Welcome to b3alien’s documentation!

Contents:

• Introduction
• Architecture
• Exemplar workflow to determine the Rate of Establishment
  • Install the b3alien Python package
  • Load the software package and additional libraries
  • Step 1: Generate a Biodiversity Data Cube from GBIF
  • Step 2: Download the GRIIS checklist of the considered country, and load it as a checklist object
  • Step 3: Load the OccurrenceCube
  • Step 4: Calculate the Rate of Establishment from the CheckList and OccurrenceCube
  • Step 5: Determine the error margings on the fitted rate of establishment
  • Step 6: Determine the survey effort
• OccurrenceCube Class
  • OccurrenceCube
  • Biodiversity data cube functions
  • aggregate_count_per_cell()
  • calculate_rate()
  • cumulative_species()
  • filter_multiple_cells()
  • filter_multiple_occ()
  • filter_time_window()
  • find_correlations()
  • get_survey_effort()
  • plot_cumsum()
  • plot_richness()
• GRIIS checklist class
  • CheckList
  • GRIIS checklist functions
  • do_taxon_matching()
  • get_speciesKey()
  • get_species_under_genus()
  • read_checklist()
  • split_event_date()
• Visualisation module
  • Visualisation of Data Cubes and the resulting simulations
  • gdf_to_ee_featurecollection()
  • initialize()
  • visualize_ee_layers()
• Simulation module
  • Simulation functions
  • get_bootstrap_errors()
  • parallel_bootstrap_solow_costello()
  • plot_with_confidence()
  • run_bootstrap_analysis()
  • simulate_solow_costello()
  • simulate_solow_costello_scipy()
• Utilitary functions
  • Utils
  • detect_runtime()
  • in_ipython()
  • in_jupyter()
  • in_script()
  • to_geoparquet()
• Acknowledgements

Indices and tables

• Index

• Module Index

• Search Page