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

[Jombart, Thibaut]

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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