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I am trying to produce rarefied species accumulation curves for two different habitat types using the rarefaction method in specaccum function of the vegan package using the code:

spa <- specaccum(Example, method = "rarefaction")

The function works for one data set but not the other where it produces this error:

Error in rarefy(t(freq), ind[i], se = TRUE) : 
  function accepts only integers (counts)

However, the data is laid out exactly the same as the other data set and when I investigate the data frame it says that all the data for the species is in integer form.

Here is a much smaller section of the data frame:

Site  AA AB AC AD AE AF AG AH AI AJ AK AL
1.1   0  0  0  0  1  0  0  2  0  0  0  0
1.2   1  0  0  0  0  0  0  0  0  0  0  0
1.3   0  0  1  0  0  0  0  0  0  0  0  0
2.1   1  0  0  0  1  0  0  0  0  0  0  0
2.2   0  1  0  0  0  0  0  0  0  0  0  0
2.3   0  0  0  0  0  0  0  1  0  0  1  1
3.2   0  2  1  0  1  0  0  0  0  0  0  0
3.3   0  0  0  0  2  0  0  3  0  0  0  0
4.1   0  0  0  0  0  0  1  1  0  0  0  0
4.2   0  0  0  0  0  0  0  0  0  0  0  0
4.3   0  0  0  0  1  0  0  1  0  0  0  0
5.1   0  1  0  0  0  1  0  3  0  0  0  0
5.2   0  0  1  0  2  0  0  1  0  0  0  0
5.3   0  0  0  1  3  2  0  4  0  0  0  0
6.1   0  0  0  0  0  0  0  0  0  0  0  0
6.2   0  2  2  0  0  2  0  0  0  0  0  0
6.3   0  0  0  0  0  0  0  0  0  0  0  0

Sites being sampling points within the habitat site, letters denoting species. I am unsure as to why it is working for one set of data but not the other when they are both laid out like this. Can someone help me understand?

Thanks

tom91
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    Try this: `specaccum(Example[-1], "rarefaction")`. I'm guessing that you are including the `Site` column on accident. – Jota Jul 05 '15 at 05:57
  • Ah yes of course, sorry was just carrying it over from a randomised curve I did before and didn't think to delete it. Thank you. – tom91 Jul 05 '15 at 06:32

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