[adegenet-forum] functions not found

[Zhian N. Kamvar]

I have update the tutorials. You can find the updated basics tutorial 
here: 
https://github.com/thibautjombart/adegenet/blob/master/tutorials/tutorial-basics.pdf

Thank you all for your patience.

All the best,
Zhian

On 6/4/21 3:00 AM, adegenet-forum-request at lists.r-forge.r-project.org 
wrote:
> Date: Thu, 3 Jun 2021 18:11:12 -0700
> From: "Zhian N. Kamvar" <zkamvar at gmail.com>
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: Re: [adegenet-forum] functions not found
> Message-ID: <5d6a9ce8-cb4d-9059-4a20-0bc70986955d at gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> 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
>>>
>>>    _______________________________________________
>>>    adegenet-forum mailing list
>>>    adegenet-forum at lists.r-forge.r-project.org
>>>    https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum
>>>
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