Hello, I am the maintainer for the poppr package, which depends on adegenet (and thus ade4). One of my users noticed a bug in the output of randtest.amova: https://groups.google.com/forum/#!topic/poppr/D1gpqgQM2F0 Basically, the alternate hypothesis for the randomization tests would be incorrect at every fourth hierarchical level. I contacted the maintainer and this bug has been fixed on the ade4 github page: https://github.com/sdray/ade4/pull/4 If you do run into this problem, there is a workaround by passing the result to as.krandtest() n <- 3 # (set this to the number of hierarchical levels) with(randomization_result, as.krandtest(sim, obs, alter = c("less", rep("greater", n)), call = call, names = names) Cheers, Zhian N. Kamvar
Bug in ade4 randtest.amova and solution
2 messages · Zhian Kamvar, Thibaut Jombart
Dear Zhian, this is great, thanks for letting us know! Best Thibaut -- Dr Thibaut Jombart Lecturer, Department of Infectious Disease Epidemiology, Imperial College London Head of RECON: repidemicsconsortium.org sites.google.com/site/thibautjombart/ github.com/thibautjombart Twitter: @TeebzR <http://twitter.com/TeebzR>
On 21 November 2016 at 19:29, Zhian Kamvar <zkamvar at gmail.com> wrote:
Hello, I am the maintainer for the poppr package, which depends on adegenet (and thus ade4). One of my users noticed a bug in the output of randtest.amova: https://groups.google.com/forum/#!topic/poppr/D1gpqgQM2F0 Basically, the alternate hypothesis for the randomization tests would be incorrect at every fourth hierarchical level. I contacted the maintainer and this bug has been fixed on the ade4 github page: https://github.com/sdray/ade4/pull/4 If you do run into this problem, there is a workaround by passing the result to as.krandtest() n <- 3 # (set this to the number of hierarchical levels) with(randomization_result, as.krandtest(sim, obs, alter = c("less", rep("greater", n)), call = call, names = names) Cheers, Zhian N. Kamvar
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