search

cran-task-views / MixedModels

CRAN Task View: Mixed, Multilevel, and Hierarchical Models in R
https://CRAN.R-project.org/view=MixedModels
27 stars 9 forks source link

What are the core packages #6

Closed jpiaskowski closed 2 years ago

jpiaskowski commented 2 years ago

Starting a list here so we can keep track of this. Core packages have to be on CRAN (which sadly, leaves out broom.mixed)

lme4 nlme brms MCMCglmm multilevelmod geepack lavaan

FYI: I found out the hard way that every time a core package is mentioned in the task view, it has to say include the tag priority = "core" to be processed correctly by ctv::ctv2html(). I tried to fixed the instances of this in the TV, but I may have missed some.

bbolker commented 2 years ago

Note that broom.mixed is on CRAN ... https://cran.r-project.org/web/packages/broom.mixed/index.html

I agree with everything on the list above. I might include performance and DHARMa (for model checking, although arguably not since they're not MM-specific); lmerTest (for LMM p-values); glmmTMB (broader range of response distributions, faster in many cases) blme, rstanarm (Bayes), ordinal, robustlmm (the most important of the 'special types', for my work ...)

Maybe the best thing would be to decide approximately how many core packages we want in total? (20?)

jpiaskowski commented 2 years ago

Good news about broom.mixed! I missed that. All those ideas sound great. There's a function in the ctv package to install all "core" packages, so keeping it to 15-20 sounds reasonable.

New list:

lme4 nlme brms MCMCglmm multilevelmod geepack lavaan broom.mixed DHARMa lmerTest glmmTMB blme rstanarm ordinal robustlmm

bbolker commented 2 years ago

The only one of these I'm not familiar with is multilevelmod (I've installed it and see what it is, I think I see why it would be included -- parallel to broom.mixed). I think I can see the argument/case for all the rest. (nlme might not count against the total as it's present in the default installation.)

jpiaskowski commented 2 years ago

yeah, currently {multilevelmod} is limited in scope, but I have high hopes that it will eventually support more functionality since it's backed by the tidymodels team.

jpiaskowski commented 2 years ago

I'm personally not in favor of adding emmeans as a core package because it doesn't do mixed modelling - it doesn't even provide BLUPs (while {marginaleffects} does). However, I don't feel that strongly about this.

palday commented 2 years ago

I also wouldn't add emmeans as core -- its functionality is very general and not at all focused on mixed models / specialized to take advantage of what mixed models can do.