Convert a taxa object to a data.frame

Convert the information in a taxa 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 = FALSE
)

Arguments

x

An object defined by taxa, 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)
#>       tax_name tax_rank tax_id tax_db tax_author tax_date tax_cite
#> 1 Homo sapiens  species   9606   ncbi   Linnaeus     1758         
#> 2     Bacillus    genus   1386   ncbi       Cohn     1872         
#> 3   Ascomycota   phylum   4890   ncbi       <NA>                  
#> 4    Ericaceae   family   4345   ncbi      Juss.     1789