The development version of the lme4 package on R-forge now passes its tests with linear mixed models, nonlinear mixed models and generalized linear mixed models. It should also be capable of fitting generalized nonlinear mixed models but I haven't written the user-callable functions for those models yet. This version represents a substantial redesign of the code (the last one, I promise) and should be both faster and simpler than previous versions. I would recommend trying it if you have large data sets and complex models (e.g. models with crossed or partially crossed grouping factors) or if you are working with generalized linear mixed models or nonlinear mixed models. For example, Sharon Goldwater recently wrote to the R-help list about peculiar relationships in her fitted GLMM models (removing a parameter decreased the deviance) from the currently released version of lme4. She was kind enough to provide me with the data and I could fit all her models, with consistent results, in the development version of the package. I'm still working on mcmcsamp so don't expect to get reasonable results from that function yet. (But soon, Ben, soon.) This version of glmer allows the quasibinomial and quasipoisson families. I plan to add the Gamma family soon. Are there any other important families that I have missed? I have added web pages documenting the C source code at http://lme4.R-forge.R-project.org/doxygen. In general you can use http://lme4.R-forge.R-project.org/ as the 'home page' for the project. There is a link there to the project summary page. You can browse the source code for the package under the SCM (source code management) tab on the project summary page. The SCM tab provides information on how you can access the svn repository. Alternatively, you can wait for the package builds to occur overnight (in Vienna) and install the new version with install.packages("lme4", repos = "http://r-forge.r-project.org") I would appreciate reports of problems with this version. Once I get mcmcsamp running I will call this the alpha release of lme4_1.0.0 It is much better to catch the bugs during the alpha and beta test phases than to need to create bug-fix releases so please test it. I think you should be able to submit bug reports directly if you have an R-forge login. There is a link to the Bugs tracker and the Feature Request tracker on the project summary page.
Development version of lme4 now passes its tests
10 messages · Austin Frank, Bernd Weiss, Martin Maechler +4 more
Dr. Bates-- Hello! Happy New Year!
This version of glmer allows the quasibinomial and quasipoisson families. I plan to add the Gamma family soon. Are there any other important families that I have missed?
I've asked on this list before[1], but since you've raised the issue again, would it be possible to model a dependent variable drawn from a multinomial distribution? I've seen the relevant link function called the "generalized logit". That function and its log likelihood are described at [2] and [3]. While the multinomial case is the one I'm most eager to see implemented the, but there are related functions that could be considered. Also useful would be the generalized probit linking function ([4]) for polychotomous choices, and the cumulative logit and probit linking functions ([5]) for ordinal multinomial responses. Thanks for considering these requests! /au Footnotes: [1] http://thread.gmane.org/gmane.comp.lang.r.lme4.devel/230 [2] http://www.statsoft.com/textbook/stglz.html#approach [3] http://support.sas.com/rnd/app/da/new/802ce/stat/chap8/sect5.htm [4] http://en.wikipedia.org/wiki/Multivariate_probit [5] http://www.asu.edu/sas/sasdoc/sashtml/stat/chap29/sect37.htm
Austin Frank http://aufrank.net GPG Public Key (D7398C2F): http://aufrank.net/personal.asc
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Douglas Bates schrieb: [...] | I have added web pages documenting the C source code at | http://lme4.R-forge.R-project.org/doxygen. In general you can use | http://lme4.R-forge.R-project.org/ as the 'home page' for the project. | There is a link there to the project summary page. You can browse | the source code for the package under the SCM (source code management) | tab on the project summary page. The SCM tab provides information on | how you can access the svn repository. Alternatively, you can wait | for the package builds to occur overnight (in Vienna) and install the | new version with | | install.packages("lme4", repos = "http://r-forge.r-project.org") I am sorry if I am missing anything but I was unable to download the windows version of the development version of lme4. Neither <install.packages("lme4", repos ...> nor the SCM approach ("win32-latest.zip") works properly. Some of my datasets are very strange... with respect to multilevel modelling, of course (N ~ 80.000, K = 15, binary dependent variable). So, it would be interesting to (1) replicate former results. In addition, (2) I would like to compare lmer results with MLWwiN and Stata (xtlogit, gllamm, xtmelogit). Regards, Bernd -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.7 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHgjSiUsbvfbd00+ERAsrwAJ4kxHLdn7i39V8Edo40zfIAoweyYQCcDb/m v95Gz8Rw4RKLM3q4pnDtwmc= =MX4w -----END PGP SIGNATURE-----
BTW: Congratulations, Doug, on your lme4 "completion" !!
"BW" == Bernd Weiss <bernd.weiss at uni-koeln.de>
on Mon, 07 Jan 2008 15:18:10 +0100 writes:
BW> -----BEGIN PGP SIGNED MESSAGE-----
BW> Hash: SHA1
BW> [...]
BW> | I have added web pages documenting the C source code at
BW> | http://lme4.R-forge.R-project.org/doxygen. In general you can use
BW> | http://lme4.R-forge.R-project.org/ as the 'home page' for the project.
BW> | There is a link there to the project summary page. You can browse
BW> | the source code for the package under the SCM (source code management)
BW> | tab on the project summary page. The SCM tab provides information on
BW> | how you can access the svn repository. Alternatively, you can wait
BW> | for the package builds to occur overnight (in Vienna) and install the
BW> | new version with
BW> |
BW> | install.packages("lme4", repos = "http://r-forge.r-project.org")
BW> I am sorry if I am missing anything but I was unable to download the
BW> windows version of the development version of lme4. Neither
BW> <install.packages("lme4", repos ...> nor the SCM approach
BW> ("win32-latest.zip") works properly.
Hmm, yes indeed; the link (on the SCM web page) goes to the
"build log" instead of to the zip file,
and the bin/windows/contrib/2.6/ or current/ directory is
completely empty.
===> a bug in the R-forge setup (or maintenance or ...),
and I think we've seen the problem before.
--> CC'ing one of the R-forge maintainers..
Martin Maechler, ETH ZUrich
You're correct, Bernd, that the versions available by install.packages from the repository at R-forge.R-packages.org appear to be out of date. Even the tar.gz file scm-latest.tar.gz is out of date (apparently from January 04). Those who can build a package from the source files can obtain the latest version from the SVN archive at R-forge (instructions are given at the SCM tab on the main project page). I have just submitted the package to Uwe's win-builder.R-project.org site to create a binary Windows package, which I will make available on my web site as http://www.stat.wisc.edu/~bates/lme4-2008-01-06-wiin32.zip Stefan: Will someone be able to check on what is happening to the nightly builds?
On Jan 7, 2008 8:18 AM, Bernd Weiss <bernd.weiss at uni-koeln.de> wrote:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Douglas Bates schrieb: [...] | I have added web pages documenting the C source code at | http://lme4.R-forge.R-project.org/doxygen. In general you can use | http://lme4.R-forge.R-project.org/ as the 'home page' for the project. | There is a link there to the project summary page. You can browse | the source code for the package under the SCM (source code management) | tab on the project summary page. The SCM tab provides information on | how you can access the svn repository. Alternatively, you can wait | for the package builds to occur overnight (in Vienna) and install the | new version with | | install.packages("lme4", repos = "http://r-forge.r-project.org") I am sorry if I am missing anything but I was unable to download the windows version of the development version of lme4. Neither <install.packages("lme4", repos ...> nor the SCM approach ("win32-latest.zip") works properly. Some of my datasets are very strange... with respect to multilevel modelling, of course (N ~ 80.000, K = 15, binary dependent variable). So, it would be interesting to (1) replicate former results. In addition, (2) I would like to compare lmer results with MLWwiN and Stata (xtlogit, gllamm, xtmelogit). Regards, Bernd -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.7 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHgjSiUsbvfbd00+ERAsrwAJ4kxHLdn7i39V8Edo40zfIAoweyYQCcDb/m v95Gz8Rw4RKLM3q4pnDtwmc= =MX4w -----END PGP SIGNATURE-----
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
Douglas Bates wrote:
You're correct, Bernd, that the versions available by install.packages from the repository at R-forge.R-packages.org appear to be out of date. Even the tar.gz file scm-latest.tar.gz is out of date (apparently from January 04). Those who can build a package from the source files can obtain the latest version from the SVN archive at R-forge (instructions are given at the SCM tab on the main project page). I have just submitted the package to Uwe's win-builder.R-project.org site to create a binary Windows package, which I will make available on my web site as http://www.stat.wisc.edu/~bates/lme4-2008-01-06-wiin32.zip Stefan: Will someone be able to check on what is happening to the nightly builds?
this is fixed. the permissions were wrong in the svn export directory. This was because of some experimenting a few days ago. the latest binaries are now available as usual. I'm sorry for the inconvenience caused. Best, Stefan
On Jan 7, 2008 8:18 AM, Bernd Weiss <bernd.weiss at uni-koeln.de> wrote:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Douglas Bates schrieb: [...] | I have added web pages documenting the C source code at | http://lme4.R-forge.R-project.org/doxygen. In general you can use | http://lme4.R-forge.R-project.org/ as the 'home page' for the project. | There is a link there to the project summary page. You can browse | the source code for the package under the SCM (source code management) | tab on the project summary page. The SCM tab provides information on | how you can access the svn repository. Alternatively, you can wait | for the package builds to occur overnight (in Vienna) and install the | new version with | | install.packages("lme4", repos = "http://r-forge.r-project.org") I am sorry if I am missing anything but I was unable to download the windows version of the development version of lme4. Neither <install.packages("lme4", repos ...> nor the SCM approach ("win32-latest.zip") works properly. Some of my datasets are very strange... with respect to multilevel modelling, of course (N ~ 80.000, K = 15, binary dependent variable). So, it would be interesting to (1) replicate former results. In addition, (2) I would like to compare lmer results with MLWwiN and Stata (xtlogit, gllamm, xtmelogit). Regards, Bernd -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.7 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHgjSiUsbvfbd00+ERAsrwAJ4kxHLdn7i39V8Edo40zfIAoweyYQCcDb/m v95Gz8Rw4RKLM3q4pnDtwmc= =MX4w -----END PGP SIGNATURE-----
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
On Jan 7, 2008 8:54 AM, Douglas Bates <bates at stat.wisc.edu> wrote:
You're correct, Bernd, that the versions available by install.packages from the repository at R-forge.R-packages.org appear to be out of date. Even the tar.gz file scm-latest.tar.gz is out of date (apparently from January 04). Those who can build a package from the source files can obtain the latest version from the SVN archive at R-forge (instructions are given at the SCM tab on the main project page). I have just submitted the package to Uwe's win-builder.R-project.org site to create a binary Windows package, which I will make available on my web site as http://www.stat.wisc.edu/~bates/lme4-2008-01-06-wiin32.zip
The Windows package is now available as http://www.stat.wisc.edu/~bates/lme4-2008-01-06-win32.zip (The URL I previously gave has win32 spelled wiin32 and won't work.)
Hello all, I'm not sure that things are fixed. See below.
On Jan 7, 2008, at 10:44 AM, Stefan Theussl wrote:
Douglas Bates wrote:
You're correct, Bernd, that the versions available by install.packages from the repository at R-forge.R-packages.org appear to be out of date. Even the tar.gz file scm-latest.tar.gz is out of date (apparently from January 04). Those who can build a package from the source files can obtain the latest version from the SVN archive at R-forge (instructions are given at the SCM tab on the main project page). I have just submitted the package to Uwe's win-builder.R-project.org site to create a binary Windows package, which I will make available on my web site as http://www.stat.wisc.edu/~bates/lme4-2008-01-06-wiin32.zip Stefan: Will someone be able to check on what is happening to the nightly builds?
this is fixed. the permissions were wrong in the svn export directory. This was because of some experimenting a few days ago. the latest binaries are now available as usual. I'm sorry for the inconvenience caused. Best, Stefan
> install.packages("lme4", repos = "http://r-forge.r-project.org")
Warning: unable to access index for repository http://r-forge.r-project.org/bin/macosx/universal/contrib/2.6
Warning message:
package 'lme4' is not available
> sessionInfo()
R version 2.6.1 (2007-11-26)
i386-apple-darwin8.10.1
locale:
C
attached base packages:
[1] grid splines grDevices graphics stats utils
methods base
other attached packages:
[1] Hmisc_3.4-3 coda_0.13-1 gmodels_2.14.1
lme4_0.99875-9
[5] Matrix_0.999375-3 lattice_0.17-4 anacor_0.9-0
car_1.2-7
[9] colorspace_0.95 fda_1.2.3 zoo_1.4-1
scatterplot3d_0.3-25
[13] rgl_0.76 JGR_1.5-8 iplots_1.1-1
JavaGD_0.4-3
[17] rJava_0.5-1
loaded via a namespace (and not attached):
[1] MASS_7.2-39 cluster_1.11.9 gdata_2.3.1 gtools_2.4.0
tools_2.6.1
_____________________________
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400 Charlottesville, VA 22904-4400
Parcels: Room 102 Gilmer Hall
McCormick Road Charlottesville, VA 22903
Office: B011 +1-434-982-4729
Lab: B019 +1-434-982-4751
Fax: +1-434-982-4766
WWW: http://www.people.virginia.edu/~mk9y/
Michael Kubovy wrote:
Hello all, I'm not sure that things are fixed. See below.
Currently we don't build mac binaries. The directory http://r-forge.r-project.org/bin/macosx/universal/contrib/2.6 does not exist yet. You may install the package from its sources in the meantime. Best regards, Stefan
On Jan 7, 2008, at 10:44 AM, Stefan Theussl wrote:
Douglas Bates wrote:
You're correct, Bernd, that the versions available by install.packages from the repository at R-forge.R-packages.org appear to be out of date. Even the tar.gz file scm-latest.tar.gz is out of date (apparently from January 04). Those who can build a package from the source files can obtain the latest version from the SVN archive at R-forge (instructions are given at the SCM tab on the main project page). I have just submitted the package to Uwe's win-builder.R-project.org site to create a binary Windows package, which I will make available on my web site as http://www.stat.wisc.edu/~bates/lme4-2008-01-06-wiin32.zip Stefan: Will someone be able to check on what is happening to the nightly builds?
this is fixed. the permissions were wrong in the svn export directory. This was because of some experimenting a few days ago. the latest binaries are now available as usual. I'm sorry for the inconvenience caused. Best, Stefan
install.packages("lme4", repos = "http://r-forge.r-project.org")
Warning: unable to access index for repository http://r-forge.r-project.org/bin/macosx/universal/contrib/2.6 Warning message: package 'lme4' is not available
sessionInfo()
R version 2.6.1 (2007-11-26) i386-apple-darwin8.10.1 locale: C attached base packages: [1] grid splines grDevices graphics stats utils methods base other attached packages: [1] Hmisc_3.4-3 coda_0.13-1 gmodels_2.14.1 lme4_0.99875-9 [5] Matrix_0.999375-3 lattice_0.17-4 anacor_0.9-0 car_1.2-7 [9] colorspace_0.95 fda_1.2.3 zoo_1.4-1 scatterplot3d_0.3-25 [13] rgl_0.76 JGR_1.5-8 iplots_1.1-1 JavaGD_0.4-3 [17] rJava_0.5-1 loaded via a namespace (and not attached): [1] MASS_7.2-39 cluster_1.11.9 gdata_2.3.1 gtools_2.4.0 tools_2.6.1
_____________________________
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400 Charlottesville, VA 22904-4400
Parcels: Room 102 Gilmer Hall
McCormick Road Charlottesville, VA 22903
Office: B011 +1-434-982-4729
Lab: B019 +1-434-982-4751
Fax: +1-434-982-4766
WWW: http://www.people.virginia.edu/~mk9y/
8 days later
Douglas Bates wrote:
This version of glmer allows the quasibinomial and quasipoisson families. I plan to add the Gamma family soon. Are there any other important families that I have missed?
This is very exciting! I would respectfully add the inverse gaussian as an important family (at least to us!). I take it from the error messages I get when using the R-forge version that this family is not supported yet? Thank you once again for all this remarkable work. Best Roger
Roger Levy Email: rlevy at ucsd.edu Assistant Professor Phone: 858-534-7219 Department of Linguistics Fax: 858-534-4789 UC San Diego Web: http://ling.ucsd.edu/~rlevy