[R-sig-ME] R-sig-mixed-models Digest, Vol 24, Issue 38
Luciano La Sala
lucianolasala at yahoo.com.ar
Sun Dec 28 17:41:33 CET 2008
Dan,
Thank you very much for your time and assistance. I think you may be right about lack of independence between ClutchSize and HO being the problem here.. I tried random slopes already, but my model fails to converge due to small sample size. I should try different models for different clutch sizes and see what happens.
Cheers!
Lucho
--- El dom 28-dic-08, r-sig-mixed-models-request at r-project.org <r-sig-mixed-models-request at r-project.org> escribió:
> De: r-sig-mixed-models-request at r-project.org <r-sig-mixed-models-request at r-project.org>
> Asunto: R-sig-mixed-models Digest, Vol 24, Issue 38
> Para: r-sig-mixed-models at r-project.org
> Fecha: domingo, 28 de diciembre de 2008, 11:00 am
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> Today's Topics:
>
> 1. Re: Commonly observed error message in lmer (Daniel
> Ezra Johnson)
> 2. Matrix messages when loading lme4 (Christopher David
> Desjardins)
> 3. Re: Matrix messages when loading lme4 (Daniel Ezra
> Johnson)
> 4. Re: Matrix messages when loading lme4
> (Christopher David Desjardins)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 27 Dec 2008 11:22:04 +0000
> From: "Daniel Ezra Johnson"
> <danielezrajohnson at gmail.com>
> Subject: Re: [R-sig-ME] Commonly observed error message in
> lmer
> To: "Luciano La Sala"
> <lucianolasala at yahoo.com.ar>
> Cc: R-mixed models mailing list
> <r-sig-mixed-models at r-project.org>
> Message-ID:
> <a46630750812270322t333fc0dcg88f4039bc642caaf at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> This error came up earlier in the year and Doug Bates
> wrote:
>
> >This call is returning a warning about evaluation of
> the gradient at
> >the initial values of the parameters. I'm not sure
> if it then goes on
> >to optimize the approximated deviance.
>
> >If the approximated deviance is not being minimized for
> this model you
> >may want to start with a simpler model, omitting some
> of the terms in
> >the fixed effects.
>
> Your fixed effects don't seem too complicated but there
> is a certain
> inherent non-independence between ClutchSize and HO
> (hatching order).
> For example if ClutchSize is 1 then HO must be 1. I wonder
> if that's
> what's causing the problem?
>
> Maybe you could try fitting separate models for each
> ClutchSize and
> observe the HO effect separately (when ClutchSize > 1)?
>
> You could also add a random slope as you said you wanted,
> that would
> be done with a term (HO|NestID).
>
> Hope this helps,
> Dan
>
> On Sat, Dec 27, 2008 at 2:39 AM, Luciano La Sala
> <lucianolasala at yahoo.com.ar> wrote:
> > Dear R-people,
> >
> > It's me again with, maybe, one more silly question
> for you. As a remainder, I am running version 2.7.1 on
> Windows Vista. I have small dataset which consists of:
> >
> > # NestID: nest indicator for each chicken. Siblings
> sharing the same nest have the same nest indicator.
> > # Chick: chick indicator consisting of a unique ID for
> each single chick.
> > # Year: 1, 2.
> > # ClutchSize: 1-, 2- , 3-eggs.
> > # HO: hatching order within each clutch (1, 2, 3
> [first, second and third-hatched chick]).
> > # SibComp: sibling competence: present/ absent (0, 1)
> > # Death10: death at ten days post-hatch (0, 1)
> >
> > In order to account for lack of independence at the
> nest level (many chicks are nested in nest), I'd like to
> run a GLMM with random slopes and intercepts for nests.
> >
> > Using lmer, whenever I try to model two-way
> interaction like specified below:
> >
> > model1 <-
> lmer(Death10~HO*ClutchSize+(1|NestID),family=binomial,1)
> >
> >
> > .... the following error message pops up:
> >
> > In mer_finalize(ans, verbose) : gr cannot be computed
> at initial par (65)
> >
> > 1. What does this error mean?
> >
> > I look forward to hearing from you soon!
> >
> > Best, Luciano
> >
> >
> >
> >
> ____________________________________________________________________________________
> > ?Busc? desde tu celular!
> >
> > Yahoo! oneSEARCH ahora est? en Claro
> >
> > http://ar.mobile.yahoo.com/onesearch
> >
> > _______________________________________________
> > R-sig-mixed-models at r-project.org mailing list
> >
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >
>
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 27 Dec 2008 12:40:20 -0600
> From: Christopher David Desjardins <desja004 at umn.edu>
> Subject: [R-sig-ME] Matrix messages when loading lme4
> To: R-mixed models mailing list
> <r-sig-mixed-models at r-project.org>
> Message-ID:
> <756D40D9-AD56-4ADE-AFEF-A6CD65145B4E at umn.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed;
> delsp=yes
>
> Hi,
> I presume these messages are benign but I thought I'd
> find out what
> they are referring to ...
>
> > library(lme4)
> Loading required package: Matrix
> Loading required package: lattice
>
> Attaching package: 'Matrix'
>
>
> The following object(s) are masked from package:stats :
>
> xtabs
>
>
> The following object(s) are masked from package:base :
>
> colMeans,
> colSums,
> rcond,
> rowMeans,
> rowSums
>
>
>
> -----------------
> Christopher David Desjardins
> Ph.D. Student
> Quantitative Methods in Education
> Department of Educational Psychology
> University of Minnesota
> http://blog.lib.umn.edu/desja004/educationalpsychology/
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 27 Dec 2008 19:06:49 +0000
> From: "Daniel Ezra Johnson"
> <danielezrajohnson at gmail.com>
> Subject: Re: [R-sig-ME] Matrix messages when loading lme4
> To: "Christopher David Desjardins"
> <desja004 at umn.edu>
> Cc: R-mixed models mailing list
> <r-sig-mixed-models at r-project.org>
> Message-ID:
> <a46630750812271106s3aa096a1kef32e1fcd6021cd3 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> It means that the Matrix package includes functions with
> the names
> listed, which as long as Matrix is loaded, supersede the
> original
> versions of those functions in the base and stats packages.
>
> If you look at one of the help pages, it should explain the
> change to
> the function. Usually this is some additional functionality
> and the
> function should be usable as before, if desired.
>
> For example, ?xtabs (or ?Matrix::xtabs) gives this notice:
> "This is a
> fully compatible extension of the standard stats package
> xtabs()
> function with the added option to produce a sparse matrix
> result via
> sparse = TRUE."
>
> Hope this helps,
> Dan
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 27 Dec 2008 15:18:43 -0600
> From: Christopher David Desjardins <desja004 at umn.edu>
> Subject: Re: [R-sig-ME] Matrix messages when loading lme4
> To: Daniel Ezra Johnson <danielezrajohnson at gmail.com>
> Cc: R-mixed models mailing list
> <r-sig-mixed-models at r-project.org>
> Message-ID:
> <05A96BCA-4D14-46DA-B557-763D2AF5B747 at umn.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> Thanks that's very helpful.
> Chris
>
> On Dec 27, 2008, at 1:06 PM, Daniel Ezra Johnson wrote:
>
> > It means that the Matrix package includes functions
> with the names
> > listed, which as long as Matrix is loaded, supersede
> the original
> > versions of those functions in the base and stats
> packages.
> >
> > If you look at one of the help pages, it should
> explain the change to
> > the function. Usually this is some additional
> functionality and the
> > function should be usable as before, if desired.
> >
> > For example, ?xtabs (or ?Matrix::xtabs) gives this
> notice: "This is a
> > fully compatible extension of the standard stats
> package xtabs()
> > function with the added option to produce a sparse
> matrix result via
> > sparse = TRUE."
> >
> > Hope this helps,
> > Dan
>
> -----------------
> Christopher David Desjardins
> Ph.D. Student
> Quantitative Methods in Education
> Department of Educational Psychology
> University of Minnesota
> http://blog.lib.umn.edu/desja004/educationalpsychology/
>
>
>
> ------------------------------
>
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> R-sig-mixed-models at r-project.org
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> End of R-sig-mixed-models Digest, Vol 24, Issue 38
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