vegan
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vegandevs
R package for community ecologists: popular ordination methods, ecological null models & diversity analysis
Dear all, the betadisper crash when all values from the distance matrix is equal to zero. I did not find where is the error, but I think the function could...
Dear all, I am analysing a microbiome dataset in which mice were sampled at two time points, before and after a treatment. I want to test if the communities are...
Hi: I saw in closed issue #317 that "vegan does not have nested PERMANOVA". Would it be possible to implement this feature, or is it something that just won't be...
Hello, I am relatively new to using vegan (and to analyzing microbiome data in general). I apologize if this seems like a silly question. I am using adonis2 to test...
I have done beta diversity analysis using phyloseq PCoA on rarefying OTU data with bray distance and now for statistical significance, I want to use adonis function from vegan so...
Since I realized that you must specify binary = T in vegdist to compute distance matrices on presence/absence data as opposed to abundance data, I keep seeing more and more...
`permatswap` and `permatfull` provided the first quantitative null models in **vegan** and they were used in simulation in `adipart` and `multipart`. Later, the quantitative null models were transfrerred to `make.commsim`...
First, I want to thank for making such a great package for multivariate and ecological community analyses! I use vegan a lot in my work. One thing I constantly miss...
Function `designdist` is currently faster than `vegdist`. With `"binary"` and `"quadratic"` terms it is much faster than `vegdist`. With `"minimum"` terms (used by most dissimilarity functions in `vegdist`) it used...
Paul and Anderson (2013) discuss 4 methods to assess how many numbers of axis might be usefull/interpretable/[putwhatyouwanthere] a) broken-stick [implemented in vegan] b) bootstrap CI for eigenvalues c) bootstrap from...
