no applicable method for 'offspring' applied to an object of class "phylo"

Question

I think my issue is actually with future and exporting methods rather than tidytree, but if someone could explain to me what is actually happening and how I should be writing my code to avoid this problem it would be greatly appreciated.

I am using tidytree to do some phylogenetic analyses. The function offspring works fine when I use lapply, but throws the following error when I use future_lapply:

Error in UseMethod("offspring") : 
  no applicable method for 'offspring' applied to an object of class "phylo"

Reproducible example:

library(ape)
library(tidytree)
library(future.apply)

tree <- rtree(4)
lapply(5:7, function(x) offspring(tree,x, tiponly=TRUE))
future_lapply(5:7, function(x) tidytree::offspring(tree,x, tiponly=TRUE))

And corresponding output:

> lapply(5:7, function(x) offspring(tree,x, tiponly=TRUE))
[[1]]
[1] 1 4 2 3

[[2]]
[1] 4 2 3

[[3]]
[1] 2 3

> future_lapply(5:7, function(x) tidytree::offspring(tree,x, tiponly=TRUE))
Error in UseMethod("offspring") : 
  no applicable method for 'offspring' applied to an object of class "phylo"

Answer 1

I can reproduce this error also using lapply();

library(ape)
library(tidytree)
tree <- rtree(4)
y <- lapply(5:7, FUN = function(x) offspring(tree, x, tiponly = TRUE))
#> Error in UseMethod("offspring") : 
#>   no applicable method for 'offspring' applied to an object of class "phylo"

And, also without lapply();

library(ape)
library(tidytree)
tree <- rtree(4)
y <- offspring(tree, 5L, tiponly = TRUE)
#> Error in UseMethod("offspring") : 
#>  no applicable method for 'offspring' applied to an object of class "phylo"

This happens because tree is of class phylo:

class(tree)
#> [1] "phylo"

but tidytree does not provide any S3 methods for this class;

methods("offspring")
#> [1] offspring.tbl_tree*
#> see '?methods' for accessing help and source code

Looking at the example in ?tidytree::offspring, it looks like you forgot:

tree <- as_tibble(tree)

Adding that makes it work, including with future.apply.

EDIT: Added the solution.