rarefaction not working with the min species number
Hi, It is exactly like Brian wrote. The R-Forge version of vegan adds a test for integer input, and stops with error if non-integer data was encountered. If you still want to proceed, you must do something with your data, and then it is on your own responsibility. The current behaviour was silently wrong with non-integer data, and truncated real values to integer. Cheers, Jari Oksanen
On 25 Apr 2012, at 17:33, Brian Inouye wrote:
Although rounding to the nearest integer will make the code run without an error, it seems like then you are making the implicit assumption that every unit of abundance is an independent sample with equal probability of occurrence, equivalent to independent individuals. While I can imagine that is justifiable for some datasets, in other cases that would be a dubious assumption. -Brian On 4/25/2012 6:00 AM, r-sig-ecology-request at r-project.org wrote:
From: Stephen Sefick<sas0025 at auburn.edu>
To: Jari Oksanen<jari.oksanen at oulu.fi>
Cc: r-sig-ecology<r-sig-ecology at r-project.org>
Subject: Re: [R-sig-eco] rarefaction not working with the min species
number
Message-ID:<4F96B0B9.1050302 at auburn.edu>
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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){
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