v2.0.0

CausalityTools v2.0.0

Diff since v1.6.0

Closed issues:

• Example systems tracker (#1)
• Example system: Thomas' cyclically symmetric attractor driving another system (#30)
• Implement directional coupling detection using rank statistics algorithm (#35)
• Animated step-wise estimation of triangulation-based transfer operator estimator. (#49)
• Animated step-wise estimation of the invariant distribution associated with a transfer operator (#54)
• Implement TriangulationInvariantMeasure type (#55)
• Sliding window causality estimators for DynamicalSystem instances. (#56)
• Recipe for visualising cross mapping algorithm (#57)
• Resampling scheme for exploration of sensitivity to dynamical systems parameters (#74)
• Why not join JuliaDynamics? (#117)
• Merge customembed(pts, positions::Positions, lags::Lags) in DelayEmbeddings.jl ? (#118)
• Consistently use DiscreteDynamicalSystem for discrete maps (#123)
• Move all example systems to DynamicalSystemsBase, or keep them here? (#147)
• Logo (#152)
• tutorial examples for each estimator (#170)
• Progress, V2 (#174)
• Design discussion (#178)
• All examples should use CairoMakie (#180)
• Tag 1.6 (#182)
• Compatibility with Entropies v2: passing ProbabilitiesEstimators is broken (#183)
• Roadmap for causal graph algorithms (#188)
• Review for 2.0: Make joint distance distribution compatible with independence tests (#195)
• Review for 2.0: Make SMeasure compatible with independence (#197)
• Review for V2: Make cross-mapping measure compatible with independence (#199)
• crossmap method lacks documentation for the variant that uses an estimator (#201)
• Review V2: Increase test coverage (#203)
• Dead link in docstring for SurrogateTest for "Quickstart example" (#205)
• LaTeX formatting error in docstring for LocalPermutationTest (#206)
• Constructor for independence test should error for MutualInformation/ConditionalMutual etc when no estimator is provided (#207)
• independence docstring should list compatible independence tests (#208)
• SurrogateTest should list compatible measures (#209)
• SurrogateTest with CMIShannon() and KSG1() estimator doesn't produce correct results (#210)
• LaTeX formatting error in docstring for PartialCorrelation, in the symbol for the joint precision matrix (#211)
• Typo in docstring for JointDistanceDistribution, abbreviated as "JJD" in example links (#212)
• Fix docstring for mutualinfo([measure::MutualInformation], est::ProbabilitiesEstimator, x, y) (#213)
• LocalPermutationTest should list available measures (#217)
• SMeasure & friends should include Theiler window (#218)
• Use StaticArraysCore.jl instead of StaticArrays.jl (#222)
• Link to CMI example in LocalPermutationTest broken (#229)
• Option to sample with/without replacement for LocalPermutationTest (#231)
• Implement Theiler window for LocalPermutationTest (#232)
• Release one more 1.X or go directly to 2.0? (#237)
• SurrogateTest overview table lists the abstract TransferEntropy instead of concrete subtypes (#239)
• Default k for Zhu1 estimator errors (#240)
• SurrogateTest with TEShannon and Zhu1 estimator errors with independence (#241)
• TEShannon and TERenyiJizba should explicitly list compatible estimators (#242)
• Lindner transfer entropy estimator subtypes DifferentialEntropyEstimator, not TransferEntropyEstimator (#243)
• When using TEShannon in SurrogateTest with embeddings with source dim > 1, check surrogate type (#245)
• Document independence test result types (#246)

Merged pull requests:

• Version 2.0 (#187) (@kahaaga)
• CompatHelper: add new compat entry for SpecialFunctions at version 2, (keep existing compat) (#189) (@github-actions[bot])
• CompatHelper: add new compat entry for Scratch at version 1, (keep existing compat) (#191) (@github-actions[bot])
• CompatHelper: add new compat entry for DSP at version 0.7, (keep existing compat) (#192) (@github-actions[bot])
• Correlation measures, with SurrogateTest compatibility (#193) (@kahaaga)
• Make JointDistanceDistribution compatible with independence testing (#196) (@kahaaga)
• Review for V2: S-measure (#198) (@kahaaga)
• Crossmap independence tests (#200) (@kahaaga)
• Review for V2: Reorganize examples and organize APIs for various methods (#202) (@kahaaga)
• Review for V2: Improve test coverage (#204) (@kahaaga)
• Gaussian estimators of MI and CMI (#214) (@kahaaga)
• Fix various issues (#215) (@kahaaga)
• Update logo (#216) (@kahaaga)
• [ImgBot] Optimize images (#219) (@imgbot[bot])
• Add HMeasure, MMeasure and LMeasure (#220) (@kahaaga)
• WIP: Examples (#221) (@kahaaga)
• mutualinfo docstring (#224) (@kahaaga)
• Add list of compatible measures to LocalPermutationTest (#227) (@kahaaga)
• Improvements to LocalPermutationTest (#233) (@kahaaga)
• Fix table (#234) (@kahaaga)
• PartialCorrelation with LocalPermutation (#235) (@kahaaga)
• Make TransferEntropyEstimators compatible with independence (#244) (@kahaaga)
• Estimator tables for transferentropy, TEShannon, TERenyiJizba (#247) (@kahaaga)
• Document test result types (#250) (@kahaaga)
• A causal graph inference API (#251) (@kahaaga)
• Predictive asymmetry, in old and new form. (#253) (@kahaaga)
• WIP: Graph algorithm improvements (#254) (@kahaaga)
• Graphs cleanup (#255) (@kahaaga)
• Convention: negative input lags for closeness measures (#256) (@kahaaga)
• Clean up causal graphs for 2.0 (#257) (@kahaaga)
• Dataset -> StateSpaceSet (#259) (@kahaaga)