run_TS: Run Taxon Sampling

In fcampelo/TaxonSampling: Hierarchical Taxonomic Sampling for Maximized Diversity at All Levels

Description

Run the TaxonSampling method to return a sample of taxonomic IDs according to the desired balance / diversity.

Usage

run_TS(
  taxlist,
  taxon,
  m,
  seq_file = NULL,
  out_file = NULL,
  method = "diversity",
  randomize = "no",
  replacement = FALSE,
  ignoreIDs = NULL,
  requireIDs = NULL,
  sampling = "agnostic",
  verbose = TRUE
)

Arguments

taxlist	list object of class _taxonsampling_, returned by [get_species_count()].
taxon	Taxon ID from which to start sampling children taxa (single character or integer value)
m	desired sample size
seq_file	character string with the path to the multifasta file containing the input sequences.
out_file	character string naming a file to save the output (a multifasta file). Ignored if 'seq_file == NULL'.
method	sampling method to use. Accepts "balanced" (favors balanced taxa representation) or "diversity" (favors maximized taxa representation)
randomize	randomization strategy: should the algorithm choose IDs randomly ("yes"), maintaining a balanced allocation ("no"), or with a balanced allocation at the top taxonomic level and randomized afterwards ("after_first_round")?
replacement	logical flag: should the algorithm allow repeated IDs in the output (if needed to reach m IDs in the output with maximized taxonomy diversity).
ignoreIDs	vector (character or integer) of IDs that must not appear in the output.
requireIDs	vector (character or integer) of IDs that must appear in the output. Notice that 'ignoreIDs' has precedence over 'requireIDs', i.e., IDs that occur in both will be ignored. 'requireIDs' that are children of any 'ignoreIDs' will also be ignored.
sampling	sampling mode. Accepts "agnostic" (sample species in a diversity-agnostic manner) or "known_species" (sample based on known species diversity).
verbose	logical: regulates function echoing to console.

Value

Input object'taxlist' updated with vector '$outputIDs' of sampled IDs and list '$outputSeqs' (if seq_file is not 'NULL') containing information about the sequences sampled.

fcampelo/TaxonSampling documentation built on Jan. 29, 2022, 7:11 a.m.