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JuliaDynamics / Attractors.jl

Find attractors of dynamical systems, their basins, and continue them across parameters. Study global stability (a.k.a. non-local, or resilience). Also tipping points functionality.
MIT License
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typos #113

Closed spaette closed 8 months ago

spaette commented 8 months ago

Convenience Minimal Silhouettes Unknown accumulated approximation arbitrarily assigns attractor construct converged choose deterministic discretization dimensional disappear disappears explicitly function guaranteed halt halting implemented initializes internal just original originally output penalize penalized perturbation perturbations silhouette statistics system system threshold unnecessary

$ grep -nr Convinience Attractors.jl
Attractors.jl/src/plotting.jl:89:Convinience combination of [`plot_basins_curves`](@ref) and [`plot_attractors_curves`](@ref)
$ grep -nr Mimimal Attractors.jl
Attractors.jl/docs/src/basins.md:39:## Mimimal Fatal Shock
$ grep -nr Silhuettes Attractors.jl
Attractors.jl/src/mapping/grouping/cluster_optimal_ϵ.jl:2:# Calculate Silhuettes
$ grep -nr Unkown Attractors.jl
Attractors.jl/src/mapping/grouping/cluster_optimal_ϵ.jl:60:        error("Unkown `optimal_radius_method`.")
$ grep -nr accummulated Attractors.jl
Attractors.jl/src/mapping/recurrences/finite_state_machine.jl:155:        # If we accummulated enough recurrences, we claim that we
$ grep -nr aproximation Attractors.jl
Attractors.jl/src/basins/fractality_of_basins.jl:130:    # Systematic error aproximation for the disk of radius ε
$ grep -nr arbitriraly Attractors.jl
Attractors.jl/src/basins/fractality_of_basins.jl:21:another initial condition that lead to another basin arbitriraly close. It provides also
$ grep -nr assings Attractors.jl
Attractors.jl/src/mapping/attractor_mapping.jl:163:`labels` returned by [`basins_fractions`](@ref) and simply assings them to a full array
$ grep -nr attarctor Attractors.jl
Attractors.jl/docs/src/examples.md:830:                    # color-code initial condition if we convegerd to attarctor
$ grep -nr constuct Attractors.jl
Attractors.jl/CHANGELOG.md:19:- New algorithm `subdivision_based_grid`. Allows user to automatically constuct the grid which simulates subdivision into regions with different discretization levels in accordance with state space flow speed.
$ grep -nr convegerd Attractors.jl
Attractors.jl/docs/src/examples.md:830:                    # color-code initial condition if we convegerd to attarctor
$ grep -nr coose Attractors.jl
Attractors.jl/docs/src/examples.md:715:    # will coose initial conditions that are only in the first 2 attractors
$ grep -nr determistic Attractors.jl
Attractors.jl/test/mapping/basins_of_attraction.jl:21:# determistic grid, we know exactly the array layout
$ grep -nr dicretization Attractors.jl
Attractors.jl/docs/src/examples.md:353:The constructed array corresponds to levels of dicretization for specific regions of the grid as a powers of 2,
$ grep -nr dimesional Attractors.jl
Attractors.jl/src/continuation/aggregate_attractor_fractions.jl:20:analysis purposes. For example, a high dimesional model of competition dynamics
$ grep -n dissapear Attractors.jl/docs/src/index.md
15:- New function [`match_continuation!`](@ref) which improves the matching during a continuation process where attractors dissapear and re-appear.
$ grep -n dissapears Attractors.jl/src/continuation/match_attractor_ids.jl
223:        # Here we always compute a next id. In this way, if an attractor dissapears
$ grep -nr explitily Attractors.jl
Attractors.jl/ext/plotting.jl:7:    # we need to explitily add here some default colors...
$ grep -nr funtion Attractors.jl
Attractors.jl/src/mapping/grouping/cluster_config.jl:118:# API funtion (group features)
$ grep -nr guaranteeed Attractors.jl
Attractors.jl/src/continuation/match_attractor_ids.jl:80:    # but also ensure that keys that have too high of a value distance are guaranteeed
$ head -n 30 Attractors.jl/src/mapping/recurrences/finite_state_machine.jl \         
> | grep hault
        # This clause here is added because sometimes the algorithm will never hault
$ grep -nr haulting Attractors.jl
Attractors.jl/src/mapping/recurrences/finite_state_machine.jl:39:            # `AttractorsViaRecurrences` algorithm exceeded safety count without haulting.
$ grep -nr imlemented Attractors.jl
Attractors.jl/src/mapping/attractor_mapping.jl:140:extract_attractors(::AttractorMapper) = error("not imlemented")
$ grep -nr initialzes Attractors.jl
Attractors.jl/src/mapping/grouping/attractor_mapping_featurizing.jl:151:# initialzes integrators for any given kind of system. But that can be done
$ grep -nr interal Attractors.jl
Attractors.jl/src/mapping/recurrences/attractor_mapping_recurrences.jl:161:    # call signature the interal basins info array of the mapper is NOT updated
$ grep -nr juuuuust Attractors.jl
Attractors.jl/test/basins/tipping_points_tests.jl:9:    # Also test analytically resolved juuuuust to be sure
$ grep -nr "orginal " Attractors.jl
Attractors.jl/test/basins/uncertainty_tests.jl:20:@testset "orginal paper" begin
$ grep -nr "orginally " Attractors.jl
Attractors.jl/src/mapping/recurrences/grids.jl:61:orginally coarse grid (a tuple of `AbstractRange`s).
$ grep -nr ouput Attractors.jl
Attractors.jl/src/basins/fractality_of_basins.jl:163:is a vector with the corresponding size of the balls. The ouput `d` is the estimation
Attractors.jl/src/basins/fractality_of_basins.jl:219:The ouput `α` is the estimation of the uncertainty exponent using the box-counting
$ grep -nr "penaltize " Attractors.jl
Attractors.jl/src/tipping/mfs.jl:186:        # penaltize if we stay in the same basin:
$ grep -nr "penaltized " Attractors.jl
Attractors.jl/src/tipping/mfs.jl:178:The algorithm uses BlackBoxOptim.jl and a penaltized objective function to minimize.
$ grep -nr "pertubation " Attractors.jl
Attractors.jl/src/tipping/mfs.jl:52:obtained pertubation it proceeds to the second step. On the second step, the algorithm
Attractors.jl/src/tipping/mfs.jl:54:norm of the pertubation found in the first step.
Attractors.jl/src/tipping/mfs.jl:90:This function generates a random pertubation of the initial point `u0` within
Attractors.jl/src/tipping/mfs.jl:93:If the pertubation is not in the same basin of attraction, it calculates the norm
Attractors.jl/src/tipping/mfs.jl:94:of the pertubation and compares it to the best pertubation found so far.
Attractors.jl/src/tipping/mfs.jl:95:If the norm is smaller, it updates the best pertubation found so far.
Attractors.jl/src/tipping/mfs.jl:96:It repeats this process total_iterations times and returns the best pertubation found.
Attractors.jl/src/tipping/mfs.jl:126:If pertubation with the same basin of attraction is found, it updates the best shock found
Attractors.jl/src/tipping/mfs.jl:128:and returns the best pertubation found.
$ grep -nr pertubations Attractors.jl
Attractors.jl/src/tipping/mfs.jl:49:the algorithm generates random pertubations within the search area and records
Attractors.jl/src/tipping/mfs.jl:53:generates random pertubations on the surface of the hypersphere with radius equal to the
Attractors.jl/src/tipping/mfs.jl:62:- `initial_iterations = 10000`: number of random pertubations to try in the first step of the
Attractors.jl/src/tipping/mfs.jl:125:the radius of the sphere on the surface of which it generates random pertubations.
$ grep -nr sillhoute Attractors.jl
Attractors.jl/src/mapping/grouping/cluster_optimal_ϵ.jl:81:    # vary ϵ to find the best one (which will maximize the mean sillhoute)
Attractors.jl/src/mapping/grouping/cluster_optimal_ϵ.jl:109:    # vary ϵ to find the best radius (which will maximize the mean sillhoute)
Attractors.jl/src/mapping/grouping/cluster_optimal_ϵ.jl:161:    # vary ϵ to find the best one (which will maximize the minimum sillhoute)
$ grep -nr statitics Attractors.jl
Attractors.jl/src/basins/fractality_of_basins.jl:98:        error("Ntotal must be larger than 1000 to gather enough statitics.")
$ grep -nr stystem Attractors.jl
Attractors.jl/src/mapping/attractor_mapping.jl:65:stystem by mapping initial conditions to attractors using `mapper`
$ grep -nr "syste " Attractors.jl
Attractors.jl/docs/src/examples.md:479:# initialize dynamical syste and sampler
$ grep -nr trehsold Attractors.jl
Attractors.jl/test/continuation/matching_attractors.jl:97:            # okay here we test the case that the trehsold becomes too large
$ grep -nr unecessary Attractors.jl
Attractors.jl/src/mapping/grouping/nearest_feature_config.jl:48:# and makes it unecessary to also implement `group_features`. The bulk version
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The use of Continuating/continuate is unusual.

$ grep -nr Continuating Attractors.jl
Attractors.jl/src/continuation/continuation_recurrences.jl:115:        desc="Continuating basins fractions:", enabled=show_progress
$ grep -nr continuate Attractors.jl
Attractors.jl/CHANGELOG.md:76:- New basins fraction continuation method `RecurrencesFindAndMatch` that utilizes a brand new algorithm to continuate basins fractions of arbitrary systems.
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spaette commented 8 months ago

@Jay-sanjay

My preference would be to mark the pull a Draft until the matters of this comment are resolved. Presumably you know how to do a soft reset if you make changes to the pull request. It would be simpler to include any such modifications in a single commit and then do a soft reset. I have found no example use of the strings Continuating/continuate in any location other than this software repository.

Incidentally, if you replace "fixing issue" in your pull comment with "Closes" this ticket will automatically close when the pull is merged.

the patch has penalized which is incorrect rather than penalize on this line

src/tipping/mfs.jl


      if mapper(u0 + perturbation) == mapper(u0)
-         # penaltize if we stay in the same basin:
+         # penalized if we stay in the same basin:
          return dist + penalty

The use of Continuating/continuate is unusual.

these were not part of this ticket

CHANGELOG.md

  - New function `continuation` that calculates basins fractions and how these change versus a parameter (given a continuation method)
- - New basins fraction continuation method `RecurrencesFindAndMatch` that utilizes a brand new algorithm to continuate basins fractions of arbitrary systems.
+ - New basins fraction continuate method `RecurrencesFindAndMatch` that utilizes a brand new algorithm to continuate basins fractions of arbitrary systems.
  - `match_attractor_ids!` has been fully overhauled to be more flexible, allow more ways to match, and also allow arbitrary user-defined ways to match.

src/continuation/continuation_recurrences.jl

      progress = ProgressMeter.Progress(length(prange);
-         desc="Continuating basins fractions:", enabled=show_progress
+         desc="continuate basins fractions:", enabled=show_progress
      )

possibly reappears/reappear could be used here

$ grep -nr re\-appear Attractors.jl
Attractors.jl/src/continuation/match_attractor_ids.jl:224:        # and re-appears, it will get a different (incremented) id as it should!
Attractors.jl/docs/src/index.md:15:- New function [`match_continuation!`](@ref) which improves the matching during a continuation process where attractors dissapear and re-appear.
$