[adegenet-forum] scaleGen error using method="binom"

[Thibaut Jombart]

Hello,

yes, this argument has been removed as it had no real use besides a
cosmetic difference in the way of computing the variances (which were
numerically the same with any method).

Best
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology
Imperial College London
https://sites.google.com/site/thibautjombart/
https://github.com/thibautjombart
Twitter: @TeebzR <https://twitter.com/TeebzR>

On 14 June 2016 at 09:11, Roman Luštrik <roman.lustrik at biolitika.si> wrote:

> Hi,
>
> I have looked at the sources on GitHub but they don't reveal anything
> interesting. Digging up stuff from 2013 on CRAN, though, shows that the
> method (R matches "met" to this argument) has been omitted in the 1.3-8
> version from May 2013. This argument is thus no longer available,
> unfortunately the documentation hasn't followed suit yet. I will open a
> ticket on GitHub so that this can be resolved, once and for all.
>
> Cheers,
> Roman
>
> ----
> In god we trust, all others bring data.
>
> ------------------------------
> *From: *"Stephen Attwood" <swahuaxi at yahoo.com>
> *To: *adegenet-forum at lists.r-forge.r-project.org
> *Sent: *Monday, June 13, 2016 3:02:24 PM
> *Subject: *[adegenet-forum] scaleGen error using method="binom"
>
> Dear All
>
> I am having a problem using scaleGen, so I tried going back to the
> adegenet tutorial and I get the same error:
>
> data(microbov)
> obj <- genind2genpop(microbov)
> X1 <- scaleGen(obj)
> X2 <- scaleGen(obj,met="bin")
> Error in .local(x, ...) : unused argument (met = "bin")
>
> I get the same error with my own data (I also tried method = "binary",
> method = "bin", etc)
>
> X1 is as expected, but X2 is obviously not assigned
>
> I have the following packages loaded:
> library(ade4)
> library(adegenet)
> library(spdep)
> library ("OpenStreetMap")
> library(ape)
>
> Using adegenet 2.0.2 and R version 3.2.5 (2016-04-14); platform
> x86_64-pc-linux-gnu
>
> If someone could suggest what I might have overlooked, that would be a
> great help - I am probably missing a package somewhere. I thought it would
> be a common problem, but I haven't found it on Google - perhaps the
> solution is so simple. At the moment it is eluding me.
>
> Thank you.
>
> Stephen
>
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