Taxonomic Check-List

Template for a taxonomic check-list generated from taxlist objects. The most important functions called in the source code are print_name(), indented_list(), write_rmd(), and render_rmd().

Usage

checklist(object, ...)

# S3 method for taxlist
checklist(
  object,
  exclude,
  indent = " ",
  prefix = "",
  suffix = "",
  print_args = list(),
  rmd_args = list(`header-includes` = "- \\setlength{\\parskip}{0pt}"),
  render_args = list(),
  title = "Taxonomic Checklist",
  output = "pdf_document",
  output_file = tempfile(),
  ...
)

Arguments

object

A taxlist object used as main input.

...

Further arguments. In taxlist-method they will be passed to the function indented_list().

exclude

A character vector including the name of taxonomic ranks that will be excluded of formatting in italics (excluded in the call to print_name()).

indent

A character value indicating the single indentation, which will be multiplied by the taxonomic rank going from the top to the bottom. Indentation can be either cancellec by indent = "" or can be specified for determined taxonomic ranks by naming elements of the input vector after the ranks.

prefix

A character value or character vector named by taxonomic ranks, which will be used as prefix.

suffix

The same as prefix but it will be placed at the end of the line.

print_args

A list with elements named after parameters (arguents) of the function print_name().

rmd_args

A list with elements named after parameters (arguments) of the function write_rmd().

render_args

A list with elements named after parameters (arguments) of the function render_rmd().

title

A character value with the title of the document.

output

A character value indicating the format of ouput using rmarkdown.

output_file

Name of the rendered otuput file. It will be passed to write_rmd().

Examples

if (FALSE) {
library(taxlist)

## Subset of family Piperaceae
Piperaceae <- subset(Easplist, TaxonName == "Piperaceae",
  slot = "taxonNames", keep_children = TRUE, keep_parents = TRUE
)

## Simple checklist
checklist(Piperaceae, output_file = "piperaceae", exclude = "family")

## Families as sections in document
checklist(Piperaceae,
  output_file = "piperaceae2", exclude = "family",
  prefix = c(family = "# ")
)

## Families as sections and small captions for the whole taxonomic list
checklist(Easplist,
  output_file = "ea-splist", exclude = "family",
  prefix = c(family = "# \\sc{"), suffix = c(family = "}")
)
}