PoPS 1.1.0

Added

• New dispersal kernels added: Uniform, Power-law, Deterministic neighbor,
  Hyperbolic-Secant, Gamma, Weibull, Normal, and Logistic (@ChrisJones687, #73).

  • These kernels are usable for both (natural_dispersal_kernel, anthropogenic_dispersal_kernel).
  • Used in the following functions (pops, pops_multirun, auto_manage, calibrate, and validate).

• Overpopulation module added to pops-core (@wenzeslaus, #83).

• Spatial Index to increase computational speed (@chrisjones, #67)

Changed

• Exposed and Infected populations can both be present at the start of a simulation (@ChrisJones687, #92).

• Internal functions for data handling have switched from the raster package to the terra package (@ChrisJones687, #79).

  • Adds terra dependency.
  • Greatly speeds up data handling and preparation.

• Mask parameter now used in pops-multirun for post processing data for visualization (@ChrisJones687, #104).

• Calibration function now takes verbose parameter (@nfkruska, #99).

• All functions now support vrt data types (@ChrisJones687, #97).

• Raster files can now be read from S3 buckets (@ChrisJones687, #75).

  • needed for model-api for dashboard

• Outputs can now be saved with write_outputs and output_folder_path parameters (@ChrisJones687, #111).

• Host map now used as initial mask for post processing and validation calculations (@ChrisJones687, #112).

• Movements now moves exposed, resistant, and mortality tracked populations (@ChrisJones687, #118).

• Mortality can now occur at various timesteps not just yearly (@ChrisJones687, #118).

  • Can be either "day", "week", "month", "year", or "every_n_steps".
  • adds parameters mortality_frequency and mortality_frequency_n.

• Validation now exports the statistics for each output and the cumulative statistics for each year (@ChrisJones687, #121).

• Treatments now update total_hosts (@ChrisJones687, #122)