[R] lme4---GLMM
Hello, I'm very sorry for my repeated question, which i asked 2 weeks ago, namely: i'm interested in possibly simple random-part specification in the call of GLMM(...) (from lme4-package) i have a random blocked structure (i.e. ~var.a1+var.a2+var.a3, ~var.b1+var.b2,~var.c1+var.c2+var.c3+var.c4), and each one part of it i would like to model as Identity-structure matrix. So i had, in symbols of nlme-package, and for only one cluster-variable my.Subject: random=list(my.Subject=pdBlocked(list(pdIdent(~var.a1+var.a2+var.a3,...),pdIdent(~var.b1+var.b2,...),pdIdent(~var.c1+var.c2+var.c3+var.c4),...))) As the lme4-package doesn't use the pdMat-classes for specification of the random-part in GLMM,i used, with advice of Douglas Bates, the explicit specification in the GLMM-call (this call can also been simplified, if i first attach the lme4 package and then the nlme-package): GLMM(., random=list(my.Subject=~var.a1+var.a2+var.a3, my.Subject=~var.b1+var.b2, my.Subject=var.c1+var.c2+var.c3+var.c4),.) and really could make estimates in such a way. The problem is how can i specify a simple matrix sructure for each block, such as pdIdent(...) in symbols of lme4. is it possible? Does the lme4 any use of pdMat-specification or something like this? If not, it seems, that i actually specify a general Covariance Matrix for each block, what i in principle don't want. thanks in advance __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] lme4 -- GLMM
hello! this is a question, how can i specify the random part in the GLMM-call (of the lme4 library) for compound matrices just in the the same way as they defined in the lme-Call (of the nlme library). For example i would just need random=list(my.Subject=pdBlocked(list(pdIdent(~... , ...),pdIdent(~... , ... this specification , if i also attach library(nlme) , is not accepted in the GLMM-call, though the simple form random=list(my.Subject=pdIdent(~...,...)) is accepted. what is the analogous of pdBlocked Co from nlme in lme4? thanks for replay __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
lme4 package etc {Re: [R] lme4 -- GLMM}
Pavel == Pavel Khomski [EMAIL PROTECTED] on Tue, 08 Feb 2005 10:20:03 +0100 writes: Pavel this is a question, how can i specify the random part Pavel in the GLMM-call (of the lme4 library) for compound Pavel matrices just in the the same way as they defined in Pavel the lme-Call (of the nlme library). ``twice in such a short paragraph -- yikes !!'' ... I'm getting convulsive... There is NO lme4 library nor an nlme one ! There's the lme4 *PACKAGE* and the nlme *PACKAGE* -- please -- (If the nlme package is built, it will rely on a nlme.so or nlme.dll (or nlme.dylib ...) *library* of compiled C code, and if packages are installed, they are installed into a library of packages; typically into one of the libraries in .libPaths() ) whooh Martin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: lme4 package etc {Re: [R] lme4 -- GLMM} | fortunes package
I guess Martin is struggling to have the most entries in the next version of fortunes ;-) Well... I hope so! Or we should really do something for new users - letting any R core team member getting convulsive is dangerous for the futuRe. Best wishes, Eric Pavel this is a question, how can i specify the random part Pavel in the GLMM-call (of the lme4 library) for compound Pavel matrices just in the the same way as they defined in Pavel the lme-Call (of the nlme library). ``twice in such a short paragraph -- yikes !!'' ... I'm getting convulsive... There is NO lme4 library nor an nlme one ! There's the lme4 *PACKAGE* and the nlme *PACKAGE* -- please -- (If the nlme package is built, it will rely on a nlme.so or nlme.dll (or nlme.dylib ...) *library* of compiled C code, and if packages are installed, they are installed into a library of packages; typically into one of the libraries in .libPaths() ) whooh Martin Eric Lecoutre UCL / Institut de Statistique Voie du Roman Pays, 20 1348 Louvain-la-Neuve Belgium tel: (+32)(0)10473050 [EMAIL PROTECTED] http://www.stat.ucl.ac.be/ISpersonnel/lecoutre If the statistics are boring, then you've got the wrong numbers. -Edward Tufte __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: lme4 package etc {Re: [R] lme4 -- GLMM}
Martin Maechler wrote: Pavel == Pavel Khomski [EMAIL PROTECTED] on Tue, 08 Feb 2005 10:20:03 +0100 writes: Pavel this is a question, how can i specify the random part Pavel in the GLMM-call (of the lme4 library) for compound Pavel matrices just in the the same way as they defined in Pavel the lme-Call (of the nlme library). The GLMM function in the lme4 package allows you to specify crossed random effects within the random argument without the need for the pdBlocked and pdIdent constructions. Simply ensure that your grouping factors are defined in such a way that each distinct group has a different level in the grouping factor (this is usually not a problem for crossed grouping factors but can be a problem with nested factors) and list them. For example random = list(rows = ~ 1, columns = ~1) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Packages and Libraries (was: Re: lme4 package etc {Re: [R] lme4 -- GLMM}
For OBVIOUS reasons, is there any chance that we could introduce package() and deprecate library()? (well, I'll also ask if we could deprecate = for assignment, but that's hopeless). best, -tony On Tue, 8 Feb 2005 11:49:39 +0100, Martin Maechler [EMAIL PROTECTED] wrote: Pavel == Pavel Khomski [EMAIL PROTECTED] on Tue, 08 Feb 2005 10:20:03 +0100 writes: Pavel this is a question, how can i specify the random part Pavel in the GLMM-call (of the lme4 library) for compound Pavel matrices just in the the same way as they defined in Pavel the lme-Call (of the nlme library). ``twice in such a short paragraph -- yikes !!'' ... I'm getting convulsive... There is NO lme4 library nor an nlme one ! There's the lme4 *PACKAGE* and the nlme *PACKAGE* -- please -- (If the nlme package is built, it will rely on a nlme.so or nlme.dll (or nlme.dylib ...) *library* of compiled C code, and if packages are installed, they are installed into a library of packages; typically into one of the libraries in .libPaths() ) whooh Martin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: Packages and Libraries (was: Re: lme4 package etc {Re: [R] lme4 -- GLMM}
A.J. Rossini [EMAIL PROTECTED] writes: For OBVIOUS reasons, is there any chance that we could introduce package() and deprecate library()? usepackage() or usePackage() has been suggested, but someone got ambitious and wanted it to be different from library(), and it sort of didn't get any further. We still have some time before feature freeze for 2.1.0 though. (well, I'll also ask if we could deprecate = for assignment, but that's hopeless). You're not *forced* to use it... -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] lme4, GLMM, var-cov matrix of fixed effects
Dear all, 1. How do I compute the fixed-effects var-cov matrix from a GLMM object (lme4 package) fitted with the Laplace method? details: the vcov method for GLMM objects does not seem to work in this case: returns a 0 * 0 matrix: fm1 - GLMM(immun ~ kid2p + mom25p + ord, + family = binomial, data = guImmun, random = ~ 1 | comm, method = Laplace) Using optimizer nlm fm1 Generalized Linear Mixed Model Family: binomial family with logit link Fixed: immun ~ kid2p + mom25p + ord Data: guImmun log-likelihood: -1400.842 Random effects: GroupsNameVarianceStd.Dev. comm (Intercept) 0.61621 0.78499 # of obs: 2159, groups: comm, 161 Estimated scale (compare to 1) 0.9702206 Fixed effects: Estimate Std. Error z value Pr(|z|) (Intercept) -0.970969 0.162467 -5.9764 2.281e-09 kid2pY 0.991837 0.119242 8.3178 2.2e-16 mom25pY -0.052423 0.129561 -0.40460.6858 ord23 -0.094408 0.140715 -0.67090.5023 ord460.040217 0.167089 0.24070.8098 ord7p0.013805 0.206611 0.06680.9467 (Intercept)kid2pY mom25pY ord23 ord46 ord7p [1,] -0.970969 0.9918369 -0.05242273 -0.09440838 0.04021697 0.01380546 vcov(fm1) 0 x 0 matrix # 2. Is it relevant and efficient to use this var-cov matrix to perform Wald-like tests for the significance of one or more fixed effects ? version information: # R _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor0.0 year 2004 month10 day 04 language R # lme4 Package: lme4 Version: 0.6-9 Date: 2004-10-04 # Matrix Package: Matrix Version: 0.8-15 Date: 2004-10-02 # Thanks, Renaud -- Dr Renaud Lancelot, vétérinaire C/0 Ambassade de France - SCAC BP 834 Antananarivo 101 - Madagascar e-mail: [EMAIL PROTECTED] tel.: +261 32 40 165 53 (cell) +261 20 22 665 36 ext. 225 (work) +261 20 22 494 37 (home) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
