Adding model.matrix() and terms() methods

[ddsjoberg]

Description

• Two new methods added for mmrm models: model.matrix() and terms().
• The model.frame() method has been updated to return a data frame the size of the number of observations utilized in the model for all combinations of the model.frame(include) argument.

Outstanding

• The default call to model.frame() does not return the outcome variable. This will be unexpected by most users, I would think. Should we update the default?
• I am using the same structure in model.frame() and model.matrix() to construct the formula passed to terms.formula(). The lme4 package returns the fixed effects and response variable only. Should this be our default as well?

[danielinteractive]

Thanks a lot @ddsjoberg for the PR! Please see first comments below. Please also add yourself to package authors in the DESCRIPTION file

[danielinteractive]

Thanks @ddsjoberg also for the questions:

• The default call to model.frame() does not return the outcome variable. This will be unexpected by most users, I would think. Should we update the default?

Yeah we can update, thanks!

• I am using the same structure in model.frame() and model.matrix() to construct the formula passed to terms.formula(). The lme4 package returns the fixed effects and response variable only. Should this be our default as well?

I just also looked at glmmTMB (we are even closer to that package re: model specification) and in this example:

library(glmmTMB)

m1 <- glmmTMB(count ~ mined + (1|site),
              zi=~mined,
              family=poisson, data=Salamanders)

terms(m1)

they also don't return site but just count and mined so I guess we can follow that pattern, yeah

Thanks!

[ddsjoberg]

A few updates:

• Following the instructions in Tests fail on Mac M1+ #322, the unit testing issue I was experiencing resolved.
• Our update to model.frame() solved the issue in weights() I originally brought up (the output from weights was the length of the non-missing rows in the fixed covariates data, rather than the length of the obs utilized in the model.)
• As discussed, I updated model.frame() to include the response column by default to be consistent with other pkgs. That said, for the same reason of maintaining consistency, model.frame()'s default should probably be to return all the columns: see example below and the same is true for lme4 models. Let's discuss when we meet later today?

m1 <- glmmTMB::glmmTMB(count ~ mined + (1|site),
              zi=~mined,
              family=poisson, data=glmmTMB::Salamanders)

model.frame(m1) |> head()
#>   count mined site
#> 1     0   yes VF-1
#> 2     0   yes VF-2
#> 3     0   yes VF-3
#> 4     2    no  R-1
#> 5     2    no  R-2
#> 6     1    no  R-3

^{Created on 2023-08-15 with reprex v2.0.2}

[danielinteractive]

Cool! Nice, yeah we can return all columns

[danielinteractive]

Nice work, thx a lot @ddsjoberg - mainly code convention comments below, please go through all new code for those (e.g. comments in sentence style also in tests etc.) thx!

[ddsjoberg]

Nice work, thx a lot @ddsjoberg - mainly code convention comments below, please go through all new code for those (e.g. comments in sentence style also in tests etc.) thx!

Thanks for the additional comments (apologies about the points already covered in your contributing guide 😳). I think everything has been addressed!