Changelog • climniche

climniche 0.3.8

Aligned the README, vignettes, reports and Reference terminology around the current climatic niche reference and the four-step fitting and projection workflow.
Separated first observed Niche Boundary Exceedance from persistent exceedance onset. A first exceedance can now occur in the final supplied projection without being treated as missing.
Added primary fields for the fraction of supplied projections beyond the niche boundary while retaining the existing temporal field names.
Revised the temporal example to map first boundary exceedance across all supplied projection years.

Clarified the mathematical relation among Climatic Displacement, Niche Distance Shift and the derived Climatic Reconfiguration term, and separated that geometry from the future-state Niche Boundary Exceedance statistic.
Corrected the upper endpoint of weighted niche percentiles and projected small numerical negative eigenvalues to the nearest positive semidefinite climatic metric.
Fitted spatial current references before applying future missing-value masks and preserved named reference weights when projecting subsets of cells.
Required fitted CENFA components to use their original variables and standardisation.
Made summary.climniche_fit() reference-weighted by default and aligned the default Pareto filter with the selected exposure direction.
Added executable controlled-geometry and Mediterranean input examples, plus a documented IHO Mediterranean boundary for rebuilding the case study.

Added a Bio-ORACLE SSP2-4.5 European anchovy time-series example with range summaries, persistent Niche Boundary Exceedance maps and the series-report workflow.
Removed an unused fill scale from single-model time plots.
Standardised user-facing names for range, temporal and climatic contribution summaries without removing existing R object fields.
Added squared_niche_distance_change as the primary climatic contribution field while retaining niche_potential_change as an exact compatibility alias.

Reframed Pareto output as ecological screening of climate exposure. exposure_direction distinguishes larger positive Niche Distance Shift from lower Climatic Displacement.
Added pareto_depth_score as the primary Pareto depth field while retaining relative_priority as an exact compatibility alias.
Reworked the Mediterranean anchovy example to compare positive Niche Distance Shift with low Climatic Displacement in paired decision planes and maps.

Added two-objective Pareto depth for climate exposure screening, including decision planes and spatial Pareto maps.
Added a European anchovy screening example and clarified that summary figure panel (c) decomposes squared niche distance change rather than SDM variable importance.
Added cell-level dominant climatic contributions, dominance shares and spatial maps, with a Mediterranean anchovy example.
Added complete variable legends for contribution maps and aligned the Mediterranean example to one six-variable climate set.
Added Pareto summary diagnostics, including first-front size and objective rank correlation.

Added fit_climniche_reference() and project_climniche() to estimate the current climatic niche reference once and reuse it across projections.
Added fit_climniche_series() for ordered future periods, climate models and scenarios. Series share one effective descriptor tolerance. Spatial references are fitted independently of future missing cells, while projections use common finite cell support.
Added weighted range summaries of Niche Boundary Exceedance: its weighted fraction, conditional relative magnitude and range mean. Reference, aggregation and raster cell area weights remain distinct.
Added continuous summaries of persistent exceedance onset, time weighted and cumulative exceedance, return below the boundary and maximum interval increase.
Added climate model agreement for ensembles with at least two models, time series reports and dynamic time and map figures.
Documented the angular identity underlying Climatic Reconfiguration.

Matched named climate rows, variables, reference weights, centres, sensitivities, metric matrices and compatible CENFA components before fitting.
Made correlation filtering deterministic and used one inverse weighted empirical distribution definition for binary and continuous reference weights.
Added stricter validation for fitted climate spaces and factor metrics. A requested factor metric now stops when its CENFA components are incomplete.
Corrected weighted summaries and plots, single-layer raster handling, non-finite raster masks, spatial layer names and original raster cell indices.
Added executable examples, a table of case-study climatic metric weights and extended tests for alignment, weighting and invalid inputs.
Kept manuscript PDF figures in the repository while excluding them from the source package built for CRAN.

Added default climate-variable preprocessing in fit_climniche() and the raster workflows. The preprocessing removes near-zero variance variables and highly correlated variables before metric fitting.
Added preprocessing metadata to fitted objects.
Documented compatibility with CENFA-style cnfa objects without requiring the CENFA package at installation time.
Refreshed the Mediterranean anchovy example outputs under the current analysis workflow.
Revised the fit_climniche() formula documentation for clearer pkgdown rendering.

Focused fitted objects, reports and figures on the four continuous reported quantities and the two descriptor fields.
Added plot_climniche_summary_figure() and climniche_summary_figure_data().
Added map controls for binary and continuous SDM reference rasters, study region boundaries and longitude-latitude labels.
Updated report, summary, map and vignette outputs to use formal metric names.
Added tests for descriptor thresholds, continuous reference weights and raster domain handling.

Added the Mediterranean European anchovy example with Bio-ORACLE v3 marine climate layers, prepared future projections and continuous SDM suitability weights.
Added radial_direction and boundary_status descriptors to fitted objects, cell tables and raster workflows.
Added plot_climniche_maps() and map controls for colour limits, palettes, legends, plotting extent, study-region boundaries and longitude-latitude labels.
Changed the package license to MIT.

Continuous SDM suitability inputs are now used as reference weights in the fitted niche centre, empirical radial boundary, niche percentiles and current-scope summaries.
occupied_threshold removes low reference weights while preserving the original continuous values above the threshold.
Raster and terra workflows now pass continuous suitability rasters through to the matrix workflow as weights instead of converting them to binary cell indices.

Added the primary R object fields climate_reconfiguration and niche_boundary_exceedance.
Retained composition_change and outside_niche_exceedance as compatibility aliases for existing code.

CRAN release: 2026-05-29