[R-sig-ME] How to specify user-defined matrix Z?

[Mollie Brooks]

Sorry, I just found this formatted version.
 https://bbolker.github.io/mixedmodels-misc/notes/phylog.html

On Mon, Oct 2, 2017 at 3:33 PM, Mollie Brooks <mollieebrooks at gmail.com>
wrote:

> This example, from Bolker and wzmli, showing how to use lme4 and glmmTMB
> seems relevant. It's a long-term goal to make these analyses easier in
> glmmTMB.
>
> https://github.com/bbolker/mixedmodels-misc/blob/master/notes/phylog.rmd
>
> cheers,
> Mollie
>
> On Sat, Sep 30, 2017 at 6:27 PM, Diogo Melo <diogro at gmail.com> wrote:
>
>> I'm pretty sure lme4qtl can handle this:
>>
>> https://www.biorxiv.org/content/early/2017/05/18/139816.1
>> https://github.com/variani/lme4qtl
>>
>> Cheers,
>> Diogo
>>
>> On Fri, Sep 29, 2017 at 4:51 PM, Zhengyang Zhou <
>> Zhengyang.Zhou at utsouthwestern.edu> wrote:
>>
>> > Hi Jacob,
>> >
>> > Thank you for your reply. I need to use lme4 because I want to test for
>> > the fixed effects (ie., beta), and the packages which can do it (eg,
>> > pbkrtest) is based on lme4.
>> >
>> > Sincerely,
>> > Zhengyang
>> > ________________________________________
>> > From: R-sig-mixed-models <r-sig-mixed-models-bounces at r-project.org> on
>> > behalf of Jacob Bergstedt <jacoba at control.lth.se>
>> > Sent: Friday, September 29, 2017 6:39 AM
>> > To: r-sig-mixed-models at r-project.org
>> > Subject: Re: [R-sig-ME] How to specify user-defined matrix Z?
>> >
>> > Hi,
>> >
>> > You can use the lmekin function in the coxme package.
>> >
>> > Best regards,
>> >
>> > Jacob
>> >
>> >
>> > On 2017-09-29 12:28, Crump, Ron wrote:
>> > > Hi Zhengyang,
>> > >
>> > >> In genetic studies, we sometimes include the genetic relatedness
>> matrix
>> > as a variance component, so we have this following model:
>> > >> Y~Xbeta+Zb+error,
>> > >>
>> > >> where beta are the fixed effects, b~N(0,sigma^2*I) are the random
>> > effects, error are the random error, Z is the cholesky decomposition of
>> the
>> > known genetic relatedness matrix. So how to use lme4 to fit this model
>> if
>> > we know X and Z beforehand? I can use the package "nlme" to do it using
>> the
>> > code like
>> > >>
>> > >> lme(y~-1+X, random=list(group=pdIdent(~-1+Z))),
>> > >> but how to do it using lme4?
>> > > I think, assuming you are using I to indicate an identity matrix, that
>> > > in neither case are you specifying a genetic relationship matrix,
>> unless
>> > > you are somehow incorporating it into Z (in which case I'd like to see
>> > how).
>> > >
>> > > I don't believe that either lme4 or nlme will allow you to do what you
>> > > want. (Somebody might correct me on this).
>> > >
>> > > Within R you could certainly use MCMCglmm or INLA to do analysis of
>> > > quantitative genetics data to obtain genetic parameters (or the
>> asremlr
>> > > interface to ASREML). I've not used it, but the pedigreemm package
>> also
>> > > looks like it would help you and there may be others. Outside of R,
>> > > Karin Meyer's wombat program will also do the job.
>> > >
>> > >
>> > > Regards,
>> > > Ron.
>> > > _______________________________________________
>> > > R-sig-mixed-models at r-project.org mailing list
>> > > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>> >
>> > _______________________________________________
>> > R-sig-mixed-models at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>> >
>> > ________________________________
>> >
>> > UT Southwestern
>> >
>> >
>> > Medical Center
>> >
>> >
>> >
>> > The future of medicine, today.
>> >
>> > _______________________________________________
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>> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>> >
>>
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