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Merge branch 'main' of github.com:JuliaStats/MixedModels.jl into glmm…
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palday committed Aug 20, 2023
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22 changes: 0 additions & 22 deletions .github/workflows/MKL.yml

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23 changes: 14 additions & 9 deletions .github/workflows/ci.yml → .github/workflows/current.yml
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name: current release
concurrency:
group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
cancel-in-progress: true
on:
push:
branches:
Expand All @@ -19,19 +22,21 @@ jobs:
matrix:
julia-version: [1]
julia-arch: [x64]
os: [ubuntu-18.04]
os: [ubuntu-20.04]
steps:
- name: Cancel Previous Runs
uses: styfle/[email protected]
with:
all_but_latest: true
access_token: ${{ github.token }}
- uses: actions/checkout@v2
- uses: julia-actions/setup-julia@v1
with:
version: ${{ matrix.julia-version }}
- uses: julia-actions/[email protected]
- uses: julia-actions/[email protected]
- uses: julia-actions/cache@v1
with:
cache-compiled: "true"
- uses: julia-actions/julia-buildpkg@v1
- uses: julia-actions/julia-runtest@v1
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- uses: julia-actions/[email protected]
- uses: julia-actions/julia-processcoverage@v1
- uses: codecov/codecov-action@v2
with:
flags: current
files: lcov.info
26 changes: 26 additions & 0 deletions .github/workflows/docs-cleanup.yml
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# remove PR previews once they're merged
# <https://juliadocs.github.io/Documenter.jl/dev/man/hosting/#gh-pages-Branch>
name: Doc Preview Cleanup
on:
pull_request:
types: [closed]
jobs:
doc-preview-cleanup:
runs-on: ubuntu-latest
steps:
- name: Checkout gh-pages branch
uses: actions/checkout@v2
with:
ref: gh-pages
- name: Delete preview and history + push changes
run: |
if [ -d "previews/PR$PRNUM" ]; then
git config user.name "Documenter.jl"
git config user.email "[email protected]"
git rm -rf "previews/PR$PRNUM"
git commit -m "delete preview"
git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
git push --force origin gh-pages-new:gh-pages
fi
env:
PRNUM: ${{ github.event.number }}
13 changes: 7 additions & 6 deletions .github/workflows/documenter.yml
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name: Documenter
concurrency:
group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
cancel-in-progress: true
on:
push:
branches: [main]
Expand All @@ -18,15 +21,13 @@ jobs:
name: Documentation
runs-on: ubuntu-20.04
steps:
- name: Cancel Previous Runs
uses: styfle/[email protected]
with:
all_but_latest: true
access_token: ${{ github.token }}
- uses: actions/checkout@v2
- uses: julia-actions/setup-julia@v1
with:
version: 1.6
version: 1.8
- uses: julia-actions/cache@v1
with:
cache-compiled: "true"
- uses: julia-actions/julia-buildpkg@latest
- uses: julia-actions/julia-docdeploy@latest
env:
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37 changes: 0 additions & 37 deletions .github/workflows/lts.yml

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42 changes: 42 additions & 0 deletions .github/workflows/minimum.yml
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name: "minimum compat"
concurrency:
group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
cancel-in-progress: true
on:
push:
branches:
- main
paths-ignore:
- 'LICENSE.md'
- 'README.md'
pull_request:
branches:
- main
paths-ignore:
- 'LICENSE.md'
- 'README.md'
jobs:
ci:
runs-on: ${{ matrix.os }}
strategy:
matrix:
julia-version: [1.8]
julia-arch: [x64]
os: [ubuntu-20.04, macos-11, windows-2019]
steps:
- uses: actions/checkout@v2
- uses: julia-actions/setup-julia@v1
with:
version: ${{ matrix.julia-version }}
- uses: julia-actions/cache@v1
with:
cache-compiled: "true"
- uses: julia-actions/julia-buildpkg@v1
- uses: julia-actions/julia-runtest@v1
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- uses: julia-actions/julia-processcoverage@v1
- uses: codecov/codecov-action@v2
with:
flags: minimum
files: lcov.info
23 changes: 14 additions & 9 deletions .github/workflows/nightly.yml
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name: nightly
concurrency:
group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
cancel-in-progress: true
on:
push:
branches:
Expand All @@ -19,19 +22,21 @@ jobs:
matrix:
julia-version: [nightly]
julia-arch: [x64]
os: [ubuntu-18.04]
os: [ubuntu-20.04]
steps:
- name: Cancel Previous Runs
uses: styfle/[email protected]
with:
all_but_latest: true
access_token: ${{ github.token }}
- uses: actions/checkout@v2
- uses: julia-actions/setup-julia@v1
with:
version: ${{ matrix.julia-version }}
- uses: julia-actions/[email protected]
- uses: julia-actions/[email protected]
- uses: julia-actions/cache@v1
with:
cache-compiled: "true"
- uses: julia-actions/julia-buildpkg@v1
- uses: julia-actions/julia-runtest@v1
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- uses: julia-actions/[email protected]
- uses: julia-actions/julia-processcoverage@v1
- uses: codecov/codecov-action@v2
with:
flags: nightly
files: lcov.info
3 changes: 3 additions & 0 deletions .github/workflows/style.yml
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name: Style-Enforcer
concurrency:
group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
cancel-in-progress: true
on:
push:
branches:
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2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -6,3 +6,5 @@ tune.json
Manifest.toml
settings.json
docs/jmd
LocalPreferences.toml

128 changes: 127 additions & 1 deletion NEWS.md
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MixedModels v4.19.0 Release Notes
==============================
* New method `StatsAPI.coefnames(::ReMat)` returns the coefficient names associated with each grouping factor. [#709]

MixedModels v4.18.0 Release Notes
==============================
* More user-friendly error messages when a formula contains variables not in the data. [#707]

MixedModels v4.17.0 Release Notes
==============================
* **EXPERIMENTAL** New kwarg `amalgamate` can be used to disable amalgation of random effects terms sharing a single grouping variable. Generally, `amalgamate=false` will result in a slower fit, but may improve convergence in some pathological cases. Note that this feature is experimental and changes to it are **not** considered breakings. [#673]
* More informative error messages when passing a `Distribution` or `Link` type instead of the desired instance. [#698]
* More informative error message on the intentional decision not to define methods for the coefficient of determination. [#698]
* **EXPERIMENTAL** Return `finitial` when PIRLS drifts into a portion of the parameter space that yields a (numerically) invalid covariance matrix. This recovery strategy may be removed in a future release. [#616]

MixedModels v4.16.0 Release Notes
==============================
* Support for check tolerances in deserialization. [#703]

MixedModels v4.15.0 Release Notes
==============================
* Support for different optimization criteria during the bootstrap. [#694]
* Support for combining bootstrap results with `vcat`. [#694]
* Support for saving and restoring bootstrap replicates with `savereplicates` and `restorereplicates`. [#694]

MixedModels v4.14.0 Release Notes
==============================
* New function `profile` for computing likelihood profiles for `LinearMixedModel`. The resultant `MixedModelProfile` can be then be used for computing confidence intervals with `confint`. Note that this API is still somewhat experimental and as such the internal storage details of `MixedModelProfile` may change in a future release without being considered breaking. [#639]
* A `confint(::LinearMixedModel)` method has been defined that returns Wald confidence intervals based on the z-statistic, i.e. treating the denominator degrees of freedom as infinite. [#639]

MixedModels v4.13.0 Release Notes
==============================
* `raneftables` returns a `NamedTuple` where the names are the grouping factor names and the values are some `Tables.jl`-compatible type. This type has been changed to a `Table` from `TypedTables.jl`. [#682]

MixedModels v4.12.1 Release Notes
==============================
* Precompilation is now handled with `PrecompileTools` instead of `SnoopPrecompile`. [#681]
* An unnecessary explicit `Vararg` in an internal method has been removed. This removal eliminates a compiler warning about the deprecated `Vararg` pattern. [#680]

MixedModels v4.12.0 Release Notes
==============================
* The pirated method `Base.:/(a::AbstractTerm, b::AbstractTerm)` is no longer defined. This does not impact the use of `/` as a nesting term in `@formula` within MixedModels, only the programmatic runtime construction of formula, e.g. `term(:a) / term(:b)`. If you require `Base.:/`, then [`RegressionFormulae.jl`](https://github.com/kleinschmidt/RegressionFormulae.jl) provides this method. (Avoiding method redefinition when using `RegressionFormulae.jl` is the motivating reason for this change.) [#677]

MixedModels v4.11.0 Release Notes
==============================
* `raneftables` returns a `NamedTuple` where the names are the grouping factor names and the values are some `Tables.jl`-compatible type. Currently this type is a `DictTable` from `TypedTables.jl`. [#634]

MixedModels v4.10.0 Release Notes
==============================
* Rank deficiency in prediction is now supported, both when the original model was fit to rank-deficient data and when the new data are rank deficient. The behavior is consistent but may be surprising when both old and new data are rank deficient. See the `predict` docstring for an example. [#676]
* Multithreading in `parametricbootstrap` with `use_threads` is now deprecated and a noop. With improvements in BLAS threading, multithreading at the Julia level did not help performance and sometimes hurt it. [#674]

MixedModels v4.9.0 Release Notes
==============================
* Support `StatsModels` 0.7, drop support for `StatsModels` 0.6. [#664]
* Revise code in benchmarks to work with recent Julia and PkgBenchmark.jl [#667]
* Julia minimum compat version raised to 1.8 because of BSplineKit [#665]

MixedModels v4.8.2 Release Notes
==============================
* Use `SnoopPrecompile` for better precompilation performance. This can dramatically increase TTFX, especially on Julia 1.9. [#663]

MixedModels v4.8.1 Release Notes
==============================
* Don't fit a GLM internally during construction of GLMM when the fixed effects are empty (better compatibility with
`dropcollinear` kwarg in newer GLM.jl) [#657]

MixedModels v4.8.0 Release Notes
==============================
* Allow predicting from a single observation, as long as `Grouping()` is used for the grouping variables. The simplified implementation of `Grouping()` also removes several now unnecessary `StatsModels` methods that should not have been called directly by the user. [#653]

MixedModels v4.7.3 Release Notes
==============================
* More informative error message for formulae lacking random effects [#651]

MixedModels v4.7.2 Release Notes
==============================
* Replace separate calls to `copyto!` and `scaleinflate!` in `updateL!` with `copyscaleinflate!` [#648]

MixedModels v4.7.1 Release Notes
==============================
* Avoid repeating initial objective evaluation in `fit!` method for `LinearMixedModel`
* Ensure that the number of function evaluations from NLopt corresponds to `length(m.optsum.fitlog) when `isone(thin)`. [#637]

MixedModels v4.7.0 Release Notes
==============================
* Relax type restriction for filename in `saveoptsum` and `restoreoptsum!`. Users can now pass any type with an appropriate `open` method, e.g. `<:AbstractPath`. [#628]

MixedModels v4.6.5 Release Notes
========================
* Attempt recovery when the initial parameter values lead to an invalid covariance matrix by rescaling [#615]
* Return `finitial` when the optimizer drifts into a portion of the parameter space that yields a (numerically) invalid covariance matrix [#615]

MixedModels v4.6.4 Release Notes
========================
* Support transformed responses in `predict` [#614]
* Simplify printing of BLAS configuration in tests. [#597]

MixedModels v4.6.3 Release Notes
========================
* Add precompile statements to speed up first `LinearMixedModel` and Bernoulli `GeneralizedLinearModel` fit [#608]
Expand Down Expand Up @@ -248,7 +346,7 @@ Principal components

* An `AbstractReMat` type has now been introduced to support [#380] work on constrained
random-effects structures and random-effects structures appropriate for applications
in GLM-based decovolution as used in fMRI and EEG (see e.g. [unfold.jl](https://github.com/unfoldtoolbox/unfold.jl).)
in GLM-based deconvolution as used in fMRI and EEG (see e.g. [unfold.jl](https://github.com/unfoldtoolbox/unfold.jl).)
* Similarly, a constructor for `FeMat{::SparseMatrixCSC,S}` has been introduced [#309].
Currently, this constructor assumes a full-rank matrix, but the work on rank
deficiency may be extended to this constructor as well.
Expand Down Expand Up @@ -336,7 +434,35 @@ Package dependencies
[#577]: https://github.com/JuliaStats/MixedModels.jl/issues/577
[#578]: https://github.com/JuliaStats/MixedModels.jl/issues/578
[#588]: https://github.com/JuliaStats/MixedModels.jl/issues/588
[#597]: https://github.com/JuliaStats/MixedModels.jl/issues/597
[#598]: https://github.com/JuliaStats/MixedModels.jl/issues/598
[#603]: https://github.com/JuliaStats/MixedModels.jl/issues/603
[#604]: https://github.com/JuliaStats/MixedModels.jl/issues/604
[#608]: https://github.com/JuliaStats/MixedModels.jl/issues/608
[#614]: https://github.com/JuliaStats/MixedModels.jl/issues/614
[#615]: https://github.com/JuliaStats/MixedModels.jl/issues/615
[#616]: https://github.com/JuliaStats/MixedModels.jl/issues/616
[#628]: https://github.com/JuliaStats/MixedModels.jl/issues/628
[#634]: https://github.com/JuliaStats/MixedModels.jl/issues/634
[#637]: https://github.com/JuliaStats/MixedModels.jl/issues/637
[#639]: https://github.com/JuliaStats/MixedModels.jl/issues/639
[#648]: https://github.com/JuliaStats/MixedModels.jl/issues/648
[#651]: https://github.com/JuliaStats/MixedModels.jl/issues/651
[#653]: https://github.com/JuliaStats/MixedModels.jl/issues/653
[#657]: https://github.com/JuliaStats/MixedModels.jl/issues/657
[#663]: https://github.com/JuliaStats/MixedModels.jl/issues/663
[#664]: https://github.com/JuliaStats/MixedModels.jl/issues/664
[#665]: https://github.com/JuliaStats/MixedModels.jl/issues/665
[#667]: https://github.com/JuliaStats/MixedModels.jl/issues/667
[#673]: https://github.com/JuliaStats/MixedModels.jl/issues/673
[#674]: https://github.com/JuliaStats/MixedModels.jl/issues/674
[#676]: https://github.com/JuliaStats/MixedModels.jl/issues/676
[#677]: https://github.com/JuliaStats/MixedModels.jl/issues/677
[#680]: https://github.com/JuliaStats/MixedModels.jl/issues/680
[#681]: https://github.com/JuliaStats/MixedModels.jl/issues/681
[#682]: https://github.com/JuliaStats/MixedModels.jl/issues/682
[#694]: https://github.com/JuliaStats/MixedModels.jl/issues/694
[#698]: https://github.com/JuliaStats/MixedModels.jl/issues/698
[#703]: https://github.com/JuliaStats/MixedModels.jl/issues/703
[#707]: https://github.com/JuliaStats/MixedModels.jl/issues/707
[#709]: https://github.com/JuliaStats/MixedModels.jl/issues/709
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