Re: [R] lme4a package loading error
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.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 10:46:16 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.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
[R] lme4a package loading error
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_1.1.9Rcpp_0.8.6 Matrix_0.999375-43 lattice_0.18-8 loaded via a namespace (and not attached): [1] grid_2.11.1nlme_3.1-96splines_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
Re: [R] 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_1.1.9Rcpp_0.8.6 Matrix_0.999375-43 lattice_0.18-8 loaded via a namespace (and not attached): [1] grid_2.11.1nlme_3.1-96splines_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
