77# ' forecast spread of the pest/pathogen into the future. This function performs
88# ' a single stochastic realization of the model and is predominantly used for
99# ' automated tests of model features.
10- # ' @param config The config with the list of parameters returned from running configuration.
10+ # ' @param config_rds_file Path to config file produced when calling `configuration`.
11+ # ' The config file includes all data necessary used to set up c++ PoPS model
1112# '
1213# ' @useDynLib PoPS, .registration = TRUE
1314# ' @importFrom terra app rast xres yres classify extract ext as.points ncol nrow project
@@ -33,85 +34,86 @@ pops <- function(config) {
3334 config $ competency_table_list <- competency_table_list_creator(config $ competency_table )
3435 config $ pest_host_table_list <- pest_host_table_list_creator(config $ pest_host_table )
3536
36- data <- pops_model(random_seed = config $ random_seed [1 ],
37- multiple_random_seeds = config $ multiple_random_seeds ,
38- random_seeds = unname(as.matrix(config $ random_seeds [1 , ])[1 , ]),
39- use_lethal_temperature = config $ use_lethal_temperature ,
40- lethal_temperature = config $ lethal_temperature ,
41- lethal_temperature_month = config $ lethal_temperature_month ,
42- use_survival_rates = config $ use_survival_rates ,
43- survival_rate_month = config $ survival_rate_month ,
44- survival_rate_day = config $ survival_rate_day ,
45- host_pools = config $ host_pools ,
46- total_populations = config $ total_populations ,
47- competency_table = config $ competency_table_list ,
48- pest_host_table = config $ pest_host_table_list ,
49- mortality_on = config $ mortality_on ,
50- quarantine_areas = config $ quarantine_areas ,
51- quarantine_directions = config $ quarantine_directions ,
52- treatment_maps = config $ treatment_maps ,
53- treatment_dates = config $ treatment_dates ,
54- pesticide_duration = config $ pesticide_duration ,
55- use_movements = config $ use_movements ,
56- movements = config $ movements ,
57- movements_dates = config $ movements_dates ,
58- weather = config $ weather ,
59- temperature = config $ temperature ,
60- survival_rates = config $ survival_rates ,
61- weather_coefficient = config $ weather_coefficient ,
62- weather_coefficient_sd = config $ weather_coefficient_sd ,
63- res = config $ res ,
64- rows_cols = config $ rows_cols ,
65- time_step = config $ time_step ,
66- reproductive_rate = config $ reproductive_rate [1 ],
67- spatial_indices = config $ spatial_indices ,
68- season_month_start_end = config $ season_month_start_end ,
69- soil_reservoirs = config $ soil_reservoirs ,
70- start_date = config $ start_date ,
71- end_date = config $ end_date ,
72- treatment_method = config $ treatment_method ,
73- natural_kernel_type = config $ natural_kernel_type ,
74- anthropogenic_kernel_type = config $ anthropogenic_kernel_type ,
75- use_anthropogenic_kernel = config $ use_anthropogenic_kernel ,
76- percent_natural_dispersal = config $ percent_natural_dispersal [1 ],
77- natural_distance_scale = config $ natural_distance_scale [1 ],
78- anthropogenic_distance_scale = config $ anthropogenic_distance_scale [1 ],
79- natural_dir = config $ natural_dir ,
80- natural_kappa = config $ natural_kappa [1 ],
81- anthropogenic_dir = config $ anthropogenic_dir ,
82- anthropogenic_kappa = config $ anthropogenic_kappa [1 ],
83- output_frequency = config $ output_frequency ,
84- output_frequency_n = config $ output_frequency_n ,
85- quarantine_frequency = config $ quarantine_frequency ,
86- quarantine_frequency_n = config $ quarantine_frequency_n ,
87- use_quarantine = config $ use_quarantine ,
88- spreadrate_frequency = config $ spreadrate_frequency ,
89- spreadrate_frequency_n = config $ spreadrate_frequency_n ,
90- mortality_frequency = config $ mortality_frequency ,
91- mortality_frequency_n = config $ mortality_frequency_n ,
92- use_spreadrates = config $ use_spreadrates ,
93- model_type_ = config $ model_type ,
94- latency_period = config $ latency_period ,
95- generate_stochasticity = config $ generate_stochasticity ,
96- establishment_stochasticity = config $ establishment_stochasticity ,
97- movement_stochasticity = config $ movement_stochasticity ,
98- dispersal_stochasticity = config $ dispersal_stochasticity ,
99- establishment_probability = config $ establishment_probability ,
100- dispersal_percentage = config $ dispersal_percentage ,
101- use_overpopulation_movements = config $ use_overpopulation_movements ,
102- overpopulation_percentage = config $ overpopulation_percentage ,
103- leaving_percentage = config $ leaving_percentage ,
104- leaving_scale_coefficient = config $ leaving_scale_coefficient ,
105- bbox = config $ bounding_box ,
106- network_min_distances = config $ network_min_distances ,
107- network_max_distances = config $ network_max_distances ,
108- network_filenames = config $ network_filenames ,
109- network_movement_types = config $ network_movement_types ,
110- network_weights = config $ network_weights ,
111- weather_size = config $ weather_size ,
112- weather_type = config $ weather_type ,
113- dispersers_to_soils_percentage = config $ dispersers_to_soils_percentage ,
114- use_soils = config $ use_soils )
37+ data <- PoPS :: pops_model(
38+ random_seed = config $ random_seed [1 ],
39+ use_multiple_random_seeds = config $ use_multiple_random_seeds ,
40+ random_seeds = as.matrix(config $ random_seeds [1 , ])[1 , ],
41+ use_lethal_temperature = config $ use_lethal_temperature ,
42+ lethal_temperature = config $ lethal_temperature ,
43+ lethal_temperature_month = config $ lethal_temperature_month ,
44+ use_overwinter_survival = config $ use_overwinter_survival ,
45+ overwinter_survival_rate_month = config $ overwinter_survival_rate_month ,
46+ overwinter_survival_rate_day = config $ overwinter_survival_rate_day ,
47+ host_pools = config $ host_pools ,
48+ total_populations = config $ total_populations ,
49+ competency_table = config $ competency_table_list ,
50+ pest_host_table = config $ pest_host_table_list ,
51+ mortality_on = config $ mortality_on ,
52+ quarantine_areas = config $ quarantine_areas ,
53+ quarantine_directions = config $ quarantine_directions ,
54+ treatment_maps = config $ treatment_maps ,
55+ treatment_dates = config $ treatment_dates ,
56+ pesticide_duration = config $ pesticide_duration ,
57+ use_movements = config $ use_movements ,
58+ movements = config $ movements ,
59+ movements_dates = config $ movements_dates ,
60+ weather = config $ weather ,
61+ temperature = config $ temperature ,
62+ survival_rates = config $ survival_rates ,
63+ weather_coefficient = config $ weather_coefficient ,
64+ weather_coefficient_sd = config $ weather_coefficient_sd ,
65+ res = config $ res ,
66+ rows_cols = config $ rows_cols ,
67+ time_step = config $ time_step ,
68+ reproductive_rate = config $ reproductive_rate ,
69+ spatial_indices = config $ spatial_indices ,
70+ season_month_start_end = config $ season_month_start_end ,
71+ soil_reservoirs = config $ soil_reservoirs ,
72+ start_date = config $ start_date ,
73+ end_date = config $ end_date ,
74+ treatment_method = config $ treatment_method ,
75+ natural_kernel_type = config $ natural_kernel_type ,
76+ anthropogenic_kernel_type = config $ anthropogenic_kernel_type ,
77+ use_anthropogenic_kernel = config $ use_anthropogenic_kernel ,
78+ percent_natural_dispersal = config $ percent_natural_dispersal [1 ],
79+ natural_distance_scale = config $ natural_distance_scale [1 ],
80+ anthropogenic_distance_scale = config $ anthropogenic_distance_scale [1 ],
81+ natural_dir = config $ natural_dir ,
82+ natural_kappa = config $ natural_kappa [1 ],
83+ anthropogenic_dir = config $ anthropogenic_dir ,
84+ anthropogenic_kappa = config $ anthropogenic_kappa [1 ],
85+ output_frequency = config $ output_frequency ,
86+ output_frequency_n = config $ output_frequency_n ,
87+ quarantine_frequency = config $ quarantine_frequency ,
88+ quarantine_frequency_n = config $ quarantine_frequency_n ,
89+ use_quarantine = config $ use_quarantine ,
90+ spreadrate_frequency = config $ spreadrate_frequency ,
91+ spreadrate_frequency_n = config $ spreadrate_frequency_n ,
92+ mortality_frequency = config $ mortality_frequency ,
93+ mortality_frequency_n = config $ mortality_frequency_n ,
94+ use_spreadrates = config $ use_spreadrates ,
95+ model_type_ = config $ model_type ,
96+ latency_period = config $ latency_period ,
97+ generate_stochasticity = config $ generate_stochasticity ,
98+ establishment_stochasticity = config $ establishment_stochasticity ,
99+ movement_stochasticity = config $ movement_stochasticity ,
100+ dispersal_stochasticity = config $ dispersal_stochasticity ,
101+ establishment_probability = config $ establishment_probability ,
102+ dispersal_percentage = config $ dispersal_percentage ,
103+ use_overpopulation_movements = config $ use_overpopulation_movements ,
104+ overpopulation_percentage = config $ overpopulation_percentage ,
105+ leaving_percentage = config $ leaving_percentage ,
106+ leaving_scale_coefficient = config $ leaving_scale_coefficient ,
107+ bbox = config $ bounding_box ,
108+ network_min_distances = config $ network_min_distances ,
109+ network_max_distances = config $ network_max_distances ,
110+ network_filenames = config $ network_filenames ,
111+ network_movement_types = config $ network_movement_types ,
112+ network_weights = config $ network_weights ,
113+ weather_size = config $ weather_size ,
114+ weather_type = config $ weather_type ,
115+ dispersers_to_soils_percentage = config $ dispersers_to_soils_percentage ,
116+ use_soils = config $ use_soils )
115117
116118 return (data )
117119}
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