EstimateR and Chao 1 standard deviation
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, "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)... 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 [[alternative HTML version deleted]]