[R-sig-eco] rarefaction not working with the min species number

[Jari Oksanen]

On 24/04/2012, at 15:39 PM, Stephen Sefick wrote:

> I will provide reproducible code if I need to.
> 
> All:
> 
> I am trying to set up a 1000 pulls of a community data frame for calculating richness measures.  I would like to be able to code the sample number based on the minimum of all of the samples.  I can do this but there is an error:
> 
> Error in sample(rep(nm, times = x[i, ]), sample[i]) :
>  cannot take a sample larger than the population when 'replace = FALSE'
> 
> when using:
> 
> rrarefy(L, min(apply(L, 1, sum)))
> 
> min is returning the lowest sample abundance of all of the samples.  rrarefy works if I subtract 5 (arbitrary) from the min(...) statement.  I am sure that I am missing something simple.
> many thanks,
> 
Stephen,

I can reproduce this if input data ('L') contain non-integer data. The function is only able to handle integer data, but it does not check the input. Probably it should: the error would still be there, but the message would be more informative.

Cheers, Jari

--
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland