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

[Stephen Sefick]

Jari,

Many thanks, that did the trick.  Here is a little bit of code that 
took my non-integer data (abundance estimates), rounds, and turns the 
numbers into a data.frame with all integers col classes.

community_round2int <- function(L){

row <- rownames(L)

a <- as.data.frame(apply(L, 2, round))

b <- as.data.frame(apply(a, 2, as.integer))

rownames(b) <- row

return(b)

}

kindest regards,

Stephen

On Tue 24 Apr 2012 08:01:16 AM CDT, Jari Oksanen wrote:
>
> 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
>
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--
Stephen Sefick
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