EstimateR and Chao 1 standard deviation

On 17 October 2014 06:44, Bob O'Hara <bohara at senckenberg.de 
<mailto:bohara at senckenberg.de>> wrote:

    On 17/10/14 13:54, "Jos? M. Blanco Moreno" wrote:

        Dear users

        I have been checking the values returned by the function estimateR
        against the formulae in the appendix to nonparametric
        estimators of
        species richness in EstimateS
        (http://viceroy.eeb.uconn.edu/EstimateS/EstimateSPages/EstSUsersGuide/EstimateSUsersGuide.htm#AppendixB).
        <http://viceroy.eeb.uconn.edu/EstimateS/EstimateSPages/EstSUsersGuide/EstimateSUsersGuide.htm#AppendixB%29.>..

        and they do not match each other.

        Where does this line of code in vegan:::estimateR.default come
        from?

        sd.Chao1 <- sqrt(a[2] * ((G^4)/4 + G^3 + (G^2)/2))

        It is from any other reference that I should have under control?

    Unless Jari added something, the functions come from my paper from
    about 10 years ago:
    O?Hara RB (2005) Species richness estimators: how many species can
    dance on the head of a pin? J Anim Ecol 74: 375?386.
    http://doi.wiley.com/10.1111/j.1365-2656.2005.00940.x, which
    refers to Chao (1987), which is cited in the estimateR
    documentation. EstimateS now uses a small sample correction:
    <http://viceroy.eeb.uconn.edu/EstimateS/EstimateSPages/EstSUsersGuide/EstimateSUsersGuide.htm#Chao1AndChao2>
    Does this account for the discrepancy?

    Bob

Yep, vegan does not include the small sample correction. The Chao1 
computation is here:

https://github.com/vegandevs/vegan/blob/master/R/estimateR.default.R#L44

but we can certainly add it if this is useful? (And I suppose it is if 
EstimateS has included it by default now...)

EstimateR and Chao 1 standard deviation

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