[adegenet-forum] functions not found
Tyler Smith
tyler at plantarum.ca
Wed Jun 2 18:10:44 CEST 2021
Hi,
I have also run into this issue when working through the official
tutorials. The basic tutorial refers to the deprecated
`hierfstat::fstat` function on line 1121:
https://github.com/thibautjombart/adegenet/blob/78be588d418f8e5b0a05ebc2880917b1c6581054/tutorials/tutorial-basics.Rnw#L1121
It also refers to the deprecated function
`hierfstat::pairwise.fst` several places. I submitted an issue on
this, and there are solutions in that thread:
https://github.com/thibautjombart/adegenet/issues/278
The tutorial hasn't been updated to reflect these underlying
changes.
I think the grunwaldlab.github.io site is more current, but I
haven't looked at it in depth, and I'm not sure how much it
focuses on adegenet (vs poppr etc).
Best,
Tyler
brian knaus <briank.lists at gmail.com> writes:
> Hi Anne,
>
> You have not specified _which_ tutorial you are attempting to
> follow. So the forum will not understand what you are trying to
> do. I suggest tutorials at the following links.
>
> http://adegenet.r-forge.r-project.org
>
> https://grunwaldlab.github.io/Population_Genetics_in_R/
>
> You have also not posted a minimal reproducible example
> (https://stackoverflow.com/a/5963610) which means the forum will
> not understand your question and therefore will not be able to
> address the issue.
>
> If you check the user's manual at the CRAN site
> (https://cran.r-project.org/web/packages/adegenet/index.html)
> you should see
> that ```fstat()``` is not a part of adegenet. So this may not be
> an appropriate forum for your question. A google search turns up
> ```fstat()``` as being part of the library ```hierfstat```,
> although the page I found was for hierfstat 0.4-22
> (https://www.rdocumentation.org/packages/hierfstat/versions/0.04-22/topics/fstat).
> The version at CRAN (0.5-7;
> https://CRAN.R-project.org/package=hierfstat) does not appear to
> include ```fstat()``` so it could be that this function is now
> legacy code.
>
> Please take a look into some of this and let us know what you
> find.
>
> Thanks!
> Brian
>
> On Mon, May 31, 2021 at 1:51 PM Anne Chenuil
> <anne.chenuil at imbe.fr> wrote:
>
> Many functions are not found when I call them using commandes
> from the tutorial (for example: fstat, gstat.randtest,
> pairwjse.fst), although I use just installed adegenet package.
>
> The adegenet version is 2.1.3 (which requires R version ≥
> 2.14)
>
> My R version is 3.6.2.
>
> Thank you in advance
>
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--
Tyler Smith
plantarum.ca
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