[R-sig-ME] lme4a package loading error
array chip
arrayprofile at yahoo.com
Sat Sep 11 08:51:38 CEST 2010
Thank you for pointing ou R-forge. I tried link from R-forge for lme4a, it
doesn't work at the time I tried (Returned "PAGE NOT FOUND".
However, the link for lme4b worked, and I installed lme4b package which can be
loaded successfully. lme4b has lmer1() instead of lmer().
However, when trying to run lmer1(), it will tell you this warning message:
Warning message:
model.Matrix() has been moved from package 'Matrix' to the new package
'MatrixModels' which is now loaded (if installed).
Its use from package 'Matrix' is deprecated.
Do use it from 'MatrixModels' instead.
I think this may be why I got error message when I try to load lme4a, which may
have not been updated to look for MatrixModels package instead of Matrix
package.
The reason I posted to both R and R-mixed-models mailing list is that it seems
that this question is more suitable to R-mixed-models, but response there is
pretty slow,......
Thanks,
John
----- Original Message ----
From: Gavin Simpson <gavin.simpson at ucl.ac.uk>
To: array chip <arrayprofile at yahoo.com>
Cc: John Sorkin <jsorkin at grecc.umaryland.edu>; r-help at r-project.org; Bert Gunter
<gunter.berton at gene.com>
Sent: Fri, September 10, 2010 10:46:16 AM
Subject: Re: lme4a package loading error
On Fri, 2010-09-10 at 10:23 -0700, array chip wrote:
> Thanks for reminding this. So I found lme4a package from Doug's UserR!2010
> presentation folder:
> http://lme4.r-forge.r-project.org/slides/2010-07-20-Gaithersburg/pkg/
What is wrong with the one on the packages tab of the lme4 project page:
https://r-forge.r-project.org/R/?group_id=60
?
You might need to make sure you have the latest Matrix as well to run
lme4a. Update Matrix via update.packages() or install the latest version
from r-forge and see if that helps.
Also, try not to cross-post to multiple lists. Stick with one, or move
the thread onto the new list.
HTH
G
> However, after installation, I got the following error message when trying to
> load the library:
>
> library(Matrix)
> > library(Rcpp)
> > library(minqa)
> > library(lme4a)
> Error : classes "modelMatrix", "denseModelMatrix", "sparseModelMatrix",
> "ddenseModelMatrix", "dsparseModelMatrix", "predModule", "dPredModule",
> "sPredModule", "respModule", "glmRespMod", "nlsRespMod" are not exported by
> 'namespace:Matrix'
> Error: package/namespace load failed for 'lme4a'
>
> Here is my sessionInfo()
> > sessionInfo()
> R version 2.11.1 (2010-05-31)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
>
>
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>
>
>
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] minqa_1.1.9 Rcpp_0.8.6 Matrix_0.999375-43 lattice_0.18-8
>
> loaded via a namespace (and not attached):
> [1] grid_2.11.1 nlme_3.1-96 splines_2.11.1 stats4_2.11.1 tools_2.11.1
>
> Any suggestions would be appreciated.
>
> John
>
>
>
>
>
> ----- Original Message ----
> From: Gavin Simpson <gavin.simpson at ucl.ac.uk>
> To: array chip <arrayprofile at yahoo.com>
> Cc: John Sorkin <jsorkin at grecc.umaryland.edu>; r-help at r-project.org; Bert
>Gunter
>
> <gunter.berton at gene.com>
> Sent: Fri, September 10, 2010 10:00:15 AM
> Subject: Re: [R] lmer fixed effects, SE, t . . . and p
>
> On Fri, 2010-09-10 at 09:51 -0700, array chip wrote:
> > But as far as I know, profile() seems to be de-activated in the lme4
package.
>
> It is beta software. The lme4a version of the lme4 "package" might have
> had profile re-enabled, IIRC.
>
> G
>
> > ----- Original Message ----
> > From: Gavin Simpson <gavin.simpson at ucl.ac.uk>
> > To: John Sorkin <jsorkin at grecc.umaryland.edu>
> > Cc: r-help at r-project.org; Bert Gunter <gunter.berton at gene.com>
> > Sent: Fri, September 10, 2010 2:05:37 AM
> > Subject: Re: [R] lmer fixed effects, SE, t . . . and p
> >
> > On Thu, 2010-09-09 at 23:40 -0400, John Sorkin wrote:
> > > Bert,
> > > I appreciate you comments, and I have read Doug Bates writing about p
> > > values in mixed effects regression. It is precisely because I read
> > > Doug's material that I asked "how are we to interpret the estimates"
> > > rather than "how can we compute a p value". My question is a simple
> > > question whose answer is undoubtedly complex, but one that needs an
> > > answer. Without p values, or confidence intervals, I am not certain
> > > what to make of the results of my analysis. Does my analysis suggest,
> > > or does it not suggest that there is a relation between time and y? If
> > > I can't answer this question after running the analysis, I don't have
> > > any more information than I did before I ran the analysis, and a fair
> > > question would be why did I run the analysis? I am asking for help not
> > > in calculation a p value or a CI, but rather to know what I can and
> > > can't say about the results of the analysis. If this basic question
> > > can not be answered, I am at a loss to interpret my results.
> > > Thank you,
> > > John
> >
> > Doug talks quite a lot about profiling lmer fits using 'profile
> > deviance' to investigate variability in fixed effects. For example, see
> > section 1.5 in the draft of chapter 1 of Doug's book on mixed models:
> >
> > http://lme4.r-forge.r-project.org/book/
> >
> > HTH
> >
> > G
> >
> > > John David Sorkin M.D., Ph.D.
> > > Chief, Biostatistics and Informatics
> > > University of Maryland School of Medicine Division of Gerontology
> > > Baltimore VA Medical Center
> > > 10 North Greene Street
> > > GRECC (BT/18/GR)
> > > Baltimore, MD 21201-1524
> > > (Phone) 410-605-7119
> > > (Fax) 410-605-7913 (Please call phone number above prior to faxing)>>> Bert
>
> > >Gunter <gunter.berton at gene.com> 9/9/2010 11:21 PM >>>
> > > John:
> > >
> > > Search on this issue in the list archives. Doug Bates has addressed it
> > > at length. Basically, he does not calculate CI's or p-values because
> > > he does not know how to reliably do so.
> > >
> > > However, the key remark in your query was:
> > >
> > > > (2) lmer does not give p values or confidence intervals for the fixed
> > >effects. How we are to interpret the estimates given that no p value or CI
>is
>
>
> > >given for the estimates?
> > >
> > > Think about it. A statistical analysis -- ANY statistical analysis --
> > > treats the data in isolation: it is not informed by physics,
> > > thermodynamics, biology, other similar data, prior experience, or,
> > > indeed, any part of the body of relevant scientific knowledge. Do you
> > > really think that any such analysis, especially when predicated upon
> > > often tenuous or even (necessarily) unverifiable assumptions and
> > > simplifications should be considered authoritative? Classical
> > > statistical inference is just another piece of the puzzle, and not
> > > even particularly useful when, as if typically the case, hypotheses
> > > are formulated AFTER seeing the data (this invalidates the probability
> > > calculations -- hypotheses must be formulated before seeing the data
> > > to be meaningfully assessed). Leo Breiman called this statistics'
> > > "quiet scandal" something like 20 years ago, and he was no dummy.
> > >
> > > It is comforting, perhaps, but illusory to believe that statistical
> > > inference can be relied on to give sound, objective scientific
> > > results. True, without such a framework, science seems rather
> > > subjective, perhaps closer to religion and arbitrary cultural
> > > archetypes than we care to admit. But see Thomas Kuhn and Paul
> > > Feuerabend for why this is neither surprising nor necessarily a bad
> > > thing.
> > >
> > > Cheers,
> > > Bert Gunter
> > >
> > >
> > >
> > >
> > > On Thu, Sep 9, 2010 at 8:00 PM, John Sorkin <jsorkin at grecc.umaryland.edu>
> > >wrote:
> > > > windows Vista
> > > > R 2.10.1
> > > >
> > > >
> > > > (1) How can I get the complete table of for the fixed effects from lmer.
>As
>
> >
> > >can be seen from the example below, fixef(fit2) only give the estimates and
> >not
> >
> > >the SE or t value
> > > >
> > > >> fit3<- lmer(y~time + (1|Subject) +
(time|Subject),data=data.frame(data))
> > > >> summary(fit3)
> > > > Linear mixed model fit by REML
> > > > Formula: y ~ time + (1 | Subject) + (time | Subject)
> > > > Data: data.frame(data)
> > > > AIC BIC logLik deviance REMLdev
> > > > -126.2 -116.4 70.1 -152.5 -140.2
> > > > Random effects:
> > > > Groups Name Variance Std.Dev. Corr
> > > > Subject (Intercept) 2.9311e+01 5.41396385
> > > > Subject (Intercept) 0.0000e+00 0.00000000
> > > > time 0.0000e+00 0.00000000 NaN
> > > > Residual 8.1591e-07 0.00090328
> > > > Number of obs: 30, groups: Subject, 10
> > > >
> > > > Fixed effects:
> > > > Estimate Std. Error t value
> > > > (Intercept) 14.998216 1.712046 9
> > > > time -0.999779 0.000202 -4950
> > > >
> > > > Correlation of Fixed Effects:
> > > > (Intr)
> > > > time -0.001
> > > >> fixef(fit3)
> > > > (Intercept) time
> > > > 14.9982158 -0.9997793
> > > >
> > > > (2) lmer does not give p values or confidence intervals for the fixed
> > >effects. How we are to interpret the estimates given that no p value or CI
>is
>
>
> > >given for the estimates?
> > > >
> > > >
> > > >
> > > >
> > > > John David Sorkin M.D., Ph.D.
> > > > Chief, Biostatistics and Informatics
> > > > University of Maryland School of Medicine Division of Gerontology
> > > > Baltimore VA Medical Center
> > > > 10 North Greene Street
> > > > GRECC (BT/18/GR)
> > > > Baltimore, MD 21201-1524
> > > > (Phone) 410-605-7119
> > > > (Fax) 410-605-7913 (Please call phone number above prior to faxing)
> > > >
> > > > Confidentiality Statement:
> > > > This email message, including any attachments, is for ...{{dropped:25}}
> > >
> > > ______________________________________________
> > > R-help at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> >
>
> --
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> Dr. Gavin Simpson [t] +44 (0)20 7679 0522
> ECRC, UCL Geography, [f] +44 (0)20 7679 0565
> Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
> Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
> UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
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