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countycal2013.R
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countycal2013.R
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library(PoPS)
library(terra)
# library(plyr)
# Note that the google drive might have a different letter
ffIn <- "Z:/Late_blight/"
ffout <- "Z:/Late_blight/modelresults/"
# This has all the time steps for a calibration/validation duration
infected_years_file = paste0(ffIn, "infections/gpkg/years/2013/inf_years_file_2013.gpkg")#"infections/rasters/2013/usa_2013_infections.tif")
number_of_observations = 347
prior_number_of_observations = 1467
prior_means = c(0, 0, 0, 0, 0, 0)
prior_cov_matrix = matrix(0, 6, 6)
params_to_estimate = c(TRUE, TRUE, TRUE, TRUE, FALSE, FALSE)
number_of_generations = 7
generation_size = 1000
pest_host_table = paste0(ffIn, "hosts/pest_host_table_lb.csv")
competency_table = paste0(ffIn, "hosts/competency_table_original.csv")
# This is the starting infection for a calibration/validation perio
infected_file_list = paste0(ffIn, "infections/gpkg/filelist/2013/inf_filelist_2013.gpkg")
host_file_list = paste0(ffIn, "hosts/host_2013_nona.tif")
total_populations_file = paste0(ffIn, "all_populations/tot_pop_2013_nona.tif")
temp = TRUE
temperature_coefficient_file = paste0(ffIn, "Weather_data/weather_us_2013.tif")
precip = FALSE
precipitation_coefficient_file = ""
model_type = "SI"
latency_period = 0
time_step = "week"
season_month_start = 1
season_month_end = 12
start_date = "2013-01-01"
end_date = "2013-12-31"
use_survival_rates = FALSE
survival_rate_month = 3
survival_rate_day = 15
survival_rates_file = ""
use_lethal_temperature = FALSE
temperature_file = ""
lethal_temperature = 5
lethal_temperature_month = 1
mortality_frequency = "week"
mortality_frequency_n = 1
management = FALSE
treatment_dates = c("")
treatments_file = ""
treatment_method = "ratio"
natural_kernel_type = "cauchy"
anthropogenic_kernel_type = "cauchy"
natural_dir = "NONE"
natural_kappa = 0
anthropogenic_dir = "NONE"
anthropogenic_kappa = 0
pesticide_duration = c(0)
pesticide_efficacy = 1
mask = NULL
output_frequency = "week"
output_frequency_n = 1
movements_file = ""
use_movements = FALSE
start_exposed = FALSE
generate_stochasticity = TRUE
establishment_stochasticity = TRUE
movement_stochasticity = TRUE
dispersal_stochasticity = TRUE
establishment_probability = 0.5
dispersal_percentage = 0.99
quarantine_areas_file = ""
use_quarantine = FALSE
use_spreadrates = FALSE
use_overpopulation_movements = FALSE
overpopulation_percentage = 0
leaving_percentage = 0
leaving_scale_coefficient = 1
calibration_method = "ABC"
number_of_iterations = 1e+05
exposed_file_list = ""
verbose = TRUE
write_outputs = "None"
output_folder_path = ffout
network_filename = ""
network_movement = "walk"
success_metric = "mcc"
use_initial_condition_uncertainty = FALSE
use_host_uncertainty = FALSE
weather_type = "deterministic"
temperature_coefficient_sd_file = ""
precipitation_coefficient_sd_file = ""
dispersers_to_soils_percentage = 0
quarantine_directions = ""
multiple_random_seeds = FALSE
file_random_seeds = NULL
use_soils = FALSE
soil_starting_pest_file = ""
start_with_soil_populations = FALSE
county_level_infection_data = TRUE
#started at 20:35 on 4/19
# Started at 9 on 2/13
lb_cal = calibrate(infected_years_file,
number_of_observations,
prior_number_of_observations,
prior_means,
prior_cov_matrix,
params_to_estimate,
number_of_generations,
generation_size,
pest_host_table,
competency_table,
infected_file_list,
host_file_list,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
model_type,
latency_period,
time_step,
season_month_start,
season_month_end,
start_date,
end_date,
use_survival_rates,
survival_rate_month,
survival_rate_day,
survival_rates_file,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_frequency,
mortality_frequency_n,
management,
treatment_dates,
treatments_file,
treatment_method,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
natural_kappa,
anthropogenic_dir,
anthropogenic_kappa,
pesticide_duration,
pesticide_efficacy,
mask,
output_frequency,
output_frequency_n,
movements_file,
use_movements,
start_exposed,
generate_stochasticity,
establishment_stochasticity,
movement_stochasticity,
dispersal_stochasticity,
establishment_probability,
dispersal_percentage,
quarantine_areas_file,
use_quarantine,
use_spreadrates,
use_overpopulation_movements,
overpopulation_percentage,
leaving_percentage,
leaving_scale_coefficient,
calibration_method,
number_of_iterations,
exposed_file_list,
verbose,
write_outputs,
output_folder_path,
network_filename,
network_movement,
success_metric,
use_initial_condition_uncertainty,
use_host_uncertainty,
weather_type,
temperature_coefficient_sd_file,
precipitation_coefficient_sd_file,
dispersers_to_soils_percentage,
quarantine_directions,
multiple_random_seeds,
file_random_seeds,
use_soils,
soil_starting_pest_file,
start_with_soil_populations,
county_level_infection_data)