PoPS 2.0.1

Added

• calibrate can now use the Mathews Correlation Coefficient as the summary statistic of
  to keep or reject parameter sets (@ChrisJones687, #145).

• validate, calibrate, pops_multirun, and pops now take use_survival_rates, survival_rate_month,
  survival_rate_day, and survival_rates_file (@ChrisJones687, #147).

• validate, calibrate, pops_multirun, and pops now take network_movement as a parameter. This
  parameter controls how dispersal occurs along the network (@ChrisJones687, #147).

Changed

• validate, calibrate, pops_multirun, auto_manage and pops no longer take
  network_min_distance and network_max_distance as these parameters are now passed
  in through the parameter_means and parameter_cov_matrix parameters and are calibrated
  as part of the calibration if network kernel is selected (@ChrisJones687, #140).

• calibrate now calibrates the network_min_distance and network_max_distance parameters
  during calibration and they are now part of the parameter_means and parameter_cov_matrix
  that are exported from the calibration (@ChrisJones687, #140).

• calibrate has more flexible success metric options removes use_distance, use_rmse, and use_mcc
  parameters and replaces it with the more flexible success_metrics parameter. Users can now
  select multiple combinations of different success metrics for the calibration
  (@ChrisJones687, #150).

• pops_multirun removed the ability to write all simulations. (@ChrisJones687, #144).

• the deterministic parameter has been renamed to dispersal_stochasticity. This
  was done to be more consistent with generate_stochasticity, movement_stochasticity, and
  establishment_stochasticity parameters (@ChrisJones687, #147).

• validate, calibrate, pops_multirun, and pops now propogate uncertainty from host and
  initial conditions. This adds the parameters use_initial_condition_uncertainty and
  use_host_uncertainty. If use_initial_condition_uncertainty is TRUE the infected_file and/or
  exposed_file need to have 2 layers a mean and standard deviation. If use_host_uncertainty is
  is TRUE the host_file needs to have 2 layers a mean and standard deviation. For each model run
  a host and/or initial conditions are drawn from the mean and sd layers so that each run has a
  unique host and/or initial conditions this will allow for both propogation of uncertainty from
  these sources but also partitioning (@ChrisJones687, #151).

Fixed

• fixed error on parameter draws in select situations (@ChrisJones687, #146).

PoPS 2.0.0

Added

• quantity_allocation_disagreement now takes in the use_distance parameter which is FALSE
  by default. This allows the model to compute the minimum total distance between observed
  and simulated infestations (@ChrisJones687, #130).

• validate, calibrate, pops_multirun, auto_manage and pops now take in
  network_min_distance, network_max_distance, and network_filename parameters these are
  used when the anthropogenic_kernel_type = "network". This allows directed spread along
  a network such as a railroad (@ChrisJones687 and @wenzeslaus, #131)

Changed

• validate now takes the variable point_file and uses it to calculate statistics based on the
  point_file in addition to the raster file also calculates new measures of model performance
  accuracy, precision, recall, and specificity (@ChrisJones687, #124).

• calibrate no longer uses success_metrics and checks parameters as these are both handled
  internally by auto-updating if the values are too far of in the first generation. This
  makes for a simpler and faster user experience (@ChrisJones687, #130).

• validate no longer uses success_metrics parameter but now has the added parameters
  use_rmse and use_distance that are used in quantity_allocation_disagreement.
  This allows for a more intuitive user interface (@ChrisJones687, #130).

• quantity_allocation_disagreement variable configuration changed to use_configuration
  to be more consistent with variable names. (@ChrisJones687, #130).

• pops_multirun can now use variable write_output = "all_simulations" to write out
  susceptible, exposed, and infected rasters from all simulations. This will allow for a
  future update where simulations can easily be started from previous simulation outputs.
  (@ChrisJones687, #133)

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)

PoPS 1.0.2

Version 1.0.2 of the PoPS Core C++ library and its interfaces: rpops R package and r.pops.spread GRASS GIS module. The release of rpops includes:

• Susceptible-infected (SI) and susceptible-exposed-infected (SEI) host phases (model_type, latency_period),
• Host mortality tracking (mortality_rate, mortality),
• Host removal and pesticide application treatments (treatments, treatment_date, pesticide_duration),
• Host resistance based on pesticide application treatments (pesticide_duration > 0),
• Treatments applied only to a ratio of hosts (treatment_application),
• Yearly pest removal based on lethal temperature (lethal_temperature, lethal_month),
• Two different dispersal kernels (natural_dispersal_kernel, anthropogenic_dispersal_kernel),
• Cauchy and exponential radial dispersal kernels use Von Mises distribution,
• Seasonal spread (seasonality in months),
• Multiple stochastic runs (pops_multirun),
• Parallel execution of multiple runs (number_of_cores in pops_multirun),
• Output of average and standard deviation of infected hosts across multiple runs and for a single stochastic run (simulation_mean, single_run, simulation_sd),
• Average and standard deviations for output averages (number_infecteds, infected_areas),
• Infection probability output in percent (probability),
• Spread rate measurement in 4 cardinal directions (west_rate, east_rate, south_rate, north_rate ),
• Distance to quarantine in 4 cardinal directions (north_distance_to_quarantine, south_distance_to_quarantine, east_distance_to_quarantine, west_distance_to_quarantine ),
• Probability of quarantine escape (escape_probability).

Version 1.0.2 Changes

• Multirun and validate draw a parameter set from the distribution for each run as intended
• Exposed populations now exported each time-step
• Fixed error when calibrating for less than 4 parameters

PoPS 1.0.0

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 rpops includes:

• Susceptible-infected (SI) and susceptible-exposed-infected (SEI) host phases (model_type, latency_period),
• Host mortality tracking (mortality_rate, mortality),
• Host removal and pesticide application treatments (treatments, treatment_date, pesticide_duration),
• Host resistance based on pesticide application treatments (pesticide_duration > 0),
• Treatments applied only to a ratio of hosts (treatment_application),
• Yearly pest removal based on lethal temperature (lethal_temperature, lethal_month),
• Two different dispersal kernels (natural_dispersal_kernel, anthropogenic_dispersal_kernel),
• Cauchy and exponential radial dispersal kernels use Von Mises distribution,
• Seasonal spread (seasonality in months),
• Multiple stochastic runs (pops_multirun),
• Parallel execution of multiple runs (number_of_cores in pops_multirun),
• Output of average and standard deviation of infected hosts across multiple runs and for a single stochastic run (simulation_mean, single_run, simulation_sd),
• Average and standard deviations for output averages (number_infecteds, infected_areas),
• Infection probability output in percent (probability),
• Spread rate measurement in 4 cardinal directions (west_rate, east_rate, south_rate, north_rate ),
• Distance to quarantine in 4 cardinal directions (north_distance_to_quarantine, south_distance_to_quarantine, east_distance_to_quarantine, west_distance_to_quarantine ),
• Probability of quarantine escape (escape_probability).

Beta 0.1

0.1.0-beta

Merge pull request #18 from ncsu-landscape-dynamics/feature/uncertain…