rarefaction not working with the min species number
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
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Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland