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.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 > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > > > > -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% 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.
