[R-sig-genetics] pegas::amova()

[Eric Crandall]

Hi Emmanuel or others,

	I was directed here to ask a question about the amova function in pegas. Hopefully this is the right place.

	 I have been using pegas::amova() in a function that loops over a database of species to calculate amova at up to three hierarchical levels. My function recently broke, apparently due to a recent update <https://cran.r-project.org/web/packages/pegas/NEWS> to Pegas - specifically this change:

    o amova() failed when the factors in the rhs of the formula were
      in a data frame. Thanks to Zhian Kamvar for the fix.

As a workaround to for pegas:amova not being able to use a dataframe of factors, I was assigning the factors to the global environment:

      level1factor<<-as.factor(sp[[l1]])
      level2factor<<-as.factor(sp[[l2]])
      amova_out<-pegas::amova(dists~level2factor/level1factor, nperm=nperm, is.squared=T)


Now, after the update, my function is throwing an error. The traceback goes

4 stop("'bin' must be numeric or a factor") 
3 FUN(X[[i]], ...) 
2 lapply(gr, tabulate) 
1 pegas::amova(dists ~ level2factor/level1factor, nperm = nperm, 
    is.squared = T) 

As far as I can tell, the objects that I am submitting to tabulate() in gr via lapply() ARE factors. 

When I try to reproduce the problem by running step by step through the pegas::amova function, everything works fine. 

So I am stumped for now. Does anyone have any ideas?


Many thanks,

Eric Crandall



PS - I’m very happy to see strata being added to genind objects in adegenet. Will these eventually be usable by pegas::amova or a similar amova function?



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