sample_n_taxa: Sample n taxa from [taxonomy()] or [taxmap()]

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

Sample n taxa from [taxonomy()] or [taxmap()]

Description

Randomly sample some number of taxa from a [taxonomy()] or [taxmap()] object. Weights can be specified for taxa or the observations assigned to them. See [dplyr::sample_n()] for the inspiration for this function.

obj$sample_n_taxa(size, taxon_weight = NULL,
  obs_weight = NULL, obs_target = NULL,
  use_subtaxa = TRUE, collapse_func = mean, ...)
sample_n_taxa(obj, size, taxon_weight = NULL,
  obs_weight = NULL, obs_target = NULL,
  use_subtaxa = TRUE, collapse_func = mean, ...)

Arguments

obj	([taxonomy()] or [taxmap()]) The object to sample from.
size	('numeric' of length 1) The number of taxa to sample.
taxon_weight	('numeric') Non-negative sampling weights of each taxon. If 'obs_weight' is also specified, the two weights are multiplied (after 'obs_weight' for each taxon is calculated).
obs_weight	('numeric') This option only applies to [taxmap()] objects. Sampling weights of each observation. The weights for each observation assigned to a given taxon are supplied to 'collapse_func' to get the taxon weight. If 'use_subtaxa' is 'TRUE' then the observations assigned to every subtaxa are also used. Any variable name that appears in [all_names()] can be used as if it was a vector on its own. If 'taxon_weight' is also specified, the two weights are multiplied (after 'obs_weight' for each observation is calculated). 'obs_target' must be used with this option.
obs_target	('character' of length 1) This option only applies to [taxmap()] objects. The name of the data set in 'obj$data' that values in 'obs_weight' corresponds to. Must be used when 'obs_weight' is used.
use_subtaxa	('logical' or 'numeric' of length 1) Affects how the 'obs_weight' option is used. If 'TRUE', the weights for each taxon in an observation's classification are multiplied to get the observation weight. If 'FALSE' just the taxonomic level the observation is assign to it considered. Positive numbers indicate the number of ranks below the each taxon to use. '0' is equivalent to 'FALSE'. Negative numbers are equivalent to 'TRUE'.
collapse_func	('function' of length 1) If 'taxon_weight' is used and ‘supertaxa' is 'TRUE', the weights for each taxon in an observation’s classification are supplied to 'collapse_func' to get the observation weight. This function should take numeric vector and return a single number.
...	Additional options are passed to [filter_taxa()].

Value

An object of type [taxonomy()] or [taxmap()]

See Also

Other taxmap manipulation functions: arrange_obs(), arrange_taxa(), filter_obs(), filter_taxa(), mutate_obs(), sample_frac_obs(), sample_frac_taxa(), sample_n_obs(), select_obs(), transmute_obs()

Examples

# Randomly sample three taxa
sample_n_taxa(ex_taxmap, 3)

# Include supertaxa
sample_n_taxa(ex_taxmap, 3, supertaxa = TRUE)

# Include subtaxa
sample_n_taxa(ex_taxmap, 1, subtaxa = TRUE)

# Sample some taxa more often then others
sample_n_taxa(ex_taxmap, 3, supertaxa = TRUE,
              obs_weight = n_legs, obs_target = "info")

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