A simulation of size-dependent diversity effects in experiments that test for diversity

mathom.R

## simulation of experiment

## to test patterns of randomization

## first set up the relationships

## volume is a uniform variable


n.mathoms <- 30
n.trts <- 3
vols.mathoms <- runif(n.mathoms,90,210)

## seven treatments (and seven replicates of each)
trts <- as.factor(rep(letters[1:n.trts],rep(n.mathoms/n.trts,n.trts)))

#potential abundance is a function of volume 

## number of species is a function of volume *and* treatment:

trt.means <- seq(from=10,to=10+5*n.trts,by=5)

## with poisson errors


n.spp.mathom <- mapply(function(vol,n.spp) {
                       rpois(1,lambda=round(0.1*vol+n.spp))},
                       vols.mathoms,
                       trt.means[trts])

plot(n.spp.mathom~vols.mathoms)
plot(n.spp.mathom~trts)

# now with the number of species, get the distribution of abundances
# among species by multiplying the 

brokestick <- function(n){
  x <- runif(n)
  x <- sort(x)
  c(x,1)-c(0,x)
}