[R-sig-genetics] Bug in ade4 randtest.amova and solution

[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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