NEWS.md
FuzzyNumbers.Ext.2, which had been archived from CRAN and prevented ConR from being installed from a clean CRAN library. The two functions used from it are now provided internally.pop.decline.test(), which was evaluating the wrong curve: the squared model coefficient was used in place of the squared year.pop.decline.test() no longer fails with object 'test' not found when the fitted parabola reaches its minimum or maximum within the assessment period. Such a trend is increasing over part of the period and decreasing over the rest, so no direction can be reported as significant. It is now classified from the net change over the period as a non-significant decline or increase. This changes the estimated continuing decline (and therefore criterion_C() results) for taxa whose population trend is best described by such a model.This entry was reconstructed retrospectively from the changes between the v1.3.0 and v2.1.0 tags, which were released without release notes.
Version 2 is a rewrite of the package. ConR 1.x provided a single assessment function covering IUCN criterion B; version 2 covers criteria A, B, C and D, separates the computation of population metrics from their conversion into IUCN categories, and replaces the retired sp/rgdal/rgeos spatial stack with sf/terra. The package went from 6 to 32 exported functions, and from a single 3,700-line source file to one file per function.
IUCN.eval() is defunct. Use criterion_B(), which covers the same criterion and can either compute the underlying metrics itself or accept them as pre-computed arguments.
map.res() is defunct; mapping of results in grid cells is not available in version 2.
Writing results to an Excel file was removed, along with the writexl dependency and the write_results argument.
Argument names were made consistently lower-case, and the arguments describing threat polygons were generalised beyond protected areas:
| 1.x | 2.x |
|---|---|
Cell_size_AOO |
cell_size_AOO |
Cell_size_locations |
cell_size_locations |
Resol_sub_pop |
resol_sub_pop |
Rel_cell_size |
rel_cell_size |
protec.areas |
threat_list |
method_protected_area |
method_polygons |
ID_shape_PA |
id_shape (default now "id_orig") |
EOO.computing() lost the Name_Sp, buff_width and write_results arguments.
Spatial outputs (export_shp = TRUE) are now sf objects instead of sp objects.
criterion_A(), criterion_B(), criterion_C() and criterion_D() assess the four IUCN criteria.cat_criterion_a(), cat_criterion_b() and cat_criterion_c() convert population metrics into IUCN categories, and are usable on their own.cat_mult_criteria() derives the consensus category across criteria, near.threatened() separates Least Concern from Near Threatened, and cat_downlist() downgrades categories, for example for regional assessments.pop.decline(), pop.decline.fit() and pop.decline.test() fit and compare models of population trend (linear, quadratic, exponential, logistic, generalised logistic and piecewise) and test for a continuing decline.pop.fluctuation() estimates extreme population fluctuations, and AOO.decline() estimates decline in the area of occupancy.AOH.estimation() estimates the area of habitat from a habitat map.severe_frag() assesses severe fragmentation, subpop.radius() and subpop.estimation() support subpopulation estimation, and EOO.sensitivity() tests how sensitive the extent of occurrence is to individual occurrences.sf and terra replace sp, rgdal, rgeos and geosphere. This was necessary because rgdal and rgeos were retired, which is also why the package was removed from CRAN.proj_type argument was added throughout, and proj_crs() resolves it. The default is the global cylindrical equal-area projection ("cea", ESRI:54034); "Antarctic" and "Africa_eac" are provided as shortcuts, and any EPSG code is accepted.EOO.computing() gained a mode argument to compute the extent of occurrence either on the spheroid ("spheroid", the default) or in a projected plane ("planar").coord.check() centralises validation of occurrence coordinates, including detection of records close to the antimeridian and of taxa with too few unique coordinates.dummy_dist() generates example occurrence data for testing and examples.example_criterionA, example_criterionC, example_criterionC_subpops, example_fluctuation and example_tutorial.terra, stars, units, data.table, dplyr, stringr, segmented, nls.multstart and lifecycle. knitr, lwgeom and rmapshaper were added as suggested packages.