metacoder (version 0.3.7)

obs_apply: 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)