[R-sig-ME] Package glmmADMB

[Paul Johnson]

Have you tried the glmmTMB package? I understand that Ben Bolker et al. are developing it as a replacement for glmmADMB. I’ve found it to be flexible*, robust, and very fast, much faster than glmmADMB (which I found unusable on large data sets), but sometimes even faster than glmer**. I’ve never had reason to use glmmADMB since finding glmmTMB. However watch out for differences between glmmTMB and glmer etc — read the Details of the glmmTMB help. There are occasional issues as expected in a new-ish package, but the developers are very active and these tend to be dealt with quickly. On the whole this is already an extremely really useful package, mainly because it can quickly fit complex (= beyond glmer) GLMMs to large data sets where glmmADMB would fail or at best take hours (a huge thank you to the developers).

*https://cran.r-project.org/web/packages/glmmTMB/vignettes/glmmTMB.pdf
"--Poisson, binomial, negative binomial (NB1 and NB2 parameterizations), Gamma, Beta, Gaussian; truncated Poisson and negative binomial
--zero-inflation with fixed and random-effects components; hurdle models via truncated Poisson/NB
--diagonal, compound-symmetric, or unstructured random effects variance-covariance matrices; first-order autoregressive (AR1) variance structures"

**E.g. binomial GLMM fitted to ~70K binary obs (of which ~700 are 1s) with 25 fixed effects and 2 crossed random effects (on an old Mac with 2.7 GHz Intel Core i7):
glmmTMB: 2.9 min
glmer: 29.4 min, but still didn’t *quite* converge (even with 'optimizer = "bobyqa"', which often helps). Log-likelihood 0.1 units below glmmTMB, so very close, and the estimates were very similar. Also I find that convergence warnings in glmer and glmer.nb are more sensitive than in glmmTMB.


> On 17 Dec 2017, at 22:53, Rodrigo Malavazi Corder <rodrigo.corder at usp.br> wrote:
> 
> Dear,
> 
> I am not able to install glmmADMB package. I have already tried different
> options, but none of them have worked. Please, find below the error message
> from R after trying to install it. May you please help me?
> 
> Thank you in advance.
> 
> Greetings,
> Rodrigo Corder
> 
> 
>> install.packages("R2admb")
> Warning in install.packages :
>  URL 'https://vps.fmvz.usp.br/CRAN/src/contrib/PACKAGES.gz': status was
> 'Couldn't connect to server'
> Warning in install.packages :
>  URL 'https://vps.fmvz.usp.br/CRAN/src/contrib/PACKAGES': status was
> 'Couldn't connect to server'
> Warning in install.packages :
>  unable to access index for repository
> https://vps.fmvz.usp.br/CRAN/src/contrib:
>  cannot download all files
> Warning in install.packages :
>  URL 'https://vps.fmvz.usp.br/CRAN/src/contrib/PACKAGES.gz': status was
> 'Couldn't connect to server'
> Warning in install.packages :
>  URL 'https://vps.fmvz.usp.br/CRAN/src/contrib/PACKAGES': status was
> 'Couldn't connect to server'
> Warning in install.packages :
>  unable to access index for repository
> https://vps.fmvz.usp.br/CRAN/src/contrib:
>  cannot download all files
> Warning in install.packages :
>  package ‘R2admb’ is not available (for R version 3.3.2)
> Warning in install.packages :
>  URL '
> https://vps.fmvz.usp.br/CRAN/bin/macosx/mavericks/contrib/3.3/PACKAGES.gz':
> status was 'Couldn't connect to server'
> Warning in install.packages :
>  URL '
> https://vps.fmvz.usp.br/CRAN/bin/macosx/mavericks/contrib/3.3/PACKAGES':
> status was 'Couldn't connect to server'
> Warning in install.packages :
>  unable to access index for repository
> https://vps.fmvz.usp.br/CRAN/bin/macosx/mavericks/contrib/3.3:
>  cannot download all files
>> install.packages("glmmADMB",
> +                  repos=c("http://glmmadmb.r-forge.r-project.org/repos",
> +                          getOption("repos")),
> +                  type="source")
> Warning in install.packages :
>  URL 'https://vps.fmvz.usp.br/CRAN/src/contrib/PACKAGES.gz': status was
> 'Couldn't connect to server'
> Warning in install.packages :
>  URL 'https://vps.fmvz.usp.br/CRAN/src/contrib/PACKAGES': status was
> 'Couldn't connect to server'
> Warning in install.packages :
>  unable to access index for repository
> https://vps.fmvz.usp.br/CRAN/src/contrib:
>  cannot download all files
> Warning in install.packages :
>  URL 'https://vps.fmvz.usp.br/CRAN/src/contrib/PACKAGES.gz': status was
> 'Couldn't connect to server'
> Warning in install.packages :
>  URL 'https://vps.fmvz.usp.br/CRAN/src/contrib/PACKAGES': status was
> 'Couldn't connect to server'
> Warning in install.packages :
>  unable to access index for repository
> https://vps.fmvz.usp.br/CRAN/src/contrib:
>  cannot download all files
> Warning in install.packages :
>  dependency ‘R2admb’ is not available
> trying URL '
> http://glmmadmb.r-forge.r-project.org/repos/src/contrib/glmmADMB_0.8.3.3.tar.gz
> '
> Content type 'application/x-gzip' length 9391177 bytes (9.0 MB)
> ==================================================
> downloaded 9.0 MB
> 
> ERROR: dependency ‘R2admb’ is not available for package ‘glmmADMB’
> * removing
> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/glmmADMB’
> Warning in install.packages :
>  installation of package ‘glmmADMB’ had non-zero exit status
> 
> The downloaded source packages are in
> 
> ‘/private/var/folders/7z/jc6r58_d49l5bgq1xf3k7smw0000gn/T/RtmpkTptDB/downloaded_packages’
>> library(glmmADMB)
> Error in library(glmmADMB) : there is no package called ‘glmmADMB’
> 
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> 
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