checknames: Function to check names on a species list or phylogeny.

In sckott/datelife_sandbox: sacbox

Description

Function to check names on a species list or phylogeny.

Usage

  checknames(phylo = NULL, charvector = NULL,
    source_ = "NCBI", splitby = NULL, writefile = FALSE)

Arguments

phylo	Phylogeny object, class phylo
source_	Source to match names to. One of ncbi, iPlant
splitby	Length of chunks by which to split species list

Examples

## Not run: 
# A phylogeny as input
library(doMC)
out <- checknames(phylo="BergmannEtAl2012", source_="NCBI", splitby=200)
out <- checknames(phylo=A"lfaroEtAl2009_tree", source_="NCBI", splitby=100)
out <- checknames(phylo="EastmanEtAlUnpublished_tree", source_="NCBI", splitby=100)
out <- checknames(phylo="HeathEtAl2012_tree", source_="NCBI")
out <- checknames(phylo="JaffeEtAl2011", source_="NCBI", splitby=100)
out <- checknames(phylo="Chaetodontidae2011", source_="NCBI")
out <- checknames(phylo="Drosophila2012_large", source_="NCBI", splitby=50, writefile=TRUE)
out <- checknames(phylo="Drosophila2012_small", source_="NCBI", splitby=50)

out <- checknames(phylo=Apogonidae2011, source_="NCBI")
out <- checknames(phylo="BinindaEmondsEtAl2007", source_="NCBI", splitby=500)
out <- checknames(phylo=FabreEtAl2009, source_="NCBI", splitby=50)
out <- checknames(phylo=HardyCook2012, source_="NCBI", writefile=TRUE)
out <- checknames(phylo="FabreEtAl2009", source_="NCBI", splitby=50, writefile=TRUE)

# A character vector as input (of species names)
out <- checknames(charvector=AlfaroEtAl2009_tree$tip.label, source_="NCBI", splitby=50)
out <- checknames(charvector=AlfaroEtAl2009_tree$tip.label[1:20], source_="NCBI")

## End(Not run)

sckott/datelife_sandbox documentation built on May 29, 2019, 3:59 p.m.