added lmm and glmm as convenience wrappers for fit

[ajinkya-k]

closes #809

Did behavior change? Did you add need features? If so, please update NEWS.md

• after opening this PR, add a reference and run docs/NEWS-update.jl to update the cross-references.
• add entry in NEWS.md

Should we release your changes right away? If so, bump the version:

• figure out new minor version no
• actually bump minor version

[ajinkya-k]

EDIT: i figured it out

issue

~can someone help me with this warning: ~ ```julia-repl ┌ MixedModels │ WARNING: Method definition lmm(StatsModels.FormulaTerm{L, R} where R where L, Any) in module MixedModels at /home/runner/work/MixedModels.jl/MixedModels.jl/src/linearmixedmodel.jl:230 overwritten at /home/runner/work/MixedModels.jl/MixedModels.jl/src/linearmixedmodel.jl:231. │ ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. └ ```

but the same doesn't seem to happen with StatsAPI.fit(LinearMixedModel, ) see lines 194-218 of src/linearmixedmodel.jl`

[palday]

MixedModels.jl had something like this in the past, but we dropped that interface. Maybe @dmbates can comment more on the why.

To actually add it, you can simply do:

lmm(args...; kwargs...) = fit(LinearMixedModel, args...; kwargs...)
glmm(args...; kwargs...) = fit(GeneralizedLinearMixedModel, args...; kwargs...)

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 97.33%. Comparing base (bcd3e9f) to head (e7b814a).
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[dmbates]

I think there should be a test involving more optional arguments, such as REML=true to lmm just to ensure that everything is getting passed on properly.

Were you going to modify the documentation to include this function?

[ajinkya-k]

Okay i will add the tests. I wanted some comments on what to write in the docstring

[ajinkya-k]

@dmbates Added a test for REML = true. It only makes sure the returned model isa LinearMixedModel . would it be worth it to test maybe the fixed effects or deviance too?

[ajinkya-k]

The lines with the yellow side bar are not being rendered in the api docs at all. Am I doing something wrong with the formatting?

[palday]

The lines with the yellow side bar are not being rendered in the api docs at all. Am I doing something wrong with the formatting?

you need to explicitly add them in docs/src/api.md.

[palday]

[ ] figure out new version no

You're adding a feature in a post 1.0 release without breaking anything, so it's a minor (major.minor.patch) version bump according to SemVer.

[ajinkya-k]

@palday I did add lmm in docs/src/api.md like this:

[ajinkya-k]

[ ] figure out new version no

You're adding a feature in a post 1.0 release without breaking anything, so it's a minor (major.minor.patch) version bump according to SemVer.

right, I meant figure out the new minor version no.

[palday]

@palday I did add lmm in docs/src/api.md like this:

you haven't committed and pushed that change yet 😉

[ajinkya-k]

@palday I meant on local, lol. I was rendering the docs locally and running LiveServer. I just did a clean build of the documentation and it worked

[ajinkya-k]

Okay! I think this is good to go!

[ajinkya-k]

The reference

[`fit`](@ref)

gives an error because there is no doc-string for fit. That error went away if I use fit! instead but fit! does not document some keywords such as wts. Should i add a docstring to fit?

[palday]

The reference

[`fit`](@ref)

gives an error because there is no doc-string for fit. That error went away if I use fit! instead but fit! does not document some keywords such as wts. Should i add a docstring to fit?

I'll push a change shortly that adds a secondary link to the type constructor and that should cover everything.

[ajinkya-k]

I don't think we need to display the output in the Quick Start section but I couldn't hide it so I left it as is. Is it possible to hide output without using a ; in an example block?

[palday]

If you don't want to display output, do you even want the code executed? If you're not executing the code, then a normal triple-backtick codeblock would work.

That said, I don't think there's harm in showing the output.

[ajinkya-k]

Let's keep the output