R/data.R

In iramosgutierrez/randtip: A generalized framework to expand incomplete phylogenies with taxonomic information

#' Phylogeny of felids
#'
#' Example phylogeny for randtip package
#'
#' @format A phylogenetic tree with 14 tips and 13 internal nodes
#' \describe{
#' Phylogenetic tree with 14 species of felids (Felidae).
#' This is a subtree extracted from the complete mammal phylogeny by Upham et al. (2019)
#' }
"cats"


#' mythology
#'
#' Data used in randtip tutorial (see Supplementary Material in https://doi.org/10.1101/2022.01.04.474924).
#'
#' @format A list with 5 slots
#'
#' \describe{
#' \item{back.tree}{Hypothetical backbone tree}
#' \item{sp.list}{List of species to expanded the backbone tree}
#' \item{info.list}{Hypothetical 'info' data frame for use under "list" mode}
#' \item{info.backbone}{Hypothetical 'info' data frame for use under "backbone" mode}
#' \item{edges}{'edges' data frame to bind the PUT "Monoceros_x_alaricornus" using a customized set of edges}
#' }
"mythology"


#' birds
#'
#' Phylogenetic tree based in Jetz et al. (2012). # ESTÁ BASADO en Jetz et al. 2012 o ES el mismo árbol?
#'
#' @format A phylo object
#' \describe{
#' Phylogenetic tree comprising 9993 species of birds.
#' Data obtained from https://github.com/megatrees/bird_20221117
#' }
"birds"


#' plants
#'
#' Phylogenetic tree obtained from Jin & Quian (2022), based on Smith & Brown (2018) and Zanne et al. (2014).
#' Nomenclature stands for World Checklist of Vascular Plants (WCVP).
#'
#' @format A phylo object
#' \describe{
#' Phylogenetic tree comprising 73011 species of vascular plants.
#' Data obtained from https://github.com/megatrees/plant_20221214
#' }
"plants"


#' fish
#'
#' Phylogenetic tree obtained from Rabosky et al. (2018).
#'
#' @format A phylo object
#' \describe{
#' Phylogenetic tree comprising 31521 species of fishes
#' Data obtained from https://github.com/megatrees/fish_20221117
#' }
"fish"


#' mammals
#'
#' Phylogenetic tree obtained from Upham et al. (2019).
#'
#' @format A phylo object
#' \describe{
#' Phylogenetic tree comprising 5911 species of mammals.
#' Data obtained from https://github.com/megatrees/mammal_20221117
#' }
"mammals"


#' squamates
#'
#' Phylogenetic tree obtained from Pyron et al. (2013).
#'
#' @format A phylo object
#' \describe{
#' Phylogenetic tree comprising 4161 species of squamates.
#' Data obtained from https://doi.org/10.1186/1471-2148-13-93
#' }
"squamates"


#' amphibians
#'
#' Phylogenetic tree obtained from Jetz & Pyron, (2018).
#'
#' @format A phylo object
#' \describe{
#' Phylogenetic tree comprising 7238 species of amphibians
#' Data obtained from https://github.com/megatrees/amphibian_20221117
#' }
"amphibians"


#' birds.info
#'
#' Info data frame with taxonomic information retrieved for the species in the bird phylogeny (Jetz et al. 2012)
#'
#' @format An info data frame
#' \describe{
#' Data frame with taxonomic information on the 9993 species of birds included in
#' 'birds' object. Taxonomic information was retrieved from 'ncbi' database taxonomy.
#'
#' }
"birds.info"


#' plants.info
#'
#' Info data frame with taxonomic information retrieved for the species in the plant phylogeny (Jin & Quian 2022)
#'
#' @format An info data frame
#' \describe{
#' Data frame with taxonomic information on the 73013 species of vascular plants
#' included in 'plants' object. Taxonomic information was retrieved from 'ncbi' database taxonomy.
#'
#' }
"plants.info"


#' fish.info
#'
#' Info data frame with taxonomic information retrieved for the species in the fish phylogeny (Rabosky et al. 2018)
#'
#' @format An info data frame
#' \describe{
#' Data frame with taxonomic information on the 31521 species of fishes
#' included in 'fish' object. Taxonomic information was retrieved from The Fish Tree of Life website.
#'
#' }
"fish.info"

#' mammals.info
#'
#' Info data frame with taxonomic information retrieved for the species in the mammal phylogeny (Upham et al. 2019)
#'
#' @format An info data frame
#' \describe{
#' Data frame with taxonomic information on the 5911 species of mammals
#' included in 'mammals' object. Taxonomic information was retrieved from 'ncbi' database taxonomy.
#'
#' }
"mammals.info"


#' squamates.info
#'
#' Info data frame with taxonomic information retrieved for the species in the squamate phylogeny (Pyron et al. 2013)
#'
#' @format An info data frame
#' \describe{
#' Data frame with taxonomic information on the 4161 species of squamates
#' included in 'squamates' object. Taxonomic information was retrieved from 'ncbi' database taxonomy.
#'
#' }
"squamates.info"


#' amphibians.info
#'
#' Info data frame with taxonomic information retrieved for the species in the amphibian phylogeny (Pyron et al. 2013)
#'
#' @format An info data frame
#' \describe{
#' Data frame with taxonomic information on the 7238 species of amphibians
#' included in 'amphibians' object. Taxonomic information was retrieved from 'ncbi' database taxonomy.
#'
#' }
"amphibians.info"