Recent Releases of ADRIA.jl

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 set_factor_bounds! 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 _sort_keys 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

Biosphere - Conservation and Restoration - Julia
Published by DanTanAtAims 9 months 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 _time_labels 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 per_loc and loc_trajectory 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 _check_discrete 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 location_selection_frequency() 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

Biosphere - Conservation and Restoration - Julia
Published by Zapiano over 1 year 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 time_series_clustering 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

Biosphere - Conservation and Restoration - Julia
Published by Rosejoycrocker over 1 year 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 loc_trajectory and per_loc function by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/438
Fix time_series_clustering 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

Biosphere - Conservation and Restoration - Julia
Published by ConnectedSystems over 1 year 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

Biosphere - Conservation and Restoration - Julia
Published by Rosejoycrocker over 1 year 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

Biosphere - Conservation and Restoration - Julia
Published by Zapiano almost 2 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 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)

Biosphere - Conservation and Restoration - Julia
Published by github-actions[bot] about 2 years ago

ADRIA.jl - v0.4.5

ADRIA v0.4.5

Diff since v0.4.4

Biosphere - Conservation and Restoration - Julia
Published by github-actions[bot] about 2 years ago

ADRIA.jl - v0.4.4

ADRIA v0.4.4

Diff since v0.4.3

Merged pull requests:

Initial documentation build (#244) (@ConnectedSystems)

Biosphere - Conservation and Restoration - Julia
Published by github-actions[bot] over 2 years ago

ADRIA.jl - v0.4.4-dev.1

ADRIA v0.4.4 Development release