metacoder (version 0.1.2)

sample_frac_obs: Sample a proportion of observations from taxmap

Description

Randomly sample some propoortion of observations from a taxmap object. Weights can be specified for observations or the taxa they are taxmap by. See sample_frac for the inspiration for this function.

Usage

sample_frac_obs(.data, size = 1, replace = FALSE, taxon_weight = NULL, obs_weight = NULL, use_supertaxa = TRUE, collapse_func = mean, ...)

Arguments

.data

(taxmap) The object to sample from.

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. The expression given is evaluated in the context of taxon_data. In other words, any column name that appears in taxon_data(.data) can be used as if it was a vector on its own. 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. The expression given is evaluated in the context of obs_data. In other words, any column name that appears in obs_data(.data) can be used as if it was a vector on its own. If taxon_weight is also specified, the two weights are multiplied (after taxon_weight for each observation is calculated).

use_supertaxa

(logical 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. Otherwise, just the taxonomic level the observation is assign to it considered.

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.

Value

An object of type taxmap

See Also

Other dplyr-like functions: arrange_obs, arrange_taxa, filter_obs, filter_taxa, mutate_obs, mutate_taxa, sample_frac_taxa, sample_n_obs, sample_n_taxa, select_obs, select_taxa, transmute_obs, transmute_taxa

Examples

# Subsample without replacement, keeping all taxa
sample_frac_obs(unite_ex_data_3, 0.1)
# Subsample without replacement and remove unsampled taxa
sample_frac_obs(unite_ex_data_3, 0.1, unobserved = FALSE)
# Subsample with taxon weight 
sample_frac_obs(unite_ex_data_3, 0.1, unobserved = FALSE, taxon_weight = 1 / n_obs)
# Sample with replacement
sample_frac_obs(unite_ex_data_3, 10, replace = TRUE)

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