taxmap: Create an instance of `taxmap`

Description

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