Packages for Animal Models & QG analyses

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Packages for Animal Models & QG analyses

Deepa Senapathi
Hi,

 

I am looking to do some quantitative genetic analyses using animal models
and was wondering if someone could suggest an appropriate package in R.  It
would help if it was similar to the ASReml genetic analyses software.

 

Thanks,

 

Deepa Senapathi

 

Deepa Senapathi
Centre for Agri-Environmental Research (CAER)
School of Agriculture, Policy & Developement.
University of Reading
Earley Gate, Whiteknights Road,
Reading RG6 6AR.
Tel: +44 (0) 118 378  5467

 


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Re: Packages for Animal Models & QG analyses

David Duffy-2

Deepa Senapathi asked:

>
> I am looking to do some quantitative genetic analyses using animal models
> and was wondering if someone could suggest an appropriate package in R.  It
> would help if it was similar to the ASReml genetic analyses software.
>
> Thanks,
>
> Deepa Senapathi
>
> Deepa Senapathi
> Centre for Agri-Environmental Research (CAER)
> School of Agriculture, Policy & Developement.
> University of Reading
> Earley Gate, Whiteknights Road,
> Reading RG6 6AR.
> Tel: +44 (0) 118 378  5467

See the R Genetics Task View.  I think kinship (which uses lme) and
perhaps regress packages.  For data amenable to an ANOVA/hierarchical
setup then lme4 as well (which does GLMMs nicely).  Have you tried Wombat
(non-R)?

David Duffy.

--
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| email: [hidden email]  ph: INT+61+7+3362-0217 fax: -0101  /     *
| Epidemiology Unit, Queensland Institute of Medical Research   \_,-._/
| 300 Herston Rd, Brisbane, Queensland 4029, Australia  GPG 4D0B994A v

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Re: Packages for Animal Models & QG analyses

Simon Blomberg-4
I don't think lme4 can handle user-specified correlation structures for
the residuals (yet), which are necessary for animal models.

Cheers,

Simon.

On Wed, 2007-11-28 at 07:50 +1000, David Duffy wrote:

> Deepa Senapathi asked:
> >
> > I am looking to do some quantitative genetic analyses using animal models
> > and was wondering if someone could suggest an appropriate package in R.  It
> > would help if it was similar to the ASReml genetic analyses software.
> >
> > Thanks,
> >
> > Deepa Senapathi
> >
> > Deepa Senapathi
> > Centre for Agri-Environmental Research (CAER)
> > School of Agriculture, Policy & Developement.
> > University of Reading
> > Earley Gate, Whiteknights Road,
> > Reading RG6 6AR.
> > Tel: +44 (0) 118 378  5467
>
> See the R Genetics Task View.  I think kinship (which uses lme) and
> perhaps regress packages.  For data amenable to an ANOVA/hierarchical
> setup then lme4 as well (which does GLMMs nicely).  Have you tried Wombat
> (non-R)?
>
> David Duffy.
>
--
Simon Blomberg, BSc (Hons), PhD, MAppStat.
Lecturer and Consultant Statistician
Faculty of Biological and Chemical Sciences
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Australia
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T: +61 7 3365 2506
email: S.Blomberg1_at_uq.edu.au

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be extracted from a given body of data. - John Tukey.

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