I would like to calculate the functional diversity measures proposed by Chiu & Chao (2014). The paper gives formulas for the calculation of functional hill numbers, mean functional diversity and (total) functional diversity. But it doesn't mention any R script or package and I don't feel confident encoding these formulas myself.
I was wondering if anyone already calculated these measures and how they did it.
Ref:
Chiu, C. H., & Chao, A. (2014). Distance-based functional diversity measures and their decomposition: A framework based on hill numbers. PLoS ONE, 9(7). doi:10.1371/journal.pone.0100014
Hello
I hope this information may help you.
«The classical diversity estimators (Shannon and Simpson entropy) can be found in many R packages. vegetarian (Charney and Record 2009) allows calculating Hill numbers and partitioning them according to Jost’s framework. Bias correction is never available except in the Entropy Estimation (Cao and Grabchak 2014) package which provides the Zhang and Grabchak’s estimators of entropy and diversity and their asymptotic variance (not included in entropart).» http://finzi.psych.upenn.edu/R/library/entropart/doc/entropart.pdf
«Functions rarefaction.individual and rarefaction.sample rarefies a series of diversity indices known as Hill numbers (Hill 1973), which can be algebraically transformed into more familiar diversity indices. The order q of the Hill number determines the weighting given to more common species, with species richness defined by q=0. Other Hill numbers are the exponential Shannon index (q=1), and the inverse Simpson index (q=2).» http://finzi.psych.upenn.edu/R/library/rareNMtests/html/rarefaction.individual.html
«Hill numbers are a family of diversity measures that quantify diversity in units of equivalent numbers of equally abundant species (Jost 2006, Gotelli and Chao 2013). EstimateS ver. 9 (and earlier versions) computes the most widely used Hill numbers (richness, exponential Shannon diversity, and reciprocal Simpson diversity) by averaging Hill number values among random resamples for the reference sample and each level of rarefaction. Chao et al. (2013) recently extended the analytical rarefaction and extrapolation tools of Colwell et al. (2012) to the full set of Hill numbers and to coverage-based rarefaction (Chao and Jost 2012). The addition of these tools is on the drawing board for future development of EstimateS.» http://onlinelibrary.wiley.com/doi/10.1111/ecog.00814/full
«The community data matrix obtained was used in a series of statistical and ecological evaluations carried out using the R software (http://cran.r-project.org/) [39] and the vegan package (http://cran.r-project.org/web/packages/v egan/index.html) [40].» http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0106662
Kind regards
Jose Macedo
Dear José,
thanks for your extensive answer. It does however not answer my question as it was about FUNCTIONAL diversity and not species diversity.
I'm specifically looking for the calculation of the functional diversity measures stated in my question.
Dear Frederik
Ok. Sorry for this misunderstanding. I was considering in fact species diversity and not functional diversity. Perhaps you can try these methodologies bellow (I have never used them) but it may be effective using HCDT entropy....
https://hal-agroparistech.archives-ouvertes.fr/hal-00989454v3/document
http://dssm.unipa.it/CRAN/web/packages/entropart/vignettes/entropart.pdf
I hope this may be effective for you
Jose
Hi José, you may be able to calculate these estimates using the entropart package. best,
I am trying to do the same thing. Check this out:
https://github.com/daijiang/hillR
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