无意落入生态学功能性多样性公式计算，R代码分享。包括FAD,MFAD,FD,FRIC,FEs，FEve,FDQ,FDiv

---
title: "Bio_diversity"
author: "jin"
date: "2018年11月18日"
output: word_document
---
```{r}
knitr::opts_chunk$set(warning = F,message = F)
```

```{r setup}
setwd("C:/Users/jack/Desktop/mission/bio diversity")
library(readxl)
library(FD)
sample <- read_excel("sample.xlsx")
feature<-as.data.frame(sample[,-c(1,length(sample))])
abundance<-as.data.frame(sample[,length(sample)])
abundance<-t(abundance)
colnames(abundance)<-sample$种名
rownames(feature)<-sample$种名
feature
```

```{r load the data}
ex1<-dbFD(feature,abundance)
```

#功能性状距离FAD

```{r 功能性状距离FAD}
sum(dist(feature))

```

#功能性状平均距离MFAD
```{r 功能性状平均距离MFAD}
sum(dist(feature))/nrow(feature)

```

#功能树状图指数 FD
```{r 功能树状图指数 FD}
#Xtree
Xtree <- function(h)
{
  species.names <- h$labels 
  H1 <- matrix(0, length(h$order), 2 * length(h$order) - 2)
  l <- vector("numeric", 2 * length(h$order) - 2)
  for(i in 1:(length(h$order) - 1)) {
    # evaluate branch lengths
    #
    if(h$merge[i, 1] < 0) {
      l[2 * i - 1] <- h$height[order(h$height)[i]]
      H1[ - h$merge[i, 1], 2 * i - 1] <- 1
    }
    else {
      l[2 * i - 1] <- h$height[order(h$height)[i]] - h$height[order(h$height)[h$merge[i, 1]]]
      H1[, 2 * i - 1] <- H1[, 2 * h$merge[i, 1] - 1] + H1[
        , 2 * h$merge[i, 1]]
    }
    if(h$merge[i, 2] < 0) {
      l[2 * i] <- h$height[order(h$height)[i]]
      H1[ - h$merge[i, 2], 2 * i] <- 1
    }
    else {
      l[2 * i] <- h$height[order(h$height)[i]] - h$height[order(h$height)[h$merge[i,