as_data_frame: Convert a taxa2 object to a 'data.frame'

In zachary-foster/taxa2: Classes for Storing and Manipulating Taxonomic Data

Description

Convert the information in a taxa2 object to a data.frame using base R vectors as columns. Use as_tibble to convert to tibbles.

Usage

as_data_frame(
  x,
  row.names = NULL,
  optional = FALSE,
  ...,
  stringsAsFactors = default.stringsAsFactors()
)

Arguments

x	An object defined by taxa2, such as taxon or taxon_id
row.names	NULL or a character vector giving the row names for the data frame. Missing values are not allowed.
optional	logical. If TRUE, setting row names and converting column names (to syntactic names: see make.names) is optional. Note that all of R's base package as.data.frame() methods use optional only for column names treatment, basically with the meaning of data.frame(*, check.names = !optional). See also the make.names argument of the matrix method.
...	additional arguments to be passed to or from methods.
stringsAsFactors	logical: should the character vector be converted to a factor?

Examples

x <- taxon(name = c('Homo sapiens', 'Bacillus', 'Ascomycota', 'Ericaceae'),
           rank = c('species', 'genus', 'phylum', 'family'),
           id = taxon_id(c('9606', '1386', '4890', '4345'), db = 'ncbi'),
           auth = c('Linnaeus, 1758', 'Cohn 1872', NA, 'Juss., 1789'))
as_data_frame(x)

zachary-foster/taxa2 documentation built on Jan. 1, 2021, 1:48 p.m.