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phyloseq and vegan not compatible #993

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chelseajkc opened this issue Aug 31, 2018 · 2 comments
Closed

phyloseq and vegan not compatible #993

chelseajkc opened this issue Aug 31, 2018 · 2 comments

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@chelseajkc
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There is still an issue with phyloseq and vegan compatibility.
I am trying to run beta diversity measures on data.
This is my code:
bray <- phyloseq::distance(physeq_object, method = "bray")
The error I get is:
Error in .C("veg_distance", x = as.double(x), nr = N, nc = ncol(x), d = double(N * :
"veg_distance" not available for .C() for package "vegan"
I have reinstalled phyloseq (by the source code, NOT Bioconductor because I read that the Bioconductor installed phyloseq has issues with dissimilarity measures) and reinstalled vegan.
My phyloseq version is 1.22.3 and my vegan version is 2.5.2.
My R version is 3.4.3.
What is going wrong?

@pstev
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pstev commented Oct 8, 2018

I'm also having this exact issue!

@cjfields
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See #921.

@joey711 joey711 closed this as completed Feb 17, 2019
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