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backport of QR to 1.x #537

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palday
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@palday palday commented Jun 7, 2023

from #507

mousum-github and others added 7 commits June 7, 2023 12:01
backport of #507

---------

Co-authored-by: Mousum <mousum@spotle.ai>
Co-authored-by: ayushpatnaikgit <ayushpatnaik@gmail.com>
Co-authored-by: Milan Bouchet-Valat <nalimilan@club.fr>
Co-authored-by: Ayush Patnaik <u6012645@anu.edu.au>
Co-authored-by: harsharora21 <harsharora1337@gmail.com>
Co-authored-by: Bogumił Kamiński <bkamins@sgh.waw.pl>
(cherry picked from commit a8016bd)
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codecov bot commented Jun 7, 2023

Codecov Report

Patch coverage: 86.79% and project coverage change: +0.72 🎉

Comparison is base (6406a70) 87.39% compared to head (cd187fb) 88.11%.

Additional details and impacted files
@@            Coverage Diff             @@
##               v1     #537      +/-   ##
==========================================
+ Coverage   87.39%   88.11%   +0.72%     
==========================================
  Files           7        7              
  Lines         952     1077     +125     
==========================================
+ Hits          832      949     +117     
- Misses        120      128       +8     
Impacted Files Coverage Δ
src/GLM.jl 60.00% <50.00%> (+10.00%) ⬆️
src/negbinfit.jl 81.81% <66.66%> (-0.85%) ⬇️
src/linpred.jl 88.55% <83.63%> (+2.94%) ⬆️
src/lm.jl 94.07% <97.14%> (+0.74%) ⬆️
src/glmfit.jl 81.33% <100.00%> (+0.31%) ⬆️

... and 1 file with indirect coverage changes

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Co-authored-by: Mousum Dutta <44145580+mousum-github@users.noreply.github.com>
@nalimilan
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Is there any particular place we should look at (i.e. where you had to adapt the original PR)?

@palday
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palday commented Jun 7, 2023

@nalimilan if you look at the diff excluding the first commit, then you can see things that were non obvious in the cherry-pick -- one exception (not including a local fit(::Type, ::FormulaTerm,...)) method, I accepted all changes from the original PR. The follow-up modifications were related to the additional redirection from TableRegressionModel.

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Thanks. Just a few comments then. There are also lines that are not covered by tests, are these real?

@@ -79,11 +79,14 @@ Using a `CategoricalVector` constructed with `categorical` or `categorical!`:
```jldoctest categorical
julia> using CategoricalArrays, DataFrames, GLM, StableRNGs


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Is this intentional?

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This is what doctest updated things to.

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Weird... :-/

@@ -139,7 +142,8 @@ function negbin(F,
regmodel = glm(F, D, NegativeBinomial(θ), args...;
dropcollinear=dropcollinear, method=method, maxiter=maxiter,
atol=atol, rtol=rtol, verbose=verbose, kwargs...)
μ = regmodel.rr.mu

μ = _rr(regmodel).mu
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Above the code seems to assume that regmodel is a TableRegressionModel, so you could just do regmodel.model.rr.mu and remove _rr.

GLM.Link(m::GeneralizedLinearModel) = Link(m.rr)
Link(r::GlmResp) = r.link
Link(m::GeneralizedLinearModel) = Link(m.rr)
Link(m::StatsModels.TableRegressionModel{<:GeneralizedLinearModel}) = Link(m.model)
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I'm a bit surprised that you need to add this, as usually method delegations were only done in StatsModels, for functions from StatsAPI. For example, below Distribution isn't defined for TableRegressionModel. Where is this method called from?

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Link is owned by GLM.

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They're called in the tests.

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Yeah but I wonder why we never needed this kind of definition before. I think the code was designed so that we never called functions on objects which could either be AbstractGLMs or TableRegressionModels.

Maybe this doesn't matter much as 1.x is a dead-end anyway.

@test coef(gm1) == coef(gm2) ≈ [10, 1]
end

@testset "formula accessor" begin
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This accessor isn't introduced by the PR, right? Why are tests added then?

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They were part of the cherry-picked commit.

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I don't see it at https://github.com/JuliaStats/GLM.jl/pull/507/files. I think this comes from the commit which removed TableRegressionModel, which isn't relevant here.

end


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Intended?

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