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RecurrenceAnalysis.jl changelog

v2.1.0

Updated to StateSpaceSets.jl v2.

v2.0.0

  • [BREAKING] The @windowed macro is removed. It was some incredibly complicated 250 lines of code that offer little benefit. Instead of using this macro, use the new windowed function. It does something simple: replaces 
    rmat = RecurrenceMatrix(...)
@windowed determinism(rmat, theiler=2, lmin=3) width=1000 step=100
    with 
    width = 1000
step = 100
windows = 1:step:(size(rmat, 1)-width)
map(1:length(windows)) do i
    rmat_view = view(
      rmat,
      windows[i]:(windows[i]+width),
      windows[i]:(windows[i]+width)
    )
    determinism(rmat_view; theiler=2, lmin=3)
end
  • [BREAKING but deprecated] The way of specifying how recurrences are counted in RecurrenceMatrix has been completely overhauled and is now based on specifying the type by using actual type instances instead of keywords. See the new docstring of RecurrenceMatrix.
  • [BREAKING but deprecated] Specifying metrics with strings in RecurrenceMatrix and co is deprecated and will be removed in the next version. Use proper Metric instances like Euclidean().
  • [BREAKING but deprecated] Giving a number as scale in RecurrenceMatrix is deprecated (because its pointless, just give ε = ε*scale instead).
  • New exported function recurrence_threshold that calculates the recurrence threshold for a given recurrence specification type.
  • RecurrenceAnalysis.jl has been updated to DynamicalSystems.jl v3 (using StateSpaceSets.jl) and hosts its own docs.

v1.8.1

  • Better support for iteration over AbstractRecurrenceMatrix with functions from Base.

v1.8.0

  • Switch to Graphs.jl from LightGraphs.jl for RNA.

v1.7.0

  • New method of skeletonizing a Recurrence Matrix skeletonize, in order to eliminate tangential motion.

v1.5.2

  • New, faster formula for rna[:averagepath] allowing disconnected graphs.

v1.5.1

  • Minor documentation fixes.

v1.5.0

  • Integration with LightGraphs to create recurrence networks, and rna function.

v1.4.0

  • New method of Fixed Amount of Neighbors (FAN) method to create recurrence plots.
  • Now AbstractRecurrenceMatrix types have a parameter with the possible values:
    • WithinRange: when neighboring points are determined by a given distance in the phase space.
    • NeighborNumber: when each point has a determined number of neighbors.
  • Input arguments of RecurrenceMatrix, etc. are generalized to AbstractStateSpaceSet.

v1.3.2

  • Bugfixes of transitivity
  • Deprecate AbstractMatrix inputs to RecurrenceMatrix etc., in favor of StateSpaceSet.

v1.3.0

  • Increased performance of RecurrenceMatrix.
  • Possible to make JointRecurrenceMatrix from input arguments.
  • New RQA measure: transitivity.
  • Dropped support for Julia 1.0, moving to new LTS 1.6.

v1.2.0

(no notable changes until so far)

  • Thread-parallelized computation of recurrence plots is now possible.

v0.12.0

  • Doc improvements
  • Return type changes in rqa
  • Breaking changes in implementations of trend and denominator of "RR"
  • name changes in plotting

v0.10.0

  • Theiler window now has default values that depend on the type: CrossRecurrenceMatrix has default 0, otherwise 1.

v0.9.0

  • Recurrence matrices are printed as a plot using UnicodePlots. See textrecurrenceplot.

v0.8.0 - v0.8.7

  • Big documentation improvements
  • Changes to return values for various rqa functions
  • Functions that return recurrence structure histograms
  • Updated and more tests
  • Performance improvements

v0.7.0

  • All recurrencematrix have been deprecate to RecurrenceMatrix which create a dedicated struct for each kind of matrix.

v0.6.0

  • Rework how recurrencematrix is computed: now a conversion to StateSpaceSet is done for small dimensions. In addition, the default metric is now Euclidean.

v0.5.0

  • With this update core functionality of delay embedding and estimating embedding dimension is moved (and used from) the Julia package DelayEmbeddings.
  • RecurrenceAnalysis is also joining JuliaDynamics and DynamicalSystems.jl from 0.5.0 onwards.
  • Extensions have been implemented so that most functionality works also with StateSpaceSets.

23-09-2018 - v0.4.0

  • Function recurrenceplot to facilitate the visualization of recurrence plots.
  • Support of Manhattan norm for the identification of recurrences.
  • Option to create matrices with fixed recurrence rate.
  • rqa option for obtaining only parameters related to diagonal structures.

12-08-2018 - v0.3.0

  • Update to support Julia 1.0.0 and 0.7.0
  • RQA functions matching outputs of crqa (R) and CRPToolbox (Matlab)

31-07-2018 - v0.2.1

  • Bugfixes:
    • sorteddistances
    • RQA functions (bugs in parameters of diagonal structures when theiler==0)

30-07-2018 - v0.3.0-beta

  • Break compatibility with 0.6
  • Breaking modifications of RQA functions, in order to match the outputs of crqa (R) and CRPToolbox (Matlab):
    • The denominator of RR is fixed to N2.
    • Theiler window added to the calculation of LAM and TT.
    • Theiler window defaults to 0 in all functions.
  • Bugfix in the calculation of diagonal structures

23-06-2018 - v0.2.0

  • Update to support Julia 0.6-0.7 (breaking compatibility with 0.5).

10-11-2016 - v0.1.0

  • Support for windowed RQA
  • Change default scale of recurrencematrix, etc.
  • Improved performance of RQA functions
  • Function rqa for all RQA parameters
  • Improved compatibility with Julia 0.5 and 0.6, backwards compatibility with 0.4
  • Bugfixes:
    • fnn
    • maxdiag
    • maxvert

25-07-2016 - v0.0.3

  • Compatibility with Julia 0.5
  • Add sorteddistances to calculate optimal thresholds

25-05-2016 - v0.0.2

  • Add functions to calculate optimal embedding dimensions
  • Include documentation and tests

18-05-2016 - v0.0.1

First release or RecurrenceAnalysis.jl