I am working with taxonomic and functional diversity of weeds in olive orchard and I am trying to use the function RaoRel using package "Cati" for R. I am to calculate alpha, betha and gamma diversity in the framework of Rao Index with Jost correction. I got to run RaoRel function but I have some questions...
1. Sample = The community matrix of abundance (c x s) of the s species for the c local communities ("Sample" in function)
I have two scenarios, and from each one of them I want to get alpha diversity and betha diversity between each of them . However, one of them is sampled with 4 sampling points while the other is sampled with 2 sampling points. Would there be any way to equalize both samples so that they were balanced?
I know that alpha, beta and gamma diversity can be analyzed through (Lande 1996) weighted by the number of samples of each of the scenarios, but I do not know if this can be done in a package.
2. STRUCTURE = A data frame containing the name of the group to which samples belong see (de Bello et al, 2011) for more details
Could I work with a multitude of scenarios at the same moment thanks to this function?
What is the best way to apply it?
Thanks in advance ¡¡
Diversity indices are sample-size dependent, especially in high diversity assemblages. So you do need to equalise samples by weighting with a biomass contribution. I think it is easier to do this before using that package :)
The package that you are using I have not used it, but in theory it should not be an inconvenience for multiple scenarios, to calculate the beta diversity I use the betapart package that was designed with that function; If you decide to do it in that one, I can help you. When you speak of matrix you refer to matrix (column x row) or to a sheet .xls, if it is a column x row then you must use the function dataframe to work with them. look at the project: R for biologists: Implementation in research and leave your questions there regards
https://www.researchgate.net/project/R-for-biologists-Implementation-in-research
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