[adegenet-forum] functions not found

[Zhian N. Kamvar]

Hello All,

Thank you for pointing out these inconsistencies in the documentation. 
Tyler is correct that the functions mentioned are coming from the 
{hierfstat} package and that many of them are deprecated[1]. I will do 
my best to update the documentation to use the current methods. Thank 
you for your patience.

All the best,
Zhian

[1]: This is in part due to the fact that, despite the fact that many of 
these functions were deprecated in 2016, a release of hierfstat was not 
sent to CRAN until August 2020.


On 6/3/21 3:00 AM, adegenet-forum-request at lists.r-forge.r-project.org wrote:
> Date: Wed, 02 Jun 2021 12:10:44 -0400
> From: Tyler Smith <tyler at plantarum.ca>
> To: brian knaus <briank.lists at gmail.com>
> Cc: adegenet-forum at lists.r-forge.r-project.org
> Subject: Re: [adegenet-forum] functions not found
> Message-ID: <xlzfck0ncme65.fsf at ONOTTRA696862XL.agr.gc.ca>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> 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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