sample_frac_obs: Sample a proportion of observations from [taxmap()]

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

Sample a proportion of observations from [taxmap()]

Description

Randomly sample some proportion of observations from a [taxmap()] object. Weights can be specified for observations or their taxa. See [dplyr::sample_frac()] for the inspiration for this function. Calling the function using the 'obj$sample_frac_obs(...)' style edits "obj" in place, unlike most R functions. However, calling the function using the 'sample_frac_obs(obj, ...)‘ imitates R’s traditional copy-on-modify semantics, so "obj" would not be changed; instead a changed version would be returned, like most R functions.

obj$sample_frac_obs(data, size, replace = FALSE,
  taxon_weight = NULL, obs_weight = NULL,
  use_supertaxa = TRUE, collapse_func = mean, ...)
sample_frac_obs(obj, data, size, replace = FALSE,
  taxon_weight = NULL, obs_weight = NULL,
  use_supertaxa = TRUE, collapse_func = mean, ...)

Arguments

obj	([taxmap()]) The object to sample from.
data	Dataset names, indexes, or a logical vector that indicates which datasets in 'obj$data' to sample. If multiple datasets are sample at once, then they must be the same length.
size	('numeric' of length 1) The proportion of observations to sample.
replace	('logical' of length 1) If 'TRUE', sample with replacement.
taxon_weight	('numeric') Non-negative sampling weights of each taxon. If 'use_supertaxa' is 'TRUE', the weights for each taxon in an observation's classification are supplied to 'collapse_func' to get the observation weight. If 'obs_weight' is also specified, the two weights are multiplied (after 'taxon_weight' for each observation is calculated).
obs_weight	('numeric') Sampling weights of each observation. If 'taxon_weight' is also specified, the two weights are multiplied (after 'taxon_weight' for each observation is calculated).
use_supertaxa	('logical' or 'numeric' of length 1) Affects how the 'taxon_weight' 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 above 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' option 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_obs()].
target	DEPRECIATED. use "data" instead.

Value

An object of type [taxmap()]

See Also

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

Examples

# Sample half of the rows fram a table
sample_frac_obs(ex_taxmap, "info", 0.5)

# Sample multiple datasets at once
sample_frac_obs(ex_taxmap, c("info", "phylopic_ids", "foods"), 0.5)

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