v0.11.0

What's Changed

• New data package version v0.6.0.
• Fix bug where cover instead of leftover space was being used in stand alone site selection by @Rosejoycrocker in #610
• Add a new ten site example domain for testing by @Rosejoycrocker in #628
• Fix mcda method bugs by @Rosejoycrocker in #629
• Fix set_factor_bounds! out of bounds for discrete factors by @Zapiano in #631
• Address MCDA error for single locations by @ConnectedSystems in #640
• Replaces distance sorting with restrictions on the number of selected locations in the same reef by @Rosejoycrocker in #635
• Changes to make ADRIA precompilable under Julia v1.10 by @ConnectedSystems in #646
• Update use of Makie/GeoMakie to address deprecation errors by @ConnectedSystems in #647
• Add connectivity data to result set storage by @Rosejoycrocker in #643
• Fix larval connectivity bug by @ConnectedSystems in #648
• Remove examples dir issue #584 by @DanTanAtAims in #651
• Update tests for new sampling method/factor definitions by @ConnectedSystems in #653
• Update factor type documentation by @ConnectedSystems in #654
• Update factor types and their use by @ConnectedSystems in #636
• Speed up calculation of truncated normal mean and cdf by @DanTanAtAims in #652
• Add a default size for scenario plots by @ConnectedSystems in #657
• CompatHelper: add new compat entry for StatsFuns at version 1, (keep existing compat) by @github-actions in #658
• CompatHelper: add new compat entry for SpecialFunctions at version 2, (keep existing compat) by @github-actions in #659
• Fix bleaching mortality by @ConnectedSystems in #660
• Clean up settler cover function to reduce confusion by @ConnectedSystems in #662
• Only load up relevant RME SSP datasets by @ConnectedSystems in #663
• Reset deployed-coral-risk-tol range by @ConnectedSystems in #664
• Clean up scenario running methods by @ConnectedSystems in #665
• Clean up use of TP matrices to align with conceptualisation of connectivity by @ConnectedSystems in #667
• Support updated domain structure by @ConnectedSystems in #669
• Adjustment to simulated events to address numerical errors by @ConnectedSystems in #668
• Return 0 in cases where lb > ub by @ConnectedSystems in #666
• Fix erroneous handling of location IDs by @ConnectedSystems in #671
• Fix error in domain loading when cluster_id is already in string format by @Rosejoycrocker in #673
• Add test domain for ReefModDomain type by @Rosejoycrocker in #675
• Additional setup instructions for code style and formatting by @ConnectedSystems in #676
• Fix cyclone sorting by @Zapiano in #683
• removed deprecate functions and function calls by @DanTanAtAims in #684
• restructured documentation image directories by @DanTanAtAims in #685
• Fix readjustment of number of slices bug in RSA by @Rosejoycrocker in #679
• Truncated normal changes by @DanTanAtAims in #687
• Allow user to set whatever bounds they wish by @ConnectedSystems in #688
• Switch to YAXArrays when runnin scenarios by @Zapiano in #690
• Remove factors input from rsa() and use scenario dataframe column names instead by @Rosejoycrocker in #696
• updated data loading test for migration to YAXArrays by @DanTanAtAims in #697
• Further updates to scenario runs with MCDA by @ConnectedSystems in #698
• Remove MKL from build process by @ConnectedSystems in #705
• Migrate metrics.jl to YAXArrays by @Zapiano in #709
• Yax cube tests by @DanTanAtAims in #704
• Yax viz by @DanTanAtAims in #703
• Yax test update by @DanTanAtAims in #700
• Remove GC workaround by @ConnectedSystems in #711
• Yax migration miscellaneous by @Zapiano in #715
• Keep metadata in results by @ConnectedSystems in #716
• CompatHelper: bump compat for DimensionalData to 0.26, (keep existing compat) by @github-actions in #714
• Finalize update of standalone MCDA methods by @ConnectedSystems in #717
• Update all tests and remove NamedDims and AxisKeys from ADRIA.jl by @Zapiano in #718
• Validating MCDA methods and initial clean/update of tests by @ConnectedSystems in #719
• Migrate from NamedDimsArrays to YAXArrays by @Zapiano in #695
• Provide a succinct overview of MCDA by @ConnectedSystems in #720
• Add support to cyclone mortality to ReefModDomain by @Zapiano in #722
• Save right intervention label at ResultSet ranks YAXArray by @Zapiano in #724
• Hacky support for later RME reef id list by @ConnectedSystems in #731
• Add support for specifying locations by @ConnectedSystems in #732
• Support more vector types for maps by @ConnectedSystems in #736
• Clean up connectivity and centrality methods by @ConnectedSystems in #737
• Additional rank methods to determine number of locations intervened on per timestep by @ConnectedSystems in #738
• Collection of miscellaneous changes by @ConnectedSystems in #740
• Fix bug, min. locations to select > available locations by @ConnectedSystems in #741
• CompatHelper: bump compat for DimensionalData to 0.27, (keep existing compat) by @github-actions in #744
• Connectivity viz by @DanTanAtAims in #742
• Fix locations selection in ReefMod datapackage cyclone mortality loading by @Zapiano in #723
• Only rank locations with available area > 0 by @ConnectedSystems in #734
• use provided centrality measures instead of defaults by @DanTanAtAims in #751
• Improved support for spatial maps by @ConnectedSystems in #750
• Repeat mention that the VS Code extension is being setup by @ConnectedSystems in #748
• Convenience plotting method for connectivity/centralities by @ConnectedSystems in #752
• Support plotting DHW and cyclone (mortality) scenarios by @ConnectedSystems in #758
• Support deactivating environmental disturbances by @ConnectedSystems in #759
• RME Result Interface by @DanTanAtAims in #745
• add range to for loop by @DanTanAtAims in #762
• Visualization for taxonomy cover. by @DanTanAtAims in #763
• Fix erroneous function call in docstrings by @ConnectedSystems in #773
• CompatHelper: bump compat for NetCDF to 0.12, (keep existing compat) by @github-actions in #765
• CompatHelper: add new compat entry for GraphMakie in [weakdeps] at version 0.5, (keep existing compat) by @github-actions in #766
• CompatHelper: add new compat entry for GeoMakie in [weakdeps] at version 0.6, (keep existing compat) by @github-actions in #767
• CompatHelper: add new compat entry for Makie in [weakdeps] at version 0.21, (keep existing compat) by @github-actions in #764
• improve load_domain docs by @arlowhite in #733
  ...

v0.10.0

What's Changed

• Add .JuliaFormatter.toml to .gitignore by @Zapiano in #499
• Update viz.clustered_scenarios to allow confidence interval plot by @Zapiano in #482
• Deprecate run_scenarios(scens, dom, ...) by @ConnectedSystems in #476
• Fix _time_labels missing last label by @Zapiano in #496
• Refactor viz.scenario by @Zapiano in #500
• CompatHelper: bump compat for SciMLBase to 2, (keep existing compat) by @github-actions in #504
• Update CSV.write writeheader parameter to header by @Zapiano in #506
• Fix bug causing Domain loading with RCP to error by @Rosejoycrocker in #511
• CompatHelper: bump compat for MLJ to 0.20, (keep existing compat) by @github-actions in #515
• Remove top_n parameter from usage by @Rosejoycrocker in #514
• Add function to find robust scenarios across several metrics by @Zapiano in #463
• Add :summary option to viz.scenarios by @Zapiano in #505
• Add support series and map binary clusters plots by @Zapiano in #521
• Fix scenarios subsetting now working by @Zapiano in #523
• Rename rs_input with scenarios by @Zapiano in #533
• Fix bug in how sensitivity.outcome_map() treats categorical variables. by @Rosejoycrocker in #491
• CompatHelper: bump compat for NCDatasets to 0.13, (keep existing compat) by @github-actions in #536
• Add interface function to query number of scenarios in result set by @ConnectedSystems in #527
• Add summarize and turn per_loc and loc_trajectory into alias by @Zapiano in #537
• Add missing scenario analysis function definitions to analysis module by @ConnectedSystems in #541
• Extract call to run scenarios inside tests to external function by @Zapiano in #540
• Broadcast _check_discrete inside update_params by @Zapiano in #539
• Adds a series of aggregation functions for location selection ranks by @Rosejoycrocker in #431
• Add functions for repeated tasks when performing location selection by @Rosejoycrocker in #434
• Update analysis docs with recent scenarios and clusters developments by @Zapiano in #545
• Resolve Out-of-Memory issues when working with larger spatial areas by @ConnectedSystems in #542
• CompatHelper: add new compat entry for TOML at version 1, (keep existing compat) by @github-actions in #553
• CompatHelper: add new compat entry for Statistics at version 1, (keep existing compat) by @github-actions in #554
• Avoid assuming where the RCP column is when adjusting scenario spec by @ConnectedSystems in #558
• Fix integer dims reference in location_selection_frequency() by @Rosejoycrocker in #563
• Add function to alter sampling bounds on parameters to specified value. by @Rosejoycrocker in #490
• Coral cover consistently represented as relative to coral habitable area by @ConnectedSystems in #555
• Fix bug due to missing default_bounds in EnvironmentalLayer and Coral model components by @Rosejoycrocker in #569
• Prevent test_rs() from creating tmp dir inside test/data by @Zapiano in #576
• Visualizations to be agnostic to Makie backend by @ConnectedSystems in #570
• Apply blue styleguide to some files by @Zapiano in #579
• Functions to plot spatial distributions of site selection frequencies by @Rosejoycrocker in #449
• Add functions used for location selection to separate decision module by @Rosejoycrocker in #571
• Update use of progress meter to resolve deprecation warning by @ConnectedSystems in #581
• Add ability to perform convergence analysis by @Rosejoycrocker in #552
• Add separate weighting parameter for depth criteria by @Rosejoycrocker in #573
• Replace package NCDatasets by NetCDF by @Zapiano in #583
• Add conversion to scientific notation by @Zapiano in #574
• CompatHelper: add new compat entry for NetCDF at version 0.11, (keep existing compat) by @github-actions in #588
• Change approach to listing supported MCDA methods by @ConnectedSystems in #593
• Use min-max normalisation for heat stress by @Rosejoycrocker in #595
• Remove defunct function for post processing results into power-BI friendly csv file by @Rosejoycrocker in #594
• Fix viz.scenarios bug introduced in changes to scenario_confint! usage by @Rosejoycrocker in #589
• Use min-max normalisation for heat stress by @Rosejoycrocker in #596
• Normalize sampled MCDA weights by @Rosejoycrocker in #582
• Handle cases where connectivity directories may be empty by @ConnectedSystems in #597
• Remove list of ignored JMcDM methods by @ConnectedSystems in #599
• Implement cyclone mortality scenarios by @Zapiano in #585
• CompatHelper: add new compat entry for DimensionalData at version 0.25, (keep existing compat) by @github-actions in #606
• CompatHelper: bump compat for Interpolations to 0.15, (keep existing compat) by @github-actions in #604
• CompatHelper: add new compat entry for YAXArrays at version 0.5, (keep existing compat) by @github-actions in #605
• Fix proportional_adjustment vector conversion computational error by @Zapiano in #607
• Fix treatment of categorical factors in regional sensitivity analysis by @Rosejoycrocker in #601
• Deactivated interventions should be considered separately by @ConnectedSystems in #598
• Adjust language in architectural overview to match recent changes by @ConnectedSystems in #612
• Add tests for figure creation by @ConnectedSystems in #608
• Attach dummy wave and cyclone data by @ConnectedSystems in #616
• CompatHelper: bump compat for SIRUS to 2, (keep existing compat) by @github-actions in #617
• Support RSA with large sample sizes by @ConnectedSystems in #614
• Add more detail regarding sequence of events by @ConnectedSystems in #611
• Changes to dhw and wave logs to store scenario and site means and stds by @Rosejoycrocker in #623
• Fix bug introduced by SIRUS v2.0.1 by @Zapiano in #625

Full Changelog: v0.9.0...v0.10.0

v0.9.0

What's Changed

• Miscellaneous changes to improve type infererability and precompilation times by @ConnectedSystems in #455
• Changes to improve performance of PAWN sensitivity analysis by @ConnectedSystems in #457
• Fix print_rules condition by @Zapiano in #460
• Update ADRIA logo by @Zapiano in #461
• Adjust PAWN function to support 1D matrix for convenience by @ConnectedSystems in #462
• Update Reef Tourism Index regression coefficient (temporary solution) by @ConnectedSystems in #466
• Include rule_extraction.jl in viz.jl by @Zapiano in #468
• Add new cluster_rules method that accepts BitVector or Vector{Bool} by @Zapiano in #467
• Add option to show GBRMPA management zones by @ConnectedSystems in #470
• Precompilation reduction by @ConnectedSystems in #469
• Update sensitivity module to follow Blue style by @ConnectedSystems in #471
• Update Doc mentioning blue style guide by @Zapiano in #472
• Update viz.rules_scatter to accept targeted clusters by @Zapiano in #475
• Remove locations with no space from consideration for interventions by @ConnectedSystems in #479
• Rename time_series_clustering and ts_cluster by @Zapiano in #478
• Fix duplicate x-axis values bug in viz.outcome_map() by @Rosejoycrocker in #442
• Add Documentation Sensitivity section for Rule Induction algorithm by @Zapiano in #477
• Update version number to 0.9.0 by @Rosejoycrocker in #497

Full Changelog: v0.8.0...v0.9.0

v0.8.0

What's Changed

• CompatHelper: bump compat for SparseArrayKit to 0.3, (keep existing compat) by @github-actions in #403
• Fix map display (default display when plotting Domain or ResultSet) by @ConnectedSystems in #407
• Fix excessive memory use (#405) by @ConnectedSystems in #409
• Update ReefMod interface to match new species list by @Rosejoycrocker in #408
• Adjustments to heritability based on feedback by @ConnectedSystems in #417
• Update docstrings with missing detail by @ConnectedSystems in #418
• Implement relevant struct to handle SIRUS rule extraction by @Zapiano in #420
• Small miscellaneous changes for scenario visualizations by @ConnectedSystems in #412
• Implement rule extracting function by @Zapiano in #421
• Updated Reef Indices by @ConnectedSystems in #415
• Remove dependency on ImageMagick in favour of ImageIO by @ConnectedSystems in #414
• Fix unnecessarily squashed figure when plotting outcome map for 1 factor by @ConnectedSystems in #425
• Move and modify behaviour of target_cluster function by @Zapiano in #424
• Fix workers crashing and leaking memory when running scenarios in parallel by @ConnectedSystems in #416
• Fix scenario metrics with field :scenario instead of :scenarios by @Zapiano in #430
• Fix error when running samples generated from sample_site_selection() by @Rosejoycrocker in #432
• Incorporate settler DHW tolerances by @ConnectedSystems in #437
• Address very slow extraction of relative cover values by @ConnectedSystems in #435
• Update prototype exploration UI to work with recent changes by @ConnectedSystems in #436
• Fix clustering map visualisation by @Zapiano in #439
• Fix loc_trajectory and per_loc function by @Zapiano in #438
• Fix time_series_clustering for variable series with k > 0 by @Zapiano in #433
• Update SIRUS StableRules type by @Zapiano in #443
• Add Blue Style Guide badge to README by @Zapiano in #441
• Fix print_rules adding & when there are two clauses by @Zapiano in #444
• Implement rule scatter plot function by @Zapiano in #422
• Documentation improvement by @Zapiano in #429
• More updates to documentation by @ConnectedSystems in #446

Full Changelog: v0.7.0...v0.8.0

v0.7.0

What's Changed

• Update docstrings for growth function by @ConnectedSystems in #375
• Add map visualization - displays k-area by @ConnectedSystems in #356
• Consider near-term conditions with greater weight than far-future conditions by @ConnectedSystems in #387
• Changes to number of species in ADRIA by @Rosejoycrocker in #380
• Temporal clustering for spatial data by @Zapiano in #382

Full Changelog: v0.6.0...v0.7.0

v0.7.0-dev.1

What's Changed

• Update use of functions due to new import approach by @ConnectedSystems in #334
• Migrate from SnoopPrecompile to PrecompileTools by @timholy in #335
• Add planning horizon factor by @ConnectedSystems in #336
• Replace use of area attribute/field with call to function site_area() to ensure correct values by @ConnectedSystems in #337
• Remove reference to defunct fields when making factors constant by @ConnectedSystems in #338
• Make use of planning horizon in sims by @ConnectedSystems in #340
• Changes to support running ADRIA with external model (ReefMod Engine) data by @ConnectedSystems in #341
• CompatHelper: add new compat entry for SimpleWeightedGraphs at version 1, (keep existing compat) by @github-actions in #343
• CompatHelper: add new compat entry for OrderedCollections at version 1, (keep existing compat) by @github-actions in #344
• CompatHelper: bump compat for StatsBase to 0.34, (keep existing compat) by @github-actions in #345
• Split ADRIA-mod domain definition by @ConnectedSystems in #346
• Add GBR zones by priority by @ConnectedSystems in #347
• Exit with error if given path is not a directory by @ConnectedSystems in #350
• Make Aviz into an extension package by @ConnectedSystems in #349
• CompatHelper: add new compat entry for Reexport at version 1, (keep existing compat) by @github-actions in #351
• CompatHelper: add new compat entry for ImageMagick at version 1, (keep existing compat) by @github-actions in #352
• Update bleaching mortality model to align with published paper by @ConnectedSystems in #354
• Add option to use JMcDM functions in ADRIA site selection by @Rosejoycrocker in #348
• Address mismatched number of elements under certain conditions by @ConnectedSystems in #358
• Remove Copras method due to erroring by @Rosejoycrocker in #359
• CompatHelper: bump compat for HypothesisTests to 0.11, (keep existing compat) by @github-actions in #363
• CompatHelper: add new compat entry for JMcDM at version 0.7, (keep existing compat) by @github-actions in #362
• Update documentation by @ConnectedSystems in #361
• Scenario discovery docs by @ConnectedSystems in #364
• Fix: Metric errors when applied to a single simulation by @ConnectedSystems in #365
• Address ranking errors in mcda outputs by @Rosejoycrocker in #367
• Add temporal clustering by @Zapiano in #370
• Fix incorrect type check by @Zapiano in #371
• CompatHelper: add new compat entry for Clustering at version 0.15, (keep existing compat) by @github-actions in #372
• CompatHelper: bump compat for Zarr to 0.9, (keep existing compat) by @github-actions in #373
• Update time series clustering and add visualization functionality by @Zapiano in #374
• Update scenario viz by @ConnectedSystems in #355
• Refactor run_scenarios to improve when running multiple rcps by @Zapiano in #376
• Bump version number and add new author by @Zapiano in #378
• Update docstrings for growth function by @ConnectedSystems in #375
• Add map visualization - displays k-area by @ConnectedSystems in #356
• Consider near-term conditions with greater weight than far-future conditions by @ConnectedSystems in #387
• Changes to number of species in ADRIA by @Rosejoycrocker in #380
• Temporal clustering for spatial data by @Zapiano in #382

New Contributors

• @timholy made their first contribution in #335
• @Zapiano made their first contribution in #370

Full Changelog: v0.5.0...v0.7.0-dev.1

v0.5.0

ADRIA v0.5.0

Diff since v0.4.5

Closed issues:

• Juvenile metric: investigate small values (#92)
• Update result set to derive spatial data from stored geopackage (#124)
• Adjust MCDA functions to be more generic (#177)
• Standardize to NamedDimsArray + AxisKeys (#200)
• Adjust scenario input IDs for clarity (#205)
• Use NamedDims+AxisKeys instead of matrix for MCDA decision matrices (#221)
• Add human-readable name to Parameter types (#230)
• Use Haversine instead of Euclidean distance (#236)
• Adjust definition or sampling of dist_thresh so that the value representing 'don't use distance sorting' is as likely as values representing using distance sorting (#238)
• Register package (#245)
• Change reference to Input Set to Domain to align with interface functions (#246)
• Update growth rates for size class 6 (#268)
• Release v0.4.5 (#272)
• Possible bug in site_selection (#284)
• Bug in site selection example (#285)
• Scenario juvenile metric returning implausible values (?) and values > 1 (#292)
• Create function which returns just the set of criteria values needed for MCDA (#296)
• map_to_discrete() erroring due to type mismatch (#304)
• run_site_selection() errors out (#308)
• [Viz/Analysis] Scenario outcomes (#311)
• [Viz/Analysis] sensitivity analysis (bar/heatmap) (#312)
• [Viz/Analysis] temporal sensitivity analysis (#313)
• [Viz/Analysis] Regional Sensitivity Analysis (#314)
• [Viz/Analysis] Outcome-based factor mapping (#315)

Merged pull requests:

• Add parameter name and description to model specification (#273) (@ConnectedSystems)
• Adjust coral growth rate for size class 6 (#274) (@ConnectedSystems)
• Remove references to Input Set (#275) (@ConnectedSystems)
• Fix: calculate distance between sites (#276) (@ConnectedSystems)
• Simplify display of model spec (#278) (@ConnectedSystems)
• Parametric ResultSet (#279) (@ConnectedSystems)
• Consolidate normalize (#280) (@ConnectedSystems)
• Changes to site selection functions (#282) (@Rosejoycrocker)
• Changes to address bug in site_selection example (addresses issue #285 ) (#286) (@Rosejoycrocker)
• Consolidate Named array types to use NamedDims+AxisKeys (#287) (@ConnectedSystems)
• Reduce allocations in load_domain() (#288) (@ConnectedSystems)
• Add criteria parameter which indicates whether distance sorting is used. (#290) (@Rosejoycrocker)
• Add function n_locations() to determine number of sites/reefs/clusters (#291) (@ConnectedSystems)
• Miscellaneous cleanup (#293) (@ConnectedSystems)
• Fix bug causing implausible juvenile indicator values (#294) (@ConnectedSystems)
• Adjust samples when use of distance thresholds is turned off (#295) (@ConnectedSystems)
• CompatHelper: add new compat entry for AxisKeys at version 0.2, (keep existing compat) (#297) (@github-actions[bot])
• Additional safety checks for sampling (#298) (@ConnectedSystems)
• Adds sampler which can sample only parameters needed for site selection (#299) (@Rosejoycrocker)
• Adds function which calculates sites selection frequency for a set of provided samples (#301) (@Rosejoycrocker)
• Fix error mapping continous samples to discrete values (#305) (@ConnectedSystems)
• Adjust shelter volume to remove hardcoded index and leverage NamedDimsArray (#306) (@ConnectedSystems)
• Fix initial slice potentially not including lowest value (#307) (@ConnectedSystems)
• Clean up Project.toml + Precompile (#309) (@ConnectedSystems)
• Correct issue with size of NamedDims array for storing ranks in run_site_selection() (#310) (@Rosejoycrocker)
• Initial indicative visualization (#318) (@ConnectedSystems)
• Fix function extension issues (#319) (@ConnectedSystems)
• Better check for constancy in RSA (#320) (@ConnectedSystems)
• Update exploration tool to latest ADRIA API (#321) (@ConnectedSystems)
• Additional docs for Domain/ResultSets (#322) (@ConnectedSystems)
• Add capability to fix factors in place (#325) (@ConnectedSystems)
• Initial ReefMod interface and functionality (#326) (@ConnectedSystems)

v0.4.5

ADRIA v0.4.5

Diff since v0.4.4

v0.4.4

ADRIA v0.4.4

Diff since v0.4.3

Merged pull requests:

• Initial documentation build (#244) (@ConnectedSystems)

v0.4.4-dev.1

ADRIA v0.4.4 Development release

What's Changed

• Initial documentation build by @ConnectedSystems in #244
• Add support for Regional Sensitivity Analysis (RSA) by @ConnectedSystems in #258
• Merge v0.4.4-dev by @ConnectedSystems in #259
• Add temporal sensitivity analyses based on the PAWN method by @ConnectedSystems in #261
• Metric restructure by @ConnectedSystems in #262
• CompatHelper: bump compat for ArchGDAL to 0.10, (keep existing compat) by @github-actions in #263

Full Changelog: v0.4.3...v0.4.4-dev.1