v2.0.0

Added

• Network kernel. (Vaclav Petras)
• Established dispersers from a cell are now tracked. (Chris Jones)
• Collection of general-use function for container handling for internal use.
• Template parameter for random number generator to Model and Simulation.
• New frequency values, every_step and time_step, can be used to schedule action every step of the simulation. (Vaclav Petras)
  • This was implemented in rpops for simple cases. The new version in Core supports all unit and n combinations for the simulation step.

Changed

• Virtual functions are used to switch between kernels instead of an ever-growing if-else statement. (Vaclav Petras)
  • This is possibly faster and it has additional cost only when compared to hardcoded simple kernels.
  • New code is potentially 4 times faster as measured with r.pops.spread in #152.
  • Kernel parameters don't need to be provided anymore when the kernel is not used.
  • Opens door for adding many kernels in a flexible way.
• Anthropogenic kernel is now different from natural kernel and contains one network kernel. (Vaclav Petras)

Fixed

• Fixed and completed documentation of function parameters. (Vaclav Petras)

Full Changelog: v1.1.0...v2.0.0

v1.1.0

Added

• Pest movement based on overpopulation (Vaclav Petras)
  • When cell contains too many pests, pests leave and move to a different cell.
• Total hosts added to run_step (Chris Jones)
  • Allows overpopulations to be based on total_hosts rather than total_populations
  • Allows movement to be based on total_hosts rather than total_populations
• Mortality timing is now more flexible (Chris Jones)
  • requires 2 new parameters mortality_frequency and mortality_frequency_n

Changed

• Model class internal attributes and functions are now protected instead of private
  to allow derived classes to access them for greater flexibility (Vaclav Petras).
• Model class kernels are now created and returned by protected functions (Vaclav Petras).
• Config class has now more defaults and subsequent setup now consistently fails when
  required values were not set (Vaclav Petras).
• Movement module has added parameters (mortality_tracker_vector, exposed, resistant,
  total_exposed, and suitable_cells) (Chris Jones).
  • Now moves exposed and resistant populations
  • Now moves total_hosts
  • Now moves moratility tracked hosts
  • Adds a new suitable_cell if a movement creates a new location with hosts.
• Treatments now modify total hosts (Chris Jones)
• Citation updated to PoPS Frontiers paper (Chris Jones)
  • Jones, C., Jones, S., Petrasova, A., Petras, V., Gaydos, D.,
    Skrip, M., Takeuchi, Y., Bigsby, K., and Meentemeyer, R., 2021.
    Iteratively forecasting biological invasions with PoPS and a little help from
    our friends.
    Frontiers in Ecology and the Environment
    DOI: 10.1002/fee.2357

PoPS 1.0.0

This is version 1.0.0 of the PoPS Core C++ library and its interfaces: rpops R package and r.pops.spread GRASS GIS module. The release of PoPS Core includes:

• Susceptible-infected (SI) and susceptible-exposed-infected (SEI) host phases,
• Host mortality tracking,
• Host removal and pesticide application treatments,
• Host resistance based on pesticide application treatments,
• Treatments applied only to a ratio of hosts,
• Seasonal spread limited to certain months,
• Limited host movement (experimental),
• Yearly pest removal based on lethal temperature,
• Two different dispersal kernels (natural and anthropogenic),
• Cauchy and exponential radial dispersal kernels,
• Reduced stochasticity options and deterministic versions of kernels,
• Spread rate measurement,
• Quarantine and study area escape measurements,
• C++ API centered around two classes: pops::Model and pops::Config.