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

[Gavin Simpson]

On 17 October 2014 10:04, Bob O'Hara <bohara at senckenberg.de> wrote:

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

Okay, I'll see about getting this into vegan 2.2-0 which is about ready for
release in the next couple of weeks.

Cheers

G


>   G
>
>
>> --
>>
>> 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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>
>
>
>  --
> 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
>
>


-- 
Gavin Simpson, PhD

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