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rrapply
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rrapply: revisiting base-R's rapply
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<!-- README.md is generated from README.Rmd. Please edit that file --> # {rrapply}: Revisiting R-base rapply() <img style="height: 139px;" src='sticker.svg' align="right" /> <!-- badges: start --> [](https://cran.r-project.org/package=rrapply) [](https://github.com/JorisChau/rrapply/actions) [](https://app.codecov.io/gh/JorisChau/rrapply) [](https://CRAN.R-project.org/package=rrapply) [](https://cran.r-project.org/package=rrapply) <!-- badges: end --> The minimal {rrapply}-package contains a single function `rrapply()`, providing an extended implementation of R-base’s `rapply()` function, which applies a function `f` to all elements of a nested list recursively and controls how to structure the returned result. `rrapply()` builds upon `rapply()`’s native C implementation and for this reason requires no external R-package dependencies. ## Installation ``` r # Install latest release from CRAN: install.packages("rrapply") # Install the development version from GitHub: # install.packages("devtools") devtools::install_github("JorisChau/rrapply") ``` ## Cheat sheet <div> <a href='https://github.com/JorisChau/rrapply/blob/master/vignettes/cheatsheet.pdf'> <img src='cheatsheet.svg' align="center" height="600" /> </a> </div> ## When to use `rrapply()` ### List pruning and unnesting #### • `how = "prune"` With base `rapply()`, there is no convenient way to prune or filter list elements from the input list object. The `rrapply()` function adds an option `how = "prune"` to prune all list elements not subject to application of `f` from a nested list, ``` r library(rrapply) ## data: renewable energy per country in 2016 (% of total energy consumption) data("renewable_energy_by_country") ## subset countries and areas in Oceania renewable_oceania <- renewable_energy_by_country[["World"]]["Oceania"] str(renewable_oceania, list.len = 3, give.attr = FALSE) #> List of 1 #> $ Oceania:List of 4 #> ..$ Australia and New Zealand:List of 6 #> .. ..$ Australia : num 9.32 #> .. ..$ Christmas Island : logi NA #> .. ..$ Cocos (Keeling) Islands : logi NA #> .. .. [list output truncated] #> ..$ Melanesia :List of 5 #> .. ..$ Fiji : num 24.4 #> .. ..$ New Caledonia : num 4.03 #> .. ..$ Papua New Guinea: num 50.3 #> .. .. [list output truncated] #> ..$ Micronesia :List of 8 #> .. ..$ Guam : num 3.03 #> .. ..$ Kiribati : num 45.4 #> .. ..$ Marshall Islands : num 11.8 #> .. .. [list output truncated] #> .. [list output truncated] ``` ``` r ## drop all logical NA's while preserving list structure rrapply( renewable_oceania, f = \(x) x, classes = "numeric", how = "prune" ) |> str(list.len = 3, give.attr = FALSE) #> List of 1 #> $ Oceania:List of 4 #> ..$ Australia and New Zealand:List of 2 #> .. ..$ Australia : num 9.32 #> .. ..$ New Zealand: num 32.8 #> ..$ Melanesia :List of 5 #> .. ..$ Fiji : num 24.4 #> .. ..$ New Caledonia : num 4.03 #> .. ..$ Papua New Guinea: num 50.3 #> .. .. [list output truncated] #> ..$ Micronesia :List of 7 #> .. ..$ Guam : num 3.03 #> .. ..$ Kiribati : num 45.4 #> .. ..$ Marshall Islands : num 11.8 #> .. .. [list output truncated] #> .. [list output truncated] ``` #### • `how = "flatten"` Instead, use `how = "flatten"` to return a flattened unnested version of the pruned list, ``` r ## drop all logical NA's and return unnested list rrapply( renewable_oceania, f = \(x) x, classes = "numeric", how = "flatten" ) |> head(n = 10) #> Australia New Zealand Fiji New Caledonia #> 9.32 32.76 24.36 4.03 #> Papua New Guinea Solomon Islands Vanuatu Guam #> 50.34 65.73 33.67 3.03 #> Kiribati Marshall Islands #> 45.43 11.75 ``` **Hint**: the `options` argument allows to avoid coercion of the flattened list to a vector and/or to include all parent list names in the result. ``` r ## flatten to simple list with full names rrapply( renewable_oceania, f = \(x) x, classes = "numeric", how = "flatten", options = list(namesep = ".", simplify = FALSE) ) |> str(list.len = 5, give.attr = FALSE) #> List of 22 #> $ Oceania.Australia and New Zealand.Australia : num 9.32 #> $ Oceania.Australia and New Zealand.New Zealand : num 32.8 #> $ Oceania.Melanesia.Fiji : num 24.4 #> $ Oceania.Melanesia.New Caledonia : num 4.03 #> $ Oceania.Melanesia.Papua New Guinea : num 50.3 #> [list output truncated] ``` #### • `how = "melt"` Or, use `how = "melt"` to return a melted data.frame of the pruned list similar in format to `reshape2::melt()` applied to a nested list. ``` r ## drop all logical NA's and return melted data.frame oceania_melt <- rrapply( renewable_oceania, f = \(x) x, classes = "numeric", how = "melt" ) head(oceania_melt) #> L1 L2 L3 value #> 1 Oceania Australia and New Zealand Australia 9.32 #> 2 Oceania Australia and New Zealand New Zealand 32.76 #> 3 Oceania Melanesia Fiji 24.36 #> 4 Oceania Melanesia New Caledonia 4.03 #> 5 Oceania Melanesia Papua New Guinea 50.34 #> 6 Oceania Melanesia Solomon Islands 65.73 ``` A melted data.frame can be used to reconstruct a nested list with `how = "unmelt"`, ``` r ## reconstruct nested list from melted data.frame rrapply(oceania_melt, how = "unmelt") |> str(list.len = 3, give.attr = FALSE) #> List of 1 #> $ Oceania:List of 4 #> ..$ Australia and New Zealand:List of 2 #> .. ..$ Australia : num 9.32 #> .. ..$ New Zealand: num 32.8 #> ..$ Melanesia :List of 5 #> .. ..$ Fiji : num 24.4 #> .. ..$ New Caledonia : num 4.03 #> .. ..$ Papua New Guinea: num 50.3 #> .. .. [list output truncated] #> ..$ Micronesia :List of 7 #> .. ..$ Guam : num 3.03 #> .. ..$ Kiribati : num 45.4 #> .. ..$ Marshall Islands : num 11.8 #> .. .. [list output truncated] #> .. [list output truncated] ``` #### • `how = "bind"` Nested lists containing repeated observations can be unnested with `how = "bind"`, which returns a wide data.frame similar in format to `dplyr::bind_rows()` applied to a list of data.frames or repeated application of `tidyr::unnest_wider()` to a nested data.frame. ``` r ## data: nested list of Pokemon properties in Pokemon GO data("pokedex") str(pokedex, list.len = 3) #> List of 1 #> $ pokemon:List of 151 #> ..$ :List of 16 #> .. ..$ id : int 1 #> .. ..$ num : chr "001" #> .. ..$ name : chr "Bulbasaur" #> .. .. [list output truncated] #> ..$ :List of 17 #> .. ..$ id : int 2 #> .. ..$ num : chr "002" #> .. ..$ name : chr "Ivysaur" #> .. .. [list output truncated] #> ..$ :List of 15 #> .. ..$ id : int 3 #> .. ..$ num : chr "003" #> .. ..$ name : chr "Venusaur" #> .. .. [list output truncated] #> .. [list output truncated] ``` ``` r ## unnest list to wide data.frame rrapply(pokedex, how = "bind")[, c(1:3, 5:8)] |> head(n = 9) #> id num name type height weight candy #> 1 1 001 Bulbasaur Grass, Poison 0.71 m 6.9 kg Bulbasaur Candy #> 2 2 002 Ivysaur Grass, Poison 0.99 m 13.0 kg Bulbasaur Candy #> 3 3 003 Venusaur Grass, Poison 2.01 m 100.0 kg Bulbasaur Candy #> 4 4 004 Charmander Fire 0.61 m 8.5 kg Charmander Candy #> 5 5 005 Charmeleon Fire 1.09 m 19.0 kg Charmander Candy #> 6 6 006 Charizard Fire, Flying 1.70 m 90.5 kg Charmander Candy #> 7 7 007 Squirtle Water 0.51 m 9.0 kg Squirtle Candy #> 8 8 008 Wartortle Water 0.99 m 22.5 kg Squirtle Candy #> 9 9 009 Blastoise Water 1.60 m 85.5 kg Squirtle Candy ``` **Hint**: set `options = list(namecols = TRUE)` to include the parent list names associated to each row in the wide data.frame as individual columns `L1`, `L2`, etc. ``` r ## bind to data.frame including parent columns rrapply(pokedex, how = "bind", options = list(namecols = TRUE))[, c(1:5, 7:10)] |> head(n = 6) #> L1 L2 id num name type height weight candy #> 1 pokemon 1 1 001 Bulbasaur Grass, Poison 0.71 m 6.9 kg Bulbasaur Candy #> 2 pokemon 2 2 002 Ivysaur Grass, Poison 0.99 m 13.0 kg Bulbasaur Candy #> 3 pokemon 3 3 003 Venusaur Grass, Poison 2.01 m 100.0 kg Bulbasaur Candy #> 4 pokemon 4 4 004 Charmander Fire 0.61 m 8.5 kg Charmander Candy #> 5 pokemon 5 5 005 Charmeleon Fire 1.09 m 19.0 kg Charmander Candy #> 6 pokemon 6 6 006 Charizard Fire, Flying 1.70 m 90.5 kg Charmander Candy ``` ### Condition function Base `rapply()` allows to apply a function `f` to list elements of certain types or classes via the `classes` argument. `rrapply()` generalizes this option via an additional `condition` argument, which accepts any function to use as a condition or predicate to apply `f` to a subset of list elements. ``` r ## drop all NA elements using condition rrapply( renewable_oceania, condition = \(x) !is.na(x), f = \(x) x, how = "prune" ) |> str(list.len = 3, give.attr = FALSE) #> List of 1 #> $ Oceania:List of 4 #> ..$ Australia and New Zealand:List of 2 #> .. ..$ Australia : num 9.32 #> .. ..$ New Zealand: num 32.8 #> ..$ Melanesia :List of 5 #> .. ..$ Fiji : num 24.4 #> .. ..$ New Caledonia : num 4.03 #> .. ..$ Papua New Guinea: num 50.3 #> .. .. [list output truncated] #> ..$ Micronesia :List of 7 #> .. ..$ Guam : num 3.03 #> .. ..$ Kiribati : num 45.4 #> .. ..$ Marshall Islands : num 11.8 #> .. .. [list output truncated] #> .. [list output truncated] ``` ``` r ## filter all countries with values > 85% rrapply( renewable_energy_by_country, condition = \(x) x > 85, how = "prune" ) |> str(give.attr = FALSE) #> List of 1 #> $ World:List of 1 #> ..$ Africa:List of 1 #> .. ..$ Sub-Saharan Africa:List of 3 #> .. .. ..$ Eastern Africa:List of 7 #> .. .. .. ..$ Burundi : num 89.2 #> .. .. .. ..$ Ethiopia : num 91.9 #> .. .. .. ..$ Rwanda : num 86 #> .. .. .. ..$ Somalia : num 94.7 #> .. .. .. ..$ Uganda : num 88.6 #> .. .. .. ..$ United Republic of Tanzania: num 86.1 #> .. .. .. ..$ Zambia : num 88.5 #> .. .. ..$ Middle Africa :List of 2 #> .. .. .. ..$ Chad : num 85.3 #> .. .. .. ..$ Democratic Republic of the Congo: num 97 #> .. .. ..$ Western Africa:List of 1 #> .. .. .. ..$ Guinea-Bissau: num 86.5 ``` ### Special arguments `.xname`, `.xpos`, `.xparents` and `.xsiblings` With base `rapply()`, the `f` function only has access to the *content* of the list element under evaluation, and there is no convenient way to access its name or location in the nested list from inside `f`. `rrapply()` defines the special arguments `.xname`, `.xpos`, `.xparents`, `.xsiblings` inside the `f` and `condition` functions (in addition to the principal function argument): - `.xname` evaluates to the name of the list element; - `.xpos` evaluates to the position of the element in the nested list structured as an integer vector; - `.xparents` evaluates to a vector of parent list names in the path to the current list element; - `.xsiblings` evaluates to the parent list containing the current list element and its direct siblings. ``` r ## apply f based on element's name rrapply( renewable_oceania, condition = \(x) !is.na(x), f = \(x, .xname) sprintf("Renewable energy in %s: %.2f%%", .xname, x), how = "flatten" ) |> head(n = 5) #> Australia #> "Renewable energy in Australia: 9.32%" #> New Zealand #> "Renewable energy in New Zealand: 32.76%" #> Fiji #> "Renewable energy in Fiji: 24.36%" #> New Caledonia #> "Renewable energy in New Caledonia: 4.03%" #> Papua New Guinea #> "Renewable energy in Papua New Guinea: 50.34%" ## filter elements by name rrapply( renewable_energy_by_country, condition = \(x, .xname) .xname %in% c("Belgium", "Netherlands", "Luxembourg"), how = "prune" ) |> str(give.attr = FALSE) #> List of 1 #> $ World:List of 1 #> ..$ Europe:List of 1 #> .. ..$ Western Europe:List of 3 #> .. .. ..$ Belgium : num 9.14 #> .. .. ..$ Luxembourg : num 13.5 #> .. .. ..$ Netherlands: num 5.78 ## filter European countries > 50% using .xpos rrapply( renewable_energy_by_country, condition = \(x, .xpos) identical(.xpos[1:2], c(1L, 5L)) && x > 50, how = "prune" ) |> str(give.attr = FALSE) #> List of 1 #> $ World:List of 1 #> ..$ Europe:List of 2 #> .. ..$ Northern Europe:List of 3 #> .. .. ..$ Iceland: num 78.1 #> .. .. ..$ Norway : num 59.5 #> .. .. ..$ Sweden : num 51.4 #> .. ..$ Western Europe :List of 1 #> .. .. ..$ Liechtenstein: num 62.9 ## filter European countries > 50% using .xparents rrapply( renewable_energy_by_country, condition = \(x, .xparents) "Europe" %in% .xparents && x > 50, how = "prune" ) |> str(give.attr = FALSE) #> List of 1 #> $ World:List of 1 #> ..$ Europe:List of 2 #> .. ..$ Northern Europe:List of 3 #> .. .. ..$ Iceland: num 78.1 #> .. .. ..$ Norway : num 59.5 #> .. .. ..$ Sweden : num 51.4 #> .. ..$ Western Europe :List of 1 #> .. .. ..$ Liechtenstein: num 62.9 ## return position of element in list rrapply( renewable_energy_by_country, condition = \(x, .xname) .xname == "Sweden", f = \(x, .xpos) .xpos, how = "flatten" ) #> $Sweden #> [1] 1 5 2 14 ## return siblings of element in list rrapply( renewable_energy_by_country, condition = \(x, .xsiblings) "Sweden" %in% names(.xsiblings), how = "flatten" ) |> head(n = 5) #> Aland Islands Denmark Estonia Faroe Islands Finland #> NA 33.06 26.55 4.24 42.03 ## filter elements and unnest list rrapply( pokedex, condition = \(x, .xpos, .xname) length(.xpos) < 4 & .xname %in% c("num", "name", "type"), how = "bind" ) |> head() #> num name type #> 1 001 Bulbasaur Grass, Poison #> 2 002 Ivysaur Grass, Poison #> 3 003 Venusaur Grass, Poison #> 4 004 Charmander Fire #> 5 005 Charmeleon Fire #> 6 006 Charizard Fire, Flying ``` ### Modifying list elements By default, both base `rapply()` and `rrapply()` recurse into any “list-like” element. Set `classes = "list"` in `rrapply()` to override and apply `f` to any list element (i.e. a sublist) that satisfies the `condition` argument. This can be useful to e.g. collapse sublists or calculate summary statistics across elements in a nested list: ``` r ## calculate mean value of Europe rrapply( renewable_energy_by_country, condition = \(x, .xname) .xname == "Europe", f = \(x) mean(unlist(x), na.rm = TRUE), classes = "list", how = "flatten" ) #> Europe #> 22.36565 ## calculate mean value for each continent ## (Antartica's value is missing) rrapply( renewable_energy_by_country, condition = \(x, .xpos) length(.xpos) == 2, f = \(x) mean(unlist(x), na.rm = TRUE), classes = "list" ) |> str(give.attr = FALSE) #> List of 1 #> $ World:List of 6 #> ..$ Africa : num 54.3 #> ..$ Americas : num 18.2 #> ..$ Antarctica: logi NA #> ..$ Asia : num 17.9 #> ..$ Europe : num 22.4 #> ..$ Oceania : num 17.8 ## simplify pokemon evolutions to character vectors rrapply( pokedex, condition = \(x, .xname) .xname %in% c("name", "next_evolution", "prev_evolution"), f = \(x) if(is.list(x)) sapply(x, `[[`, "name") else x, classes = c("character", "list"), how = "bind" ) |> head(n = 9) #> name next_evolution prev_evolution #> 1 Bulbasaur Ivysaur, Venusaur NA #> 2 Ivysaur Venusaur Bulbasaur #> 3 Venusaur NA Bulbasaur, Ivysaur #> 4 Charmander Charmeleon, Charizard NA #> 5 Charmeleon Charizard Charmander #> 6 Charizard NA Charmander, Charmeleon #> 7 Squirtle Wartortle, Blastoise NA #> 8 Wartortle Blastoise Squirtle #> 9 Blastoise NA Squirtle, Wartortle ``` **Hint**: as data.frames are also list-like objects, `rrapply()` applies `f` to individual data.frame columns by default. Set `classes = "data.frame"` to avoid this behavior and apply the `f` and `condition` functions to complete data.frame objects instead of individual data.frame columns. ### Recursive list updating #### • `how = "recurse"` If `classes = "list"` and `how = "recurse"`, `rrapply()` applies the `f` function to any list element that satisfies the `condition` argument similar to the previous section, but recurses further into any *updated* list-like element after application of `f`. This can be useful to e.g. recursively update the class or other attributes of all elements in a nested list: ``` r ## recursively remove all list attributes rrapply( renewable_oceania, f = \(x) c(x), classes = c("list", "ANY"), how = "recurse" ) |> str(list.len = 3, give.attr = TRUE) #> List of 1 #> $ Oceania:List of 4 #> ..$ Australia and New Zealand:List of 6 #> .. ..$ Australia : num 9.32 #> .. ..$ Christmas Island : logi NA #> .. ..$ Cocos (Keeling) Islands : logi NA #> .. .. [list output truncated] #> ..$ Melanesia :List of 5 #> .. ..$ Fiji : num 24.4 #> .. ..$ New Caledonia : num 4.03 #> .. ..$ Papua New Guinea: num 50.3 #> .. .. [list output truncated] #> ..$ Micronesia :List of 8 #> .. ..$ Guam : num 3.03 #> .. ..$ Kiribati : num 45.4 #> .. ..$ Marshall Islands : num 11.8 #> .. .. [list output truncated] #> .. [list output truncated] ``` #### • `how = "names"` The option `how = "names"` is a special case of `how = "recurse"`, where the value of `f` is used to replace the *name* of the evaluated list element instead of its *content* (as with all other `how` options). By default, `how = "names"` uses `classes = c("list", "ANY")` in order to allow updating of all names in the nested list. ``` r ## recursively replace all names by M49-codes rrapply( renewable_oceania, f = \(x) attr(x, "M49-code"), how = "names" ) |> str(list.len = 3, give.attr = FALSE) #> List of 1 #> $ 009:List of 4 #> ..$ 053:List of 6 #> .. ..$ 036: num 9.32 #> .. ..$ 162: logi NA #> .. ..$ 166: logi NA #> .. .. [list output truncated] #> ..$ 054:List of 5 #> .. ..$ 242: num 24.4 #> .. ..$ 540: num 4.03 #> .. ..$ 598: num 50.3 #> .. .. [list output truncated] #> ..$ 057:List of 8 #> .. ..$ 316: num 3.03 #> .. ..$ 296: num 45.4 #> .. ..$ 584: num 11.8 #> .. .. [list output truncated] #> .. [list output truncated] ``` ### Expression objects Base `rapply()` does not include recursion for expression objects. In contrast `rrapply()` supports recursion of call objects and expression vectors, which are treated as nested lists based on their abstract syntax trees. As such, all functionality that applies to nested lists extends directly to call objects and expression vectors. To update the abstract syntax tree of a call object, use `how = "replace"`: ``` r ## language object (lang <- quote(y <- x <- 1 + TRUE)) #> y <- x <- 1 + TRUE ## replace logicals by integers rrapply(lang, classes = "logical", f = as.numeric, how = "replace") #> y <- x <- 1 + 1 ``` To update the abstract syntax tree and return it as a nested list, use `how = "list"`: ``` r ## update and decompose call object rrapply(lang, f = function(x) ifelse(is.logical(x), as.numeric(x), x), how = "list") |> str() #> List of 3 #> $ : symbol <- #> $ : symbol y #> $ :List of 3 #> ..$ : symbol <- #> ..$ : symbol x #> ..$ :List of 3 #> .. ..$ : symbol + #> .. ..$ : num 1 #> .. ..$ : num 1 ``` The modes `how = "prune"`, `how = "flatten"` and `how = "melt"` return the pruned abstract syntax tree as: a nested list, a flattened list and a melted data.frame respectively. This is identical to application of `rrapply()` to the abstract syntax tree formatted as a nested list. To illustrate, we return all names (i.e. symbols) in the abstract syntax tree that not part of base R: ``` r ## expression vector expr <- expression(y <- x <- 1, f(g(2 * pi))) is_new_name <- function(x) !exists(as.character(x), envir = baseenv()) ## prune and decompose expression rrapply(expr, classes = "name", condition = is_new_name, how = "prune") |> str() #> List of 2 #> $ :List of 2 #> ..$ : symbol y #> ..$ :List of 1 #> .. ..$ : symbol x #> $ :List of 2 #> ..$ : symbol f #> ..$ :List of 1 #> .. ..$ : symbol g ## prune and flatten expression rrapply(expr, classes = "name", condition = is_new_name, how = "flatten") |> str() #> List of 4 #> $ : symbol y #> $ : symbol x #> $ : symbol f #> $ : symbol g ## prune and melt expression rrapply(expr, classes = "name", condition = is_new_name, f = as.character, how = "melt") #> L1 L2 L3 value #> 1 1 2 <NA> y #> 2 1 3 2 x #> 3 2 1 <NA> f #> 4 2 2 1 g ``` For more details and examples on how to use the `rrapply()` function see the accompanying package vignette in the vignettes folder or the Articles section at <https://jorischau.github.io/rrapply/>.
