ADRIA-v0.17.0

ADRIA ADRIA-v0.17.0

What's Changed

• docs: document where definition of maximum shelter volume is defined by @DanTanAtAims in #1120
• Fixes NaN in Dirichlet sampling by @ConnectedSystems in #1124
• Overhaul documentation system by @ConnectedSystems in #1121
• fix: when a domain is loaded with no wave data it still samples scena… by @DanTanAtAims in #1122
• fix: support dynamic year axis in Plotly backend by @DanTanAtAims in #1123
• Updates to visualization system for consistency by @ConnectedSystems in #1126
• Package reorg to monorepo by @ConnectedSystems in #1127
• Improves DHW attenuation at depth for bleaching mortality by @ConnectedSystems and @Zapiano in #1128

Breaking changes

ADRIA has been separated into subpackages:

• ADRIA: Provides core simulation and assessment infrastructure
• ADRIAanalysis: Provides the decision analysis and assessment functionality
• ADRIAviz: Provides the visualization capability

See the documentation for an overview.

Full Changelog: v0.16.0...v0.17.0

Merged pull requests:

• CompatHelper: add new compat entry for CSV at version 0.10, (keep existing compat) (#2) (@github-actions[bot])
• CompatHelper: add new compat entry for ModelingToolkit at version 8, (keep existing compat) (#3) (@github-actions[bot])
• CompatHelper: add new compat entry for Compose at version 0.9, (keep existing compat) (#4) (@github-actions[bot])
• CompatHelper: add new compat entry for BlackBoxOptim at version 0.6, (keep existing compat) (#5) (@github-actions[bot])
• CompatHelper: add new compat entry for IJulia at version 1, (keep existing compat) (#6) (@github-actions[bot])
• CompatHelper: add new compat entry for MATLAB at version 0.8, (keep existing compat) (#7) (@github-actions[bot])
• CompatHelper: add new compat entry for ProfileView at version 1, (keep existing compat) (#8) (@github-actions[bot])
• CompatHelper: add new compat entry for DataFrames at version 1, (keep existing compat) (#9) (@github-actions[bot])
• CompatHelper: add new compat entry for Graphs at version 1, (keep existing compat) (#10) (@github-actions[bot])
• CompatHelper: add new compat entry for StaticArrays at version 1, (keep existing compat) (#11) (@github-actions[bot])
• CompatHelper: add new compat entry for ModelParameters at version 0.3, (keep existing compat) (#12) (@github-actions[bot])
• CompatHelper: add new compat entry for Setfield at version 0.8, (keep existing compat) (#13) (@github-actions[bot])
• CompatHelper: add new compat entry for WinRPM at version 1, (keep existing compat) (#14) (@github-actions[bot])
• CompatHelper: add new compat entry for BenchmarkTools at version 1, (keep existing compat) (#15) (@github-actions[bot])
• CompatHelper: add new compat entry for Plots at version 1, (keep existing compat) (#16) (@github-actions[bot])
• CompatHelper: add new compat entry for DifferentialEquations at version 7, (keep existing compat) (#17) (@github-actions[bot])
• CompatHelper: add new compat entry for OrdinaryDiffEq at version 6, (keep existing compat) (#18) (@github-actions[bot])
• CompatHelper: add new compat entry for GraphPlot at version 0.5, (keep existing compat) (#19) (@github-actions[bot])
• CompatHelper: add new compat entry for GeoDataFrames at version 0.2, (keep existing compat) (#20) (@github-actions[bot])
• CompatHelper: add new compat entry for ProgressMeter at version 1, (keep existing compat) (#67) (@github-actions[bot])
• CompatHelper: bump compat for Setfield to 1, (keep existing compat) (#72) (@github-actions[bot])
• CompatHelper: add new compat entry for GR at version 0.64, (keep existing compat) (#73) (@github-actions[bot])
• CompatHelper: add new compat entry for CpuId at version 0.3, (keep existing compat) (#74) (@github-actions[bot])
• Site population cap (#76) (@ConnectedSystems)
• Adding new total_cover function to RCI calculation (#80) (@Rosejoycrocker)
• Changes to support site level metrics (#84) (@ConnectedSystems)
• Changes to scaling for MCDA criteria (site capacity) (attempts to address #79) (#85) (@Rosejoycrocker)
• Relative cover input to RCI be relative to the sites max coral cover? (#89) (@ConnectedSystems)
• Scenario focused metrics (#93) (@ConnectedSystems)
• More appropriate indication of cluster-wide outcomes (#97) (@ConnectedSystems)
• Address TODO: Extract non-coral parameters to reduce memory use (#105) (@ConnectedSystems)
• Ensure proportional adjustment of coral cover remain in bounds (#106) (@ConnectedSystems)
• Expand docstring for proportional_adjustment() for clarity (#107) (@ConnectedSystems)
• Address small Shelter Volume outcomes (#91) (#108) (@ConnectedSystems)
• Unguided selection (#112) (@ConnectedSystems)
• Sysimage builder (#115) (@ConnectedSystems)
• Fix log scaling error in MCDA coral cover criteria (#117) (@Rosejoycrocker)
• Detailed docstrings added + shading matrix function added (#118) (@Rosejoycrocker)
• Environmental data layer component for ADRIA ecosystem model (#120) (@ConnectedSystems)
• Fixes small issue introduced by compartmentalising SE and SH matrix creation (#122) (@Rosejoycrocker)
• Adding function to generate csv summary result set (#125) (@Rosejoycrocker)
• Fixes typos which were not picked up in previous PR (#126) (@Rosejoycrocker)
• Include PowerBI post processing file in module (#131) (@ConnectedSystems)
• Fixes for recruitment issue (#137) (@ConnectedSystems)
• Fix site ranking log (#140) (@ConnectedSystems)
• Correct simplified settler cover calculation (#141) (@ConnectedSystems)
• Fixes undefined absolute_site_coral_cover (#142) (@Rosejoycrocker)
• Remove tf from simulation constants (#143) (@ConnectedSystems)
• Fixes missed tf definition (#144) (@Rosejoycrocker)
• Distributes seeded corals at selected sites according to space available (#145) (@Rosejoycrocker)
• Add timeframe datapackage property (#147) (@ConnectedSystems)
• Adds function to distribute seeded corals at selected sites according to space available (addresses #146) (#148) (@Rosejoycrocker)
• Update bleaching mortality model (#149) (@ConnectedSystems)
• CompatHelper: bump compat for PkgVersion to 0.3, (keep existing compat) (#150) (@github-actions[bot])
• Additional metrics for site rank analysis (#153) (@ConnectedSystems)
• Applying depth offset to align with IPMF (#154) (@ConnectedSystems)
• Add copy of model spec to ResultSet (#155) (@ConnectedSystems)
• Add incoming and outgoing connectivity ranks and criteria (#156) (@ConnectedSystems)
• Adds function to find top n sites in result set for each scenario (#159) (@Rosejoycrocker)
• Adding coral cover area criteria in terms of absolute coral cover (#160) (@Rosejoycrocker)
• Miscellaneous changes to clean up code (#161) (@ConnectedSystems)
• Mix normalisation bug in MCDA (#162) (@Rosejoycrocker)
• Support runs across multiple RCPs (#163) (@ConnectedSystems)
• Scenario relative cover metric to return cluster wide values (#164) (@ConnectedSystems)
• Fixes to ODE formulation and indexing (#165) (@Rosejoycrocker)
• CompatHelper: add new compat entry for Distributions at version 0.25, (keep existing compat) (#166) (@github-actions[bot])
• Changes to top_N_sites rank metric (#167) (@ConnectedSystems)
• Support extraction of geometry data from inconsistent column names (#169) (@ConnectedSystems)
• Robustness metrics (#172) (@ConnectedSystems)
• Replace bleaching resistance with uncertain bleaching sensitivity (#174) (@ConnectedSystems)
• Incorporation of zoning criteria in MCDA (#175) (@Rosejoycrocker)
• Add sampling methods (#176) (@ConnectedSystems)
• Spread site selection (#180) (@ConnectedSystems)
• Add dhw summary statistics to ResultSet (#181) (@Rosejoycrocker)
• Corrections to assignment of growth rates and tests for coral_spec() parameters (#183) (@Rosejoycrocker)
• Coral model adjustments (#184) (@ConnectedSystems)
• Switch to netCDF (#185) (@ConnectedSystems)
• Correct connectivity alignment (#186) (@ConnectedSystems)
• Update example domain with netCDF format datacubes (#187) (@ConnectedSystems)
• Changes to support Multi-Objective Optimization (#188) (@ConnectedSystems)
• Tentative support for Multi-Objective Robust Optimization (#189) (@ConnectedSystems)
• Bug fix for ODE + change to definition of basal area (#190) (@Rosejoycrocker)
• Consolidate site area calcs #170 (#191) (@ConnectedSystems)
• Performance changes (#192) (@ConnectedSystems)
• Reorganize data loading functions (#193) (@ConnectedSystems)
• Adjust coral wave mortalities following recommendation by Ken (#195) (@Rosejoycrocker)
• Adding within size class growth for size class 6 back in for ODE and adjusting within size class growth rates (#196) (@Rosejoycrocker)
• Connectivity update (#197) (@ConnectedSystems)
• Add distance sorting to MCDA (#198) (@Rosejoycrocker)
• Update metrics (#199) (@ConnectedSystems)
• Updated background mortality values (#201) (@ConnectedSystems)
• Minor changes to get visualizations working for v0.4.2 (#202) (@ConnectedSystems)
• v0.4.2 dev merge (#203) (@ConnectedSystems)
• CompatHelper: add new compat entry for GeoInterface at version 1, (keep existing compat) (#206) (@github-actions[bot])
• CompatHelper: add new compat entry for RelocatableFolders at version 1, (keep existing compat) (#207) (@github-actions[bot])
• CompatHelper: add new compat entry for Surrogates at version 6, (keep existing compat) (#208) (@github-actions[bot])
• CompatHelper: add new compat entry for FileIO at version 1, (keep existing compat) (#209) (@github-actions[bot])
• CompatHelper: add new compat entry for DecisionTree at version 0.11, (keep existing compat) (#210) (@github-actions[bot])
• CompatHelper: add new compat entry for Distances at version 0.10, (keep existing compat) (#211) (@github-actions[bot])
• CompatHelper: add new compat entry for Combinatorics at version 1, (keep existing compat) (#212) (@github-actions[bot])
• CompatHelper: add new compat entry for BlackBoxOptim at version 0.6, (keep existing compat) (#213) (@github-actions[bot])
• CompatHelper: add new compat entry for SnoopPrecompile at version 1, (keep existing compat) (#214) (@github-actions[bot])
• CompatHelper: add new compat entry for Bootstrap at version 2, (keep existing compat) (#215) (@github-actions[bot])
• CompatHelper: add new compat entry for HypothesisTests at version 0.10, (keep existing compat) (#216) (@github-actions[bot])
• CompatHelper: add new compat entry for GeoFormatTypes at version 0.4, (keep existing compat) (#217) (@github-actions[bot])
• CompatHelper: add new compat entry for NCDatasets at version 0.12, (keep existing compat) (#218) (@github-actions[bot])
• CompatHelper: add new compat entry for GLMakie at version 0.7, (keep existing compat) (#219) (@github-actions[bot])
• CompatHelper: add new compat entry for GeoMakie at version 0.4, (keep existing compat) (#220) (@github-actions[bot])
• Adjust rankings to match site reordering due to distance sorting (#224) (@Rosejoycrocker)
• Add depth column to MCDA decision matrix to be used in seeding and shading decision matrices (#225) (@Rosejoycrocker)
• Remove additional weighting that is no longer needed (#227) (@ConnectedSystems)
• Re-order site data by unique site id column to align logged site ids (#228) (@ConnectedSystems)
• CompatHelper: bump compat for GLMakie to 0.8, (keep existing compat) (#233) (@github-actions[bot])
• v0.4.3 merge (#241) (@ConnectedSystems)
• Initial documentation build (#244) (@ConnectedSystems)
• Add support for Regional Sensitivity Analysis (RSA) (#258) (@ConnectedSystems)
• Merge v0.4.4-dev (#259) (@ConnectedSystems)
• Add temporal sensitivity analyses based on the PAWN method (#261) (@ConnectedSystems)
• Metric restructure (#262) (@ConnectedSystems)
• CompatHelper: bump compat for ArchGDAL to 0.10, (keep existing compat) (#263) (@github-actions[bot])
• v0.4.4-dev.1 (#266) (@ConnectedSystems)
• 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)
• Move n_adapt from Intervention component to Coral component (#332) (@ConnectedSystems)
• Update use of functions due to new import approach (#334) (@ConnectedSystems)
• Migrate from SnoopPrecompile to PrecompileTools (#335) (@timholy)
• Add planning horizon factor (#336) (@ConnectedSystems)
• Replace use of area attribute/field with call to function site_area() to ensure correct values (#337) (@ConnectedSystems)
• Remove reference to defunct fields when making factors constant (#338) (@ConnectedSystems)
• Fix error caused by mismatched locations (#339) (@ConnectedSystems)
• Make use of planning horizon in sims (#340) (@ConnectedSystems)
• Changes to support running ADRIA with external model (ReefMod Engine) data (#341) (@ConnectedSystems)
• CompatHelper: add new compat entry for SimpleWeightedGraphs at version 1, (keep existing compat) (#343) (@github-actions[bot])
• CompatHelper: add new compat entry for OrderedCollections at version 1, (keep existing compat) (#344) (@github-actions[bot])
• CompatHelper: bump compat for StatsBase to 0.34, (keep existing compat) (#345) (@github-actions[bot])
• Split ADRIA-mod domain definition (#346) (@ConnectedSystems)
• Add GBR zones by priority (#347) (@ConnectedSystems)
• Add option to use JMcDM functions in ADRIA site selection (#348) (@Rosejoycrocker)
• Make Aviz into an extension package (#349) (@ConnectedSystems)
• Exit with error if given path is not a directory (#350) (@ConnectedSystems)
• CompatHelper: add new compat entry for Reexport at version 1, (keep existing compat) (#351) (@github-actions[bot])
• CompatHelper: add new compat entry for ImageMagick at version 1, (keep existing compat) (#352) (@github-actions[bot])
• Update bleaching mortality model to align with published paper (#354) (@ConnectedSystems)
• Update scenario viz (#355) (@ConnectedSystems)
• Add map visualization - displays k-area (#356) (@ConnectedSystems)
• Address mismatched number of elements under certain conditions (#358) (@ConnectedSystems)
• Remove Copras method due to erroring (#359) (@Rosejoycrocker)
• Update documentation (#361) (@ConnectedSystems)
• CompatHelper: add new compat entry for JMcDM at version 0.7, (keep existing compat) (#362) (@github-actions[bot])
• CompatHelper: bump compat for HypothesisTests to 0.11, (keep existing compat) (#363) (@github-actions[bot])
• Scenario discovery docs (#364) (@ConnectedSystems)
• Fix: Metric errors when applied to a single simulation (#365) (@ConnectedSystems)
• Address ranking errors in mcda outputs (#367) (@Rosejoycrocker)
• Add temporal clustering (#370) (@Zapiano)
• Fix incorrect type check (#371) (@Zapiano)
• CompatHelper: add new compat entry for Clustering at version 0.15, (keep existing compat) (#372) (@github-actions[bot])
• CompatHelper: bump compat for Zarr to 0.9, (keep existing compat) (#373) (@github-actions[bot])
• Update time series clustering and add visualization functionality (#374) (@Zapiano)
• Update docstrings for growth function (#375) (@ConnectedSystems)
• Refactor run_scenarios to improve when running multiple rcps (#376) (@Zapiano)
• Bump version number and add new author (#378) (@Zapiano)
• Changes to number of species in ADRIA (#380) (@Rosejoycrocker)
• Distribution-based bleaching mortality to capture natural adaptation and heritability (#381) (@ConnectedSystems)
• Temporal clustering for spatial data (#382) (@Zapiano)
• Remove duplicate function recruitment (#385) (@ConnectedSystems)
• Reorganize package structure (#386) (@ConnectedSystems)
• Consider near-term conditions with greater weight than far-future conditions (#387) (@ConnectedSystems)
• Update release guide (#389) (@ConnectedSystems)
• Changes to ode solver and time step for efficiency improvements (#390) (@Rosejoycrocker)
• Add adaptive=false specification and remove tolerances (#391) (@Rosejoycrocker)
• Scenario viz change (#393) (@ConnectedSystems)
• CompatHelper: add new compat entry for JuliennedArrays at version 0.4, (keep existing compat) (#395) (@github-actions[bot])
• CompatHelper: add new compat entry for FLoops at version 0.2, (keep existing compat) (#396) (@github-actions[bot])
• Fix bug: Use wave condition for current timestep, not previous (#397) (@ConnectedSystems)
• Update comment to reflect changes for wave condition usage (#398) (@ConnectedSystems)
• Incorrect function being called (#400) (@ConnectedSystems)
• Remove use of batch sizes when running parallel scenarios (#401) (@ConnectedSystems)
• CompatHelper: bump compat for SparseArrayKit to 0.3, (keep existing compat) (#403) (@github-actions[bot])
• Fix map display (default display when plotting Domain or ResultSet) (#407) (@ConnectedSystems)
• Update ReefMod interface to match new species list (#408) (@Rosejoycrocker)
• Fix excessive memory use (#405) (#409) (@ConnectedSystems)
• Small miscellaneous changes for scenario visualizations (#412) (@ConnectedSystems)
• Remove dependency on ImageMagick in favour of ImageIO (#414) (@ConnectedSystems)
• Updated Reef Indices (#415) (@ConnectedSystems)
• Fix workers crashing and leaking memory when running scenarios in parallel (#416) (@ConnectedSystems)
• Adjustments to heritability based on feedback (#417) (@ConnectedSystems)
• Update docstrings with missing detail (#418) (@ConnectedSystems)
• Implement relevant struct to handle SIRUS rule extraction (#420) (@Zapiano)
• Implement rule extracting function (#421) (@Zapiano)
• Implement rule scatter plot function (#422) (@Zapiano)
• Move and modify behaviour of target_cluster function (#424) (@Zapiano)
• Fix unnecessarily squashed figure when plotting outcome map for 1 factor (#425) (@ConnectedSystems)
• Documentation improvement (#429) (@Zapiano)
• Fix scenario metrics with field :scenario instead of :scenarios (#430) (@Zapiano)
• Adds a series of aggregation functions for location selection ranks (#431) (@Rosejoycrocker)
• Fix error when running samples generated from sample_site_selection() (#432) (@Rosejoycrocker)
• Fix time_series_clustering for variable series with k > 0 (#433) (@Zapiano)
• Add functions for repeated tasks when performing location selection (#434) (@Rosejoycrocker)
• Address very slow extraction of relative cover values (#435) (@ConnectedSystems)
• Update prototype exploration UI to work with recent changes (#436) (@ConnectedSystems)
• Incorporate settler DHW tolerances (#437) (@ConnectedSystems)
• Fix loc_trajectory and per_loc function (#438) (@Zapiano)
• Fix clustering map visualisation (#439) (@Zapiano)
• Add Blue Style Guide badge to README (#441) (@Zapiano)
• Fix duplicate x-axis values bug in viz.outcome_map() (#442) (@Rosejoycrocker)
• Update SIRUS StableRules type (#443) (@Zapiano)
• Fix print_rules adding & when there are two clauses (#444) (@Zapiano)
• More updates to documentation (#446) (@ConnectedSystems)
• Functions to plot spatial distributions of site selection frequencies (#449) (@Rosejoycrocker)
• Miscellaneous changes to improve type infererability and precompilation times (#455) (@ConnectedSystems)
• Changes to improve performance of PAWN sensitivity analysis (#457) (@ConnectedSystems)
• Fix print_rules condition (#460) (@Zapiano)
• Update ADRIA logo (#461) (@Zapiano)
• Adjust PAWN function to support 1D matrix for convenience (#462) (@ConnectedSystems)
• Add function to find robust scenarios across several metrics (#463) (@Zapiano)
• Update Reef Tourism Index regression coefficient (temporary solution) (#466) (@ConnectedSystems)
• Add new cluster_rules method that accepts BitVector or Vector{Bool} (#467) (@Zapiano)
• Include rule_extraction.jl in viz.jl (#468) (@Zapiano)
• Precompilation reduction (#469) (@ConnectedSystems)
• Add option to show GBRMPA management zones (#470) (@ConnectedSystems)
• Update sensitivity module to follow Blue style (#471) (@ConnectedSystems)
• Update Doc mentioning blue style guide (#472) (@Zapiano)
• Update viz.rules_scatter to accept targeted clusters (#475) (@Zapiano)
• Deprecate run_scenarios(scens, dom, ...) (#476) (@ConnectedSystems)
• Add Documentation Sensitivity section for Rule Induction algorithm (#477) (@Zapiano)
• Rename time_series_clustering and ts_cluster (#478) (@Zapiano)
• Remove locations with no space from consideration for interventions (#479) (@ConnectedSystems)
• Adjust run_model() to only require values relative to $k$ area (#481) (@ConnectedSystems)
• Update viz.clustered_scenarios to allow confidence interval plot (#482) (@Zapiano)
• Consistent treatment of k area on data load (#485) (@ConnectedSystems)
• Transform ICC from relative to absolute area to relative to k area (#486) (@ConnectedSystems)
• Add function to alter sampling bounds on parameters to specified value. (#490) (@Rosejoycrocker)
• Fix bug in how sensitivity.outcome_map() treats categorical variables. (#491) (@Rosejoycrocker)
• Fix _time_labels missing last label (#496) (@Zapiano)
• Update version number to 0.9.0 (#497) (@Rosejoycrocker)
• Add .JuliaFormatter.toml to .gitignore (#499) (@Zapiano)
• Refactor viz.scenario (#500) (@Zapiano)
• CompatHelper: bump compat for SciMLBase to 2, (keep existing compat) (#504) (@github-actions[bot])
• Add :summary option to viz.scenarios (#505) (@Zapiano)
• Update CSV.write writeheader parameter to header (#506) (@Zapiano)
• Fix bug causing Domain loading with RCP to error (#511) (@Rosejoycrocker)
• Remove top_n parameter from usage (#514) (@Rosejoycrocker)
• CompatHelper: bump compat for MLJ to 0.20, (keep existing compat) (#515) (@github-actions[bot])
• Add support series and map binary clusters plots (#521) (@Zapiano)
• Fix scenarios subsetting now working (#523) (@Zapiano)
• Add interface function to query number of scenarios in result set (#527) (@ConnectedSystems)
• Rename rs_input with scenarios (#533) (@Zapiano)
• CompatHelper: bump compat for NCDatasets to 0.13, (keep existing compat) (#536) (@github-actions[bot])
• Add summarize and turn per_loc and loc_trajectory into alias (#537) (@Zapiano)
• Broadcast _check_discrete inside update_params (#539) (@Zapiano)
• Extract call to run scenarios inside tests to external function (#540) (@Zapiano)
• Add missing scenario analysis function definitions to analysis module (#541) (@ConnectedSystems)
• Resolve Out-of-Memory issues when working with larger spatial areas (#542) (@ConnectedSystems)
• Update analysis docs with recent scenarios and clusters developments (#545) (@Zapiano)
• Fix failing test cases due to recent changes (#546) (@ConnectedSystems)
• Changes to mcda functions to reflect coral cover being in terms of k area (#547) (@Rosejoycrocker)
• Add ability to perform convergence analysis (#552) (@Rosejoycrocker)
• CompatHelper: add new compat entry for TOML at version 1, (keep existing compat) (#553) (@github-actions[bot])
• CompatHelper: add new compat entry for Statistics at version 1, (keep existing compat) (#554) (@github-actions[bot])
• Coral cover consistently represented as relative to coral habitable area (#555) (@ConnectedSystems)
• Avoid assuming where the RCP column is when adjusting scenario spec (#558) (@ConnectedSystems)
• Fix integer dims reference in location_selection_frequency() (#563) (@Rosejoycrocker)
• Fix bug due to missing default_bounds in EnvironmentalLayer and Coral model components (#569) (@Rosejoycrocker)
• Visualizations to be agnostic to Makie backend (#570) (@ConnectedSystems)
• Add functions used for location selection to separate decision module (#571) (@Rosejoycrocker)
• Add separate weighting parameter for depth criteria (#573) (@Rosejoycrocker)
• Add conversion to scientific notation (#574) (@Zapiano)
• Fix plot map (#575) (@Zapiano)
• Prevent test_rs() from creating tmp dir inside test/data (#576) (@Zapiano)
• Apply blue styleguide to some files (#579) (@Zapiano)
• Update use of progress meter to resolve deprecation warning (#581) (@ConnectedSystems)
• Normalize sampled MCDA weights (#582) (@Rosejoycrocker)
• Replace package NCDatasets by NetCDF (#583) (@Zapiano)
• Implement cyclone mortality scenarios (#585) (@Zapiano)
• CompatHelper: add new compat entry for NetCDF at version 0.11, (keep existing compat) (#588) (@github-actions[bot])
• Fix viz.scenarios bug introduced in changes to scenario_confint! usage (#589) (@Rosejoycrocker)
• Change approach to listing supported MCDA methods (#593) (@ConnectedSystems)
• Remove defunct function for post processing results into power-BI friendly csv file (#594) (@Rosejoycrocker)
• Use min-max normalisation for heat stress (#595) (@Rosejoycrocker)
• Use min-max normalisation for heat stress (#596) (@Rosejoycrocker)
• Handle cases where connectivity directories may be empty (#597) (@ConnectedSystems)
• Deactivated interventions should be considered separately (#598) (@ConnectedSystems)
• Remove list of ignored JMcDM methods (#599) (@ConnectedSystems)
• Fix treatment of categorical factors in regional sensitivity analysis (#601) (@Rosejoycrocker)
• Separate shading and fogging timing parameters (#602) (@Rosejoycrocker)
• CompatHelper: bump compat for Interpolations to 0.15, (keep existing compat) (#604) (@github-actions[bot])
• CompatHelper: add new compat entry for YAXArrays at version 0.5, (keep existing compat) (#605) (@github-actions[bot])
• CompatHelper: add new compat entry for DimensionalData at version 0.25, (keep existing compat) (#606) (@github-actions[bot])
• Fix proportional_adjustment vector conversion computational error (#607) (@Zapiano)
• Add tests for figure creation (#608) (@ConnectedSystems)
• Fix bug where cover instead of leftover space was being used in stand alone site selection (#610) (@Rosejoycrocker)
• Add more detail regarding sequence of events (#611) (@ConnectedSystems)
• Adjust language in architectural overview to match recent changes (#612) (@ConnectedSystems)
• Support RSA with large sample sizes (#614) (@ConnectedSystems)
• Attach dummy wave and cyclone data (#616) (@ConnectedSystems)
• CompatHelper: bump compat for SIRUS to 2, (keep existing compat) (#617) (@github-actions[bot])
• Changes to dhw and wave logs to store scenario and site means and stds (#623) (@Rosejoycrocker)
• Fix bug introduced by SIRUS v2.0.1 (#625) (@Zapiano)
• Add a new ten site example domain for testing (#628) (@Rosejoycrocker)
• Fix mcda method bugs (#629) (@Rosejoycrocker)
• Fix set_factor_bounds! out of bounds for discrete factors (#631) (@Zapiano)
• Consolidate methods that transform factor values into sampling.jl (#632) (@ConnectedSystems)
• Replaces distance sorting with restrictions on the number of selected locations in the same reef (#635) (@Rosejoycrocker)
• Update factor types and their use (#636) (@ConnectedSystems)
• Update factor definitions to use custom constructor (#637) (@ConnectedSystems)
• Update sampling methods for newly defined factor definitions (#638) (@ConnectedSystems)
• Update interactions with Param types across ADRIA more generally (#639) (@ConnectedSystems)
• Address MCDA error for single locations (#640) (@ConnectedSystems)
• Add connectivity data to result set storage (#643) (@Rosejoycrocker)
• Changes to make ADRIA precompilable under Julia v1.10 (#646) (@ConnectedSystems)
• Update use of Makie/GeoMakie to address deprecation errors (#647) (@ConnectedSystems)
• Fix larval connectivity bug (#648) (@ConnectedSystems)
• Remove examples dir issue #584 (#651) (@DanTanAtAims)
• Speed up calculation of truncated normal mean and cdf (#652) (@DanTanAtAims)
• Update tests for new sampling method/factor definitions (#653) (@ConnectedSystems)
• Update factor type documentation (#654) (@ConnectedSystems)
• Add a default size for scenario plots (#657) (@ConnectedSystems)
• CompatHelper: add new compat entry for StatsFuns at version 1, (keep existing compat) (#658) (@github-actions[bot])
• CompatHelper: add new compat entry for SpecialFunctions at version 2, (keep existing compat) (#659) (@github-actions[bot])
• Fix bleaching mortality (#660) (@ConnectedSystems)
• Clean up settler cover function to reduce confusion (#662) (@ConnectedSystems)
• Only load up relevant RME SSP datasets (#663) (@ConnectedSystems)
• Reset deployed-coral-risk-tol range (#664) (@ConnectedSystems)
• Clean up scenario running methods (#665) (@ConnectedSystems)
• Return 0 in cases where lb > ub (#666) (@ConnectedSystems)
• Clean up use of TP matrices to align with conceptualisation of connectivity (#667) (@ConnectedSystems)
• Adjustment to simulated events to address numerical errors (#668) (@ConnectedSystems)
• Support updated domain structure (#669) (@ConnectedSystems)
• Fix erroneous handling of location IDs (#671) (@ConnectedSystems)
• Fix error in domain loading when cluster_id is already in string format (#673) (@Rosejoycrocker)
• Add test domain for ReefModDomain type (#675) (@Rosejoycrocker)
• Additional setup instructions for code style and formatting (#676) (@ConnectedSystems)
• Implementation of new MCDA types (#678) (@ConnectedSystems)
• Fix readjustment of number of slices bug in RSA (#679) (@Rosejoycrocker)
• Fix cyclone sorting (#683) (@Zapiano)
• removed deprecate functions and function calls (#684) (@DanTanAtAims)
• restructured documentation image directories (#685) (@DanTanAtAims)
• Truncated normal changes (#687) (@DanTanAtAims)
• Allow user to set whatever bounds they wish (#688) (@ConnectedSystems)
• Yax loaddomain (#689) (@Zapiano)
• Switch to YAXArrays when runnin scenarios (#690) (@Zapiano)
• Adjustments to allow loading newest Domain datasets (#691) (@ConnectedSystems)
• Update rank metrics to use YAXArrays (#693) (@ConnectedSystems)
• Update viz.clustering to expect AbstractMatrix (#694) (@ConnectedSystems)
• Migrate from NamedDimsArrays to YAXArrays (#695) (@Zapiano)
• Remove factors input from rsa() and use scenario dataframe column names instead (#696) (@Rosejoycrocker)
• updated data loading test for migration to YAXArrays (#697) (@DanTanAtAims)
• Further updates to scenario runs with MCDA (#698) (@ConnectedSystems)
• Update support for standalone MCDA use (#699) (@ConnectedSystems)
• Yax test update (#700) (@DanTanAtAims)
• added nameddimsarray2yaxarray (#701) (@DanTanAtAims)
• Fix error in bin size for sensitivity.outcome_map (#702) (@Rosejoycrocker)
• Yax viz (#703) (@DanTanAtAims)
• Yax cube tests (#704) (@DanTanAtAims)
• Remove MKL from build process (#705) (@ConnectedSystems)
• Reef mod matlab domain (#706) (@DanTanAtAims)
• Yax analysis (#707) (@DanTanAtAims)
• Migrate metrics.jl to YAXArrays (#709) (@Zapiano)
• Yax sensitivity (#710) (@DanTanAtAims)
• Remove GC workaround (#711) (@ConnectedSystems)
• CompatHelper: bump compat for DimensionalData to 0.26, (keep existing compat) (#714) (@github-actions[bot])
• Yax migration miscellaneous (#715) (@Zapiano)
• Keep metadata in results (#716) (@ConnectedSystems)
• Finalize update of standalone MCDA methods (#717) (@ConnectedSystems)
• Update all tests and remove NamedDims and AxisKeys from ADRIA.jl (#718) (@Zapiano)
• Validating MCDA methods and initial clean/update of tests (#719) (@ConnectedSystems)
• Provide a succinct overview of MCDA (#720) (@ConnectedSystems)
• Add support to cyclone mortality to ReefModDomain (#722) (@Zapiano)
• Fix locations selection in ReefMod datapackage cyclone mortality loading (#723) (@Zapiano)
• Save right intervention label at ResultSet ranks YAXArray (#724) (@Zapiano)
• Add counterfactual minus guided/unguided diff at location level (#726) (@Zapiano)
• Hacky support for later RME reef id list (#731) (@ConnectedSystems)
• Add support for specifying locations (#732) (@ConnectedSystems)
• improve load_domain docs (#733) (@arlowhite)
• Only rank locations with available area > 0 (#734) (@ConnectedSystems)
• Support more vector types for maps (#736) (@ConnectedSystems)
• Clean up connectivity and centrality methods (#737) (@ConnectedSystems)
• Additional rank methods to determine number of locations intervened on per timestep (#738) (@ConnectedSystems)
• Collection of miscellaneous changes (#740) (@ConnectedSystems)
• Fix bug, min. locations to select > available locations (#741) (@ConnectedSystems)
• Connectivity viz (#742) (@DanTanAtAims)
• CompatHelper: bump compat for DimensionalData to 0.27, (keep existing compat) (#744) (@github-actions[bot])
• RME Result Interface (#745) (@DanTanAtAims)
• Working example of CUDA-fied settler_cover() (#747) (@ConnectedSystems)
• Repeat mention that the VS Code extension is being setup (#748) (@ConnectedSystems)
• Improved support for spatial maps (#750) (@ConnectedSystems)
• use provided centrality measures instead of defaults (#751) (@DanTanAtAims)
• Convenience plotting method for connectivity/centralities (#752) (@ConnectedSystems)
• Misc cleanup (coral dynamics) (#753) (@ConnectedSystems)
• Changes to make use of expected multi-dimensional data structure (#754) (@ConnectedSystems)
• remove hardcoded coral spec from metrics and data store (#755) (@DanTanAtAims)
• fix initial cover block constructor (#757) (@DanTanAtAims)
• Support plotting DHW and cyclone (mortality) scenarios (#758) (@ConnectedSystems)
• Support deactivating environmental disturbances (#759) (@ConnectedSystems)
• Multidimensional cover (#761) (@DanTanAtAims)
• add range to for loop (#762) (@DanTanAtAims)
• Visualization for taxonomy cover. (#763) (@DanTanAtAims)
• CompatHelper: add new compat entry for Makie in [weakdeps] at version 0.21, (keep existing compat) (#764) (@github-actions[bot])
• CompatHelper: bump compat for NetCDF to 0.12, (keep existing compat) (#765) (@github-actions[bot])
• CompatHelper: add new compat entry for GraphMakie in [weakdeps] at version 0.5, (keep existing compat) (#766) (@github-actions[bot])
• CompatHelper: add new compat entry for GeoMakie in [weakdeps] at version 0.6, (keep existing compat) (#767) (@github-actions[bot])
• Change assisted adaptation to a Discrete Uniform value (#770) (@ConnectedSystems)
• Use underlying data instead of YAXArray type (#771) (@ConnectedSystems)
• Increase compression level for ResultSet (#772) (@ConnectedSystems)
• Fix erroneous function call in docstrings (#773) (@ConnectedSystems)
• Add methods to extract deployment location info (#774) (@ConnectedSystems)
• Clean up defunct dependencies (#776) (@ConnectedSystems)
• Fix visualization type error (#777) (@DanTanAtAims)
• Fix mismatched function name in docstring (#778) (@ConnectedSystems)
• constrain growth by available area (#779) (@DanTanAtAims)
• Fix site_level dosctring (#782) (@Zapiano)
• remove breakpoint in code (#784) (@DanTanAtAims)
• Assortment of improvements to SIRUS and Time Series Clustering (#786) (@Zapiano)
• Add default option to _sort_keys (#787) (@Zapiano)
• Julia format GH workflow, format all files (#790) (@arlowhite)
• julia-actions recommended dependabot.yml (#791) (@arlowhite)
• Coerce to MultiPolygon instead of Polygon (#793) (@ConnectedSystems)
• Bump julia-actions/cache from 1 to 2 (#795) (@dependabot[bot])
• Bump julia-actions/setup-julia from 1 to 2 (#796) (@dependabot[bot])
• Bump actions/checkout from 2 to 4 (#797) (@dependabot[bot])
• Minor updates to geospatial functions/handling (#798) (@ConnectedSystems)
• use apply_mortality not apply_survival (#799) (@DanTanAtAims)
• Address tests failing due to type mismatch (scenario confint) (#801) (@ConnectedSystems)
• Fix depth min/offset being sampled for counterfactual scenarios (#802) (@ConnectedSystems)
• Use CoralBlox linear_extension_scale_factor (#805) (@Zapiano)
• Implement linear extension scale factor (#806) (@Zapiano)
• Fix add run_model method that do not require functional_groups (#807) (@Zapiano)
• build: prototype CD integration with Provena to update model (#808) (@PeterBaker0)
• Fix broken tests (#809) (@Zapiano)
• update fecundity min area variable name for clarity (#810) (@eco-ben)
• fix permutation of initial cover dimensions (#811) (@DanTanAtAims)
• Breaks new initial_cover.nc file into size classes assuming a LogNormal distribution (#812) (@Zapiano)
• Fix miscellaneous of broken tests (#813) (@Zapiano)
• Fix sampling test (#814) (@Zapiano)
• Increase release version (#815) (@DanTanAtAims)
• Apply changes to ADRIA to make it compatible with CoralBlox model (#817) (@Zapiano)
• CompatHelper: add new compat entry for CoralBlox at version 1, (keep existing compat) (#821) (@github-actions[bot])
• Fix docs builder, add .git-blame-ignore-revs and document (#823) (@arlowhite)
• fix helper dimension size error (#824) (@DanTanAtAims)
• Add reshape to fix dimension mismatch when logging dhw tolerances (#827) (@Rosejoycrocker)
• updates docs github action to use Julia 1.10.* (#829) (@arlowhite)
• Remove Manifest from gitignore (#830) (@Zapiano)
• Rename metrics :sites dimension with :locations (#831) (@Zapiano)
• Fix docs errors (#832) (@arlowhite)
• Fix cover loading and size class lower bound (#833) (@DanTanAtAims)
• convert recruitment from relative area to area before use (#834) (@DanTanAtAims)
• lowercase png extensions to fix Documenter (#837) (@arlowhite)
• Cscape interface improvements (#838) (@ConnectedSystems)
• feat: migrating and updating docker functionality + publish pipeline (#839) (@PeterBaker0)
• fix: stale links in docker docs (#843) (@PeterBaker0)
• Overly constrained argument types causing tests to fail (#844) (@ConnectedSystems)
• feat: restore unit testing and add julia caching (#845) (@PeterBaker0)
• fix reefmod domain load initial cover (#846) (@DanTanAtAims)
• Add metadata to metrics YAXArrays (#847) (@Zapiano)
• Update interface to use correct gpkg (#850) (@DanTanAtAims)
• correct calculation of relative cover (#853) (@DanTanAtAims)
• Speed up CScape Result Interface (#854) (@DanTanAtAims)
• rename dimension from sites to locations (#857) (@DanTanAtAims)
• throw more informative error message (#858) (@DanTanAtAims)
• add scenario id to scenario dataframe (#860) (@DanTanAtAims)
• Improve summarize performance by using mapslices (#862) (@Zapiano)
• Viz metadata (#863) (@Zapiano)
• Pin NetCDF.jl and Zarr.jl in order to pin DiskArrays.jl (#864) (@Zapiano)
• Bump actions/checkout from 3 to 4 (#865) (@dependabot[bot])
• Bump docker/login-action from 2 to 3 (#866) (@dependabot[bot])
• Bump docker/build-push-action from 4 to 6 (#867) (@dependabot[bot])
• Bump docker/metadata-action from 4 to 5 (#868) (@dependabot[bot])
• Fix rule extraction to handle constant factors (#870) (@Zapiano)
• Improvements to model performance by reducing allocations (#871) (@ConnectedSystems)
• Julia 1.11 Manifest and Pkg update (#876) (@arlowhite)
• Minor change for performance (#877) (@ConnectedSystems)
• Apply CompatHelper suggestions, free NetCDF,Zarr; add & pin DiskArrays (#878) (@arlowhite)
• LERC_jll 3 to 4, downgrade DimensionalData to 0.27.9, Julia Pkg update (#879) (@arlowhite)
• Update code and dependencies to GeoMakie v0.7.x (#884) (@ConnectedSystems)
• Cyclone mortalities assigned to wrong group (#888) (@DanTanAtAims)
• DiskArrays 0.4.5, Pkg update (#889) (@arlowhite)
• Fix StackOverflow error when plotting maps (#891) (@ConnectedSystems)
• Add spatial visualisations for decision matrices (#893) (@Rosejoycrocker)
• Add DEA functions and plotting to ADRIA.analysis (#896) (@Rosejoycrocker)
• Remove duplicate rules (#899) (@Zapiano)
• Bump codecov/codecov-action from 4 to 5 (#901) (@dependabot[bot])
• Fix DHW scenario viz again (#903) (@ConnectedSystems)
• Incorporate recruitment to growth constraints and cap seeding to habitable area (#906) (@DanTanAtAims)
• Add extraction of feature set to support analyses and assessment (#907) (@ConnectedSystems)
• Add additional convenience functions and update docstrings (#908) (@ConnectedSystems)
• Remove defunct method seed_corals! (#909) (@ConnectedSystems)
• Switch to logging number of coral deployed (#910) (@ConnectedSystems)
• Add method to display all DHW scenarios for the currently set RCP/SSP (#914) (@ConnectedSystems)
• Minor tweaks to taxa visualization (#915) (@ConnectedSystems)
• Updated factor bounds setting method (#917) (@ConnectedSystems)
• Minor fix on docs (#920) (@vitorhirata)
• Pin DiskArrays to 0.4.9 (#922) (@vitorhirata)
• Fix tests of viz/spatial and metrics/spatial (#923) (@vitorhirata)
• Pin DiskArrays to 0.4.9 in docs Manifest and v1.11 Manifest (#924) (@vitorhirata)
• Custom categorical distribution (#927) (@DanTanAtAims)
• Small change to parameter description to avoid confusion (#928) (@ConnectedSystems)
• Replace and deprecate remaining use of site_k_area (#929) (@ConnectedSystems)
• CompatHelper: bump compat for Makie in [weakdeps] to 0.22, (keep existing compat) (#930) (@github-actions[bot])
• CompatHelper: bump compat for DimensionalData to 0.29, (keep existing compat) (#931) (@github-actions[bot])
• CompatHelper: bump compat for YAXArrays to 0.6, (keep existing compat) (#932) (@github-actions[bot])
• Avoid reshape for performance (#933) (@ConnectedSystems)
• Considering spatial dispersal of intervention locations (#934) (@ConnectedSystems)
• Add cyclone mortality to documentation (#936) (@Zapiano)
• Correct RCP identifier in result directory (#937) (@ConnectedSystems)
• Remove synopsis from documentation (#938) (@Zapiano)
• Update docs to configure Julia Formatter extension (#939) (@ConnectedSystems)
• Fix docs build (#945) (@Zapiano)
• CompatHelper: bump compat for JMcDM to 0.8, (keep existing compat) (#946) (@github-actions[bot])
• Fix rounding problem, leading to coral overgrowth, when cover plus recruits fill an entire reef (#947) (@Zapiano)
• Bump julia-actions/julia-format from 3 to 4 (#948) (@dependabot[bot])
• Speed up timeseries clustering (#949) (@Zapiano)
• add bin edges used in calibration to ADRIA (#950) (@DanTanAtAims)
• Fix multiple tests (#951) (@Zapiano)
• Changes to enable recent RME domain loading (#952) (@Zapiano)
• CompatHelper: bump compat for Interpolations to 0.16, (keep existing compat) (#953) (@github-actions[bot])
• Speedup bleaching (#954) (@Zapiano)
• Add plot for single scenario stratified by size class and functional group (#955) (@Zapiano)
• CompatHelper: bump compat for Makie in [weakdeps] to 0.23, (keep existing compat) (#956) (@github-actions[bot])
• Update Manifest (#957) (@Zapiano)
• CompatHelper: bump compat for Makie in [weakdeps] to 0.24, (keep existing compat) (#958) (@github-actions[bot])
• Update calibrated factors (#960) (@Zapiano)
• docs: minor clarification to Makie backend selection (#961) (@PeterBaker0)
• CompatHelper: bump compat for GraphMakie in [weakdeps] to 0.6, (keep existing compat) (#964) (@github-actions[bot])
• Fix tests prior to merging global-calib to main (#965) (@Zapiano)
• CompatHelper: bump compat for DataStructures to 0.19, (keep existing compat) (#966) (@github-actions[bot])
• Calibration and SA changes (#967) (@Zapiano)
• Bump project version prior to new release (#968) (@Zapiano)
• Fix conn data load location selection when force_single_reef is true (#970) (@Zapiano)
• Update compatible datapackage version to 0.8.0 (#972) (@Zapiano)
• Deactivate criteria factors when running deactivate_interventions (#973) (@Zapiano)
• Fix _init_cover_weights dicstring (#974) (@Zapiano)
• Specify timeframe when loading RME dhw_scens (#975) (@Zapiano)
• Bump actions/checkout from 4 to 5 (#976) (@dependabot[bot])
• Doc guided sampling (#977) (@Zapiano)
• Support independent scenarios viz legend rendering (#978) (@Zapiano)
• CompatHelper: bump compat for YAXArrays to 0.7, (keep existing compat) (#979) (@github-actions[bot])
• CompatHelper: bump compat for MLJ to 0.21, (keep existing compat) (#981) (@github-actions[bot])
• Refactor Reef Index Metrics (#982) (@DanTanAtAims)
• Export bin_edges (#983) (@Zapiano)
• CompatHelper: bump compat for JSON to 1, (keep existing compat) (#984) (@github-actions[bot])
• Update calibrated parameter base values (#985) (@Zapiano)
• CompatHelper: bump compat for JSON to 1, (keep existing compat) (#986) (@github-actions[bot])
• Fix factor update bug (#988) (@ConnectedSystems)
• Update key dependencies and bump version (#989) (@ConnectedSystems)
• Bump project version prior to new release (#990) (@Zapiano)
• fix: Correct growth constraint calculation in scenario.jl (#992) (@DanTanAtAims)
• CompatHelper: bump compat for MLJ to 0.22, (keep existing compat) (#993) (@github-actions[bot])
• CompatHelper: bump compat for SIRUS to 3, (keep existing compat) (#994) (@github-actions[bot])
• Refactor out recruitment constraint from timestep loop (#996) (@Zapiano)
• Remove MAT dependency (#997) (@ConnectedSystems)
• Update GeoDataFrame handling (#998) (@ConnectedSystems)
• Remove broadcasting to avoid intermediate allocations (#999) (@ConnectedSystems)
• Remove intermediate array (#1000) (@ConnectedSystems)
• fix: fix input type declaration for _render_legend (#1001) (@DanTanAtAims)
• Initial cleanup in prep for restructure (#1002) (@ConnectedSystems)
• Support arbitrary number of time series clusters (#1003) (@ConnectedSystems)
• Reorganizing code structure (#1004) (@ConnectedSystems)
• Bump actions/checkout from 5 to 6 (#1005) (@dependabot[bot])
• Adjusted scenario sampling and default parameters (#1006) (@ConnectedSystems)
• Refactor Spatial Data Loading and Update Input Data Handling (#1007) (@DanTanAtAims)
• Speedups (#1008) (@DanTanAtAims)
• Fix incorrect use of single reef idx (#1009) (@DanTanAtAims)
• fix: Fix categorical bug where bounds are passed instead of categories (#1010) (@DanTanAtAims)
• Improves scenario assessment workflow (#1011) (@ConnectedSystems)
• Pin YAXArray dependency (#1013) (@ConnectedSystems)
• Implements decision strategies (#1019) (@ConnectedSystems)
• Mention use of shared depot paths (#1020) (@ConnectedSystems)
• Fix single reef load and sampling (#1023) (@Zapiano)
• Bump project version prior to new release (#1024) (@Zapiano)
• Restrict minimum compatible Julia version to 1.11 (#1026) (@Zapiano)
• Improve fecundity (#1027) (@Zapiano)
• Add Allee effect (#1031) (@Zapiano)
• Fix: All axis values were being stripped when creating new DataCube (#1033) (@ConnectedSystems)
• Fix LTMP Taxa Cover and Metric Metadata (#1034) (@DanTanAtAims)
• reformat with JuliaFormatter V1 (#1035) (@arlowhite)
• Fix wrong use of reactive strategy index (#1036) (@Zapiano)
• Fix sampling tests (and others) (#1037) (@Zapiano)
• Update documentation project (#1038) (@Zapiano)
• Update Julia version used in github doc build to 1.11 (#1039) (@Zapiano)
• Extend seeding intervention to all functional groups (#1040) (@Zapiano)
• Rename ENV variable TEST to ADRIA_TEST (#1041) (@Zapiano)
• Remove ODE related code (and clean up) (#1042) (@Zapiano)
• Fix fog and seed location fixing (#1043) (@Zapiano)
• Fix fog strategy builder (#1047) (@Zapiano)
• Limit environmental data loading to timeframe in datapackage.json (#1048) (@DanTanAtAims)
• Use newest version of ADRIAIndicators (#1049) (@DanTanAtAims)
• Enforce location ids in environmental data. (#1050) (@DanTanAtAims)
• Implement moving corals intervention (#1052) (@Zapiano)
• Allow target locations for MCB (#1053) (@Zapiano)
• Use seeding device density to distribute seeded corals (#1056) (@Zapiano)
• Assisted adaptation relative to recent past (#1057) (@Zapiano)
• Update Breeder's equation usage (#1058) (@Zapiano)
• Add min_iv_locs param specific for moving corals (#1059) (@Zapiano)
• Add moving corals stats to feature set (#1060) (@Zapiano)
• Add Marine Cloud Brightening with Multi-dimensional DHW NetCDFs (#1062) (@DanTanAtAims)
• Bump codecov/codecov-action from 5 to 6 (#1063) (@dependabot[bot])
• Bump docker/login-action from 3 to 4 (#1064) (@dependabot[bot])
• Bump julia-actions/cache from 2 to 3 (#1065) (@dependabot[bot])

Closed issues:

• Core functionality to be ported from ADRIA (MATLAB) (#1)
• Pretty display for ResultSet (#68)
• Include site area data in result set (#69)
• Precompilation step to include dummy runs (#70)
• Example and test data packages (#71)
• Investigate optimizations to improve precompilation times (#75)
• Add total coral cover metric (#77)
• Adjust RCI to use new total coral cover (#78)
• Investigate alternative site selection weightings for coral cover (#79)
• Separate coral_cover() metric into individual functions (#81)
• Switch default behaviour of ADRIA.jl to store aggregated results? (#82)
• Use NamedDims and NamedArrays (#83)
• Adapt siteselection() to use dMCDA to avoid code repetition (#86)
• Shelter Volume: investigate very small values (#91)
• Juvenile metric: investigate small values (#92)
• Auto-adjust site offset/depth bounds on loading Domain (#94)
• Add an additional model component for environmental layers (#95)
• Coral evenness: Metric returns NaNs (#96)
• Replace duplicate proportional growth constraint with single function (#99)
• Make relative_cover() relative to site max coral cover area (k) instead of total site area (#109)
• ADRIA specific sampling functions (#119)
• Update result set to derive spatial data from stored geopackage (#124)
• Distribute seeded corals acording to available space, not k (#128)
• Exporting to PowerBI format very slow (#132)
• Double check recruitment calculation? (#133)
• Add scenario index to csv created by result_post_processing.jl and filter counterfactual according to dhw scenario (#136)
• Bleaching mortality may be over-estimated (#138)
• DHW dataset may over-represent extreme DHW trajectories (#139)
• Refactor seeding step into its own function with tests (#146)
• Use measure of dhw time distribution for MCDA heat stress criteria (#151)
• Check scaling of coral real estate criteria in MCDA function and add measure of space for coral to be seeded. (#152)
• Make shading of seeded sites user controllable (#157)
• Metric function to extract the top N performing sites (#158)
• Process area data on file read (#170)
• Add support for NetCDF data files (#173)
• Adjust MCDA functions to be more generic (#177)
• Deprecate support for .mat files (#182)
• Update site_selection() function in Domain.jl and use within ADRIA model site selection process to reduce replication (#194)
• Standardize to NamedDimsArray + AxisKeys (#200)
• Standardize relative cover metric to report values relative to k area (#204)
• Adjust scenario input IDs for clarity (#205)
• Use NamedDims+AxisKeys instead of matrix for MCDA decision matrices (#221)
• Site ranks are never updated after distance sorting (#223)
• Update the bleaching response to formally account for depth, surface shading and water quality. (#226)
• Move natural adaptation parameter to be part of the Coral component (#229)
• Add human-readable name to Parameter types (#230)
• List management zones in order of preference for targeted deployment (#231)
• Change triangular distributions to specify peak in absolute terms (#234)
• Use Haversine instead of Euclidean distance (#236)
• Use mean distance threshold and change in aggregate criteria value threshold instead of site by site distance threshold and top_n in distance sorting (#237)
• 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)
• Investigate bounds used for coral_cover_tol (#239)
• Set up documentation system and website (#240)
• Consider using JMcDM (#242)
• Register package (#245)
• Change reference to Input Set to Domain to align with interface functions (#246)
• Address possible double switching of RCPs (#248)
• Make plotting functions more generic to support rapid workflows (#249)
• Better separation of Aviz sub-system (#250)
• Make MCDA functions generic (#252)
• Move example scripts into documentation (#253)
• pareto analysis (#256)
• Regional Sensitivity Analysis (#257)
• Temporal Sensitivity Analysis (#260)
• Favicon for Documentation site (#265)
• Use LTMP observations (#267)
• Update growth rates for size class 6 (#268)
• TagBot trigger issue (#269)
• [Discussion] Natural adaptation (#270)
• Release v0.4.5 (#272)
• Separate fogging from shading (#277)
• 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)
• Re-enable tests/CI when Julia v1.9 is released (#300)
• Connectivity data cubes (#302)
• First conversion of model specification to DataFrame is excruciatingly slow (#303)
• 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)
• [Viz/Analysis] maps for/of site selection (#316)
• [Viz/Analysis] Naive Bayes (#323)
• Make run_site_selection() more user-friendly (#324)
• Investigate alternative method for sampling mcda weights (#327)
• Checking centrality is correctly calculated (#329)
• Release v0.5.0 (#331)
• MCDA crashes with mismatched array sizes for rankings and rankingsin (#333)
• Create single ResultSet (#342)
• MCDA method errors (#357)
• Make n_sites a perturbable model factor (#360)
• align_rankings! giving incorrect output rankings (#366)
• Time series clustering (#368)
• [Viz/Analysis] Clustering of scenarios to aid in MORDM (#369)
• Separate model factors (#377)
• Register v0.6.0 (#379)
• Spatial clustering based on outcomes (#383)
• [Viz/Analysis] Spatial plots of locations clustered by outcome (#384)
• Register v0.7.0 (#388)
• Remove coral cover conversion for ReefModEngine interface (#399)
• Add Rule Induction (with SIRUS) (#404)
• ADRIAmod uses excessive amounts of memory during runs (#405)
• Errors when running scenarios in parallel when nworkers() > 1 (#413)
• Change the way target_cluster function is works (#423)
• Duplicate RCP issue when running scenarios generated using sample_site_selection() (#426)
• Error: loc_trajectory and per_loc not qualifying dim (#427)
• Error: non_null_sites (#428)
• viz.outcome_map() gives duplicate x-axis values when plotting :guided factor (#440)
• Register v0.8.0 (#447)
• Update code style section in docs (#448)
• Out of memory error when calculating PAWN sensitivity for 8192 scenarios (#450)
• Target clusters with lower values of some metric (#451)
• Show labels and units of measurement automatically for plots by default (#453)
• Rule Extraction viz function is not included int viz extension (#454)
• Relevant features/properties for rule induction (and scenario decision making) (#458)
• Regional sensiyivity analysis gives duplicate values for categorical factors (#459)
• Summarized vizualisation for time series clustering (#464)
• Add example of Rule Induction usage to the Documentation (#473)
• Update rule ADRIA.viz.rules_scatter to accept target_clusters vector instead of clusters (#474)
• Conceptually align all coral cover calculations to be relative to k area (#480)
• Make $k$ area in geospatial data consistent (#483)
• Load initial coral cover data consistently across different Domain types (#484)
• Scenario running methods to be refactored to expect only values relative to $k$ area (#487)
• All metrics to be adjusted to expect $k$ area values (#488)
• Duplicate x-axis values in outcome maps (Part 2) (#489)
• Robust Decision Making (#493)
• Properly handle plotting binary (target vs non-target) clusters (#494)
• _time_labels gives duplicate labels in some cases (#495)
• Register v0.9.0 (#498)
• Adjust usage of k site area in location selection to align with coral cover being relative to k (#501)
• Possible issue with settler_cover() when moving to k area based processes (#502)
• Update deprecated writeheader=true at Domain.jl model_spec function (#503)
• Create a function that uses Slices to compute some aggregation metric over given axis (#508)
• Remove top_n from distance sorting as no longer needed (#509)
• Fix bug when loading Domain due to DHWs containing missing values (#510)
• [RFC] Change factors marked as "integer" types to "discrete" (#512)
• Refactor tests so we have an available ResultSet instance (#513)
• Incorporate cyclone mortality into ADRIAmod (#516)
• Implement n_scenarios(rs) (#517)
• Skip RCP entry from scenario specification by name rather than assuming position (#518)
• Add method for selecting all parameters associated with a particular intervention (#520)
• [Bug] Plotting subset of scenarios fail as not all scenario types may be included (#522)
• Use more descriptive dimension/axis labels for ResultSet logs storage now that AxisKeys is in use (#524)
• Make SRM apply to Reef clusters not whole of GBR (#525)
• Generalise creation of MCDA decision matrices (#526)
• Switch to YAXArrays (#528)
• Develop cyclone mortality models based on R implementation (#529)
• Filter coral species/site by branching_below_5, branching_above_5 and massive (#530)
• Use cyclone mortality model and filter to implement cyclone mortality in ADRIAmod (#531)
• Switch to WGLMakie for visualizations (#532)
• Increase default worker timeout (#534)
• Out of memory error for parallelised runs for whole of GBR domain (#535)
• Error runing test/runtests.jl (#538)
• Create plotting functions for sensitivity analysis convergence (#543)
• Add documentation for Cyclone mortality (#544)
• Add load_latest_results() (#548)
• Cluster maps not working (#549)
• Record/Log of DHW and wave stats in result sets are broken (#550)
• Fix error in growth ODE test (#551)
• Deployment location analysis methods/metrics leak into package namespace (#556)
• Add MCDA weighting normalisation to scenario sampling post-processing (#559)
• Delete/remove deprecated functions in prep for v1.0 release (#560)
• Make all indices used in site selection aggregation functions symbols (#562)
• Find and deprecate inconsistent methods (#564)
• Separate weighting parameters for heat_stress and depth in the MCDA (#565)
• Reorganize files/images for documentation (#567)
• Error when tests run scenarios (#568)
• Compute mean of truncated distribution using a Burman series (#572)
• Remove unused version check (#580)
• Move example scripts into the cookbook (#584)
• Adjust sampling approach for flexibility (#586)
• Changes in PR#552 breaks scenario visualizations (#587)
• Tests raising error (#590)
• Add function which returns list of MCDA methods which can be used in ADRIA (#591)
• Use min-max normalisation for heat stress criteria (#592)
• Update use of Makie (v0.20.0) to avoid deprecations (#600)
• Loading RME datasets are broken due to cyclone data requirement (#609)
• Fix "surprising" readjustment of the number of slices used to perform RSA/outcome mapping (#615)
• Adjust distribute_seeded_corals to account for cases where the top 5 sites do not have enough space for seeded corals (#618)
• Change log for dhws and waves to store mean and std for scenarios and sites/reefs (#619)
• Add new 10 site test Domain to testing folder in ADRIA (#622)
• Make decision matrices NamedDimsArrays (#624)
• Register v0.10.0 (#626)
• set_factor_bounds! setting value outside range for discrete variables (#630)
• Priority sites criteria expecting different structure for strong_pred than what is implemented (#633)
• Add connectivity matrix to ResultSet (#641)
• Error precompiling ADRIA.jl (#645)
• Support use of cluster identifier in spatial dataset (#655)
• Fix bug in constrain_reef_cluster which assumes there will always be enough locations to satisfy the reef constraint (#656)
• Add test domain for ReefModDomain type (#670)
• Ignore constant factors when applying SIRUS (#672)
• Add tests for standalone site selection using rank_locations (#680)
• Larval spread via connectivity is not working as expected (#686)
• Method Call error during testing from rsa function type. (#692)
• Documentation image links are broken (#712)
• viz.outcome_map not working when :guided is one of the factors of interest (#713)
• Fix sampling of guided MCDA methods (#725)
• Remove connectivity data from Domain types (#735)
• Example given in #742 no longer works (#749)
• Revisit use of temporary geojson (#768)
• Order of scenarios plotted are inconsistent (#769)
• Docstring example missing ending backticks (#781)
• Delete stale branches (#783)
• Improve loc_trajectory() function performance (#788)
• Makie spatial plotting maps color vector to each polygon in a multipolygon, leaving white polygons for unmapped shapes (#792)
• Geospatial dataset for the Test domain does not define a valid CRS (#800)
• Register v0.11.0 (#816)
• Delete defunct code after implementing changes to use CoralBlox.jl (#819)
• ReefModDomain loading is not working (#825)
• Dimension mismatch when logging DHW tolerances in debug mode (#826)
• CoralBlox apparent incompatibility (#828)
• Absolute cover calculations consider wrong area (#841)
• mismatch of naming in Cscape results set (#849)
• Investigate alternate chunking strategy for Zarr store (#851)
• data saved as relative cover is actually absolute cover (#852)
• Error when calculating total cover (#855)
• Errors/issues in _get_result_paths() (C~scape interface) (#856)
• Retrieve scenario IDs from CScapeResultsSet (#859)
• DimensionalData compat 0.27 (#881)
• GeoMakie compat 0.6 (#882)
• DiskArrays pinned to 0.3.23 (#883)
• StackOverflowError in tests failing on main branch (#890)
• Rule extraction print_rules error attempting to access 1-element Vector{Float64} at index [2] (#900)
• Seeding Intervention Habitable Area limit (#905)
• NaNs in growth_constraints vector raising error at global_calib branch (#963)
• Release v0.12.0 (#969)
• Register v0.13.0 (#991)
• Release v0.14.0 (#1012)
• Release v0.14.1 (#1014)
• Release v0.15.0 (#1015)
• Release v0.15.1 (#1025)
• JuliaFormatter workflow blocking well formatted files (#1029)