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/
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.simp...@ucl.ac.uk> To: array chip <arrayprof...@yahoo.com> Cc: John Sorkin <jsor...@grecc.umaryland.edu>; r-help@r-project.org; Bert Gunter <gunter.ber...@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.simp...@ucl.ac.uk> > To: John Sorkin <jsor...@grecc.umaryland.edu> > Cc: r-help@r-project.org; Bert Gunter <gunter.ber...@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.ber...@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 <jsor...@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@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. > -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% 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 %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ______________________________________________ R-help@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.
