数据格式如下：

library(openxlsx)

library(reshape2)

library(vegan)

herb.data <- read.xlsx("D:/R/XX.xlsx")

#计算Pr1多样性

pr1<-herb.data[1:13,1:4]

herb.mat <- acast(pr1, 

                  formula = repeatname ~ species , 

                  value.var = "abundance", 

                  fill = 0)

Shannon.Wiener <- diversity(herb.mat, index = "shannon")

Simpson <- diversity(herb.mat, index = "simpson")

S <- specnumber(herb.mat)

plot(S)

J <- Shannon.Wiener/log(S)

hdataexport <- rbind(Shannon.Wiener,Simpson,S,J)

write.csv(hdataexport, file = "D:/R/XX R.csv")

#将结果剪切到新的excel并标注Pr1

#计算Pr2多样性

pr2<-herb.data[14:24,1:4]

herb.mat <- acast(pr2, 

                  formula = repeatname ~ species , 

                  value.var = "abundance", 

                  fill = 0)

Shannon.Wiener <- diversity(herb.mat, index = "shannon")

Simpson <- diversity(herb.mat, index = "simpson")

S <- specnumber(herb.mat)

plot(S)

J <- Shannon.Wiener/log(S)

hdataexport <- rbind(Shannon.Wiener,Simpson,S,J)

write.csv(hdataexport, file = "D:/R/XX R.csv")

#将结果剪切到新的excel并标注Pr2

#计算Pr3多样性

pr3<-herb.data[25:34,1:4]

herb.mat <- acast(pr3, 

                  formula = repeatname ~ species , 

                  value.var = "abundance", 

                  fill = 0)

Shannon.Wiener <- diversity(herb.mat, index = "shannon")

Simpson <- diversity(herb.mat, index = "simpson")

S <- specnumber(herb.mat)

plot(S)

J <- Shannon.Wiener/log(S)

hdataexport <- rbind(Shannon.Wiener,Simpson,S,J)

write.csv(hdataexport, file = "D:/R/XX R.csv")

#将结果剪切到新的excel并标注Pr3

#计算Pa多样性

pa<-herb.data[35:51,1:4]

herb.mat <- acast(pa, 

                  formula = repeatname ~ species , 

                  value.var = "abundance", 

                  fill = 0)

Shannon.Wiener <- diversity(herb.mat, index = "shannon")

Simpson <- diversity(herb.mat, index = "simpson")

S <- specnumber(herb.mat)

plot(S)

J <- Shannon.Wiener/log(S)

hdataexport <- rbind(Shannon.Wiener,Simpson,S,J)

write.csv(hdataexport, file = "D:/R/XX R.csv")

代码主要来自于 张金龙老师的博客（https://blog.sciencenet.cn/blog-255662-310032.html），自己发挥了一点分处理计算，最后应该输出到一个Excel表格中，没能做到，有会做的朋友请留言指教，多谢！