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NEWS.md

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aoh 0.0.2.15

  • Update terra_gdal_rasterize() to remove the verbose parameter. This is because the underlying gdalUtilities::gdal_rasterize() function no longer supports the q parameter with recent GDAL versions (i.e., 3.9.3+).
  • Fix URLs.

aoh 0.0.2.14

  • Update create_spp_info_data() to make data cleaning functionality more robust for the BirdLife species' range dataset.
  • Update built-in helper script for processing area of habitat data to include (i) mammal species with terrestrial and freshwater distributions and (ii) mammal species with terrestrial and marine distributions (see inst/scripts/aoh-data.R)
  • New built-in helper script to download all species identifiers from the IUCN Red List (see inst/scripts/iucn-species-list.R)

aoh 0.0.2.13

  • Update read_spp_range_data() and create_spp_info_data() to fix incompatibility issue with latest version of the BirdLife species range dataset (#57). Thanks to Jianqiao Zhao for the bug report.
  • Update create_spp_aoh_data() and create_spp_frc_data() so that they provide a correct error message when the argument to x does not contain an "id_no" column.

aoh 0.0.2.12

  • Fix bug in create_spp_info_data() in assigning habitat types for resident distributions of migratory and non-migratory species. This bug meant that (i) habitat types for resident distributions of migratory species would include those exclusively affiliated with the species' passage distributions and (ii) habitat types for resident distributions of non-migratory species would not include those exclusively affiliated with the species' passage distributions. Thanks to Jianqiao Zhao for bug report.
  • Update built-in testing data to include multiple migratory species.
  • Update internal R script for creating test dataset (i.e., inst/scripts/test-data.R) to be compatible with current version of the package.
  • Update is_gdal_calc_available() to be more robust.
  • Fix URLs.

aoh 0.0.2.11

  • Fix bug in create_spp_info_data() so that the IUCN Red List API key can be specified using the key parameter.
  • Fix aliasing for package manual entry.

aoh 0.0.2.10

  • Update prepr and ggmap package dependencies.

aoh 0.0.2.9

  • Remove rgdal package dependency.
  • Updates URLs.
  • Update functions for downloading preprocessed data from Zenodo.
  • Update plot_spp_aoh_data() and plot_spp_frc_data() to be compatible with changes to the ggmap package for creating maps with a basemap.

aoh 0.0.2.8

  • Fix failing tests on continuous integration services (due to issues unzipping test files).

aoh 0.0.2.7

  • Update read_spp_range_data() to that it can import data from a zip file that contains multiple ESRI Shapefiles (e.g., the 2022-2 IUCN Red List release for reptile data).

aoh 0.0.2.6

  • Update create_spp_aoh_data() and create_spp_frc_data() to have a new rasterize_touches parameter (#48). This parameter can be toggled so that when rasterizing species' range data, raster cells that partially overlap with any part of the species' range are treated as covered by the species' range. This functionality may be especially useful for species with very small geographic ranges.
  • Fix bug in create_spp_aoh_data() and create_spp_frc_data() that causes Python errors when using the GDAL engine and a habitat_data or elevation_data raster that is stored only in memory (and not associated with any file on disk).
  • Fix bug in create_spp_aoh_data() and create_spp_frc_data() that causes the GRASS engine to throws errors.
  • Update package dependency versions.

aoh 0.0.2.5

  • Fix compatibility with updates to terra::compareGeom().

aoh 0.0.2.4

  • Update data cleaning procedures for create_spp_info_data() so that a useful error message is provided if all species are excluded.

aoh 0.0.2.3

  • Fix bug in create_spp_aoh_data() when using GRASS engine that caused the function to throw an error because it failed to initialize a new GRASS project correctly.
  • Update get_spp_habitat_data(), get_spp_summary_data(), get_spp_threat_data(), get_spp_summary_data() functions so that they do not throw warnings related to the dplyr package.

aoh 0.0.2.2

  • New iucn_threat_data built-in dataset denoting threat information on the IUCN Red List Threat Classification.
  • Fix compatibility of tests with updates to IUCN Red List.
  • Fix compatibility with tidyselect package (>= 1.2.0).
  • Fix badges in README.
  • The rgrass package is now used for GRASS functionality (due to upcoming deprecation of the rgrass7 package).

aoh 0.0.2.1

  • Update create_spp_info_data() so that data cleaning procedures replace 0 m lower elevation limits with 500 m (#39). This is because the IUCN Red List assigns lower limit values of 0 m for many species that have parts of their distribution in areas below sea level.
  • Update create_spp_info_data() so that data can be processed using EPSG:4326 coordinate reference system. Instead of throwing an error, the function will now display an alert.
  • Fix bug in create_spp_aoh_data() with the terra engine that caused negative elevations to be rounded to zero.

aoh 0.0.2.0

  • Initial stable release.
  • Add tests for st_repair_geometry().
  • Add URLs to citations in README.
  • Update references in documentation.

aoh 0.0.1.6

  • Fix spelling and formatting mistakes in vignette.
  • Update st_repair_geometry() to be more robust to geometry issues.

aoh 0.0.1.5

  • Update documentation for the create_spp_info_data() function.
  • Update create_spp_info_data() function so that the methodology used to correct errors in species' elevational limits now follows best practices. This behavior is controlled using the adjust_elevational_limits. If elevational limits should not be altered during processing, this can be specified by setting adjust_elevational_limits = FALSE.
  • Update create_spp_info_data() function so that IUCN habitat codes are adjusted to be assigned based on guidelines for the identification of Key Biodiversity Areas. Broadly speaking, these guidelines assign IUCN habitat codes to species' distributions in a manner to minimize omission errors. This behavior is controlled by the adjust_habitat_codes parameter. If habitat codes should be assigned based on exact matches (e.g., Resident distributions should only be associated with habitat codes described for Resident distributions), this can be specified by setting adjust_habitat_codes = FALSE.
  • Update create_spp_info_data(), create_spp_aoh_data(), create_spp_frc_data(), and calc_spp_frc_data() functions so that the returned sf::st_sf() object now contains an additional migratory column indicating if the species was processed as a migratory species or not.
  • Update create_spp_info_data(), create_spp_aoh_data(), create_spp_frc_data(), and calc_spp_frc_data() functions so that the order of the columns now places the IUCN threat status information (i.e., "category" column) closer to the start of the table.
  • Update tests to be robust to Zenodo website outages.

aoh 0.0.1.4

  • Updatest_repair_geometry() to avoid unneeded geometry duplication. This reduces memory requirements forcrate_spp_info_data().

aoh 0.0.1.3

  • Fix issues with using GDAL engine for processing data on Windows. Specifically, the package will now correctly work with the GDAL Python bindings that are installed as part of the OSGeo4W software (#32).
  • Fix issues where functions for downloading datasets would fail to load data from cache, and needlessly re-download data.
  • Fix issue where attempting to download data or query data version numbers would throw an error due to errors with the Zenodo API.

aoh 0.0.1.2

  • Suppress meaningless warnings triggered for GRASS on macOS.
  • Increase version requirement for terra package.
  • Fix IUCN Red List API tests.

aoh 0.0.1.1

  • Improve test coverage.
  • Convenience functions for applying GDAL commands to terra package objects are now exported. These functions include terra_gdal_calc(), terra_gdal_crop(), terra_gdal_project(), and terra_gdal_rasterize().
  • Fix bug in terra_gdal_project().

aoh 0.0.1.0

  • Initial developmental release.

aoh 0.0.0.99999

  • Initial work on developing package.