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ChrisJones687ChrisJones687
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update remaining pops single run tests and add configs.
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‎inst/extdata/configs_pops/ts28_config_t1.yaml‎

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# File paths for input and output data
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input_path: "C:/Users/cjone/Projects/rpops/inst/extdata"
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output_path: "C:/Users/cjone/Projects/rpops/inst/extdata/simple2x2/outputs"
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# pest parameters
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starting_infected_files: ["extdata/simple2x2/infected_oak_wsd.tif", "extdata/simple2x2/infected_tanoak_wsd.tif", "extdata/simple2x2/infected_baylaurel_wsd.tif"]
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parameter_means_file: "extdata/parameter_means_default.csv"
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parameter_cov_matrix_file: "extdata/parameter_cov_matrix_default.csv"
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pest_host_table: "extdata/pest_host_table.csv"
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competency_table: "extdata/competency_table_multihost.csv"
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county_level_infection_data: false
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use_initial_condition_uncertainty: false
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start_exposed: false
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latency_period: 2
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exposed_files: [""]
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# host data
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host_files: ["extdata/simple2x2/host_oak_wsd.tif", "extdata/simple2x2/host_tanoak_wsd.tif", "extdata/simple2x2/host_baylaurel_wsd.tif"]
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total_populations_file: "extdata/simple2x2/total_plants.tif"
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use_host_uncertainty: true
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# simulation settings
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random_seed: 42
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start_date: "2008-01-01"
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end_date: "2009-12-31"
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time_step: "month"
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model_type: "SI"
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season_month_start: 1
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season_month_end: 12
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number_of_iterations: 10
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number_of_cores: 2
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output_frequency: "year"
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output_frequency_n: 1
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mask: null
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# weather
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use_lethal_temperature: false
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lethal_temperature_file: "extdata/simple2x2/critical_temp_all_below_threshold.tif"
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lethal_temperature: -14
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lethal_temperature_month: 1
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use_overwinter_survival: false
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overwinter_survival_rate_month: 3
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overwinter_survival_rate_day: 15
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overwinter_survival_rates_file: "extdata/simple2x2/survival_rates.tif"
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use_temperature: true
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temperature_coefficient_file: "extdata/simple2x2/temperature_coefficient.tif"
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temperature_coefficient_sd_file: "extdata/simple2x2/coefficient_sd.tif"
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use_precipitation: false
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precipitation_coefficient_file: "extdata/simple2x2/temperature_coefficient.tif"
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precipitation_coefficient_sd_file: "extdata/simple2x2/coefficient_sd.tif"
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weather_type: "deterministic"
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# mortality
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mortality_frequency: "year"
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mortality_frequency_n: 1
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# treatments
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use_treatment: false
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treatments_file: "extdata/simple2x2/treatments.tif"
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treatment_dates: ["2009-05-01"]
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treatment_method: "ratio"
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pesticide_durations: [120]
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pesticide_efficacy: 0.5
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use_quarantine: false
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quarantine_areas_file: ""
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quarantine_directions: ""
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# dispersal
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natural_kernel_type: "cauchy"
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natural_dir: "NONE"
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anthropogenic_kernel_type: "cauchy"
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anthropogenic_dir: "NONE"
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# only used if anthropogenic_kernel_type == "network"
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network_files: [""]
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network_movement_types: ["walk"]
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network_min_distances: [0]
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network_max_distances: [0]
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network_weights: [1]
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# host movement
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use_movements: false
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movements_file: ""
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# stochasticity
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use_multiple_random_seeds: false
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multiple_random_seeds_file: null
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generate_stochasticity: true
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establishment_stochasticity: true
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movement_stochasticity: true
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dispersal_stochasticity: true
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establishment_probability: 0.5
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dispersal_percentage: 0.99
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use_spreadrates: false
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use_overpopulation_movements: false
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overpopulation_percentage: 0.75
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leaving_percentage: 0.5
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leaving_scale_coefficient: 5
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# soil_pests
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use_soils: false
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soil_starting_pest_file: ""
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start_with_soil_populations: false
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dispersers_to_soils_percentage: 0
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# validation and calibration
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infected_val_cal_file: ""
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# calibration only parameters
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perform_calibration: false
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params_to_estimate: [true, true, true, true, false, false]
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prior_means: [0, 0, 0, 0, 0, 0]
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prior_cov_matrix: [[0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0]]
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prior_number_of_observations: 0
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number_of_observations: 0
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success_metric: "MCC"
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verbose: true
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natural_kappa: 0
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anthropogenic_kappa: 0
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calibration_method: "ABC"
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# ABC Parameters
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generation_size: 1000
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number_of_generations: 7
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# validation only
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perform_validation: false
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point_file: ""
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use_configuration: false
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# Model API only never used unless you are pulling data from an S3 bucket in the cloud
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use_s3: false
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bucket: ""

‎inst/extdata/configs_pops/ts28_config_t2.yaml‎

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# File paths for input and output data
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input_path: "C:/Users/cjone/Projects/rpops/inst/extdata"
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output_path: "C:/Users/cjone/Projects/rpops/inst/extdata/simple2x2/outputs"
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# pest parameters
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starting_infected_files: ["extdata/simple2x2/infected_oak_wsd.tif", "extdata/simple2x2/infected_tanoak_wsd.tif"]
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parameter_means_file: "extdata/parameter_means_rr5.csv"
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parameter_cov_matrix_file: "extdata/parameter_cov_matrix_rr5.csv"
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pest_host_table: "extdata/pest_host_table_2host.csv"
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competency_table: "extdata/competency_table_2host.csv"
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county_level_infection_data: false
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use_initial_condition_uncertainty: false
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start_exposed: false
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latency_period: 2
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exposed_files: [""]
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# host data
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host_files: ["extdata/simple2x2/host_oak_wsd.tif", "extdata/simple2x2/host_tanoak_wsd.tif"]
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total_populations_file: "extdata/simple2x2/total_plants.tif"
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use_host_uncertainty: true
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# simulation settings
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random_seed: 42
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start_date: "2008-01-01"
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end_date: "2009-12-31"
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time_step: "month"
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model_type: "SI"
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season_month_start: 1
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season_month_end: 12
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number_of_iterations: 10
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number_of_cores: 2
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output_frequency: "year"
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output_frequency_n: 1
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mask: null
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# weather
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use_lethal_temperature: false
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lethal_temperature_file: "extdata/simple2x2/critical_temp_all_below_threshold.tif"
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lethal_temperature: -14
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lethal_temperature_month: 1
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use_overwinter_survival: false
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overwinter_survival_rate_month: 3
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overwinter_survival_rate_day: 15
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overwinter_survival_rates_file: "extdata/simple2x2/survival_rates.tif"
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use_temperature: true
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temperature_coefficient_file: "extdata/simple2x2/temperature_coefficient.tif"
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temperature_coefficient_sd_file: "extdata/simple2x2/coefficient_sd.tif"
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use_precipitation: false
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precipitation_coefficient_file: "extdata/simple2x2/temperature_coefficient.tif"
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precipitation_coefficient_sd_file: "extdata/simple2x2/coefficient_sd.tif"
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weather_type: "deterministic"
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# mortality
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mortality_frequency: "year"
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mortality_frequency_n: 1
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# treatments
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use_treatment: false
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treatments_file: "extdata/simple2x2/treatments.tif"
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treatment_dates: ["2009-05-01"]
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treatment_method: "ratio"
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pesticide_durations: [120]
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pesticide_efficacy: 0.5
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use_quarantine: false
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quarantine_areas_file: ""
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quarantine_directions: ""
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# dispersal
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natural_kernel_type: "cauchy"
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natural_dir: "NONE"
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anthropogenic_kernel_type: "cauchy"
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anthropogenic_dir: "NONE"
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# only used if anthropogenic_kernel_type == "network"
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network_files: [""]
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network_movement_types: ["walk"]
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network_min_distances: [0]
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network_max_distances: [0]
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network_weights: [1]
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# host movement
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use_movements: false
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movements_file: ""
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# stochasticity
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use_multiple_random_seeds: false
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multiple_random_seeds_file: null
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generate_stochasticity: true
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establishment_stochasticity: true
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movement_stochasticity: true
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dispersal_stochasticity: true
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establishment_probability: 0.5
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dispersal_percentage: 0.99
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use_spreadrates: false
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use_overpopulation_movements: false
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overpopulation_percentage: 0.75
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leaving_percentage: 0.5
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leaving_scale_coefficient: 5
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# soil_pests
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use_soils: false
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soil_starting_pest_file: ""
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start_with_soil_populations: false
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dispersers_to_soils_percentage: 0
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# validation and calibration
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infected_val_cal_file: ""
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# calibration only parameters
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perform_calibration: false
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params_to_estimate: [true, true, true, true, false, false]
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prior_means: [0, 0, 0, 0, 0, 0]
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prior_cov_matrix: [[0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0]]
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prior_number_of_observations: 0
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number_of_observations: 0
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success_metric: "MCC"
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verbose: true
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natural_kappa: 0
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anthropogenic_kappa: 0
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calibration_method: "ABC"
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# ABC Parameters
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generation_size: 1000
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number_of_generations: 7
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# validation only
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perform_validation: false
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point_file: ""
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use_configuration: false
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# Model API only never used unless you are pulling data from an S3 bucket in the cloud
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use_s3: false
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bucket: ""

‎inst/extdata/configs_pops/ts29_config_t1.yaml‎

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# File paths for input and output data
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input_path: "C:/Users/cjone/Projects/rpops/inst/extdata"
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output_path: "C:/Users/cjone/Projects/rpops/inst/extdata/simple2x2/outputs"
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# pest parameters
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starting_infected_files: ["extdata/simple20x20/county_infected.gpkg"]
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parameter_means_file: "extdata/parameter_means_default.csv"
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parameter_cov_matrix_file: "extdata/parameter_cov_matrix_default.csv"
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pest_host_table: "extdata/pest_host_table_singlehost_nomort.csv"
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competency_table: "extdata/competency_table_singlehost.csv"
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county_level_infection_data: true
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use_initial_condition_uncertainty: false
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start_exposed: false
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latency_period: 2
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exposed_files: [""]
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# host data
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host_files: ["extdata/simple20x20/host_w_sd2.tif"]
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total_populations_file: "extdata/simple20x20/all_plants.tif"
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use_host_uncertainty: false
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# simulation settings
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random_seed: null
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start_date: "2008-01-01"
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end_date: "2008-03-31"
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time_step: "month"
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model_type: "SI"
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season_month_start: 1
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season_month_end: 12
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number_of_iterations: 10
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number_of_cores: 2
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output_frequency: "month"
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output_frequency_n: 1
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mask: null
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# weather
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use_lethal_temperature: false
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lethal_temperature_file: "extdata/simple2x2/critical_temp_all_below_threshold.tif"
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lethal_temperature: -14
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lethal_temperature_month: 1
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use_overwinter_survival: false
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overwinter_survival_rate_month: 3
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overwinter_survival_rate_day: 15
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overwinter_survival_rates_file: "extdata/simple2x2/survival_rates.tif"
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use_temperature: false
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temperature_coefficient_file: "extdata/simple2x2/temperature_coefficient.tif"
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temperature_coefficient_sd_file: "extdata/simple2x2/coefficient_sd.tif"
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use_precipitation: false
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precipitation_coefficient_file: "extdata/simple2x2/temperature_coefficient.tif"
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precipitation_coefficient_sd_file: "extdata/simple2x2/coefficient_sd.tif"
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weather_type: "deterministic"
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# mortality
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mortality_frequency: "month"
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mortality_frequency_n: 1
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# treatments
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use_treatment: false
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treatments_file: "extdata/simple2x2/treatments.tif"
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treatment_dates: ["2008-02-01"]
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treatment_method: "ratio"
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pesticide_durations: [0]
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pesticide_efficacy: 0.5
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use_quarantine: false
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quarantine_areas_file: "extdata/simple20x20/initial_infection.tif"
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quarantine_directions: ""
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# dispersal
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natural_kernel_type: "cauchy"
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natural_dir: "NONE"
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anthropogenic_kernel_type: "cauchy"
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anthropogenic_dir: "NONE"
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# only used if anthropogenic_kernel_type == "network"
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network_files: ["extdata/simple20x20/segments1.csv", "extdata/simple20x20/segments2.csv"]
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network_movement_types: ["walk", "walk"]
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network_min_distances: [100, 100]
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network_max_distances: [1000, 1000]
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network_weights: [1, 1000]
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# host movement
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use_movements: false
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movements_file: ""
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# stochasticity
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use_multiple_random_seeds: false
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multiple_random_seeds_file: null
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generate_stochasticity: true
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establishment_stochasticity: true
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movement_stochasticity: true
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dispersal_stochasticity: true
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establishment_probability: 0.5
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dispersal_percentage: 0.99
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use_spreadrates: false
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use_overpopulation_movements: false
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overpopulation_percentage: 0.75
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leaving_percentage: 0.5
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leaving_scale_coefficient: 5
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# soil_pests
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use_soils: false
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soil_starting_pest_file: ""
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start_with_soil_populations: false
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dispersers_to_soils_percentage: 0
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# validation and calibration
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infected_val_cal_file: ""
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# calibration only parameters
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perform_calibration: false
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params_to_estimate: [true, true, true, true, false, false]
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prior_means: [0, 0, 0, 0, 0, 0]
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prior_cov_matrix: [[0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0]]
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prior_number_of_observations: 0
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number_of_observations: 0
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success_metric: "MCC"
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verbose: true
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natural_kappa: 0
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anthropogenic_kappa: 0
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calibration_method: "ABC"
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# ABC Parameters
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generation_size: 1000
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number_of_generations: 7
123+
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# validation only
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perform_validation: false
126+
point_file: ""
127+
use_configuration: false
128+
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# Model API only never used unless you are pulling data from an S3 bucket in the cloud
130+
use_s3: false
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bucket: ""

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