Use mutate inside a function called by an apply family function - r

Question

I am trying to change some of my data that are stored as tibbles inside a list.
This list of tibbles was generated by a package.
I do not understand why my function does not work.
If I extract a tibble element manually, the function works but not inside a lapply.
my function:
changesomethingtaxize <- function(x, whatchange=NULL, applyfunction=NULL){
library(lazyeval) ;
mutate_call <- lazyeval::interp(~ a(b), a = match.fun(applyfunction), b = as.name(whatchange) )
x %<>% mutate_(.dots = setNames(list(mutate_call), whatchange) )
return(x)
}
I want to do
mydata <- lapply(mydata, function(x) changesomethingtaxize(x, whatchange=rank, applyfunction=str_to_sentence) )
I could use a loop to extract each tibbles (in this case I only have 5) but I would like to understand what I do wrong :)
From dput()
mydata <- structure(list(`Zostera marina` = structure(list(name = c("Plantae",
"Viridiplantae", "Streptophyta", "Embryophyta", "Tracheophyta",
"Spermatophytina", "Magnoliopsida", "Lilianae", "Alismatales",
"Zosteraceae", "Zostera", "Zostera marina"), rank = c("kingdom",
"subkingdom", "infrakingdom", "superdivision", "division", "subdivision",
"class", "superorder", "order", "family", "genus", "species"),
id = c("202422", "954898", "846494", "954900", "846496",
"846504", "18063", "846542", "38883", "39069", "39073", "39074"
)), row.names = c(NA, 12L), class = "data.frame"), `Vascular plants` = structure(list(
name = c("Plantae", "Viridiplantae", "Streptophyta", "Embryophyta",
"Tracheophyta"), rank = c("kingdom", "subkingdom", "infrakingdom",
"superdivision", "division"), id = c("202422", "954898",
"846494", "954900", "846496")), row.names = c(NA, 5L), class = "data.frame"),
`Fucus vesiculosus` = structure(list(name = c("Chromista",
"Chromista", "Phaeophyta", "Phaeophyceae", "Fucales", "Fucaceae",
"Fucus", "Fucus vesiculosus"), rank = c("kingdom", "subkingdom",
"division", "class", "order", "family", "genus", "species"
), id = c("630578", "590735", "660055", "10686", "11328",
"11329", "11334", "11335")), row.names = c(NA, 8L), class = "data.frame"),
Macroalgae = NA, `Filamentous algae` = NA), class = "classification", db = "itis")

Answer 1

I think I actually found why... :D
The lapply works but was not returning anything because of the NAs (empty elements of the list).
I added an if() that only mutates a tibble if the tibble actually contains something.
It is always an NA issue somewhere!
Well hope that piece of code could help someone someday.

Answer 2

The functions you provided aren't usable by themselves, but it looks like you're attempting to use a function meant to modify a data frame on non-dataframe objects, which mydata contains.
I'm using dplyr::mutate() just to illustrate here.
Your data contain NAs (which in this case are logical). dplyr::mutate() doesnt' have a method for logicals and I'm assuming the function you're trying to use doesn't either (or simply doesn't have a way of handling NA values).
You should be getting an error that's at least conceptually similar to the following ...
lapply(mydata, function(x) dplyr::mutate(x, col_to_modify = toupper(rank)))
#> Error in UseMethod("mutate_"): no applicable method for 'mutate_' applied to an object of class "logical"
To get around this, you can check your list ahead of time and note which elements are indeed data frames.
df_indices <- vapply(mydata, is.data.frame, logical(1L))
df_indices
#> Zostera marina Vascular plants Fucus vesiculosus Macroalgae
#> TRUE TRUE TRUE FALSE
#> Filamentous algae
#> FALSE
Using df_indices, we can modify only those elements in mydata like so...
mydata[df_indices] <- lapply(
mydata[df_indices],
function(x) dplyr::mutate(x, col_to_modify = toupper(rank))
)
mydata
#> $`Zostera marina`
#> name rank id col_to_modify
#> 1 Plantae kingdom 202422 KINGDOM
#> 2 Viridiplantae subkingdom 954898 SUBKINGDOM
#> 3 Streptophyta infrakingdom 846494 INFRAKINGDOM
#> 4 Embryophyta superdivision 954900 SUPERDIVISION
#> 5 Tracheophyta division 846496 DIVISION
#> 6 Spermatophytina subdivision 846504 SUBDIVISION
#> 7 Magnoliopsida class 18063 CLASS
#> 8 Lilianae superorder 846542 SUPERORDER
#> 9 Alismatales order 38883 ORDER
#> 10 Zosteraceae family 39069 FAMILY
#> 11 Zostera genus 39073 GENUS
#> 12 Zostera marina species 39074 SPECIES
#>
#> $`Vascular plants`
#> name rank id col_to_modify
#> 1 Plantae kingdom 202422 KINGDOM
#> 2 Viridiplantae subkingdom 954898 SUBKINGDOM
#> 3 Streptophyta infrakingdom 846494 INFRAKINGDOM
#> 4 Embryophyta superdivision 954900 SUPERDIVISION
#> 5 Tracheophyta division 846496 DIVISION
#>
#> $`Fucus vesiculosus`
#> name rank id col_to_modify
#> 1 Chromista kingdom 630578 KINGDOM
#> 2 Chromista subkingdom 590735 SUBKINGDOM
#> 3 Phaeophyta division 660055 DIVISION
#> 4 Phaeophyceae class 10686 CLASS
#> 5 Fucales order 11328 ORDER
#> 6 Fucaceae family 11329 FAMILY
#> 7 Fucus genus 11334 GENUS
#> 8 Fucus vesiculosus species 11335 SPECIES
#>
#> $Macroalgae
#> [1] NA
#>
#> $`Filamentous algae`
#> [1] NA
#>
#> attr(,"class")
#> [1] "classification"
#> attr(,"db")
#> [1] "itis"
Note that {purrr} has a nice map() variant designed to handle this very situation. purrr::map_if() takes a .p (predicate) argument to which you can provide a function that it applies to .x and returns TRUE or FALSE. Only those elements that return TRUE are modified by the function you provide to .f
purrr::map_if(.x = mydata, .p = is.data.frame,
.f = ~ dplyr::mutate(.x, col_to_modify = toupper(rank)))
#> $`Zostera marina`
#> name rank id col_to_modify
#> 1 Plantae kingdom 202422 KINGDOM
#> 2 Viridiplantae subkingdom 954898 SUBKINGDOM
#> 3 Streptophyta infrakingdom 846494 INFRAKINGDOM
#> 4 Embryophyta superdivision 954900 SUPERDIVISION
#> 5 Tracheophyta division 846496 DIVISION
#> 6 Spermatophytina subdivision 846504 SUBDIVISION
#> 7 Magnoliopsida class 18063 CLASS
#> 8 Lilianae superorder 846542 SUPERORDER
#> 9 Alismatales order 38883 ORDER
#> 10 Zosteraceae family 39069 FAMILY
#> 11 Zostera genus 39073 GENUS
#> 12 Zostera marina species 39074 SPECIES
#>
#> $`Vascular plants`
#> name rank id col_to_modify
#> 1 Plantae kingdom 202422 KINGDOM
#> 2 Viridiplantae subkingdom 954898 SUBKINGDOM
#> 3 Streptophyta infrakingdom 846494 INFRAKINGDOM
#> 4 Embryophyta superdivision 954900 SUPERDIVISION
#> 5 Tracheophyta division 846496 DIVISION
#>
#> $`Fucus vesiculosus`
#> name rank id col_to_modify
#> 1 Chromista kingdom 630578 KINGDOM
#> 2 Chromista subkingdom 590735 SUBKINGDOM
#> 3 Phaeophyta division 660055 DIVISION
#> 4 Phaeophyceae class 10686 CLASS
#> 5 Fucales order 11328 ORDER
#> 6 Fucaceae family 11329 FAMILY
#> 7 Fucus genus 11334 GENUS
#> 8 Fucus vesiculosus species 11335 SPECIES
#>
#> $Macroalgae
#> [1] NA
#>
#> $`Filamentous algae`
#> [1] NA