[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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