Release ADRIAanalysis-v0.1.0 · open-AIMS/ADRIA.jl

ADRIAanalysis ADRIAanalysis-v0.1.0

ADRIAanalysis v0.1.0: Release Notes

Overview

ADRIAanalysis is a new Julia sub-package that provides post-simulation analysis tools
for ADRIA (Adaptive Dynamic Reef Intervention Assessments) results. It was extracted from the core
ADRIA package into a standalone package to keep the main package lean, reduce
time-to-first-execution (TTFX), and allow optional heavy dependencies to load only when
needed.

What's Included

Sensitivity Analysis (`ADRIAanalysis.sensitivity`)

pawn: Moment-independent global sensitivity analysis using the
Kolmogorov-Smirnov statistic. Returns a summary DataFrame of
min/mean/median/max/std/cv across binned factor samples.
tsa: Temporal Sensitivity Analysis: applies PAWN at each time step to reveal
how driver importance evolves over time.
rsa: Regional Sensitivity Analysis using the Anderson-Darling test to identify
factor ranges associated with behavioural vs. non-behavioural scenarios.
outcome_map: Maps desirable outcomes to discretized factor space, with
bootstrapped confidence intervals, to identify which input ranges reliably produce
target outputs.
convergence: Assesses how sensitivity indices stabilize as sample size grows,
supporting confidence in results with limited runs.

Scenario Classification

target_clusters: Classifies scenario clusters into target / non-target groups
based on outcome temporal variability.
find_scenarios: Selects scenarios from cluster assignments using user-supplied
filter functions; works with 2D and 3D outcome arrays.
scenario_clusters: Converts cluster assignment vectors into a Dict mapping
cluster IDs to BitVector masks for downstream filtering.
screen_scenarios: Rule-based scenario screening: returns indices of scenarios
satisfying a normalized criterion across all output columns.

Pareto & Robustness Analysis

find_pareto_optimal: Identifies Pareto-optimal scenarios across multiple RCP
climate scenarios.
find_robust: Filters Pareto-optimal scenarios by an additional user-defined
robustness rule.

Data Envelopment Analysis

data_envelopment_analysis: Wraps DataEnvelopmentAnalysis.jl to benchmark
scenario efficiency against a frontier (CRS/VRS/FDH models, input- or
output-oriented). Returns a DEAResult with efficiency scores and peer groups.

Feature Engineering

feature_set: Assembles a cleaned feature DataFrame from a ResultSet,
including DHW statistics, deployment indicators, and coral volumes. Automatically
removes constant and highly correlated columns for use in downstream ML workflows.

Interpretable Rule Extraction (optional extension)

ADRIAanalysisRulesExt activates when both SIRUS.jl and MLJ.jl are loaded:

cluster_rules: Fits a SIRUS classifier to scenario clusters and returns the
top-N interpretable decision rules.
rules: Converts raw SIRUS.StableRules to the Rule struct.
print_rules: Pretty-prints rules as human-readable if/else conditions.

Architecture & Design

Aspect	Detail
Package type	Standalone sub-package under `ADRIAanalysis/`
ADRIA compat	`0.16`, `0.17`
Julia requirement	`≥ 1.11`
Optional extension	`ADRIAanalysisRulesExt` (requires `MLJ` + `SIRUS`)
Array backend	`YAXArrays` for labelled multi-dimensional outputs

MLJ and SIRUS are declared as weak dependencies. The package loads and functions
normally without them. Rule extraction stubs error with a clear message if the extension
is not active, guarding against silent missing-dependency failures.

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)

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ADRIAanalysis ADRIAanalysis-v0.1.0

ADRIAanalysis v0.1.0: Release Notes

Overview

What's Included

Sensitivity Analysis (`ADRIAanalysis.sensitivity`)

Scenario Classification

Pareto & Robustness Analysis

Data Envelopment Analysis

Feature Engineering

Interpretable Rule Extraction (optional extension)

Architecture & Design

Contributors

Uh oh!

Uh oh!

ADRIAanalysis-v0.1.0

ADRIAanalysis ADRIAanalysis-v0.1.0

ADRIAanalysis v0.1.0: Release Notes

Overview

What's Included

Sensitivity Analysis (ADRIAanalysis.sensitivity)

Scenario Classification

Pareto & Robustness Analysis

Data Envelopment Analysis

Feature Engineering

Interpretable Rule Extraction (optional extension)

Architecture & Design

Contributors

Uh oh!

Sensitivity Analysis (`ADRIAanalysis.sensitivity`)