R计算 PD Calculate Faith’s Phylogenetic Diversity
网址： cran.r-project.org/web/package…
Description： Calculate the sum of the total phylogenetic branch length for one or multiple samples.
Usage： pd(samp, tree, include.root=TRUE)
Arguments
samp： Community data matrix
tree：A phylo tree object
include.root： Should the root node be included in all PD calculations (default = TRUE)
#加载包 library(picante)
library(ape)
#测试数据 data(phylocom)
pd(phylocomphylo)
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读取树文件： tree= read.tree("D:/timberproject2021/sp_tree20210707.tre")
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读取samp数据矩阵 b = read.csv("D:/timberproject2021/GridsID-species2.csv", header = T, row.names=1)
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计算pd c = pd(b, tree, include.root=TRUE)
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导出计算结果 write.csv(c,file = "D:/aaa.csv")
报错：修改树： If youwant the root ofyour tree to correspond to the most recent ancestor of the taxaactually present in your sample, you should prune the tree before running pd:
prunedTree<-prune.sample(b,tree)
参考资料：