[R-sig-ME] Advice for the R-package of lme4
Ben Bolker
bbo|ker @end|ng |rom gm@||@com
Thu Aug 26 23:58:33 CEST 2021
[Please keep r-sig-mixed-models using r-project.org in the Cc: list!]
The warning message is *probably* irrelevant; to make it go away you
would need to install the Matrix package from source on your machine
(the binary packages on CRAN are built with the latest R version of a
particular release series).
A preliminary investigation on my side had the same general
conclusions (fitting with 1.1-23 and 1.1-26 gave identical answers). I'm
afraid that if you have tried with both versions of the package and
can't replicate your former results exactly then, logically, *the
lme4/lmerTest package versions cannot be the source of the problem*;
some other aspect of your setup must have changed. Numerical
computations are, unfortunately, subject to a great deal of
(small-scale) instability due to changes in underlying linear algebra
packages, compilers, etc..
I'm not sure what else we can do to help.
sincerely
Ben Bolker
On 8/25/21 11:17 PM, 市川 淳 wrote:
> Thank you for your kind advice.
>
> I installed the package of remotes and compilers.
> I tried to analyze using the combination of lme4 1.1-20, 1.1-21,
> 1.1-23, or 1.1-25 and lmerTest 3.0-1 or lmerTest 3.1-3;
> however, I can't get the same results as before.
>
> Incidentally, the following message is always displayed.
>
> ====
> Warning message:
> Package 'Matrix' was built under R in version 3.6.3.
> //Actually, the message is in Japanese.
> =====
>
> Very sorry to bother you while you are busy, but I appreciate your
> cooperation.
>
> Best regards
> Jun Ichikawa
>
>
> 2021年8月26日(木) 11:02 Ben Bolker <bbolker using gmail.com
> <mailto:bbolker using gmail.com>>:
>
> If you want to check for yourself, you can retrieve older
> versions of
> the tarballs (.tar.gz files) from
> https://cran.r-project.org/src/contrib/Archive/lme4/
> <https://cran.r-project.org/src/contrib/Archive/lme4/>
>
> Alternatively, if you install the 'remotes' package, you can use
>
> remotes::install_version("lme4", "1.1-23")
>
> - this basically automates the process of downloading the tarball and
> installing it.
>
> You *will* need development tools (compilers etc.) installed to do
> this (an alternative is to use the 'checkpoint' package to retrieve old
> package versions from MRAN (a versioned mirror of CRAN maintained by
> Microsoft).
>
>
>
> On 8/25/21 9:10 PM, 市川 淳 wrote:
> > Sorry for the sudden email.
> > I would like you to give me your advice.
> > This is my first post.
> >
> > I have often used the package of lme4 and lmerTest to conduct a
> linear
> > mixed model analysis.
> > Meanwhile, I have been in trouble of whichthe values in the
> output are
> > slightly different between late April 2021 and August 2021.
> > The source code, R environment, and csv files are the same
> (R-3.6.1 in
> > Windows 10).
> >
> > I surveyed and found out the following.
> > Around June 2020, (maybe) I installed lme4 1.1-23 and lmerTest 3.0-1.
> > I used these packages for a while; however I (maybe) updated lme4
> 1.1-26
> > and lmerTest 3.1-3 a few days ago (in August 2021).
> >
> > I have checked the values of estimate, SE, p-value and so on in the
> > output, and have noticed that these were different between the
> packages
> > mentioned above.
> >
> > Please advise me on the problem.
> > I uploaded samples of the source code and csv file.
> >
> https://drive.google.com/drive/folders/1gbP-Ib-nW7-zrmUyrpuLmbODCuw3Zuot?usp=sharing
> <https://drive.google.com/drive/folders/1gbP-Ib-nW7-zrmUyrpuLmbODCuw3Zuot?usp=sharing>
>
> >
> <https://drive.google.com/drive/folders/1gbP-Ib-nW7-zrmUyrpuLmbODCuw3Zuot?usp=sharing
> <https://drive.google.com/drive/folders/1gbP-Ib-nW7-zrmUyrpuLmbODCuw3Zuot?usp=sharing>>
> >
> > I look forward to hearing from you.
> > Very sorry to bother you while you are busy, but I appreciate your
> > cooperation.
> >
> > Best regards
> > Anonymity X
>
> --
> Dr. Benjamin Bolker
> Professor, Mathematics & Statistics and Biology, McMaster University
> Director, School of Computational Science and Engineering
> Graduate chair, Mathematics & Statistics
>
--
Dr. Benjamin Bolker
Professor, Mathematics & Statistics and Biology, McMaster University
Director, School of Computational Science and Engineering
Graduate chair, Mathematics & Statistics
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