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

[Bob O'Hara]

On 10/17/2014 05:36 PM, Gavin Simpson wrote:
> 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, "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).
>         <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...)
>
Might as well. it looks like it shouldn't make a huge difference unless 
sample sizes are small.

Bob

> G
>
>     -- 
>
>     Bob O'Hara
>
>     Biodiversity and Climate Research Centre
>     Senckenberganlage 25
>     D-60325 Frankfurt am Main,
>     Germany
>
>     Tel: +49 69 7542 1863 <tel:%2B49%2069%207542%201863>
>     Mobile: +49 1515 888 5440 <tel:%2B49%201515%20888%205440>
>     WWW: http://www.bik-f.de/root/index.php?page_id=219
>     Blog: http://blogs.nature.com/boboh
>     Journal of Negative Results - EEB: www.jnr-eeb.org
>     <http://www.jnr-eeb.org>
>
>
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>
>
> -- 
> Gavin Simpson, PhD


-- 
Bob O'Hara

Biodiversity and Climate Research Centre
Senckenberganlage 25
D-60325 Frankfurt am Main,
Germany

Tel: +49 69 7542 1863
Mobile: +49 1515 888 5440
WWW:   http://www.bik-f.de/root/index.php?page_id=219
Blog: http://blogs.nature.com/boboh
Journal of Negative Results - EEB: www.jnr-eeb.org


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