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willpearse/trees_for_managers.R

Created March 5, 2017 00:10
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Calculating PD for managers
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trees_for_managers.R
#Loading a package
library(pez)
#Building a tree
tree <- read.tree("Vascular_Plants_rooted.dated.tre") #file from http://datadryad.org/resource/doi:10.5061/dryad.63q27
species <- c("Quercus_notreal","Pinus_notreal","Blasia_notreal","Riccia_notreal")
tree <- congeneric.merge(tree, species)
tree <- drop.tip(tree, setdiff(tree$tip.label, species))
#Calculating PD
c.data <- comparative.comm(tree, community.data)
.pd(c.data)
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