R/brranching-package.R

In ropensci/brranching: Fetch 'Phylogenies' from Many Sources

#' @title brranching
#' @description Phylogenies from many sources
#' @importFrom crul HttpClient
#' @importFrom curl curl_escape
#' @importFrom ape read.tree write.tree
#' @importFrom taxize tax_name
#' @importFrom phytools read.newick
#' @importFrom phylocomr ph_bladj ph_phylomatic
#' @importFrom conditionz ConditionKeeper
#' @name brranching-package
#' @aliases brranching
#' @docType package
#' @author Scott Chamberlain <myrmecocystus@@gmail.com>
#' @keywords package
NULL

#' Lookup-table for family, genus, and species names for ThePlantList 
#' gymnosperms
#'
#' These names are from <http://www.theplantlist.org/>, collected
#' on 2015-11-11, and are from version 1.1 of their data. This data is
#' used in the function [phylomatic_names()]
#'
#' @format A data frame with 23,801 rows and 2 variables:
#' 
#' - family: family name
#' - genus: genus name
#' 
#' @source <http://www.theplantlist.org/>
#' @name tpl
#' @docType data
#' @keywords data
NULL

#' Phylogenies to use with phylomatic
#'
#' @format A list with 4 character strings:
#' 
#' - R20120829 - 2401 tips, 1801 internal nodes
#' - binindaemonds2007 - 4510 tips, 2108 internal nodes
#' - zanne2014 - 31749 tips, 31748 internal nodes
#' - smith2011 - 55473 tips, 55338 internal nodes
#' 
#' @source phylocom
#' @name phylomatic_trees
#' @docType data
#' @keywords data
NULL