[adegenet-forum] read.genepop (adegenet 2.0.0 with R v. 3.2.1)

[Paul Maier]

Thanks, Thibaut, for clearing that up.
Paul


----------------------------------------------
Paul Maier

San Diego State, PhD Student
US Geological Survey, Biologist
The Biodiversity Group, Science Advisor


On Tue, Jul 14, 2015 at 1:01 PM, Jombart, Thibaut <t.jombart at imperial.ac.uk>
wrote:

>
> Hello,
>
> yes, this change is on purpose. adegenet 2.0.0 includes a lot of reforms
> of the code, with some breaking backward compatibility.
>
> Here is a good example: storing replacement of missing values inside a
> genind object was bad practice - one ends up not knowing if all values are
> genuine, or if some are merely NAs that have been replaced. In the new
> version, missing data are stored as missing, but they can be easily
> replaced when extracting a table of allele counts or frequencies (see
> ?tab).
>
> Cheers
> Thibaut
>
>
> ==============================
> Dr Thibaut Jombart
> MRC Centre for Outbreak Analysis and Modelling
> Department of Infectious Disease Epidemiology
> Imperial College - School of Public Health
> Norfolk Place, London W2 1PG, UK
> Tel. : 0044 (0)20 7594 3658
> http://sites.google.com/site/thibautjombart/
> http://sites.google.com/site/therepiproject/
> http://adegenet.r-forge.r-project.org/
> Twitter: @thibautjombart
>
>
>    ------------------------------
> *From:* adegenet-forum-bounces at lists.r-forge.r-project.org [
> adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Paul
> Maier [maierpa at gmail.com]
> *Sent:* 14 July 2015 20:50
> *To:* adegenet-forum at lists.r-forge.r-project.org
> *Subject:* [adegenet-forum] read.genepop (adegenet 2.0.0 with R v. 3.2.1)
>
>   Hi all,
> It appears the new version of this function (read.genepop) doesn't have
> the 'missing' option. Can someone either post an older version of adegenet
> compatible with R 3.2.1, or post R code for the earlier version of the
> read.genepop function? I hadn't anticipated trying to figure this out
> manually.
> Thanks!
> Paul
>
>  ----------------------------------------------
> Paul Maier
>
>  San Diego State, PhD Student
> US Geological Survey, Biologist
> The Biodiversity Group, Science Advisor
>
>
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