accumulation curve in R

Question

I have data of species at 4 sites over several months. I have successfully created accumulation graphs using package vegan in R but I would like to plot all 4

Answer 1

Ok, so @jlhoward's solution is of course much simpler, and more sensible. But, since I hadn't thought of the obvious, and coded this up, I figured I may as well share it. It might be useful for related questions where the function at hand doesn't accept add.

Load library and some example data:

library(vegan)
data(BCI)
sp1 <- specaccum(BCI, 'random')

# random modification to BCI data to create data for a second curve
BCI2 <- as.matrix(BCI)
BCI2[sample(prod(dim(BCI2)), 10000)] <- 0
sp2 <- specaccum(BCI2, 'random')

Plotting

# Combine the specaccum objects into a list 
l <- list(sp1, sp2) 

# Calculate required y-axis limits
ylm <- range(sapply(l, '[[', 'richness') + 
           sapply(l, '[[', 'sd') * c(-2, 2))

# Apply a plotting function over the indices of the list
sapply(seq_along(l), function(i) {
  if (i==1) { # If it's the first list element, use plot()
    with(l[[i]], {
      plot(sites, richness, type='l', ylim=ylm, 
           xlab='Sites', ylab='random', las=1)
      segments(seq_len(max(sites)), y0=richness - 2*sd, 
               y1=richness + 2*sd)
    })    
  } else {
    with(l[[i]], { # for subsequent elements, use lines()
      lines(sites, richness, col=i)
      segments(seq_len(max(sites)), y0=richness - 2*sd, 
               y1=richness + 2*sd, col=i)
    })     
  }
})

legend('bottomright', c('Site 1', 'Site 2'), col=1:2, lty=1, 
       bty='n', inset=0.025)