taxa (version 0.3.3)

supertaxa_apply: Apply function to supertaxa of each taxon

Description

Apply a function to the supertaxa for each taxon. This is similar to using supertaxa() with lapply() or sapply().

obj$supertaxa_apply(func, subset = NULL, recursive = TRUE,
  simplify = FALSE, include_input = FALSE, value = "taxon_indexes",
  na = FALSE, ...)
supertaxa_apply(obj, func, subset = NULL, recursive = TRUE,
  simplify = FALSE, include_input = FALSE, value = "taxon_indexes",
  na = FALSE, ....)

Arguments

obj

The taxonomy() or taxmap() object containing taxon information to be queried.

func

(function) The function to apply.

subset

Taxon IDs, TRUE/FALSE vector, or taxon indexes of taxa to use. Default: All taxa in obj will be used. Any variable name that appears in all_names() can be used as if it was a vector on its own.

recursive

(logical or numeric) If FALSE, only return the supertaxa one rank above the target taxa. If TRUE, return all the supertaxa of every supertaxa, etc. Positive numbers indicate the number of recursions (i.e. number of ranks above the target taxon to return). 1 is equivalent to FALSE. Negative numbers are equivalent to TRUE.

simplify

(logical) If TRUE, then combine all the results into a single vector of unique values.

include_input

(logical) If TRUE, the input taxa are included in the output

value

What data to give to the function. Any result of all_names(obj) can be used, but it usually only makes sense to use data that has an associated taxon id.

na

(logical) If TRUE, return NA where information is not available.

...

Extra arguments are passed to the function.

Examples

# NOT RUN {
# Get number of supertaxa that each taxon is contained in
supertaxa_apply(ex_taxmap, length)

# Get classifications for each taxon
# Note; this can be done with `classifications()` easier
supertaxa_apply(ex_taxmap, paste, collapse = ";", include_input = TRUE,
                value = "taxon_names")

# }

Run the code above in your browser using DataCamp Workspace