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Separate OutcomeSpace and ProbabilitiesEstimator #285

Merged
merged 74 commits into from
Aug 18, 2023
Merged

Separate OutcomeSpace and ProbabilitiesEstimator #285

merged 74 commits into from
Aug 18, 2023

Commits on Aug 1, 2023

  1. Discrete estimators and start of API

    @kahaaga
    kahaaga committed Aug 1, 2023
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Commits on Aug 11, 2023

  1. Total rewrite for OutcomeSpace and ProbabilitiesEstimator`

    @kahaaga
    kahaaga committed Aug 11, 2023
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  2. Convert to SSSet if input is array

    @kahaaga
    kahaaga committed Aug 11, 2023
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  3. Silently deprecate. Remove warning. 

    Fixes #283
    @kahaaga
    kahaaga committed Aug 11, 2023
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  4. New API for SpatialSymbolicPermutation too 

    Fixes a bug too, where repeated outcomes were returned by `probabilities_and_outcomes`. This wasn't caught before, because the tests were wrong too.
    @kahaaga
    kahaaga committed Aug 11, 2023
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  5. Test outcome spaces

    @kahaaga
    kahaaga committed Aug 11, 2023
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  6. Update deprecations

    @kahaaga
    kahaaga committed Aug 11, 2023
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  7. Remove link to deleted file

    @kahaaga
    kahaaga committed Aug 11, 2023
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  8. Notation

    @kahaaga
    kahaaga committed Aug 11, 2023
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  9. Simplify docstring

    @kahaaga
    kahaaga committed Aug 11, 2023
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  10. "Outcome spaces" before "Probabilities"

    @kahaaga
    kahaaga committed Aug 11, 2023
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  11. Clarify what m is

    @kahaaga
    kahaaga committed Aug 11, 2023
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  12. Consistent symbols

    @kahaaga
    kahaaga committed Aug 11, 2023
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  13. Update probabilities docstring

    @kahaaga
    kahaaga committed Aug 11, 2023
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  14. Update summary page

    @kahaaga
    kahaaga committed Aug 11, 2023
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Commits on Aug 15, 2023

  1. Bug fix: outcome_space for Dispersion was not sorted

    @kahaaga
    kahaaga committed Aug 15, 2023
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  2. Use fasthist! for dispersion too. 

    No need for the intermediate function, since normalization happens later.
    @kahaaga
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  3. More generic dispatch 

    This saves many lines of code, and makes extension easier
    @kahaaga
    kahaaga committed Aug 15, 2023
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  4. Update StatisticalComplexity docstring

    @kahaaga
    kahaaga committed Aug 15, 2023
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  5. Generic dispatch

    @kahaaga
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  6. Function is removed, don't test it

    @kahaaga
    kahaaga committed Aug 15, 2023
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  7. Update changelog for StatisticalComplexity

    @kahaaga
    kahaaga committed Aug 15, 2023
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  8. Document is_counting_based

    @kahaaga
    kahaaga committed Aug 15, 2023
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  9. NaiveKernel should work for AbstractVector{<:Real} too

    @kahaaga
    kahaaga committed Aug 15, 2023
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  10. Fix outcome_space bug for TransferOperator

    @kahaaga
    kahaaga committed Aug 15, 2023
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  11. Update docstring for probabilities

    @kahaaga
    kahaaga committed Aug 15, 2023
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  12. AddConstant probabilities estimator

    @kahaaga
    kahaaga committed Aug 15, 2023
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  13. Clean up Shrinkage

    @kahaaga
    kahaaga committed Aug 15, 2023
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  14. Gather tests in one file

    @kahaaga
    kahaaga committed Aug 15, 2023
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  15. Fix ProbabilitiesEstimator tests

    @kahaaga
    kahaaga committed Aug 15, 2023
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  16. Add note for use with missing_probabilities

    @kahaaga
    kahaaga committed Aug 15, 2023
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  17. Include probabilities estimators test suite

    @kahaaga
    kahaaga committed Aug 15, 2023
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  18. Remove unfinished line

    @kahaaga
    kahaaga committed Aug 15, 2023
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  19. Update Project.toml

    @kahaaga
    kahaaga committed Aug 15, 2023
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  20. Bug fix: scaling coefficients shouldn't be included

    @kahaaga
    kahaaga committed Aug 15, 2023
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  21. encoded_space_cardinality for all outcome spaces

    @kahaaga
    kahaaga committed Aug 15, 2023
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  22. Remove @show statement

    @kahaaga
    kahaaga committed Aug 15, 2023
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  23. Remove generic dispatch

    @kahaaga
    kahaaga committed Aug 15, 2023
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  24. Dedicated test files

    @kahaaga
    kahaaga committed Aug 15, 2023
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  25. Shrinkage is generic; update docs

    @kahaaga
    kahaaga committed Aug 15, 2023
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  26. Update Wavelet test after scaling coefficients were discarded

    @kahaaga
    kahaaga committed Aug 15, 2023
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Commits on Aug 18, 2023

  1. In-place sort

    @kahaaga
    kahaaga committed Aug 18, 2023
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  2. Define all counting functions for probabilities estimators

    @kahaaga
    kahaaga committed Aug 18, 2023
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  3. Define outcomes generically

    @kahaaga
    kahaaga committed Aug 18, 2023
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  4. export allcounts

    @kahaaga
    kahaaga committed Aug 18, 2023
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  5. Define outcomes for ValueHistogram

    @kahaaga
    kahaaga committed Aug 18, 2023
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  6. Move tests to correct folder

    @kahaaga
    kahaaga committed Aug 18, 2023
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  7. Test all outcome and probability related funnctions

    @kahaaga
    kahaaga committed Aug 18, 2023
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  8. More tests

    @kahaaga
    kahaaga committed Aug 18, 2023
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  9. Define number of encoded points for Diversity

    @kahaaga
    kahaaga committed Aug 18, 2023
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  10. Tests for Diversity

    @kahaaga
    kahaaga committed Aug 18, 2023
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  11. Diversity and NaiveKernel are counting-based

    @kahaaga
    kahaaga committed Aug 18, 2023
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  12. NaiveKernel isn't counting based

    @kahaaga
    kahaaga committed Aug 18, 2023
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  13. Add tests for AddConstant estimator

    @kahaaga
    kahaaga committed Aug 18, 2023
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  14. Better description

    @kahaaga
    kahaaga committed Aug 18, 2023
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  15. Restrict outcome spaces in constructors

    @kahaaga
    kahaaga committed Aug 18, 2023
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  16. (merge small doc work of Datseris into PR#285 (#287) 

    * re-wrote the terminology first wto paragraphs

* re-write readme
    @Datseris
    Datseris committed Aug 18, 2023
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  17. re-write outcome space function

    @Datseris
    Datseris committed Aug 18, 2023
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  18. restructure is_counting_based function

    @Datseris
    Datseris committed Aug 18, 2023
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  19. rename MLE to RelativeAmount.

    @Datseris
    Datseris committed Aug 18, 2023
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  20. fix missing count based declaration for TOP and Spatial

    @Datseris
    Datseris committed Aug 18, 2023
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  21. outcome space docstring improv

    @Datseris
    Datseris committed Aug 18, 2023
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  22. reorg probabilities file

    @Datseris
    Datseris committed Aug 18, 2023
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  23. make default all = true for missing outcomes

    @Datseris
    Datseris committed Aug 18, 2023
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  24. non-duplicate estimation of L in missing outcomes

    @Datseris
    Datseris committed Aug 18, 2023
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  25. seprate counts core into new file

    @Datseris
    Datseris committed Aug 18, 2023
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  26. simplify internal encoded_space_cardinality function

    @Datseris
    Datseris committed Aug 18, 2023
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  27. fix Sample Coverage

    @Datseris
    Datseris committed Aug 18, 2023
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  28. correct usage of verify_counting_based

    @Datseris
    Datseris committed Aug 18, 2023
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  29. typo in Shrinkage docs

    @Datseris
    Datseris committed Aug 18, 2023
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  30. delete samplecoverage

    @Datseris
    Datseris committed Aug 18, 2023
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  31. Test file has changed name

    @kahaaga
    kahaaga committed Aug 18, 2023
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  32. Fix tests for weighted permutation based outcome spaces

    @kahaaga
    kahaaga committed Aug 18, 2023
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  33. Use correct terminology in OutcomeSpace docstrings

    @kahaaga
    kahaaga committed Aug 18, 2023
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