R/givemeDIVERSITY.R

In henrycstevens/ccomm: Analyze and visualize ecological community datasets

#' givemeDIVERSITY
#' 
#' This function takes a sites (rows) x species (columns) matrix, 
#' uses the package 'BAT' to perform alpha and beta diversity calculations,
#' and returns (1) boxplots depicting alpha diversity across sites, 
#' and (2) pairwise estimates for beta diversity across sites and overall
#' beta diversity for all sites (including relative contributions of 
#' richness and replacement in determining overall beta).
#' 
#' @export givemeDIVERSITY

givemeDIVERSITY <- function(community) {
  
  library(BAT)
  
  td <- alpha(community, raref = 1)
  
  cols = colorRampPalette(c("white", "black"))
  boxplot(t(td), names = rownames(test) , col=cols(length(td)), main="Alpha diversity", 
          xlab = "Site", pars = list
          (boxwex = 0.8, staplewex = 0, outwex = 0.5), range=1.5,
          lwd=0.8, lty=1, ylab = expression(alpha))
  
  beta.multi(community)
}