsa… <nam… FALSE https:/… Run Code i… FALSE http…
#> 2 40500181 argufy gaborcsa… <nam… FALSE https:/… Declarativ… FALSE http…
#> 3 36442442 ask gaborcsa… <nam… FALSE https:/… Friendly C… FALSE http…
#> 4 34924886 baseimports gaborcsa… <nam… FALSE https:/… Do we get … FALSE http…
#> 5 61620661 citest gaborcsa… <nam… FALSE https:/… Test R pac… TRUE http…
#> 6 33907457 clisymbols gaborcsa… <nam… FALSE https:/… Unicode sy… FALSE http…
#> 7 37236467 cmaker gaborcsa… <nam… FALSE https:/… port of cm… TRUE http…
#> 8 67959624 cmark gaborcsa… <nam… FALSE https:/… CommonMark… TRUE http…
#> 9 63152619 conditions gaborcsa… <nam… FALSE https:/… <NA> TRUE http…
#> 10 24343686 crayon gaborcsa… <nam… FALSE https:/… R package … FALSE http…
#> # … with 166 more rows, and 58 more variables: forks_url <chr>, keys_url <chr>,
#> # collaborators_url <chr>, teams_url <chr>, hooks_url <chr>,
#> # issue_events_url <chr>, events_url <chr>, assignees_url <chr>,
#> # branches_url <chr>, tags_url <chr>, blobs_url <chr>, git_tags_url <chr>,
#> # git_refs_url <chr>, trees_url <chr>, statuses_url <chr>,
#> # languages_url <chr>, stargazers_url <chr>, contributors_url <chr>,
#> # subscribers_url <chr>, subscription_url <chr>, commits_url <chr>, …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 father
#> <chr> <int> <chr> <chr> <chr> <chr> <chr> <lgl> <list> <list> <chr>
#> 1 https:… 1022 Theon… Male "Ironb… "In 2… "" TRUE <chr … <chr [… ""
#> 2 https:… 1052 Tyrio… Male "" "In 2… "" TRUE <chr … <chr [… ""
#> 3 https:… 1074 Victa… Male "Ironb… "In 2… "" TRUE <chr … <chr [… ""
#> 4 https:… 1109 Will Male "" "" "In 2… FALSE <chr … <chr [… ""
#> 5 https:… 1166 Areo … Male "Norvo… "In 2… "" TRUE <chr … <chr [… ""
#> 6 https:… 1267 Chett Male "" "At H… "In 2… FALSE <chr … <chr [… ""
#> 7 https:… 1295 Cress… Male "" "In 2… "In 2… FALSE <chr … <chr [… ""
#> 8 https:… 130 Arian… Female "Dorni… "In 2… "" TRUE <chr … <chr [… ""
#> 9 https:… 1303 Daene… Female "Valyr… "In 2… "" TRUE <chr … <chr [… ""
#> 10 https:… 1319 Davos… Male "Weste… "In 2… "" TRUE <chr … <chr [… ""
#> # … with 20 more rows, and 7 more variables: 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 [1]>
#> 2 <chr [2]> <chr [11]> <chr [1]> <chr [2]> <chr [4]> <chr [6]> <chr [1]>
#> 3 <chr [2]> <chr [1]> <chr [1]> <chr [3]> <chr [2]> <chr [1]> <chr [1]>
#> 4 <chr [1]> <chr [1]> <NULL> <chr [1]> <chr [1]> <chr [1]> <chr [1]>
#> 5 <chr [1]> <chr [1]> <chr [1]> <chr [3]> <chr [2]> <chr [2]> <chr [1]>
#> 6 <chr [1]> <chr [1]> <NULL> <chr [2]> <chr [1]> <chr [1]> <chr [1]>
#> 7 <chr [1]> <chr [1]> <NULL> <chr [2]> <chr [1]> <chr [1]> <chr [1]>
#> 8 <chr [1]> <chr [1]> <chr [1]> <chr [4]> <chr [1]> <chr [1]> <chr [1]>
#> 9 <chr [5]> <chr [11]> <chr [1]> <chr [1]> <chr [4]> <chr [6]> <chr [1]>
#> 10 <chr [4]> <chr [5]> <chr [2]> <chr [1]> <chr [3]> <chr [5]> <chr [1]>
#> # … with 20 more rowsWhat 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 rowsOr 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.)
Again, we could rewrite using unnest_auto(). This is convenient for exploration, but I wouldn’t rely on it in the long term - unnest_auto() has the undesirable property that it will always succeed. That means if your data structure changes, unnest_auto() will continue to work, but might give very different output that causes cryptic failures from downstream functions.
tibble(char = got_chars) %>%
unnest_auto(char) %>%
select(name, title = titles) %>%
unnest_auto(title)
#> Using `unnest_wider(char)`; elements have 18 names in common
#> Using `unnest_longer(title)`; no element has names
#> # 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 rowsNext 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)
locThe 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)Again, unnest_auto() makes this simpler with the small risk of failing in unexpected ways if the input structure changes:
loc %>%
unnest_auto(json) %>%
unnest_auto(results) %>%
unnest_auto(results) %>%
unnest_auto(geometry) %>%
unnest_auto(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:
I’d normally use readr::parse_datetime() or lubridate::ymd_hms(), but I can’t here because it’s a vignette and I don’t want to add a dependency to tidyr just to simplify one example.↩︎