taxmap

0th

Percentile

Create an instance of taxmap

Create an instance of taxmap containing observations taxmap by a taxonomy.

Usage
taxmap(taxon_ids, supertaxon_ids, taxa = taxon_ids, obs_taxon_ids = numeric(0), taxon_data = NULL, obs_data = NULL, taxon_funcs = list(n_obs = n_obs, n_obs_1 = n_obs_1, n_supertaxa = n_supertaxa, n_subtaxa = n_subtaxa, n_subtaxa_1 = n_subtaxa_1, hierarchies = hierarchies), obs_funcs = list())
Arguments
taxon_ids
(character) These are unique identifiers for taxa. They will be coerced into characters.
supertaxon_ids
(character OR (numeric)) Supertaxa of taxa. If a character vector, then these should be in the same format as taxon_ids. If a numeric vector, then it is interpreted as the indexes of taxon_ids. Taxa without parents should be NA.
taxa
(character) Objects representing taxa. Currently, these can be anything, but this might change in the future.
obs_taxon_ids
(character OR (numeric)) Taxon assignments of observations. Supertaxa of taxa. If a character vector, then these should be in the same format as taxon_ids. If a numeric vector, then it is interpreted as the indexes of taxon_ids.
taxon_data
(data.frame) A table with rows pretaining to taxa
obs_data
A (data.frame) A table with rows pretaining to obs_taxa
taxon_funcs
(list of named functions) These the values produced by these functions will be accessible as a column in taxon_data. The first parameter of each function should be a single taxmap object.
obs_funcs
(list of named functions) These the values produced by these functions will be accessible as a column in obs_data. The first parameter of each function should be a single taxmap object.
Value

An object of type taxmap

Aliases
  • taxmap
Documentation reproduced from package metacoder, version 0.1.2, License: GPL-2 | GPL-3

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