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Profile the objective #639

Merged
merged 103 commits into from
May 4, 2023
Merged

Profile the objective #639

merged 103 commits into from
May 4, 2023

Commits on Sep 13, 2022

  1. Revising profiling of fixed-effects parameters.

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Commits on Sep 14, 2022

  1. Create a single Table from profileβ

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Commits on Sep 15, 2022

  1. Incorporate some of Phillip's suggestions.

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  2. use a copy of remat.λ when profiling, change initial

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Commits on Sep 16, 2022

  1. shallow copy ReMats

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  2. contravariance

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  3. Add tests, names in MixedModelProfile, export

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Commits on Sep 19, 2022

  1. using BSplineKit, add confint for model and prof

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  2. Add tests for confint, be more careful of types

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Commits on Sep 20, 2022

  1. Shuffle fields in profile object and adjust test

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  2. Document functions and structs

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Commits on Sep 21, 2022

  1. Initial profilelogσ with fixed stepsz

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  2. Add profilelogσ and tests

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    dmbates committed Sep 21, 2022
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  3. reformat

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  4. Suppress progress display on refits

    @dmbates
    dmbates committed Sep 21, 2022
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  5. Avoid destructuring to allow for LTS test

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Commits on Sep 22, 2022

  1. use Compat.jl for destructuring syntax

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Commits on Oct 2, 2022

  1. Add BSplineKit and TypedTables to Project.toml

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Commits on Oct 4, 2022

  1. New version of BSplineKit (w periodic splines)

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Commits on Oct 11, 2022

  1. Merge branch 'main' into profile

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Commits on Oct 18, 2022

  1. Merge branch 'main' into profile

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  2. Allow [email protected] for testing on LTS julia

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Commits on Oct 25, 2022

  1. Use profile generic, return a table.

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  2. Back out a comment, fix tests.

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Commits on Oct 26, 2022

  1. Merge branch 'main' of github.com:JuliaStats/MixedModels.jl into profile

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Commits on Nov 2, 2022

  1. Be more careful with initial values in profileσ

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  2. Copy the vector, not just the reference to it

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Commits on Nov 15, 2022

  1. profile function with sigma, beta and theta

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  2. Fix confint method and comparison values in tests.

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Commits on Nov 16, 2022

  1. Add estimate to confint table, smaller δj, tests

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Commits on Nov 20, 2022

  1. Store m and the vc's values. Use Tuples.

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Commits on Nov 23, 2022

  1. Per discussion of #639

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Commits on Nov 24, 2022

  1. Bump version of BSplineKit to allow extrapolation

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Commits on Nov 25, 2022

  1. Add and export objective! methods.

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Commits on Jan 7, 2023

  1. Split and update src/profile.jl

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  2. Minor correction in a test.

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    dmbates committed Jan 7, 2023
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  3. Merge branch 'main' into profile

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Commits on Jan 27, 2023

  1. Remove unused definition.

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  2. Export Table, add .tbl property for bootstrap.

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  3. Interim version of profiling, σs have problems.

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Commits on Jan 28, 2023

  1. Fix σ profiles by moving lowerbd on θ

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Commits on Jan 29, 2023

  1. Merge current main

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Commits on Jan 31, 2023

  1. Add documentation.

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Commits on Feb 3, 2023

  1. Require julia version 1.8 (b/c BSplineKit 0.14)

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  2. Add confint for bootstrap, clean up for profile.

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  3. Modify test to match current code

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  4. Bump julia version for documenter to 1,8

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Commits on Feb 7, 2023

  1. Bump version of Aqua

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  2. Check monotone splines. Comment out unused method

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  3. Add more tests of profiling. Clean up method use.

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Commits on Feb 8, 2023

  1. Merge branch 'main' of github.com:JuliaStats/MixedModels.jl into profile

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  2. Merge branch 'profile' of https://github.com/JuliaStats/MixedModels.jl … 

    …into profile
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Commits on Feb 10, 2023

  1. 'tbl' field of MixedModelProfile as a Table

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Commits on Feb 16, 2023

  1. JuliaFormatter 

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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Commits on Feb 21, 2023

  1. JuliaFormatter.format("src")

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Commits on Feb 22, 2023

  1. Merge branch 'main' into profile

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    dmbates committed Feb 22, 2023
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  2. Clean up warning message.

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    dmbates committed Feb 22, 2023
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Commits on Feb 28, 2023

  1. Merge branch 'main' into profile

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  2. Return raneftables as a NamedTuple of DictTables

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  3. Update src/mixedmodel.jl 

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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Commits on Mar 1, 2023

  1. Return a NamedTuple of Tables - easier to sort.

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Commits on Mar 10, 2023

  1. Merge branch 'main' into profile

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Commits on Mar 17, 2023

  1. drop Compat

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Commits on Mar 20, 2023

  1. Update src/profile/fixefpr.jl 

    Co-authored-by: Phillip Alday <[email protected]>
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  2. Update src/MixedModels.jl 

    Co-authored-by: Phillip Alday <[email protected]>
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    dmbates and palday authored Mar 20, 2023
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  3. Update src/linearmixedmodel.jl 

    Co-authored-by: Phillip Alday <[email protected]>
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    dmbates and palday authored Mar 20, 2023
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  4. Update src/profile/fixefpr.jl 

    Co-authored-by: Phillip Alday <[email protected]>
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  5. Update src/profile/utilities.jl 

    Co-authored-by: Phillip Alday <[email protected]>
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  6. Replace Tuple type with stronger NTuple{N,Symbol} 

    type
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  7. Update src/profile/sigmapr.jl 

    Co-authored-by: Phillip Alday <[email protected]>
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    dmbates and palday authored Mar 20, 2023
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Commits on Mar 21, 2023

  1. add CI method comparison

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  2. Merge branch 'profile' of github.com:JuliaStats/MixedModels.jl into p… 

    …rofile
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  3. Update src/profile/vcpr.jl 

    Co-authored-by: Phillip Alday <[email protected]>
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    dmbates and palday authored Mar 21, 2023
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Commits on Mar 22, 2023

  1. Fix a syntax error

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    dmbates committed Mar 22, 2023
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  2. Remove unnecessary qualifiers

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Commits on Apr 12, 2023

  1. Merge branch 'main' of github.com:JuliaStats/MixedModels.jl into profile

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  2. Merge branch 'main' into profile

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Commits on Apr 13, 2023

  1. Bump compat for BSplineKit

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  2. JuliaFormatter change

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Commits on Apr 15, 2023

  1. Merge branch 'main' into profile

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Commits on Apr 17, 2023

  1. Changes suggested in palday's review.

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Commits on Apr 26, 2023

  1. Merge branch 'main' into profile

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Commits on May 3, 2023

  1. Merge branch 'main' of github.com:JuliaStats/MixedModels.jl into profile

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  2. Add news

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  3. version bump

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Commits on May 4, 2023

  1. Add docstring and drop type parameter 

    Co-authored-by: Phillip Alday <[email protected]>
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  2. Document MixedModelProfile struct 

    Co-authored-by: Phillip Alday <[email protected]>
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    dmbates and palday authored May 4, 2023
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  3. Document a method as internal and potentially volatile 

    Co-authored-by: Phillip Alday <[email protected]>
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  4. Document a method src/profile/sigmapr.jl as volatile 

    Co-authored-by: Phillip Alday <[email protected]>
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  5. Document a method as internal and potentially volatile 

    Co-authored-by: Phillip Alday <[email protected]>
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    dmbates and palday authored May 4, 2023
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  6. Document confint method 

    Co-authored-by: Phillip Alday <[email protected]>
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  7. Document confint method 

    Co-authored-by: Phillip Alday <[email protected]>
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    dmbates and palday authored May 4, 2023
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  8. Document an internal method 

    Co-authored-by: Phillip Alday <[email protected]>
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    dmbates and palday authored May 4, 2023
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  9. Document confint method 

    Co-authored-by: Phillip Alday <[email protected]>
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    dmbates and palday authored May 4, 2023
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  10. Document profilevcl 

    Co-authored-by: Phillip Alday <[email protected]>
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  11. Document the internal method profileσs! 

    Co-authored-by: Phillip Alday <[email protected]>
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  12. Refine target values in test/pls.jl 

    Co-authored-by: Phillip Alday <[email protected]>
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  13. correct a typo of dot as separator

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  14. Generalize a type comparison in test/pls.jl 

    Co-authored-by: Phillip Alday <[email protected]>
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  15. Generalize a type comparison in test/pls.jl [ci skip] 

    Co-authored-by: Phillip Alday <[email protected]>
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  16. Suppress progress updates in profile in tests [ci skip] 

    Co-authored-by: Phillip Alday <[email protected]>
    @dmbates @palday
    dmbates and palday authored May 4, 2023
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  17. Gene 

    Co-authored-by: Phillip Alday <[email protected]>
    @dmbates @palday
    dmbates and palday authored May 4, 2023
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  18. fix indents

    @palday
    palday committed May 4, 2023
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