alpha多样性计算

library(picante)  

alpha <- function(x, tree = NULL, base = exp(1)) {
  est <- estimateR(x)
  Richness <- est[1, ]
  Chao1 <- est[2, ]
  ACE <- est[4, ]
  Shannon <- diversity(x, index = 'shannon', base = base)
  Simpson <- diversity(x, index = 'simpson')    #Gini-Simpson 指数
  Pielou <- Shannon / log(Richness, base)
  goods_coverage <- 1 - rowSums(x == 1) / rowSums(x)
  
  result <- data.frame(Richness, Shannon, Simpson, Pielou, Chao1, ACE, goods_coverage)
  if (!is.null(tree)) {
    PD_whole_tree <- pd(x, tree, include.root = FALSE)[1]
    names(PD_whole_tree) <- 'PD_whole_tree'
    result <- cbind(result, PD_whole_tree)
  }
  result
}
otu <- read.csv("salmonDNA.csv",row.names=1,stringsAsFactors=F,header=T,check.names=F)
otu &