obs_apply: Apply function to observations per taxon

In metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Apply function to observations per taxon

Description

Apply a function to data for the observations for each taxon. This is similar to using [obs()] with [lapply()] or [sapply()].

obj$obs_apply(data, func, simplify = FALSE, value = NULL,
  subset = NULL, recursive = TRUE, ...)
obs_apply(obj, data, func, simplify = FALSE, value = NULL,
  subset = NULL, recursive = TRUE, ...)

Arguments

obj	The [taxmap()] object containing taxon information to be queried.
data	Either the name of something in 'obj$data' that has taxon information or a an external object with taxon information. For tables, there must be a column named "taxon_id" and lists/vectors must be named by taxon ID.
func	('function') The function to apply.
simplify	('logical') If 'TRUE', convert lists to vectors.
value	What data to give to the function. This is usually the name of column in a table in 'obj$data'. Any result of 'all_names(obj)' can be used, but it usually only makes sense to use columns in the dataset specified by the 'data' option. By default, the indexes of observation in 'data' are returned.
subset	Taxon IDs, TRUE/FALSE vector, or taxon indexes 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 observation assigned to the specified input taxa, not subtaxa. If 'TRUE', return all the observations of every subtaxa, etc. Positive numbers indicate the number of ranks below the each taxon to get observations for '0' is equivalent to 'FALSE'. Negative numbers are equivalent to 'TRUE'.
...	Extra arguments are passed to the function.

Examples

# Find the average number of legs in each taxon
obs_apply(ex_taxmap, "info", mean, value = "n_legs", simplify = TRUE)

# One way to implement `n_obs` and find the number of observations per taxon
obs_apply(ex_taxmap, "info", length, simplify = TRUE)

metacoder documentation built on April 4, 2023, 9:08 a.m.