WIP: Overarching review tracker for V2

[kahaaga]

This issue tracks the status of everything we need to check before releasing v2.0.

ProbabilitiesEstimators

Docstrings

TODO:

• Clarity
• Eliminate typos
• Verify that all examples are runnable.
• Outcome space is described.

Do this for:

• [x] CountOccurrences.
• [x] ValueHistogram.
• [ ] TransferOperator. NOTE: we'll leave the TransferOperator rework for when I do #55
• [x] Dispersion
• [x] SpatialDispersion. Updated and verified in #210.
• [x] WaveletOverlap
• [x] PowerSpectrum
• [x] SymbolicPermutation. Updated and verified in #207.
• [x] SymbolicWeightedPermutation
• [x] SymbolicAmplitudeAwarePermutation
• [x] SpatialSymbolicPermutation. Updated and verified in #210.
• [x] NaiveKernel

API

Verify that all necessary methods are implemented and tested.

• [x] CountOccurrences.
• [x] ValueHistogram.
• [ ] TransferOperator. See comment above.
• [x] Dispersion
• [x] SpatialDispersion
• [x] WaveletOverlap
• [x] PowerSpectrum
• [x] SymbolicPermutation
• [x] SymbolicWeightedPermutation
• [x] SymbolicAmplitudeAwarePermutation
• [x] SpatialSymbolicPermutation. Added missing test in #224
• [x] NaiveKernel

Entropy types

Docstrings

• [x] Shannon
• [x] Renyi
• [x] Tsallis
• [x] Kaniadakis
• [x] Curado
• [x] StretchedExponential

Additionally,

• [x] All Entropy types must be referenced with a @ref in the docstring for Entropy.
• [x] All ProbabilitiesEstimators appear in the overview table in the documentation.

  API

Check that all (mandatory) methods are implemented and tested.

• [x] Shannon
• [x] Renyi
• [x] Tsallis
• [x] Kaniadakis
• [x] Curado
• [x] StretchedExponential

EntropyEstimators

Documentation

Docstrings should include a description (preferentially a formula) for the quantity it computes.

• [x] KozachenkoLeonenko
• [x] Kraskov
• [x] Zhu
• [x] ZhuSingh
• [x] Vasicek
• [x] Ebrahimi
• [x] Correa
• [x] AlizadehArghami

Tests

We need

• Analytical tests (i.e. generate data from known probability distributions) and see if we can approximate it

• Test default values (i.e. the estimators we have now default to Shannon(; base = 2)

• [x] KozachenkoLeonenko

• [x] Kraskov

• [x] Zhu

• [x] ZhuSingh

• [x] Vasicek

• [x] Ebrahimi

• [x] Correa

• [x] AlizadehArghami

Additionally,

• [x] All EntropEstimator sybtypes are referenced with a @ref in the docstring for EntropyEstimator.
• [x] All EntropyEstimators appear in the overview table in the documentation.

[Datseris]

I am assigning to myself all probability estimators except the tranasfer operator and everything related to symbolic permutations. I am also assiging to myself all "discrete" entropies.

[kahaaga]

I am assigning to myself all probability estimators except the tranasfer operator and everything related to symbolic permutations. I am also assiging to myself all "discrete" entropies.

Ok! FYI: in #210, I already updated the docstrings for SpatialDispersion and SpatialSymbolicPermutation and made sure the examples are now runnable. Feel free to merge that PR whenever.

EDIT: ah, I see. except the symbolic stuff. Then I'll take care of that too.

[kahaaga]

I am assigning myself to all EntropyEstimators. EDIT: done.

[Datseris]

I am doing my review now, which will also result in a PR. I think it is best for me to finish my review first before you do a second one. So that we don't get confused, as the review will touch many aspects of the documentation.

[kahaaga]

I am doing my review now, which will also result in a PR. I think it is best for me to finish my review first before you do a second one. So that we don't get confused, as the review will touch many aspects of the documentation

Noted. I won't touch anything until you give a notice that you're done.

[kahaaga]

Ok, I'm closing this. I went through the entire list again, and I don't think we've missed anything.