obs: Get data indexes associated with taxa

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

Get data indexes associated with taxa

Description

Given a [taxmap()] object, return data associated with each taxon in a given table included in that [taxmap()] object.

obj$obs(data, value = NULL, subset = NULL,
  recursive = TRUE, simplify = FALSE)
obs(obj, data, value = NULL, subset = NULL,
  recursive = TRUE, simplify = FALSE)

Arguments

obj	([taxmap()]) The [taxmap()] object containing taxon information to be queried.
data	Either the name of something in 'obj$data' that has taxon information or a an external object with taxon information. For tables, there must be a column named "taxon_id" and lists/vectors must be named by taxon ID.
value	What data to return. This is usually the name of column in a table in 'obj$data'. Any result of 'all_names(obj)' can be used. If the value used has names, it is assumed that the names are taxon ids and the taxon ids are used to look up the correct values.
subset	Taxon IDs, TRUE/FALSE vector, or taxon indexes to find observations for. Default: All taxa in 'obj' will be used. Any variable name that appears in [all_names()] can be used as if it was a vector on its own.
recursive	('logical' or 'numeric') If 'FALSE', only return the observation assigned to the specified input taxa, not subtaxa. If 'TRUE', return all the observations of every subtaxa, etc. Positive numbers indicate the number of ranks below the each taxon to get observations for '0' is equivalent to 'FALSE'. Negative numbers are equivalent to 'TRUE'.
simplify	('logical') If 'TRUE', then combine all the results into a single vector of unique observation indexes.

Value

If 'simplify = FALSE', then a list of vectors of observation indexes are returned corresponding to the 'data' argument. If 'simplify = TRUE', then the observation indexes for all 'data' taxa are returned in a single vector.

Examples

# Get indexes of rows corresponding to each taxon
obs(ex_taxmap, "info")

# Get only a subset of taxon indexes
obs(ex_taxmap, "info", subset = 1:2)

# Get only a subset of taxon IDs
obs(ex_taxmap, "info", subset = c("b", "c"))

# Get only a subset of taxa using logical tests
obs(ex_taxmap, "info", subset = taxon_ranks == "genus")

# Only return indexes of rows assinged to each taxon explicitly
obs(ex_taxmap, "info", recursive = FALSE)

# Lump all row indexes in a single vector
obs(ex_taxmap, "info", simplify = TRUE)

# Return values from a dataset instead of indexes
obs(ex_taxmap, "info", value = "name")

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