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Recent Releases of adria.jl

adria.jl - v0.12.0

What's Changed

  • update fecundity min area variable name for clarity by @eco-ben in https://github.com/open-AIMS/ADRIA.jl/pull/810
  • Apply changes to ADRIA to make it compatible with CoralBlox model by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/817
  • CompatHelper: add new compat entry for CoralBlox at version 1, (keep existing compat) by @github-actions[bot] in https://github.com/open-AIMS/ADRIA.jl/pull/821
  • Julia format GH workflow, format all files by @arlowhite in https://github.com/open-AIMS/ADRIA.jl/pull/790
  • Fix docs builder, add .git-blame-ignore-revs and document by @arlowhite in https://github.com/open-AIMS/ADRIA.jl/pull/823
  • fix helper dimension size error by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/824
  • Add reshape to fix dimension mismatch when logging dhw tolerances by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/827
  • updates docs github action to use Julia 1.10.* by @arlowhite in https://github.com/open-AIMS/ADRIA.jl/pull/829
  • Remove Manifest from gitignore by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/830
  • Fix docs errors by @arlowhite in https://github.com/open-AIMS/ADRIA.jl/pull/832
  • convert recruitment from relative area to area before use by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/834
  • Rename metrics :sites dimension with :locations by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/831
  • lowercase png extensions to fix Documenter by @arlowhite in https://github.com/open-AIMS/ADRIA.jl/pull/837
  • Fix cover loading and size class lower bound by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/833
  • feat: migrating and updating docker functionality + publish pipeline by @PeterBaker0 in https://github.com/open-AIMS/ADRIA.jl/pull/839
  • fix: stale links in docker docs by @PeterBaker0 in https://github.com/open-AIMS/ADRIA.jl/pull/843
  • Fix error in bin size for sensitivity.outcome_map by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/702
  • Overly constrained argument types causing tests to fail by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/844
  • feat: restore unit testing and add julia caching by @PeterBaker0 in https://github.com/open-AIMS/ADRIA.jl/pull/845
  • fix reefmod domain load initial cover by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/846
  • Add metadata to metrics YAXArrays by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/847
  • Improve summarize performance by using mapslices by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/862
  • Pin NetCDF.jl and Zarr.jl in order to pin DiskArrays.jl by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/864
  • Bump actions/checkout from 3 to 4 by @dependabot[bot] in https://github.com/open-AIMS/ADRIA.jl/pull/865
  • Bump docker/login-action from 2 to 3 by @dependabot[bot] in https://github.com/open-AIMS/ADRIA.jl/pull/866
  • Bump docker/build-push-action from 4 to 6 by @dependabot[bot] in https://github.com/open-AIMS/ADRIA.jl/pull/867
  • Bump docker/metadata-action from 4 to 5 by @dependabot[bot] in https://github.com/open-AIMS/ADRIA.jl/pull/868
  • Improvements to model performance by reducing allocations by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/871
  • Minor change for performance by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/877
  • Julia 1.11 Manifest and Pkg update by @arlowhite in https://github.com/open-AIMS/ADRIA.jl/pull/876
  • Apply CompatHelper suggestions, free NetCDF,Zarr; add & pin DiskArrays by @arlowhite in https://github.com/open-AIMS/ADRIA.jl/pull/878
  • LERC_jll 3 to 4, downgrade DimensionalData to 0.27.9, Julia Pkg update by @arlowhite in https://github.com/open-AIMS/ADRIA.jl/pull/879
  • Cyclone mortalities assigned to wrong group by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/888
  • Update code and dependencies to GeoMakie v0.7.x by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/884
  • DiskArrays 0.4.5, Pkg update by @arlowhite in https://github.com/open-AIMS/ADRIA.jl/pull/889
  • Viz metadata by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/863
  • Fix StackOverflow error when plotting maps by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/891
  • Add counterfactual minus guided/unguided diff at location level by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/726
  • Remove duplicate rules by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/899
  • Fix rule extraction to handle constant factors by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/870
  • Incorporate recruitment to growth constraints and cap seeding to habitable area by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/906
  • Add additional convenience functions and update docstrings by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/908
  • Remove defunct method seed_corals! by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/909
  • Fix DHW scenario viz again by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/903
  • Switch to logging number of coral deployed by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/910
  • Add DEA functions and plotting to ADRIA.analysis by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/896
  • Add method to display all DHW scenarios for the currently set RCP/SSP by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/914
  • Minor fix on docs by @vitorhirata in https://github.com/open-AIMS/ADRIA.jl/pull/920
  • Pin DiskArrays to 0.4.9 by @vitorhirata in https://github.com/open-AIMS/ADRIA.jl/pull/922
  • Updated factor bounds setting method by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/917
  • Pin DiskArrays to 0.4.9 in docs Manifest and v1.11 Manifest by @vitorhirata in https://github.com/open-AIMS/ADRIA.jl/pull/924
  • Small change to parameter description to avoid confusion by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/928
  • Add extraction of feature set to support analyses and assessment by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/907
  • Bump codecov/codecov-action from 4 to 5 by @dependabot[bot] in https://github.com/open-AIMS/ADRIA.jl/pull/901
  • CompatHelper: bump compat for DimensionalData to 0.29, (keep existing compat) by @github-actions[bot] in https://github.com/open-AIMS/ADRIA.jl/pull/931
  • CompatHelper: bump compat for Makie in [weakdeps] to 0.22, (keep existing compat) by @github-actions[bot] in https://github.com/open-AIMS/ADRIA.jl/pull/930
  • CompatHelper: bump compat for YAXArrays to 0.6, (keep existing compat) by @github-actions[bot] in https://github.com/open-AIMS/ADRIA.jl/pull/932
  • Fix tests of viz/spatial and metrics/spatial by @vitorhirata in https://github.com/open-AIMS/ADRIA.jl/pull/923
  • Avoid reshape for performance by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/933
  • Custom categorical distribution by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/927
  • Add spatial visualisations for decision matrices by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/893
  • Correct RCP identifier in result directory by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/937
  • Add cyclone mortality to documentation by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/936
  • Remove synopsis from documentation by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/938
  • Minor tweaks to taxa visualization by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/915
  • Update docs to configure Julia Formatter extension by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/939
  • Replace and deprecate remaining use of site_k_area by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/929
  • Considering spatial dispersal of intervention locations by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/934
  • Fix docs build by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/945
  • Bump julia-actions/julia-format from 3 to 4 by @dependabot[bot] in https://github.com/open-AIMS/ADRIA.jl/pull/948
  • Speed up timeseries clustering by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/949
  • Fix multiple tests by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/951
  • Changes to enable recent RME domain loading by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/952
  • Speedup bleaching by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/954
  • Update Manifest by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/957
  • Bump project version prior to new release by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/968

New Contributors

  • @eco-ben made their first contribution in https://github.com/open-AIMS/ADRIA.jl/pull/810
  • @vitorhirata made their first contribution in https://github.com/open-AIMS/ADRIA.jl/pull/920

Full Changelog: https://github.com/open-AIMS/ADRIA.jl/compare/v0.11.0...v0.12.0

- Julia
Published by Zapiano 10 months ago

adria.jl - 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 https://github.com/open-AIMS/ADRIA.jl/pull/610
  • Add a new ten site example domain for testing by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/628
  • Fix mcda method bugs by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/629
  • Fix setfactorbounds! out of bounds for discrete factors by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/631
  • Address MCDA error for single locations by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/640
  • Replaces distance sorting with restrictions on the number of selected locations in the same reef by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/635
  • Changes to make ADRIA precompilable under Julia v1.10 by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/646
  • Update use of Makie/GeoMakie to address deprecation errors by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/647
  • Add connectivity data to result set storage by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/643
  • Fix larval connectivity bug by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/648
  • Remove examples dir issue #584 by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/651
  • Update tests for new sampling method/factor definitions by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/653
  • Update factor type documentation by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/654
  • Update factor types and their use by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/636
  • Speed up calculation of truncated normal mean and cdf by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/652
  • Add a default size for scenario plots by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/657
  • CompatHelper: add new compat entry for StatsFuns at version 1, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/658
  • CompatHelper: add new compat entry for SpecialFunctions at version 2, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/659
  • Fix bleaching mortality by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/660
  • Clean up settler cover function to reduce confusion by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/662
  • Only load up relevant RME SSP datasets by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/663
  • Reset deployed-coral-risk-tol range by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/664
  • Clean up scenario running methods by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/665
  • Clean up use of TP matrices to align with conceptualisation of connectivity by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/667
  • Support updated domain structure by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/669
  • Adjustment to simulated events to address numerical errors by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/668
  • Return 0 in cases where lb > ub by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/666
  • Fix erroneous handling of location IDs by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/671
  • Fix error in domain loading when cluster_id is already in string format by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/673
  • Add test domain for ReefModDomain type by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/675
  • Additional setup instructions for code style and formatting by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/676
  • Fix cyclone sorting by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/683
  • removed deprecate functions and function calls by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/684
  • restructured documentation image directories by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/685
  • Fix readjustment of number of slices bug in RSA by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/679
  • Truncated normal changes by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/687
  • Allow user to set whatever bounds they wish by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/688
  • Switch to YAXArrays when runnin scenarios by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/690
  • Remove factors input from rsa() and use scenario dataframe column names instead by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/696
  • updated data loading test for migration to YAXArrays by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/697
  • Further updates to scenario runs with MCDA by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/698
  • Remove MKL from build process by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/705
  • Migrate metrics.jl to YAXArrays by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/709
  • Yax cube tests by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/704
  • Yax viz by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/703
  • Yax test update by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/700
  • Remove GC workaround by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/711
  • Yax migration miscellaneous by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/715
  • Keep metadata in results by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/716
  • CompatHelper: bump compat for DimensionalData to 0.26, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/714
  • Finalize update of standalone MCDA methods by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/717
  • Update all tests and remove NamedDims and AxisKeys from ADRIA.jl by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/718
  • Validating MCDA methods and initial clean/update of tests by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/719
  • Migrate from NamedDimsArrays to YAXArrays by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/695
  • Provide a succinct overview of MCDA by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/720
  • Add support to cyclone mortality to ReefModDomain by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/722
  • Save right intervention label at ResultSet ranks YAXArray by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/724
  • Hacky support for later RME reef id list by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/731
  • Add support for specifying locations by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/732
  • Support more vector types for maps by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/736
  • Clean up connectivity and centrality methods by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/737
  • Additional rank methods to determine number of locations intervened on per timestep by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/738
  • Collection of miscellaneous changes by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/740
  • Fix bug, min. locations to select > available locations by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/741
  • CompatHelper: bump compat for DimensionalData to 0.27, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/744
  • Connectivity viz by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/742
  • Fix locations selection in ReefMod datapackage cyclone mortality loading by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/723
  • Only rank locations with available area > 0 by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/734
  • use provided centrality measures instead of defaults by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/751
  • Improved support for spatial maps by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/750
  • Repeat mention that the VS Code extension is being setup by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/748
  • Convenience plotting method for connectivity/centralities by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/752
  • Support plotting DHW and cyclone (mortality) scenarios by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/758
  • Support deactivating environmental disturbances by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/759
  • RME Result Interface by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/745
  • add range to for loop by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/762
  • Visualization for taxonomy cover. by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/763
  • Fix erroneous function call in docstrings by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/773
  • CompatHelper: bump compat for NetCDF to 0.12, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/765
  • CompatHelper: add new compat entry for GraphMakie in [weakdeps] at version 0.5, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/766
  • CompatHelper: add new compat entry for GeoMakie in [weakdeps] at version 0.6, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/767
  • CompatHelper: add new compat entry for Makie in [weakdeps] at version 0.21, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/764
  • improve load_domain docs by @arlowhite in https://github.com/open-AIMS/ADRIA.jl/pull/733
  • Change assisted adaptation to a Discrete Uniform value by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/770
  • Use underlying data instead of YAXArray type by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/771
  • Fix mismatched function name in docstring by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/778
  • Fix site_level dosctring by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/782
  • Fix visualization type error by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/777
  • Add methods to extract deployment location info by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/774
  • Increase compression level for ResultSet by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/772
  • remove breakpoint in code by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/784
  • Clean up defunct dependencies by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/776
  • Add default option to sortkeys by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/787
  • Assortment of improvements to SIRUS and Time Series Clustering by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/786
  • Coerce to MultiPolygon instead of Polygon by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/793
  • julia-actions recommended dependabot.yml by @arlowhite in https://github.com/open-AIMS/ADRIA.jl/pull/791
  • Bump julia-actions/cache from 1 to 2 by @dependabot in https://github.com/open-AIMS/ADRIA.jl/pull/795
  • Bump julia-actions/setup-julia from 1 to 2 by @dependabot in https://github.com/open-AIMS/ADRIA.jl/pull/796
  • Bump actions/checkout from 2 to 4 by @dependabot in https://github.com/open-AIMS/ADRIA.jl/pull/797
  • Minor updates to geospatial functions/handling by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/798
  • Address tests failing due to type mismatch (scenario confint) by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/801
  • Fix depth min/offset being sampled for counterfactual scenarios by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/802
  • build: prototype CD integration with Provena to update model by @PeterBaker0 in https://github.com/open-AIMS/ADRIA.jl/pull/808
  • Fix broken tests by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/809
  • Fix sampling test by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/814
  • Increase release version by @DanTanAtAims in https://github.com/open-AIMS/ADRIA.jl/pull/815

New Contributors

  • @arlowhite made their first contribution in https://github.com/open-AIMS/ADRIA.jl/pull/733
  • @dependabot made their first contribution in https://github.com/open-AIMS/ADRIA.jl/pull/795
  • @PeterBaker0 made their first contribution in https://github.com/open-AIMS/ADRIA.jl/pull/808

Full Changelog: https://github.com/open-AIMS/ADRIA.jl/compare/v0.10.0...v0.11.0

- Julia
Published by DanTanAtAims almost 2 years ago

adria.jl - v0.10.0

What's Changed

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

Full Changelog: https://github.com/open-AIMS/ADRIA.jl/compare/v0.9.0...v0.10.0

- Julia
Published by Zapiano over 2 years ago

adria.jl - v0.9.0

What's Changed

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

Full Changelog: https://github.com/open-AIMS/ADRIA.jl/compare/v0.8.0...v0.9.0

- Julia
Published by Rosejoycrocker over 2 years ago

adria.jl - v0.8.0

What's Changed

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

Full Changelog: https://github.com/open-AIMS/ADRIA.jl/compare/v0.7.0...v0.8.0

- Julia
Published by ConnectedSystems almost 3 years ago

adria.jl - v0.7.0

What's Changed

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

Full Changelog: https://github.com/open-AIMS/ADRIA.jl/compare/v0.6.0...v0.7.0

- Julia
Published by Rosejoycrocker almost 3 years ago

adria.jl - v0.7.0-dev.1

What's Changed

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

New Contributors

  • @timholy made their first contribution in https://github.com/open-AIMS/ADRIA.jl/pull/335
  • @Zapiano made their first contribution in https://github.com/open-AIMS/ADRIA.jl/pull/370

Full Changelog: https://github.com/open-AIMS/ADRIA.jl/compare/v0.5.0...v0.7.0-dev.1

- Julia
Published by Zapiano almost 3 years ago

adria.jl - 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 distthresh 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 `siteselection(#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) -maptodiscrete()erroring due to type mismatch (#304) -runsiteselection()` 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 siteselection example (addresses issue #285 ) (#286) (@Rosejoycrocker) - Consolidate Named array types to use NamedDims+AxisKeys (#287) (@ConnectedSystems) - Reduce allocations in `loaddomain()(#288) (@ConnectedSystems) - Add criteria parameter which indicates whether distance sorting is used. (#290) (@Rosejoycrocker) - Add functionnlocations()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 inrunsite_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)

- Julia
Published by github-actions[bot] about 3 years ago

adria.jl - v0.4.5

ADRIA v0.4.5

Diff since v0.4.4

- Julia
Published by github-actions[bot] over 3 years ago

adria.jl - v0.4.4

ADRIA v0.4.4

Diff since v0.4.3

Merged pull requests: - Initial documentation build (#244) (@ConnectedSystems)

- Julia
Published by github-actions[bot] over 3 years ago

adria.jl - v0.4.4-dev.1

ADRIA v0.4.4 Development release

What's Changed

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

Full Changelog: https://github.com/open-AIMS/ADRIA.jl/compare/v0.4.3...v0.4.4-dev.1

- Julia
Published by ConnectedSystems over 3 years ago

adria.jl - v0.4.3

What's Changed

  • Improved model performance
  • Support for multi-objective analysis
  • Adjust rankings to match site reordering due to distance sorting by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/224
  • Add depth column to MCDA decision matrix to be used in seeding and shading decision matrices by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/225
  • Remove additional weighting that is no longer needed by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/227
  • Re-order site data by unique site id column to align logged site ids by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/228
  • CompatHelper: bump compat for GLMakie to 0.8, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/233
  • v0.4.3 merge by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/241
  • Various package dependency version bumps via CompatHelper

Full Changelog: https://github.com/open-AIMS/ADRIA.jl/compare/v0.4.2...v0.4.3

- Julia
Published by ConnectedSystems over 3 years ago

adria.jl - v0.4.2

What's Changed

  • Mix normalisation bug in MCDA by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/162
  • Miscellaneous changes to clean up code by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/161
  • Scenario relative cover metric to return cluster wide values by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/164
  • Fixes to ODE formulation and indexing by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/165
  • CompatHelper: add new compat entry for Distributions at version 0.25, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/166
  • Changes to top_N_sites rank metric by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/167
  • Support runs across multiple RCPs by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/163
  • Support extraction of geometry data from inconsistent column names by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/169
  • Robustness metrics by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/172
  • Replace bleaching resistance with uncertain bleaching sensitivity by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/174
  • Incorporation of zoning criteria in MCDA by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/175
  • Add sampling methods by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/176
  • Add dhw summary statistics to ResultSet by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/181
  • Spread site selection by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/180
  • Corrections to assignment of growth rates and tests for coral_spec() parameters by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/183
  • Coral model adjustments by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/184
  • Switch to netCDF by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/185
  • Correct connectivity alignment by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/186
  • Changes to support Multi-Objective Optimization by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/188
  • Bug fix for ODE + change to definition of basal area by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/190
  • Update example domain with netCDF format datacubes by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/187
  • Tentative support for Multi-Objective Robust Optimization by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/189
  • Reorganize data loading functions by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/193
  • Adjust coral wave mortalities following recommendation by Ken by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/195
  • Consolidate site area calcs #170 by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/191
  • Performance changes by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/192
  • Connectivity update by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/197
  • Adding within size class growth for size class 6 back in for ODE and adjusting within size class growth rates by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/196
  • Update metrics by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/199
  • Updated background mortality values by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/201
  • Minor changes to get visualizations working for v0.4.2 by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/202
  • Add distance sorting to MCDA by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/198
  • v0.4.2 dev merge by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/203

Full Changelog: https://github.com/open-AIMS/ADRIA.jl/compare/v0.4.1...v0.4.2

- Julia
Published by ConnectedSystems over 3 years ago

adria.jl - v0.4.1

What's Changed

  • Adding function to generate csv summary result set by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/125
  • Fixes typos which were not picked up in previous PR by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/126
  • Include PowerBI post processing file in module by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/131
  • Fixes for recruitment issue by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/137
  • Fix site ranking log by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/140
  • Correct simplified settler cover calculation by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/141
  • Fixes undefined absolutesitecoral_cover by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/142
  • Remove tf from simulation constants by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/143
  • Fixes missed tf definition by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/144
  • Distributes seeded corals at selected sites according to space available by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/145
  • Add timeframe datapackage property by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/147
  • Adds function to distribute seeded corals at selected sites according to space available (addresses #146) by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/148
  • Update bleaching mortality model by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/149
  • Applying depth offset to align with IPMF by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/154
  • Additional metrics for site rank analysis by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/153
  • Add copy of model spec to ResultSet by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/155
  • Add incoming and outgoing connectivity ranks and criteria by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/156
  • Adds function to find top n sites in result set for each scenario by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/159
  • Adding coral cover area criteria in terms of absolute coral cover by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/160

Full Changelog: https://github.com/open-AIMS/ADRIA.jl/compare/v0.4...v0.4.1

- Julia
Published by ConnectedSystems almost 4 years ago

adria.jl - v0.4

What's Changed

  • More appropriate indication of cluster-wide outcomes by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/97
  • Expand docstring for proportional_adjustment() for clarity by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/107
  • Ensure proportional adjustment of coral cover remain in bounds by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/106
  • Address TODO: Extract non-coral parameters to reduce memory use by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/105
  • Unguided selection by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/112
  • Sysimage builder by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/115
  • Fix log scaling error in MCDA coral cover criteria by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/117
  • Detailed docstrings added + shading matrix function added by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/118
  • Address small Shelter Volume outcomes (#91) by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/108
  • Fixes small issue introduced by compartmentalising SE and SH matrix creation by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/122

Full Changelog: https://github.com/open-AIMS/ADRIA.jl/compare/v0.3.2...v0.4

- Julia
Published by ConnectedSystems almost 4 years ago

adria.jl - v0.3.2 dev release

What's Changed

  • Adding new total_cover function to RCI calculation by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/80
  • Changes to support site level metrics by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/84
  • Changes to scaling for MCDA criteria (site capacity) (address #79) by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/85
  • Relative cover input to RCI be relative to the sites max coral cover? by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/89
  • Scenario focused metrics by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/93

New Contributors

  • @Rosejoycrocker made their first contribution in https://github.com/open-AIMS/ADRIA.jl/pull/80

Full Changelog: https://github.com/open-AIMS/ADRIA.jl/compare/v0.2.1...v0.3.2

- Julia
Published by ConnectedSystems almost 4 years ago

adria.jl - v0.2.1

Includes minor bug fixes to address:

  • Error when handling missing sites in site data and connectivity
  • Mismatched return types from summarized relative cover metric
  • Default value for deployed_coral_risk_tol out of bounds
  • Include upper/lower bounds when filtering sites based on depth.

- Julia
Published by ConnectedSystems about 4 years ago

adria.jl - v0.2

First stable development release

What's Changed

  • CompatHelper: add new compat entry for GeoDataFrames at version 0.2, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/20
  • CompatHelper: add new compat entry for GraphPlot at version 0.5, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/19
  • CompatHelper: add new compat entry for OrdinaryDiffEq at version 6, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/18
  • CompatHelper: add new compat entry for CSV at version 0.10, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/2
  • CompatHelper: add new compat entry for WinRPM at version 1, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/14
  • CompatHelper: add new compat entry for Plots at version 1, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/16
  • CompatHelper: add new compat entry for ModelParameters at version 0.3, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/12
  • CompatHelper: add new compat entry for StaticArrays at version 1, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/11
  • CompatHelper: add new compat entry for BenchmarkTools at version 1, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/15
  • CompatHelper: add new compat entry for Graphs at version 1, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/10
  • CompatHelper: add new compat entry for DifferentialEquations at version 7, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/17
  • CompatHelper: add new compat entry for Setfield at version 0.8, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/13
  • CompatHelper: add new compat entry for ModelingToolkit at version 8, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/3
  • CompatHelper: add new compat entry for DataFrames at version 1, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/9
  • CompatHelper: add new compat entry for IJulia at version 1, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/6
  • CompatHelper: add new compat entry for ProfileView at version 1, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/8
  • CompatHelper: add new compat entry for Compose at version 0.9, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/4
  • CompatHelper: add new compat entry for BlackBoxOptim at version 0.6, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/5
  • CompatHelper: add new compat entry for MATLAB at version 0.8, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/7
  • CompatHelper: add new compat entry for ProgressMeter at version 1, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/67
  • CompatHelper: bump compat for Setfield to 1, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/72
  • CompatHelper: add new compat entry for GR at version 0.64, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/73
  • CompatHelper: add new compat entry for CpuId at version 0.3, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/74
  • Site population cap by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/76

New Contributors

  • @github-actions made their first contribution in https://github.com/open-AIMS/ADRIA.jl/pull/20
  • @ConnectedSystems made their first contribution in https://github.com/open-AIMS/ADRIA.jl/pull/76

Full Changelog: https://github.com/open-AIMS/ADRIA.jl/commits/v0.2

- Julia
Published by ConnectedSystems about 4 years ago