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
pd(phylocom$sample, phylocom$phylo)
1. 读取树文件：
tree= read.tree("D:/xxxxx.tre")
2. 读取sample数据矩阵
b = read.csv("D:/xxxxxxxx.csv", header = T, row.names=1)
#纵坐标代表的是每个物种，横坐标代表每个群落或者区域包括的物种组成。 Pen1中有Arre-elat,Brom_tect，其他pen2等同理
0代表这个物种（列名）在这个居群中不存在;数字代表一个程度、频率等数值，代表物种在某个区域出现的程度
3. 计算pd
c = pd(b, tree, include.root=TRUE)
4. 导出计算结果
write.csv(c,file = "D:/xxxxx.csv")
报错：修改树命令：
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/
