R—计算系统发育多样性PD (Calculate Faith’s Phylogenetic Diversity)

R计算 PD Calculate Faith’s Phylogenetic Diversity

网址： https://cran.r-project.org/web/packages/picante/index.html

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(phylocom$sample,phylocom$phylo)

1. 读取树文件：
   tree= read.tree(“D:/timberproject2021/sp_tree20210707.tre”)

2. 读取samp数据矩阵
   b = read.csv(“D:/timberproject2021/GridsID-species2.csv”, header = T, row.names=1)

3. 计算pd
   c = pd(b, tree, include.root=TRUE)

4. 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：

https://daijiang.name/en/2014/05/04/notes-func-phylo-book-1/

原文网址：https://www.jianshu.com/p/789a93c2f62a