[R-sig-eco] singletons and doubletons in vegan

[Jari Oksanen]

On 01/02/2012, at 14:34 PM, Canning-Clode, Joao wrote:

> Hi all,
> 
> I am running species accumulation curves for several data-sets, and am also playing with some estimators with this function in vegan:
> 
> SF.estimators<-poolaccum(SF.data,permutations=1000)
> SF.estimators # shows data for Sobs, Chao, both Jacks and bootstrap
> plot(SF.estimators) # illustrates graphs for all estimators
> summary(SF.estimators,display="jack2") # gives jack2 stats
> 
> Does any of you know how can I get the info about singletons and doubletons?
> 
What information do you need? If you want to know the names of singleton and doubleton *occurrences* on plots, you can use (with the BCI data in vegan):

freq <- colSums(BCI>0)
which(freq==1)
which(freq==2)

If you want to something similar for counts (individuals), you just change the command to find the 'freq'.

If you want to know how many singleton and doubleton species you have in each of your sampling units, you can use

rowSums(BCI[, freq==1] > 0)
rowSums(BCI[, freq==2] > 0)

If you want to know how may species have exactly one individual (stem) in a sampling unit, just use

rowSums(BCI==1)

Was the information you asked among these things, or do you want to have something more?

Cheers, Jari Oksanen
-- 
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
jari.oksanen at oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa