[R-sig-eco] diversityresult function - BiodiversityR package

[Jari Oksanen]

I think the difference is like documented. Citing your own message:

""all" calculates the diversity of the entire
community (all sites pooled), ..., "mean" calculates the average diversity of the sites"

So "all" uses pooled data (colSums(<data>)), and "mean" uses non-pooled data but calculates the average of results. That is, it first calculates the diversities (as with method = "s"), and then takes their average.

Cheers, Jari Oksanen
________________________________________
From: r-sig-ecology-bounces at r-project.org [r-sig-ecology-bounces at r-project.org] on behalf of Gian Maria Niccolò Benucci [gian.benucci at gmail.com]
Sent: 30 March 2012 11:57
To: r-sig-ecology at r-project.org
Subject: [R-sig-eco] diversityresult function - BiodiversityR package

Hi all,

I would compare the diversity of two groups of samples through the use of
diversity indices such as richness, shannon, simpson, evennes etc.
I then used the diversityresult() to calculate such indices. Once I got
diversity for each sample and tested for data normality I used simple ANOVA
to evaluate differences between such groups.

-Do this apprach be correct?

Moreover, in the help of the function is written: "Method of calculating
the diversity statistics: "all" calculates the diversity of the entire
community (all sites pooled), "s" calculates the diversity of each site
separatedly, "mean" calculates the average diversity of the sites, "sd"
calculates the standard deviation of the diversity of the sites"

- What is the differenc in calculation between "all" and "mean" methods?
maybe "all" first pools sites and then calculate diversity while "mean"
first average the sites and then calculate diversity?

Thanks a lot for replies,

--
Gian

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