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Allow specifying sigma in LinearMixedModel #551

Merged
merged 11 commits into from
Aug 17, 2021
Merged

Allow specifying sigma in LinearMixedModel #551

merged 11 commits into from
Aug 17, 2021

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palday
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@palday palday commented Aug 17, 2021

This was done to support meta-analytic type models. There might be other cases where we can use a fixed residual variation to do tricks with observation-level random effects, but I'm not sure.

I've also done some formatting tweaks that take advantage of kwarg syntax in Julia 1.5+ (since we now require Julia 1.6).

I'll tackle #549 after this is merged (or rejected) as some of the changes would create a merge conflict.

If we one day allow specifying constraints on the betas, I would suggest doing this as a new type ConstrainedLinearMixedModel and then define a separate objective method for that so that we don't keep adding conditionals to objective. (And reallistically, we should should also define separate setβ!, setθ! and setβθ! methods.)

@palday palday changed the title Allow specifying sigma in LinearMixedModels Allow specifying sigma in LinearMixedModel Aug 17, 2021
@palday palday requested a review from dmbates August 17, 2021 02:56
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codecov bot commented Aug 17, 2021

Codecov Report

Merging #551 (3a26237) into main (5fe9112) will increase coverage by 0.09%.
The diff coverage is 100.00%.

❗ Current head 3a26237 differs from pull request most recent head 83bc987. Consider uploading reports for the commit 83bc987 to get more accurate results
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@@            Coverage Diff             @@
##             main     #551      +/-   ##
==========================================
+ Coverage   96.16%   96.25%   +0.09%     
==========================================
  Files          27       27              
  Lines        2425     2431       +6     
==========================================
+ Hits         2332     2340       +8     
+ Misses         93       91       -2     
Impacted Files Coverage Δ
src/optsummary.jl 97.67% <ø> (ø)
src/linearmixedmodel.jl 98.43% <100.00%> (+0.01%) ⬆️
src/linalg/cholUnblocked.jl 100.00% <0.00%> (+9.09%) ⬆️

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Co-authored-by: Douglas Bates <[email protected]>
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@palday palday merged commit fd79f39 into main Aug 17, 2021
@palday palday deleted the pa/sigma branch August 17, 2021 15:21
@palday palday mentioned this pull request Aug 17, 2021
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2 participants