update config yamls

Author: ChrisJones687

inst/extdata/configs_configuration/test_config.yaml

@@ -3,24 +3,23 @@ input_path: "C:/Users/cjone/Projects/rpops/inst/extdata" # folder with inputs
 output_path: "C:/Users/cjone/Projects/rpops/inst/extdata/simple20x20/outputs" # folder to write outputs to
 
 # pest parameters
-starting_infected_files: ["extdata/simple20x20/infected_single.tif"] # GeoTiff File with the locations of initial infections to start the simulation
-parameter_means_file: "extdata/parameter_means_default.csv" # CSV File with the parameter means from the calibration
-parameter_cov_matrix_file: "extdata/parameter_cov_matrix_default.csv" # CSV File with the parameter covariance matrix from the calibration
-pest_host_table: "extdata/pest_host_table_singlehost.csv" # CSV file with the pest host table
-competency_table: "extdata/competency_table_singlehost.csv" # CSV file with the compentency table
+starting_infected_files: ["simple20x20/infected_single.tif"] # GeoTiff File with the locations of initial infections to start the simulation
+parameter_means_file: "parameter_means_default.csv" # CSV File with the parameter means from the calibration
+parameter_cov_matrix_file: "parameter_cov_matrix_default.csv" # CSV File with the parameter covariance matrix from the calibration
+pest_host_table_file: "pest_host_table_singlehost.csv" # CSV file with the pest host table
+competency_table_file: "competency_table_singlehost.csv" # CSV file with the compentency table
 county_level_infection_data: false # is your infection data county level only
 use_initial_condition_uncertainty: false # Are you providing a mean and standard deviation for your starting infection files. This allows for propogating uncertainty through the model.
 start_exposed: false # Should you start with your known infections as exposed. Useful for simulating inoculation experiments.
 latency_period: 0 # what is the lantent period of your pathogen?
 exposed_files: [""] # A list of GeoTiff files with location of exposed infections at start of simulation.
 
 # host data
-host_files: ["extdata/simple20x20/host.tif"]
-total_populations_file: "extdata/simple20x20/all_plants.tif"
+host_files: ["simple20x20/host.tif"]
+total_populations_file: "simple20x20/all_plants.tif"
 use_host_uncertainty: false
 
 # simulation settings
-random_seed: null # no need to set this primarily used for tests to ensure identical random draws.
 start_date: "2024-01-01"
 end_date: "2024-12-31"
 time_step: "week"
@@ -31,7 +30,6 @@ number_of_iterations: 10
 number_of_cores: 2
 output_frequency: "year"
 output_frequency_n: 1
-mask: null
 
 # weather
 use_lethal_temperature: false
@@ -102,14 +100,18 @@ soil_starting_pest_file: ""
 start_with_soil_populations: false
 dispersers_to_soils_percentage: 0
 
+# Mask out areas for comparison (e.g. water, or other landcover types)
+use_mask: FALSE
+mask_file: ""
+
 # validation and calibration
 infected_val_cal_file: "" # GeoTiff file with the infections in which to compare the validation/calibration results with.
 
 # calibration only parameters
 perform_calibration: false
 params_to_estimate: [true, true, true, true, false, false] # Position 1 = reproductive rate, 2 =
-prior_means: [0, 0, 0, 0, 0, 0]
-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]]
+prior_means_file: ""
+prior_cov_matrix_file: ""
 prior_number_of_observations: 0 # observations that have been conducted at the start of the simulation
 number_of_observations: 0 # observations that were conducted during the simulation for validation/calibration (these are samples taken to confirm presence/absence and/or abundance)
 success_metric: "MCC"
@@ -125,7 +127,12 @@ number_of_generations: 7
 perform_validation: false
 point_file: "" # only if you want to validate to specific point data ()
 use_configuration: false # Use if you want to calculate configuration disagreement. This takes longer to compute simulation statistics and success metrics).
+use_distance: false
 
 # Model API only never used unless you are pulling data from an S3 bucket in the cloud
 use_s3: false
 bucket: ""
+
+# testing only ignore for normal use
+random_seed: null
+testing: FALSE

inst/extdata/configs_configuration/test_config_anthropogenic_kernel_error.yml

@@ -3,24 +3,23 @@ input_path: "C:/Users/cjone/Projects/rpops/inst/extdata" # folder with inputs
 output_path: "C:/Users/cjone/Projects/rpops/inst/extdata/simple20x20/outputs" # folder to write outputs to
 
 # pest parameters
-starting_infected_files: ["extdata/simple20x20/infected_single.tif"] # GeoTiff File with the locations of initial infections to start the simulation
-parameter_means_file: "extdata/parameter_means_default.csv" # CSV File with the parameter means from the calibration
-parameter_cov_matrix_file: "extdata/parameter_cov_matrix_default.csv" # CSV File with the parameter covariance matrix from the calibration
-pest_host_table: "extdata/pest_host_table_singlehost.csv" # CSV file with the pest host table
-competency_table: "extdata/competency_table_singlehost.csv" # CSV file with the compentency table
+starting_infected_files: ["simple20x20/infected_single.tif"] # GeoTiff File with the locations of initial infections to start the simulation
+parameter_means_file: "parameter_means_default.csv" # CSV File with the parameter means from the calibration
+parameter_cov_matrix_file: "parameter_cov_matrix_default.csv" # CSV File with the parameter covariance matrix from the calibration
+pest_host_table_file: "pest_host_table_singlehost.csv" # CSV file with the pest host table
+competency_table_file: "competency_table_singlehost.csv" # CSV file with the compentency table
 county_level_infection_data: false # is your infection data county level only
 use_initial_condition_uncertainty: false # Are you providing a mean and standard deviation for your starting infection files. This allows for propogating uncertainty through the model.
 start_exposed: false # Should you start with your known infections as exposed. Useful for simulating inoculation experiments.
 latency_period: 0 # what is the lantent period of your pathogen?
 exposed_files: [""] # A list of GeoTiff files with location of exposed infections at start of simulation.
 
 # host data
-host_files: ["extdata/simple20x20/host.tif"]
-total_populations_file: "extdata/simple20x20/all_plants.tif"
+host_files: ["simple20x20/host.tif"]
+total_populations_file: "simple20x20/all_plants.tif"
 use_host_uncertainty: false
 
 # simulation settings
-random_seed: null # no need to set this primarily used for tests to ensure identical random draws.
 start_date: "2024-01-01"
 end_date: "2024-12-31"
 time_step: "week"
@@ -31,7 +30,6 @@ number_of_iterations: 10
 number_of_cores: 2
 output_frequency: "year"
 output_frequency_n: 1
-mask: null
 
 # weather
 use_lethal_temperature: false
@@ -102,6 +100,10 @@ soil_starting_pest_file: ""
 start_with_soil_populations: false
 dispersers_to_soils_percentage: 0
 
+# Mask out areas for comparison (e.g. water, or other landcover types)
+use_mask: FALSE
+mask_file: ""
+
 # validation and calibration
 infected_val_cal_file: "" # GeoTiff file with the infections in which to compare the validation/calibration results with.
 
@@ -125,7 +127,12 @@ number_of_generations: 7
 perform_validation: false
 point_file: "" # only if you want to validate to specific point data ()
 use_configuration: false # Use if you want to calculate configuration disagreement. This takes longer to compute simulation statistics and success metrics).
+use_distance: false
 
 # Model API only never used unless you are pulling data from an S3 bucket in the cloud
 use_s3: false
 bucket: ""
+
+# testing only ignore for normal use
+random_seed: null
+testing: FALSE

inst/extdata/configs_configuration/test_config_host_uncert_error.yml

@@ -3,24 +3,23 @@ input_path: "C:/Users/cjone/Projects/rpops/inst/extdata" # folder with inputs
 output_path: "C:/Users/cjone/Projects/rpops/inst/extdata/simple20x20/outputs" # folder to write outputs to
 
 # pest parameters
-starting_infected_files: ["extdata/simple20x20/infected_single.tif"] # GeoTiff File with the locations of initial infections to start the simulation
-parameter_means_file: "extdata/parameter_means_default.csv" # CSV File with the parameter means from the calibration
-parameter_cov_matrix_file: "extdata/parameter_cov_matrix_default.csv" # CSV File with the parameter covariance matrix from the calibration
-pest_host_table: "extdata/pest_host_table_singlehost.csv" # CSV file with the pest host table
-competency_table: "extdata/competency_table_singlehost.csv" # CSV file with the compentency table
+starting_infected_files: ["simple20x20/infected_single.tif"] # GeoTiff File with the locations of initial infections to start the simulation
+parameter_means_file: "parameter_means_default.csv" # CSV File with the parameter means from the calibration
+parameter_cov_matrix_file: "parameter_cov_matrix_default.csv" # CSV File with the parameter covariance matrix from the calibration
+pest_host_table_file: "pest_host_table_singlehost.csv" # CSV file with the pest host table
+competency_table_file: "competency_table_singlehost.csv" # CSV file with the compentency table
 county_level_infection_data: false # is your infection data county level only
 use_initial_condition_uncertainty: false # Are you providing a mean and standard deviation for your starting infection files. This allows for propogating uncertainty through the model.
 start_exposed: false # Should you start with your known infections as exposed. Useful for simulating inoculation experiments.
 latency_period: 0 # what is the lantent period of your pathogen?
 exposed_files: [""] # A list of GeoTiff files with location of exposed infections at start of simulation.
 
 # host data
-host_files: ["extdata/simple20x20/host.tif"]
-total_populations_file: "extdata/simple20x20/all_plants.tif"
+host_files: ["simple20x20/host.tif"]
+total_populations_file: "simple20x20/all_plants.tif"
 use_host_uncertainty: true
 
 # simulation settings
-random_seed: null # no need to set this primarily used for tests to ensure identical random draws.
 start_date: "2024-01-01"
 end_date: "2024-12-31"
 time_step: "week"
@@ -31,7 +30,6 @@ number_of_iterations: 10
 number_of_cores: 2
 output_frequency: "year"
 output_frequency_n: 1
-mask: null
 
 # weather
 use_lethal_temperature: false
@@ -102,14 +100,18 @@ soil_starting_pest_file: ""
 start_with_soil_populations: false
 dispersers_to_soils_percentage: 0
 
+# Mask out areas for comparison (e.g. water, or other landcover types)
+use_mask: FALSE
+mask_file: ""
+
 # validation and calibration
 infected_val_cal_file: "" # GeoTiff file with the infections in which to compare the validation/calibration results with.
 
 # calibration only parameters
 perform_calibration: false
 params_to_estimate: [true, true, true, true, false, false] # Position 1 = reproductive rate, 2 =
-prior_means: [0, 0, 0, 0, 0, 0]
-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]]
+prior_means_file: ""
+prior_cov_matrix_file: ""
 prior_number_of_observations: 0 # observations that have been conducted at the start of the simulation
 number_of_observations: 0 # observations that were conducted during the simulation for validation/calibration (these are samples taken to confirm presence/absence and/or abundance)
 success_metric: "MCC"
@@ -125,7 +127,12 @@ number_of_generations: 7
 perform_validation: false
 point_file: "" # only if you want to validate to specific point data ()
 use_configuration: false # Use if you want to calculate configuration disagreement. This takes longer to compute simulation statistics and success metrics).
+use_distance: false
 
 # Model API only never used unless you are pulling data from an S3 bucket in the cloud
 use_s3: false
 bucket: ""
+
+# testing only ignore for normal use
+random_seed: null
+testing: FALSE

inst/extdata/configs_configuration/test_config_initial_cond_uncert_error.yml

@@ -3,24 +3,23 @@ input_path: "C:/Users/cjone/Projects/rpops/inst/extdata" # folder with inputs
 output_path: "C:/Users/cjone/Projects/rpops/inst/extdata/simple20x20/outputs" # folder to write outputs to
 
 # pest parameters
-starting_infected_files: ["extdata/simple20x20/infected_single.tif"] # GeoTiff File with the locations of initial infections to start the simulation
-parameter_means_file: "extdata/parameter_means_default.csv" # CSV File with the parameter means from the calibration
-parameter_cov_matrix_file: "extdata/parameter_cov_matrix_default.csv" # CSV File with the parameter covariance matrix from the calibration
-pest_host_table: "extdata/pest_host_table_singlehost.csv" # CSV file with the pest host table
-competency_table: "extdata/competency_table_singlehost.csv" # CSV file with the compentency table
+starting_infected_files: ["simple20x20/infected_single.tif"] # GeoTiff File with the locations of initial infections to start the simulation
+parameter_means_file: "parameter_means_default.csv" # CSV File with the parameter means from the calibration
+parameter_cov_matrix_file: "parameter_cov_matrix_default.csv" # CSV File with the parameter covariance matrix from the calibration
+pest_host_table_file: "pest_host_table_singlehost.csv" # CSV file with the pest host table
+competency_table_file: "competency_table_singlehost.csv" # CSV file with the compentency table
 county_level_infection_data: false # is your infection data county level only
 use_initial_condition_uncertainty: true # Are you providing a mean and standard deviation for your starting infection files. This allows for propogating uncertainty through the model.
 start_exposed: false # Should you start with your known infections as exposed. Useful for simulating inoculation experiments.
 latency_period: 0 # what is the lantent period of your pathogen?
 exposed_files: [""] # A list of GeoTiff files with location of exposed infections at start of simulation.
 
 # host data
-host_files: ["extdata/simple20x20/host.tif"]
-total_populations_file: "extdata/simple20x20/all_plants.tif"
+host_files: ["simple20x20/host.tif"]
+total_populations_file: "simple20x20/all_plants.tif"
 use_host_uncertainty: false
 
 # simulation settings
-random_seed: null # no need to set this primarily used for tests to ensure identical random draws.
 start_date: "2024-01-01"
 end_date: "2024-12-31"
 time_step: "week"
@@ -31,7 +30,6 @@ number_of_iterations: 10
 number_of_cores: 2
 output_frequency: "year"
 output_frequency_n: 1
-mask: null
 
 # weather
 use_lethal_temperature: false
@@ -102,14 +100,18 @@ soil_starting_pest_file: ""
 start_with_soil_populations: false
 dispersers_to_soils_percentage: 0
 
+# Mask out areas for comparison (e.g. water, or other landcover types)
+use_mask: FALSE
+mask_file: ""
+
 # validation and calibration
 infected_val_cal_file: "" # GeoTiff file with the infections in which to compare the validation/calibration results with.
 
 # calibration only parameters
 perform_calibration: false
 params_to_estimate: [true, true, true, true, false, false] # Position 1 = reproductive rate, 2 =
-prior_means: [0, 0, 0, 0, 0, 0]
-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]]
+prior_means_file: ""
+prior_cov_matrix_file: ""
 prior_number_of_observations: 0 # observations that have been conducted at the start of the simulation
 number_of_observations: 0 # observations that were conducted during the simulation for validation/calibration (these are samples taken to confirm presence/absence and/or abundance)
 success_metric: "MCC"
@@ -125,7 +127,12 @@ number_of_generations: 7
 perform_validation: false
 point_file: "" # only if you want to validate to specific point data ()
 use_configuration: false # Use if you want to calculate configuration disagreement. This takes longer to compute simulation statistics and success metrics).
+use_distance: false
 
 # Model API only never used unless you are pulling data from an S3 bucket in the cloud
 use_s3: false
 bucket: ""
+
+# testing only ignore for normal use
+random_seed: null
+testing: FALSE

inst/extdata/configs_configuration/test_config_latency_period_error.yml

@@ -3,24 +3,23 @@ input_path: "C:/Users/cjone/Projects/rpops/inst/extdata" # folder with inputs
 output_path: "C:/Users/cjone/Projects/rpops/inst/extdata/simple20x20/outputs" # folder to write outputs to
 
 # pest parameters
-starting_infected_files: ["extdata/simple20x20/infected_single.tif"] # GeoTiff File with the locations of initial infections to start the simulation
-parameter_means_file: "extdata/parameter_means_default.csv" # CSV File with the parameter means from the calibration
-parameter_cov_matrix_file: "extdata/parameter_cov_matrix_default.csv" # CSV File with the parameter covariance matrix from the calibration
-pest_host_table: "extdata/pest_host_table_singlehost.csv" # CSV file with the pest host table
-competency_table: "extdata/competency_table_singlehost.csv" # CSV file with the compentency table
+starting_infected_files: ["simple20x20/infected_single.tif"] # GeoTiff File with the locations of initial infections to start the simulation
+parameter_means_file: "parameter_means_default.csv" # CSV File with the parameter means from the calibration
+parameter_cov_matrix_file: "parameter_cov_matrix_default.csv" # CSV File with the parameter covariance matrix from the calibration
+pest_host_table_file: "pest_host_table_singlehost.csv" # CSV file with the pest host table
+competency_table_file: "competency_table_singlehost.csv" # CSV file with the compentency table
 county_level_infection_data: false # is your infection data county level only
 use_initial_condition_uncertainty: false # Are you providing a mean and standard deviation for your starting infection files. This allows for propogating uncertainty through the model.
 start_exposed: false # Should you start with your known infections as exposed. Useful for simulating inoculation experiments.
 latency_period: 0 # what is the lantent period of your pathogen?
 exposed_files: [""] # A list of GeoTiff files with location of exposed infections at start of simulation.
 
 # host data
-host_files: ["extdata/simple20x20/host.tif"]
-total_populations_file: "extdata/simple20x20/all_plants.tif"
+host_files: ["simple20x20/host.tif"]
+total_populations_file: "simple20x20/all_plants.tif"
 use_host_uncertainty: false
 
 # simulation settings
-random_seed: null # no need to set this primarily used for tests to ensure identical random draws.
 start_date: "2024-01-01"
 end_date: "2024-12-31"
 time_step: "week"
@@ -31,7 +30,6 @@ number_of_iterations: 10
 number_of_cores: 2
 output_frequency: "year"
 output_frequency_n: 1
-mask: null
 
 # weather
 use_lethal_temperature: false
@@ -102,14 +100,18 @@ soil_starting_pest_file: ""
 start_with_soil_populations: false
 dispersers_to_soils_percentage: 0
 
+# Mask out areas for comparison (e.g. water, or other landcover types)
+use_mask: FALSE
+mask_file: ""
+
 # validation and calibration
 infected_val_cal_file: "" # GeoTiff file with the infections in which to compare the validation/calibration results with.
 
 # calibration only parameters
 perform_calibration: false
 params_to_estimate: [true, true, true, true, false, false] # Position 1 = reproductive rate, 2 =
-prior_means: [0, 0, 0, 0, 0, 0]
-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]]
+prior_means_file: ""
+prior_cov_matrix_file: ""
 prior_number_of_observations: 0 # observations that have been conducted at the start of the simulation
 number_of_observations: 0 # observations that were conducted during the simulation for validation/calibration (these are samples taken to confirm presence/absence and/or abundance)
 success_metric: "MCC"
@@ -125,7 +127,12 @@ number_of_generations: 7
 perform_validation: false
 point_file: "" # only if you want to validate to specific point data ()
 use_configuration: false # Use if you want to calculate configuration disagreement. This takes longer to compute simulation statistics and success metrics).
+use_distance: false
 
 # Model API only never used unless you are pulling data from an S3 bucket in the cloud
 use_s3: false
 bucket: ""
+
+# testing only ignore for normal use
+random_seed: null
+testing: FALSE