[R-sig-ME] MCMCglmm
Iasonas Lamprianou
lamprianou at yahoo.com
Thu Apr 8 15:58:15 CEST 2010
Dear all,
I recently experimented with MCMCglmm and I loved (really loved) the fact that it will give me confidence intervals for the variance of the random effects. It seems that MCMC is a reasonable method to do so, in contrast to REML which seems to have problems on this front. However, MCMCglmm is painfully slower than lmer which is more familiar to me. The good news is that the point estimates of lmer are near the centre of the confidence intervals by MCMCglmm.
I reduced my sample size a bit and managed to fit those two models with lmer (the second would not fit because it needed 1.5GB or RAM). Both seem to have a reasonable fit (at least at first look).
m4 <- lmer(score ~ 1+(1|marker/day)+(1|candidate)+(1|batch), mg2006)
m5 <- lmer(score ~ 1+(1+day|marker)+(1|candidate)+(1|batch), mg2006)
I would like to run these two models above with MCMCglmm. Does anyone know how to do it?
Thank you for the help
Jason
Dr. Iasonas Lamprianou
Assistant Professor (Educational Research and Evaluation)
Department of Education Sciences
European University-Cyprus
P.O. Box 22006
1516 Nicosia
Cyprus
Tel.: +357-22-713178
Fax: +357-22-590539
Honorary Research Fellow
Department of Education
The University of Manchester
Oxford Road, Manchester M13 9PL, UK
Tel. 0044 161 275 3485
iasonas.lamprianou at manchester.ac.uk
--- On Thu, 8/4/10, r-sig-mixed-models-request at r-project.org <r-sig-mixed-models-request at r-project.org> wrote:
> From: r-sig-mixed-models-request at r-project.org <r-sig-mixed-models-request at r-project.org>
> Subject: R-sig-mixed-models Digest, Vol 40, Issue 15
> To: r-sig-mixed-models at r-project.org
> Date: Thursday, 8 April, 2010, 12:13
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> Today's Topics:
>
> 1. Re: Multi-level models Odds ratio (E
> T)
> 2. Re: Multi-level models Odds ratio
> (ONKELINX, Thierry)
> 3. Re: Multi-level models Odds ratio (E
> T)
> 4. Re: Multi-level models Odds ratio
> (Andy Fugard (Work))
> 5. Re: Multi-level models Odds ratio (E
> T)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 8 Apr 2010 11:27:49 +0100
> From: E T <2nuzzbot at gmail.com>
> To: Daniel Ezra Johnson <danielezrajohnson at gmail.com>
> Cc: "r-sig-mixed-models at r-project.org"
> <r-sig-mixed-models at r-project.org>
> Subject: Re: [R-sig-ME] Multi-level models Odds ratio
> Message-ID:
> <l2w706f8d1f1004080327re8708f46mc7d334f41ae19a10 at mail.gmail.com>
> Content-Type: text/plain
>
> odds.ratios = exp(coefs(model))
>
> Thanks, however unfortunately when I try the above command
> I receive the
> following error:
>
> Error: could not find function "coefs"
>
> Regards
>
> Et
>
>
>
> On Wed, Apr 7, 2010 at 5:47 PM, Daniel Ezra Johnson <
> danielezrajohnson at gmail.com>
> wrote:
>
> > something like odds.ratios = exp(coefs(model))
> >
> >
> > On Apr 7, 2010, at 12:28 PM, E T <2nuzzbot at gmail.com>
> wrote:
> >
> > Hi all,
> >>
> >> Apologies for the simplicity of my question....
> however any advice is
> >> greatly appreciated. Thanks
> >>
> >> Is there a specific command available to obtain
> the odds ratios produced
> >> from a multilevel logistic model?
> >>
> >> I have estimated a multi-level logistic model
> using the lme4 package. I
> >> can
> >> obtain results using the 'summary' command,
> however I would like to obtain
> >> the computed odds ratios.
> >> (Similar to the output that can be produced for
> logistic GLM using the
> >> logistic.display command from the epicalc
> package).
> >>
> >> [[alternative HTML version
> deleted]]
> >>
> >> _______________________________________________
> >> R-sig-mixed-models at r-project.org
> mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >>
> >
>
> [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 8 Apr 2010 12:32:01 +0200
> From: "ONKELINX, Thierry" <Thierry.ONKELINX at inbo.be>
> To: "E T" <2nuzzbot at gmail.com>,
> "Daniel Ezra Johnson"
> <danielezrajohnson at gmail.com>
> Cc: r-sig-mixed-models at r-project.org
> Subject: Re: [R-sig-ME] Multi-level models Odds ratio
> Message-ID:
> <2E9C414912813E4EB981326983E0A104071B69A6 at inboexch.inbo.be>
> Content-Type: text/plain;
> charset="us-ascii"
>
> It should be
>
> exp(coef(model))
>
> Without the "s"
>
> HTH,
>
> Thierry
> ------------------------------------------------------------------------
> ----
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek
> team Biometrie & Kwaliteitszorg
> Gaverstraat 4
> 9500 Geraardsbergen
> Belgium
>
> Research Institute for Nature and Forest
> team Biometrics & Quality Assurance
> Gaverstraat 4
> 9500 Geraardsbergen
> Belgium
>
> tel. + 32 54/436 185
> Thierry.Onkelinx at inbo.be
> www.inbo.be
>
> To call in the statistician after the experiment is done
> may be no more
> than asking him to perform a post-mortem examination: he
> may be able to
> say what the experiment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an
> answer does not
> ensure that a reasonable answer can be extracted from a
> given body of
> data.
> ~ John Tukey
>
>
> > -----Oorspronkelijk bericht-----
> > Van: r-sig-mixed-models-bounces at r-project.org
>
> > [mailto:r-sig-mixed-models-bounces at r-project.org]
> Namens E T
> > Verzonden: donderdag 8 april 2010 12:28
> > Aan: Daniel Ezra Johnson
> > CC: r-sig-mixed-models at r-project.org
> > Onderwerp: Re: [R-sig-ME] Multi-level models Odds
> ratio
> >
> > odds.ratios = exp(coefs(model))
> >
> > Thanks, however unfortunately when I try the above
> command I
> > receive the following error:
> >
> > Error: could not find function "coefs"
> >
> > Regards
> >
> > Et
> >
> >
> >
> > On Wed, Apr 7, 2010 at 5:47 PM, Daniel Ezra Johnson
> <
> > danielezrajohnson at gmail.com>
> wrote:
> >
> > > something like odds.ratios = exp(coefs(model))
> > >
> > >
> > > On Apr 7, 2010, at 12:28 PM, E T <2nuzzbot at gmail.com>
> wrote:
> > >
> > > Hi all,
> > >>
> > >> Apologies for the simplicity of my
> question.... however
> > any advice is
> > >> greatly appreciated. Thanks
> > >>
> > >> Is there a specific command available to
> obtain the odds ratios
> > >> produced from a multilevel logistic model?
> > >>
> > >> I have estimated a multi-level logistic model
> using the
> > lme4 package.
> > >> I can obtain results using the 'summary'
> command, however I would
> > >> like to obtain the computed odds ratios.
> > >> (Similar to the output that can be produced
> for logistic GLM using
> > >> the logistic.display command from the epicalc
> package).
> > >>
> > >> [[alternative HTML version
> deleted]]
> > >>
> > >>
> _______________________________________________
> > >> R-sig-mixed-models at r-project.org
> mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> > >>
> > >
> >
> > [[alternative HTML version
> deleted]]
> >
> > _______________________________________________
> > R-sig-mixed-models at r-project.org
> mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >
>
> Druk dit bericht a.u.b. niet onnodig af.
> Please do not print this message unnecessarily.
>
> Dit bericht en eventuele bijlagen geven enkel de visie van
> de schrijver weer
> en binden het INBO onder geen enkel beding, zolang dit
> bericht niet bevestigd is
> door een geldig ondertekend document. The views expressed
> in this message
> and any annex are purely those of the writer and may not be
> regarded as stating
> an official position of INBO, as long as the message is not
> confirmed by a duly
> signed document.
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 8 Apr 2010 11:35:03 +0100
> From: E T <2nuzzbot at gmail.com>
> To: Daniel Ezra Johnson <danielezrajohnson at gmail.com>
> Cc: "r-sig-mixed-models at r-project.org"
> <r-sig-mixed-models at r-project.org>
> Subject: Re: [R-sig-ME] Multi-level models Odds ratio
> Message-ID:
> <i2y706f8d1f1004080335q84f61b78u8c7b656b67a08a8e at mail.gmail.com>
> Content-Type: text/plain
>
> If I use the command coef(model) this extracts the
> coefficients in the
> model, however if I try exp(coef(model)) I receive an
> error:
>
> Error in exp(coef(model)) : Non-numeric argument to
> mathematical function
>
> I could manually get the exp of each factor in my
> model..... but as I have a
> large model (and also have numerous other models to
> produce), I was
> wondering if there was an automated method
>
> Regards
>
> Et
>
> On Thu, Apr 8, 2010 at 11:27 AM, E T <2nuzzbot at gmail.com>
> wrote:
>
> > odds.ratios = exp(coefs(model))
> >
> > Thanks, however unfortunately when I try the above
> command I receive the
> > following error:
> >
> > Error: could not find function "coefs"
> >
> > Regards
> >
> > Et
> >
> >
> >
> >
> > On Wed, Apr 7, 2010 at 5:47 PM, Daniel Ezra Johnson
> <
> > danielezrajohnson at gmail.com>
> wrote:
> >
> >> something like odds.ratios = exp(coefs(model))
> >>
> >>
> >> On Apr 7, 2010, at 12:28 PM, E T <2nuzzbot at gmail.com>
> wrote:
> >>
> >> Hi all,
> >>>
> >>> Apologies for the simplicity of my
> question.... however any advice is
> >>> greatly appreciated. Thanks
> >>>
> >>> Is there a specific command available to
> obtain the odds ratios produced
> >>> from a multilevel logistic model?
> >>>
> >>> I have estimated a multi-level logistic model
> using the lme4 package. I
> >>> can
> >>> obtain results using the 'summary' command,
> however I would like to
> >>> obtain
> >>> the computed odds ratios.
> >>> (Similar to the output that can be produced
> for logistic GLM using the
> >>> logistic.display command from the epicalc
> package).
> >>>
> >>> [[alternative HTML version
> deleted]]
> >>>
> >>>
> _______________________________________________
> >>> R-sig-mixed-models at r-project.org
> mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >>>
> >>
> >
>
> [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 08 Apr 2010 12:48:30 +0200
> From: "Andy Fugard (Work)" <andy.fugard at sbg.ac.at>
> To: E T <2nuzzbot at gmail.com>
> Cc: "r-sig-mixed-models at r-project.org"
> <r-sig-mixed-models at r-project.org>
> Subject: Re: [R-sig-ME] Multi-level models Odds ratio
> Message-ID: <4BBDB47E.8030305 at sbg.ac.at>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Here's another example, borrowed from the help for "lmer":
>
> > gm1 <- glmer(cbind(incidence, size - incidence) ~
> period + (1 | herd),
> family =
> binomial, data = cbpp)
>
> As you say, coef works:
>
> > coef(gm1)
> $herd
> (Intercept)
> period2 period3 period4
> 1 -0.8085096 -0.9923347 -1.128675
> -1.580374
> 2 -1.6974292 -0.9923347 -1.128675
> -1.580374
> 3 -0.9922697 -0.9923347 -1.128675
> -1.580374
> 4 -1.3592525 -0.9923347 -1.128675
> -1.580374
> 5 -1.5885461 -0.9923347 -1.128675
> -1.580374
> 6 -1.7987950 -0.9923347 -1.128675
> -1.580374
> 7 -0.5091313 -0.9923347 -1.128675
> -1.580374
> 8 -0.7991613 -0.9923347 -1.128675
> -1.580374
> 9 -1.6361848 -0.9923347 -1.128675
> -1.580374
> 10 -1.9394614 -0.9923347 -1.128675 -1.580374
> 11 -1.4831632 -0.9923347 -1.128675 -1.580374
> 12 -1.4633469 -0.9923347 -1.128675 -1.580374
> 13 -2.0884474 -0.9923347 -1.128675 -1.580374
> 14 -0.4278151 -0.9923347 -1.128675 -1.580374
> 15 -1.9290041 -0.9923347 -1.128675 -1.580374
>
> But note the "$herd" bit. Since this model has a
> varying intercept by
> herd, you get a column in the resulting data frame called
> "herd".
>
> So you could try, for this example:
>
> > exp(coef(gm1)$herd)
> (Intercept) period2 period3 period4
> 1 0.4455216 0.3707102 0.3234614 0.2058981
> 2 0.1831538 0.3707102 0.3234614 0.2058981
> 3 0.3707343 0.3707102 0.3234614 0.2058981
> 4 0.2568527 0.3707102 0.3234614 0.2058981
> 5 0.2042223 0.3707102 0.3234614 0.2058981
> 6 0.1654982 0.3707102 0.3234614 0.2058981
> 7 0.6010174 0.3707102 0.3234614 0.2058981
> 8 0.4497060 0.3707102 0.3234614 0.2058981
> 9 0.1947215 0.3707102 0.3234614 0.2058981
> 10 0.1437814 0.3707102 0.3234614
> 0.2058981
> 11 0.2269188 0.3707102 0.3234614
> 0.2058981
> 12 0.2314603 0.3707102 0.3234614
> 0.2058981
> 13 0.1238793 0.3707102 0.3234614
> 0.2058981
> 14 0.6519320 0.3707102 0.3234614
> 0.2058981
> 15 0.1452928 0.3707102 0.3234614
> 0.2058981
>
> Since the slopes don't vary by herd, you might also want
> just the fixed
> effects:
>
> > exp(fixef(gm1))
> (Intercept) period2
> period3 period4
>
> 0.2469585 0.3707102 0.3234614 0.2058981
>
> HTH,
>
> Andy
>
>
> E T wrote:
> > If I use the command coef(model) this extracts the
> coefficients in the
> > model, however if I try exp(coef(model)) I receive an
> error:
> >
> > Error in exp(coef(model)) : Non-numeric argument to
> mathematical function
> >
> > I could manually get the exp of each factor in my
> model..... but as I have a
> > large model (and also have numerous other models to
> produce), I was
> > wondering if there was an automated method
> >
> > Regards
> >
> > Et
> >
> > On Thu, Apr 8, 2010 at 11:27 AM, E T <2nuzzbot at gmail.com>
> wrote:
> >
> >> odds.ratios = exp(coefs(model))
> >>
> >> Thanks, however unfortunately when I try the above
> command I receive the
> >> following error:
> >>
> >> Error: could not find function "coefs"
> >>
> >> Regards
> >>
> >> Et
> >>
> >>
> >>
> >>
> >> On Wed, Apr 7, 2010 at 5:47 PM, Daniel Ezra
> Johnson <
> >> danielezrajohnson at gmail.com>
> wrote:
> >>
> >>> something like odds.ratios =
> exp(coefs(model))
> >>>
> >>>
> >>> On Apr 7, 2010, at 12:28 PM, E T <2nuzzbot at gmail.com>
> wrote:
> >>>
> >>> Hi all,
> >>>> Apologies for the simplicity of my
> question.... however any advice is
> >>>> greatly appreciated. Thanks
> >>>>
> >>>> Is there a specific command available to
> obtain the odds ratios produced
> >>>> from a multilevel logistic model?
> >>>>
> >>>> I have estimated a multi-level logistic
> model using the lme4 package. I
> >>>> can
> >>>> obtain results using the 'summary'
> command, however I would like to
> >>>> obtain
> >>>> the computed odds ratios.
> >>>> (Similar to the output that can be
> produced for logistic GLM using the
> >>>> logistic.display command from the epicalc
> package).
> >>>>
> >>>> [[alternative HTML
> version deleted]]
> >>>>
> >>>>
> _______________________________________________
> >>>> R-sig-mixed-models at r-project.org
> mailing list
> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >>>>
> >
> > [[alternative HTML version
> deleted]]
> >
> > _______________________________________________
> > R-sig-mixed-models at r-project.org
> mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
>
> --
> Andy Fugard, Postdoctoral researcher, ESF LogICCC project
> "Modeling human inference within the framework of
> probability logic"
> Department of Psychology, University of Salzburg, Austria
> http://www.andyfugard.info
>
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 8 Apr 2010 12:13:23 +0100
> From: E T <2nuzzbot at gmail.com>
> To: "Andy Fugard (Work)" <andy.fugard at sbg.ac.at>
> Cc: "r-sig-mixed-models at r-project.org"
> <r-sig-mixed-models at r-project.org>
> Subject: Re: [R-sig-ME] Multi-level models Odds ratio
> Message-ID:
> <p2p706f8d1f1004080413k3014fe10q444382c927c2f90e at mail.gmail.com>
> Content-Type: text/plain
>
> exp(coef(model)$group)
>
> exp(fixef(model))
>
> Thanks.... yes this worked successfully :o)
>
> Et
>
> On Thu, Apr 8, 2010 at 11:48 AM, Andy Fugard (Work)
> <andy.fugard at sbg.ac.at>wrote:
>
> > Here's another example, borrowed from the help for
> "lmer":
> >
> > > gm1 <- glmer(cbind(incidence, size -
> incidence) ~ period + (1 | herd),
> > family
> = binomial, data = cbpp)
> >
> > As you say, coef works:
> >
> > > coef(gm1)
> > $herd
> > (Intercept)
> period2 period3 period4
> > 1 -0.8085096 -0.9923347 -1.128675
> -1.580374
> > 2 -1.6974292 -0.9923347 -1.128675
> -1.580374
> > 3 -0.9922697 -0.9923347 -1.128675
> -1.580374
> > 4 -1.3592525 -0.9923347 -1.128675
> -1.580374
> > 5 -1.5885461 -0.9923347 -1.128675
> -1.580374
> > 6 -1.7987950 -0.9923347 -1.128675
> -1.580374
> > 7 -0.5091313 -0.9923347 -1.128675
> -1.580374
> > 8 -0.7991613 -0.9923347 -1.128675
> -1.580374
> > 9 -1.6361848 -0.9923347 -1.128675
> -1.580374
> > 10 -1.9394614 -0.9923347 -1.128675 -1.580374
> > 11 -1.4831632 -0.9923347 -1.128675 -1.580374
> > 12 -1.4633469 -0.9923347 -1.128675 -1.580374
> > 13 -2.0884474 -0.9923347 -1.128675 -1.580374
> > 14 -0.4278151 -0.9923347 -1.128675 -1.580374
> > 15 -1.9290041 -0.9923347 -1.128675 -1.580374
> >
> > But note the "$herd" bit. Since this model has a
> varying intercept by
> > herd, you get a column in the resulting data frame
> called "herd".
> >
> > So you could try, for this example:
> >
> > > exp(coef(gm1)$herd)
> > (Intercept) period2 period3 period4
> > 1 0.4455216 0.3707102 0.3234614
> 0.2058981
> > 2 0.1831538 0.3707102 0.3234614
> 0.2058981
> > 3 0.3707343 0.3707102 0.3234614
> 0.2058981
> > 4 0.2568527 0.3707102 0.3234614
> 0.2058981
> > 5 0.2042223 0.3707102 0.3234614
> 0.2058981
> > 6 0.1654982 0.3707102 0.3234614
> 0.2058981
> > 7 0.6010174 0.3707102 0.3234614
> 0.2058981
> > 8 0.4497060 0.3707102 0.3234614
> 0.2058981
> > 9 0.1947215 0.3707102 0.3234614
> 0.2058981
> > 10 0.1437814 0.3707102 0.3234614
> 0.2058981
> > 11 0.2269188 0.3707102 0.3234614
> 0.2058981
> > 12 0.2314603 0.3707102 0.3234614
> 0.2058981
> > 13 0.1238793 0.3707102 0.3234614
> 0.2058981
> > 14 0.6519320 0.3707102 0.3234614
> 0.2058981
> > 15 0.1452928 0.3707102 0.3234614
> 0.2058981
> >
> > Since the slopes don't vary by herd, you might also
> want just the fixed
> > effects:
> >
> > > exp(fixef(gm1))
> > (Intercept) period2
> period3 period4
> >
> 0.2469585 0.3707102 0.3234614 0.2058981
> >
> > HTH,
> >
> > Andy
> >
> >
> > E T wrote:
> > > If I use the command coef(model) this extracts
> the coefficients in the
> > > model, however if I try exp(coef(model)) I
> receive an error:
> > >
> > > Error in exp(coef(model)) : Non-numeric argument
> to mathematical function
> > >
> > > I could manually get the exp of each factor in my
> model..... but as I
> > have a
> > > large model (and also have numerous other models
> to produce), I was
> > > wondering if there was an automated method
> > >
> > > Regards
> > >
> > > Et
> > >
> > > On Thu, Apr 8, 2010 at 11:27 AM, E T <2nuzzbot at gmail.com>
> wrote:
> > >
> > >> odds.ratios = exp(coefs(model))
> > >>
> > >> Thanks, however unfortunately when I try the
> above command I receive the
> > >> following error:
> > >>
> > >> Error: could not find function "coefs"
> > >>
> > >> Regards
> > >>
> > >> Et
> > >>
> > >>
> > >>
> > >>
> > >> On Wed, Apr 7, 2010 at 5:47 PM, Daniel Ezra
> Johnson <
> > >> danielezrajohnson at gmail.com>
> wrote:
> > >>
> > >>> something like odds.ratios =
> exp(coefs(model))
> > >>>
> > >>>
> > >>> On Apr 7, 2010, at 12:28 PM, E T <2nuzzbot at gmail.com>
> wrote:
> > >>>
> > >>> Hi all,
> > >>>> Apologies for the simplicity of my
> question.... however any advice is
> > >>>> greatly appreciated. Thanks
> > >>>>
> > >>>> Is there a specific command available
> to obtain the odds ratios
> > produced
> > >>>> from a multilevel logistic model?
> > >>>>
> > >>>> I have estimated a multi-level
> logistic model using the lme4 package.
> > I
> > >>>> can
> > >>>> obtain results using the 'summary'
> command, however I would like to
> > >>>> obtain
> > >>>> the computed odds ratios.
> > >>>> (Similar to the output that can be
> produced for logistic GLM using the
> > >>>> logistic.display command from the
> epicalc package).
> > >>>>
> > >>>> [[alternative HTML
> version deleted]]
> > >>>>
> > >>>>
> _______________________________________________
> > >>>> R-sig-mixed-models at r-project.org
> mailing list
> > >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> > >>>>
> > >
> > > [[alternative HTML
> version deleted]]
> > >
> > > _______________________________________________
> > > R-sig-mixed-models at r-project.org
> mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >
> >
> > --
> > Andy Fugard, Postdoctoral researcher, ESF LogICCC
> project
> > "Modeling human inference within the framework of
> probability logic"
> > Department of Psychology, University of Salzburg,
> Austria
> > http://www.andyfugard.info
> >
>
> [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
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>
>
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