I have previously used Primer to output species accumulation curve results (including Chao, Jacknife and Bootstrap estimators), and from memory if I had 40 study sites, there would be 40 numbers for each on the x axis.
In R, the species accumulation curve runs the entire x axis, but the estimators always fall short (N minus 3?) ... when working with a small number of sampling sites, the curves of the estimators are going to cause questions as Primer curves look better. Can anyone explain why this occurs in R, and whether there is a way to fix it (or at least justify why this is the case)?
Thanks!
This is a totally lost question. One can not compare two different
software and their results unless the analysis parameters are taken into consideration.
That is fair. The Primer output was created using: Plots > Species-Accum Plot, with max 999 permutations, and indices S, Chao1, Jackknife1, Jackknife2 and Bootstrap.
In R, I used vegan::poolaccum(data, permutations =999).
Both used the identical data set with 40 sites. The resulting numbers for each only vary slightly, but my confusion is because R only gives 38 rows of data while Primer gives 40.
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