[R-sig-ME] Side effects from mcmcsamp()
Juan Pedro Steibel
steibelj at msu.edu
Fri May 15 22:16:53 CEST 2009
Hello,
I noticed this a wile ago. One thing that occurred to me was to copy to
another object before running mcmcsamp, example:
obmix0<-obmix
where obmix is the lmer object.
then do: mcmcsamp(obmix)....
For some reason obmix0 gets modified too.
It's been a while since I checked this so it may have been fixed.
Anyways, a way around this is to extract all the info needed from your
lmer object to other variables before running mcmcsamp, that's what I do
now and it works fine.
Thanks
JP
John Maindonald wrote:
> Dear Douglas -
> The following is at the very least a serious trap! The output
> from VarCorr() and print() changes remarkably after running
> mcmcsamp() with the lmer object as argument. The estimate
> of sigma is always (for these data) high, but roughly in the
> middle of the range of values that come out of ant111b.samp at sigma
>
> I have also been able to reproduce this behaviour
> (a) under lme4_0.999375-28 [below, I use 30]
> (b) under Mac OSX. In fact, I thought initially that this
> was an OSX problem!
>
> While mcmcsamp() is in view, it would be very helpful
> to have a progress report on where it is at.
>
> Many thanks
> John Maindonald.
>
> I run the following code:
>
> library(DAAG)
> library(lme4)
> ant111b.lmer <- lmer(harvwt ~ 1 + (1 | site), data=ant111b)
> ant111b.lmer
> VarCorr(ant111b.lmer)
> ant111b.samp <- mcmcsamp(ant111b.lmer, n=1000)
>
> ## Now, extract the VarCorr and summary correlations
> VarCorr(ant111b.lmer)
> summary(ant111b.lmer)
>
> > ant111b.lmer <- lmer(harvwt ~ 1 + (1 | site), data=ant111b)
> > ant111b.lmer
> Linear mixed model fit by REML
> Formula: harvwt ~ 1 + (1 | site)
> Data: ant111b
> AIC BIC logLik deviance REMLdev
> 100.4 104.8 -47.21 95.08 94.42
> Random effects:
> Groups Name Variance Std.Dev.
> site (Intercept) 2.36773 1.53874
> Residual 0.57754 0.75996
> Number of obs: 32, groups: site, 8
>
> Fixed effects:
> Estimate Std. Error t value
> (Intercept) 4.2917 0.5603 7.659
> > library(DAAG)
> > library(lme4)
> > ant111b.lmer <- lmer(harvwt ~ 1 + (1 | site), data=ant111b)
> > ant111b.lmer
> Linear mixed model fit by REML
> Formula: harvwt ~ 1 + (1 | site)
> Data: ant111b
> AIC BIC logLik deviance REMLdev
> 100.4 104.8 -47.21 95.08 94.42
> Random effects:
> Groups Name Variance Std.Dev.
> site (Intercept) 2.36773 1.53874
> Residual 0.57754 0.75996
> Number of obs: 32, groups: site, 8
>
> Fixed effects:
> Estimate Std. Error t value
> (Intercept) 4.2917 0.5603 7.659
> > ant111b.samp <- mcmcsamp(ant111b.lmer, n=1000)
> > VarCorr(ant111b.lmer)
> $site
> (Intercept)
> (Intercept) 8.363436
> attr(,"stddev")
> (Intercept)
> 2.891961
> attr(,"correlation")
> (Intercept)
> (Intercept) 1
>
> attr(,"sc")
> sigmaREML
> 1.428289
> > summary(ant111b.lmer)
> Linear mixed model fit by REML
> Formula: harvwt ~ 1 + (1 | site)
> Data: ant111b
> AIC BIC logLik deviance REMLdev
> 112.1 116.5 -53.04 105.7 106.1
> Random effects:
> Groups Name Variance Std.Dev.
> site (Intercept) 8.3634 2.8920
> Residual 2.0400 1.4283
> Number of obs: 32, groups: site, 8
>
> Fixed effects:
> Estimate Std. Error t value
> (Intercept) 4.2917 0.4171 10.29
>
> > sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] lme4_0.999375-30 Matrix_0.999375-26 lattice_0.17-22
> [4] DAAG_0.99-1 MASS_7.2-47
>
> loaded via a namespace (and not attached):
> [1] grid_2.9.0
>
>
>
> John Maindonald email: john.maindonald at anu.edu.au
> phone : +61 2 (6125)3473 fax : +61 2(6125)5549
> Centre for Mathematics & Its Applications, Room 1194,
> John Dedman Mathematical Sciences Building (Building 27)
> Australian National University, Canberra ACT 0200.
>
> _______________________________________________
> R-sig-mixed-models at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
>
--
=============================
Juan Pedro Steibel
Assistant Professor
Statistical Genetics and Genomics
Department of Animal Science &
Department of Fisheries and Wildlife
Michigan State University
1205-I Anthony Hall
East Lansing, MI
48824 USA
Phone: 1-517-353-5102
E-mail: steibelj at msu.edu
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