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Changelog

Source: NEWS.md

b3gbi 0.8.3 - Minor update:

  • Improved and updated the introductory tutorial

b3gbi 0.8.2 - Minor update:

  • Fixed the way Hill diversity is calculated for maps. It now uses years as sampling units instead of aggregating across years, and estimates from incidence data (presence/absence) instead of using observations as an abundance proxy.

b3gbi 0.8.1 - Minor update:

  • Fixed multiple small bugs that led to incorrect grid cell calculation and assignment for quarter-degree and eea grids.

b3gbi 0.8.0 - Major update:

  • The grid is now intersected with the shapefile polygon if one is provided, so the grid is clipped to the shape polygon instead of the bounding box.
  • The user can now choose to exclude occurrences on land, whereas previously only oceanic occurrences could be excluded. This can be changed using the parameter include_land = FALSE. By default, both ocean and land occurrences are included. Please note: this are geographical filters, they do not discriminate by taxa. Furthermore, since cubes contain pre-aggregated data, occurrences within grid cells that overlap both land and ocean cannot be excluded, regardless of whether the occurrences themselves are on land or ocean.
  • The user can now select the output CRS when plotting, independently of the CRS of the indicator object. This can be done using the parameter output_crs. By default, output_crs is NULL and will use the CRS of the indicator object.
  • Grid line width and colour, and the fill colour of empty grid cells can now be customized using the parameters grid_line_width, grid_line_colour, and grid_fill_colour.
  • The width and colour of the grid outline can also be customized using the parameters grid_outline_width and grid_outline_colour.
  • The grid outline is turned off by default, but can be turned on using the parameter visible_grid_outline = TRUE.
  • The grid outline can be plotted as a complete rectangle even when the grid is not, using complete_grid_outline. Set this to ‘original’ to use an outline that is generally rectangular but follows the distortions of the grid caused by the chosen projection. Use ‘transformed’ to force a proper rectangular shape regardless of the projection. By default, complete_grid_outline is set to FALSE.
  • It is now possible to crop a map according to the boundaries of the geographical regions you selected when calculating the indicator, even if they are different from the bounding box of the cube. This can be done using the parameter crop_by_region = TRUE. Note that this only works if you specified one or more region(s) when calculating the indicator, not if you used level = ‘cube’. By default, crop_by_region is set to FALSE.
  • Colours and fill colours for each rnaturalearth layer that the user specifies when plotting a map can now be customized using the parameters layer_colours and layer_fill_colours. The user must provide a vector of colours that matches the order and number of layers specified in the layers parameter.
  • Panel grid lines can now be turned on using the parameter visible_panel_gridlines. By default, panel grid lines are turned off (visible_panel_gridlines = FALSE).
  • The parameter panel_bg has been renamed to ocean_fill_colour to better reflect its function.
  • The parameter ne_type, which specifies the type of rnaturalearth data used, is now retained in the metadata of the calculated indicator (the level and region are still retained as well).
  • Area-based automatic cell size determination now has more categories.
  • Plotting code has been restructured and simplified to improve efficiency and readability.
  • Documentation has been updated and improved.

b3gbi 0.7.6 - Minor update:

  • Fixed a bug that caused rnaturalearth to keep downloading the same layer data. It now downloads the data to a cache folder and loads it from there the next time it needs it.

b3gbi 0.7.5 - Minor update:

  • Fixed a bug that caused maps to sometimes fail to plot with an error about wrong object class.
  • Fixed errors in the way Pielou’s evenness, Williams’ evenness, and taxonomic distinctness were calculated.
  • Some code restructuring to reduce the size of the codebase and improve readability.

b3gbi 0.7.4 - Minor update:

  • Refactored code in main plotting functions to improve efficiency and readability.
  • Fixed many style inconsistencies across the package.
  • This update does not significantly affect functionality of the package. It is mostly about cleaner, more efficient, more readable code.

b3gbi 0.7.3 - Minor update:

  • Hill diversity maps now calculate without error.
  • Hill diversity maps now use observations as an abundance proxy instead of attempting to use matrices of raw incidence data.
  • Hill diversity maps no longer calculate confidence intervals as visualization is not supported at this time.

b3gbi 0.7.2 - Minor update:

  • Hill diversity time series indicators now calculate without error.
  • The number of bootstrap confidence intervals for Hill diversity time series can now be set by the user, and confidence intervals can be turned off.
  • The confidence level for Hill diversity time series can now be set by the user (default is 0.95).
  • Taxonomic distinctness no longer tries to calculate confidence intervals
  • If no shapefile is selected and no grid cells are required for calculation, time series now bypass all geometric operations and are thus extremely fast.
  • The x and y axis expansions for plot_ts and plot_species_ts now default to 0.05 instead of 0.This makes time series plots look less cramped.

b3gbi 0.7.1 - Minor update:

  • Reorganized code in some indicator calculations to improve efficiency.

  • Fixed area_rarity_ts() that was broken by the previous update.

  • Note that the Hill functions are not working properly. This will hopefully be fixed in the next update.

b3gbi 0.7.0 - Major update:

  • Ocean occurrences are now included by default when calculating indicators (previously they were ignored entirely). They can be turned off using include_ocean = FALSE. Alternatively, you can set include_ocean = “buffered_coast” to include only occurrences within a set distance from the coast, measured in km (e.g., buffer_dist = 50).
  • Shape files can now be .wkt format. The CRS cannot be automatically determined from .wkt files, so it is assumed to be EPSG:4326 unless specified using the parameter shapefile_crs.
  • All geometry processing within the workflow is now done using a projected CRS, and conversion to the user-specified output_crs happens at the end. This allows for a simplified workflow and ensures more accurate calculations.
  • The user now has the option to add any rnaturalearth layer(s) to map plots using the layers parameter.
  • Automatic cell_size determination now takes total cube area into account instead of just the level (‘country’, ‘continent’, etc). Note, however, that the user still has the ability to manually set cell_size.
  • Warnings from the sf package should no longer appear due to improvements in the way geometry operations are handled by b3gbi.
  • The scale (resolution) of rnaturalearth data is now user-selectable when plotting (using the ‘scale’ parameter). The default is ‘medium’.
  • Indicators are now calculated much faster as geometric operations have been simplified and reduced and code has been reorganized and simplified to improve efficiency.
  • Grid offsets are now correct.
  • Additional error checking included.
  • Many minor bug fixes.

b3gbi 0.6.3 - Minor update:

  • Fixed a bug that caused quarter-degree grid codes to be translated incorrectly for some geographic locations. They should now work correctly in all cases.

b3gbi 0.6.2 - Minor update:

  • Fixed a bug related to MGRS grids that caused southern hemisphere MGRS codes to be associated northern hemisphere EPSG codes.

b3gbi 0.6.1 - Minor update:

  • Fixed a bug that caused an error when calculating time series from MGRS cube.

b3gbi 0.6.0 - Major update:

  • Fixed the way that MGRS grid codes are processed. Previously they were converted to lat/long and a global CRS was used. The package instead now converts to UTM codes and chooses the most appropriate local CRS.

b3gbi 0.5.6 - Minor update:

  • Fixed a bug in that caused quarter-degree grid codes to be translated incorrectly.
  • Removed minimum size limitation for grid cells. Very high resolution grids now just give a message warning the user that it could take a while and suggesting a larger cell size.

b3gbi 0.5.5 - Minor update:

  • Fixed bugs in ab_rarity_map() and area_rarity_map() that caused incorrect calculations.
  • Added more unit tests.
  • Improved error handling in some functions.

b3gbi 0.5.4 - Minor update:

  • Fixed an error where spherical geometry was being turned off without a good reason. Spherical geometry is now only turned off to retry failed st_intersection() or st_difference() operations or when the user explicitly sets it to FALSE.
  • Additional error handling was added to many functions.
  • process_cube() now checks for contamination in the grid code column and throws an error if any false grid codes are found.
  • Some code was cleaned up and made more efficient.
  • Unit tests were added to the package for some functions to prevent breakage in future updates.

b3gbi 0.5.3 - Minor update:

  • Updated old and non-working example in process_cube() documentation.

b3gbi 0.5.2 - Minor update:

  • Fixed species occurrence and species range plots when selecting only one species (previously it was not possible to add additional ggplot code when only one species was plotted due to a bug in the plotting code).

b3gbi 0.5.1 - Minor update:

  • Equations in pkgdown help website now display correctly.
  • Fixed bad example in spec_occ_ts() documentation.

b3gbi 0.5.0 - Major update:

  • Conversion between input and output coordinate reference systems is now handled correctly even if they have different units (e.g. degrees vs km).
  • Conversion between CRSs with different units (e.g. degrees vs km) must now be forced by the user, and a warning is given.
  • More extensive documentation is now provided for indicator functions, including formulas and background information.
  • Users can now provide external shapefiles to limit indicator calculations to feature boundaries.
  • Removed compatibility with previous generation cubes (created using TriAs project code).

b3gbi 0.4.4 - Minor update:

  • Area is no longer calculated for projections that use degrees.
  • Occurrence density now refuses to calculate for projections that use degrees.
  • Object metadata now displays ‘degrees’ instead of ‘degrees^2’.

b3gbi 0.4.3

04.03.2025 - Minor update:

  • Add power parameter for map legend scale transformations. This enables the use of Box-Cox, modulus, and Yeo-Johnson transformations.

b3gbi 0.4.2

20.02.2025 - Minor update:

  • Bug fix: Coordinates now display correctly after using process_cube() with custom grid codes

b3gbi 0.4.1

19.02.2025 - Minor update:

  • All R CMD checks are now passing without any errors, warnings or notes
  • The ‘taxize’ package is no longer a dependency, but must be installed if you want to calculate taxonomic distinctness

b3gbi 0.4

14.02.2025 - Major update:

  • Better integration with rnaturalearth
  • Fully supports b3gbi GUI functions
  • Hill diversity functions are now exported and can be used

b3gbi 0.3.1

12.02.2025 - Minor update:

  • Get dependencies from recognised repositories
  • Join the R-universe!

b3gbi 0.3

05.12.2024 - Major update:

  • Added bootstrapped confidence intervals to most indicators.
  • Added many additional customization parameters for time series plots. See plot_ts() documentation.
  • Defaults for some visualization parameters have changed.
  • Fixed bug that caused errors about incorrect cell sizes when they were actually correct.

b3gbi 0.2.3.1

20.11.2024 - Minor update:

  • User-supplied resolutions for ‘km’-based grid systems are now properly handled

b3gbi 0.2.3

07.11.2024 - Minor update:

Compatible with gcube output:

  • added class sim_cube for objects without grid codes
  • added ‘none’ to grid_type options

Bug fixes:

  • No longer returns an error when you correctly specify a cell size when calculating indicators with mgrs grid

b3gbi 0.2.2

16.07.2024 - Minor update:

  • Cubes processed using process_cube_old() now have a column called minCoordinateUncertaintyInMeters, containing the spatial uncertainty from the cube. Previously the spatial uncertainty column was made available when using process_cube() but was ignored by process_cube_old().

b3gbi 0.2.1

27.06.2024 - Minor update:

  • Added options to improve control of plot output. The argument land_fill_colour allows you to change the colour of the land area outside of the grid.The argument crop_to_grid will snap the plot edges to the gridded area. This will improve the way the plot looks if e.g. your data is sparse and does not extend to the edges of a country or continent.
  • Fixed a bug in process_cube_old that caused it to fail.
  • Fixed a bug that caused calculated indicator objects to retain too many data columns.

b3gbi 0.2.0

24.06.2024 - Major update:

  • Added occupancy turnover to available indicators.
  • All indicators in the package now working (you can get a list by typing ‘available_indicators’).
  • The process_cube function now expects a current generation cube (created using the GBIF API) by default. Previous generation cubes (created using the TriAS project code) can still be used but must now be processed using a separate function, process_cube_old.
  • Added support for non-standard column names (you can manually input column names when processing your cube, and the process_cube function will rename them to the Darwin Core standard expected by the rest of the package).
  • Added support for Quarter Degree and Military grids (note that the Military grids are translated by an external package that is not on CRAN. It is hoped to replace this with native code in a later update).
  • Process_cube function can now automatically find the column containing the grid cell codes and detect the type of grid (there are options to manually input the column name and grid cell type but in most cases it is better to leave it on automatic to avoid potential downstream problems).
  • You can now select the output CRS you want to use for your calculated indicator.

b3gbi 0.1.0