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

[Gavin Simpson]

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

> 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
>

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...)

G


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> Bob O'Hara
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-- 
Gavin Simpson, PhD

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