R/bdiv.R

In Listen-Lii/abdiv: Get alpha and beta diversity index

#' abdiv
#' This package get alpha and beta diversity index from OTU tables by high-throuthput sequencing data in microbiology.
#' function adiv() get alpha diversity indexes, which including Shannon, Inv_Simpson, Pielou_evenness, and Simpson_evenness indexes.
#' function bdiv() get beta diversity indexes, which including jaccard and bray-curtis distances.
#' @param x is the standard OTU table. Rowname is OTU, colname is sample. Data must be anundance. Presence/absence data is not suitable.
#' examples:
#' library(abdiv)
#' bdiv(mtcars)


bdiv = function(x){
  #requireNamespace(vegan)
  #library("vegan")
  x[is.na(x)]=0
  jaccard.dist = vegdist(t(x), method="jaccard",binary=T)
  ja = as.matrix(jaccard.dist)
  bray.dist = vegdist(t(x), method="bray")
  br = as.matrix(bray.dist)
  list(jaccard=ja,bray=br)
}