[R-sig-eco] EstimateR and Chao 1 standard deviation

[Bob O'Hara]

On 17/10/14 13:54, "José 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)... 
>
> 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

-- 

Bob O'Hara

Biodiversity and Climate Research Centre
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