tests/testthat/test-pops-multirun.R
In ncsu-landscape-dynamics/rpops: Pest or Pathogen Spread Model
context("test-pops-multirun")
test_that("Model stops if files don't exist or aren't the correct extension", {
infected_file_list <-
system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
expect_error(pops_multirun(infected_file_list = "",
host_file_list = host_file_list,
total_populations_file = host_file_list,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
file_exists_error)
expect_error(pops_multirun(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
mask = ""),
file_exists_error)
})
test_that("Multirun model outputs work", {
skip_on_os("windows")
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
temperature_file <- ""
temperature_coefficient_file <- ""
precipitation_coefficient_file <- ""
use_lethal_temperature <- FALSE
temp <- FALSE
precip <- FALSE
season_month_start <- 5
season_month_end <- 11
time_step <- "month"
start_date <- "2019-01-01"
end_date <- "2019-12-31"
lethal_temperature <- -35
lethal_temperature_month <- 1
random_seed <- 42
treatments_file <- ""
treatment_dates <- c("2019-11-01")
treatment_method <- "ratio"
management <- FALSE
mortality_frequency <- "Year"
mortality_frequency_n <- 1
natural_kernel_type <- "cauchy"
anthropogenic_kernel_type <- "cauchy"
natural_dir <- "NONE"
anthropogenic_dir <- "NONE"
pesticide_duration <- c(0)
pesticide_efficacy <- 1.0
random_seed <- NULL
output_frequency <- "year"
movements_file <- ""
use_movements <- FALSE
number_of_iterations <- 2
number_of_cores <- 2
model_type <- "SI"
latency_period <- 0
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
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
output_frequency_n <- 1
use_spreadrates <- TRUE
use_overpopulation_movements <- FALSE
overpopulation_percentage <- 0
leaving_percentage <- 0
leaving_scale_coefficient <- 1
exposed_file_list <- ""
mask <- NULL
write_outputs <- "None"
output_folder_path <- tempdir()
network_filename <- ""
use_survival_rates <- FALSE
survival_rate_month <- 3
survival_rate_day <- 15
survival_rates_file <- ""
network_movement <- "walk"
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
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
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,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
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,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement,
use_initial_condition_uncertainty,
use_host_uncertainty)
expect_equal(length(data), 18)
expect_equal(terra::as.matrix(data$median_run[[1]], wide = TRUE),
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
# expect_equal(terra::as.matrix(data$susceptible_run[[1]], wide = TRUE),
# matrix(c(10, 6, 14, 15), nrow = 2, ncol = 2))
expect_equal(terra::as.matrix(data$probability[[1]], wide = TRUE),
matrix(c(100, 0, 0, 0), nrow = 2, ncol = 2))
expect_equal(data$number_infecteds[[1]], 5)
expect_equal(data$number_infecteds[[2]], 0)
expect_equal(data$infected_areas[[1]], 900)
expect_equal(data$infected_areas[[2]], 0)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
output_frequency <- "month"
write_outputs <- "None"
output_folder_path <- ""
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
model_type,
latency_period,
time_step,
season_month_start,
season_month_end,
start_date,
end_date,
use_survival_rates,
survival_rate_month,
survival_rate_day,
survival_rates_file,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_frequency,
mortality_frequency_n,
management,
treatment_dates,
treatments_file,
treatment_method,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
output_frequency,
output_frequency_n,
movements_file,
use_movements,
start_exposed,
generate_stochasticity,
establishment_stochasticity,
movement_stochasticity,
dispersal_stochasticity,
establishment_probability,
dispersal_percentage,
quarantine_areas_file,
use_quarantine,
use_spreadrates,
use_overpopulation_movements,
overpopulation_percentage,
leaving_percentage,
leaving_scale_coefficient,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement,
use_initial_condition_uncertainty = FALSE,
use_host_uncertainty = FALSE,
weather_type = "deterministic",
temperature_coefficient_sd_file = "",
precipitation_coefficient_sd_file = "",
dispersers_to_soils_percentage = 0,
quarantine_directions = "",
multiple_random_seeds = FALSE,
file_random_seeds = NULL,
use_soils = FALSE,
soil_starting_pest_file = "",
start_with_soil_populations = FALSE)
expect_equal(length(data), 18)
expect_equal(terra::as.matrix(data$median_run[[1]], wide = TRUE),
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
# expect_equal(terra::as.matrix(data$susceptible_run[[1]], wide = TRUE),
# matrix(c(10, 6, 14, 15), nrow = 2, ncol = 2))
expect_equal(terra::as.matrix(data$probability[[1]], wide = TRUE),
matrix(c(100, 0, 0, 0), nrow = 2, ncol = 2))
expect_equal(data$number_infecteds[[1]], 5)
expect_equal(data$number_infecteds[[2]], 0)
expect_equal(data$infected_areas[[1]], 900)
expect_equal(data$infected_areas[[2]], 0)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
output_frequency <- "year"
quarantine_areas_file <-
system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
use_quarantine <- TRUE
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
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,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
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,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement)
expect_equal(length(data), 18)
expect_equal(terra::as.matrix(data$median_run[[1]], wide = TRUE),
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
# expect_equal(terra::as.matrix(data$susceptible_run[[1]], wide = TRUE),
# matrix(c(10, 6, 14, 15), nrow = 2, ncol = 2))
expect_equal(terra::as.matrix(data$probability[[1]], wide = TRUE),
matrix(c(100, 0, 0, 0), nrow = 2, ncol = 2))
expect_equal(data$number_infecteds[[1]], 5)
expect_equal(data$number_infecteds[[2]], 0)
expect_equal(data$infected_areas[[1]], 900)
expect_equal(data$infected_areas[[2]], 0)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
output_frequency <- "month"
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
model_type,
latency_period,
time_step,
season_month_start,
season_month_end,
start_date,
end_date,
use_survival_rates,
survival_rate_month,
survival_rate_day,
survival_rates_file,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_frequency,
mortality_frequency_n,
management,
treatment_dates,
treatments_file,
treatment_method,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
output_frequency,
output_frequency_n,
movements_file,
use_movements,
start_exposed,
generate_stochasticity,
establishment_stochasticity,
movement_stochasticity,
dispersal_stochasticity,
establishment_probability,
dispersal_percentage,
quarantine_areas_file,
use_quarantine,
use_spreadrates,
use_overpopulation_movements,
overpopulation_percentage,
leaving_percentage,
leaving_scale_coefficient,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement)
expect_equal(length(data), 18)
expect_equal(terra::as.matrix(data$median_run[[1]], wide = TRUE),
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
# expect_equal(terra::as.matrix(data$susceptible_run[[1]], wide = TRUE),
# matrix(c(10, 6, 14, 15), nrow = 2, ncol = 2))
expect_equal(terra::as.matrix(data$probability[[1]], wide = TRUE),
matrix(c(100, 0, 0, 0), nrow = 2, ncol = 2))
expect_equal(data$number_infecteds[[1]], 5)
expect_equal(data$number_infecteds[[2]], 0)
expect_equal(data$infected_areas[[1]], 900)
expect_equal(data$infected_areas[[2]], 0)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
})
test_that("Multirun model outputs work with mask", {
skip_on_os("windows")
infected_file_list <-
system.file("extdata", "simple20x20", "initial_infection.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple20x20", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
temperature_file <- ""
temperature_coefficient_file <- ""
precipitation_coefficient_file <- ""
use_lethal_temperature <- FALSE
temp <- FALSE
precip <- FALSE
season_month_start <- 5
season_month_end <- 11
time_step <- "month"
start_date <- "2019-01-01"
end_date <- "2019-12-31"
lethal_temperature <- -35
lethal_temperature_month <- 1
random_seed <- NA
treatments_file <- ""
treatment_dates <- c("2019-11-01")
treatment_method <- "ratio"
management <- FALSE
mortality_frequency <- "Year"
mortality_frequency_n <- 1
natural_kernel_type <- "cauchy"
anthropogenic_kernel_type <- "cauchy"
natural_dir <- "NONE"
anthropogenic_dir <- "NONE"
pesticide_duration <- c(0)
pesticide_efficacy <- 1.0
random_seed <- NULL
output_frequency <- "year"
movements_file <- ""
use_movements <- FALSE
number_of_iterations <- 2
number_of_cores <- 2
model_type <- "SI"
latency_period <- 0
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
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
output_frequency_n <- 1
use_spreadrates <- TRUE
mask <- system.file("extdata", "simple20x20", "mask.tif", package = "PoPS")
use_survival_rates <- FALSE
survival_rate_month <- 3
survival_rate_day <- 15
survival_rates_file <- ""
network_movement <- "walk"
use_overpopulation_movements <- FALSE
overpopulation_percentage <- 0
leaving_percentage <- 0
leaving_scale_coefficient <- 1
exposed_file_list <- ""
write_outputs <- "None"
output_folder_path <- tempdir()
network_filename <- ""
quarantine_directions <- ""
multiple_random_seeds <- TRUE
file_random_seeds <- NULL
use_soils <- FALSE
soil_starting_pest_file <- ""
start_with_soil_populations <- FALSE
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
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
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,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
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,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement,
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)
expect_equal(length(data), 18)
expect_equal(terra::as.matrix(data$median_run[[1]], wide = TRUE),
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(data$number_infecteds[[1]], 1)
expect_equal(data$number_infecteds[[2]], 0)
expect_equal(data$infected_areas[[1]], 10000)
expect_equal(data$infected_areas[[2]], 0)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
use_initial_condition_uncertainty <- TRUE
use_host_uncertainty <- TRUE
infected_file_list <-
system.file("extdata", "simple20x20", "infected_wsd.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple20x20", "host_w_sd2.tif", package = "PoPS")
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
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,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
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,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement,
use_initial_condition_uncertainty,
use_host_uncertainty,
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)
expect_equal(length(data), 18)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
use_initial_condition_uncertainty <- TRUE
use_host_uncertainty <- FALSE
infected_file_list <-
system.file("extdata", "simple20x20", "infected_wsd.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple20x20", "host_w_sd2.tif", package = "PoPS")
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
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,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
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,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement,
use_initial_condition_uncertainty,
use_host_uncertainty,
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)
expect_equal(length(data), 18)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
use_initial_condition_uncertainty <- FALSE
use_host_uncertainty <- TRUE
infected_file_list <-
system.file("extdata", "simple20x20", "infected_wsd.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple20x20", "host_w_sd2.tif", package = "PoPS")
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
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,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
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,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement,
use_initial_condition_uncertainty,
use_host_uncertainty,
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)
expect_equal(length(data), 18)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
use_initial_condition_uncertainty <- FALSE
use_host_uncertainty <- FALSE
infected_file_list <-
system.file("extdata", "simple20x20", "infected_wsd.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple20x20", "host_w_sd2.tif", package = "PoPS")
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
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,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
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,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement,
use_initial_condition_uncertainty,
use_host_uncertainty,
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)
expect_equal(length(data), 18)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
})
test_that("Multirun model outputs work with writing all simulations and random seeds", {
skip_on_os("windows")
infected_file_list <-
system.file("extdata", "simple20x20", "initial_infection.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple20x20", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
temperature_file <- ""
temperature_coefficient_file <- ""
precipitation_coefficient_file <- ""
use_lethal_temperature <- FALSE
temp <- FALSE
precip <- FALSE
season_month_start <- 5
season_month_end <- 11
time_step <- "month"
start_date <- "2019-01-01"
end_date <- "2019-12-31"
lethal_temperature <- -35
lethal_temperature_month <- 1
random_seed <- 42
treatments_file <- ""
treatment_dates <- c("2019-11-01")
treatment_method <- "ratio"
management <- FALSE
mortality_frequency <- "Year"
mortality_frequency_n <- 1
natural_kernel_type <- "cauchy"
anthropogenic_kernel_type <- "cauchy"
natural_dir <- "NONE"
anthropogenic_dir <- "NONE"
pesticide_duration <- c(0)
pesticide_efficacy <- 1.0
random_seed <- NULL
output_frequency <- "year"
movements_file <- ""
use_movements <- FALSE
number_of_iterations <- 2
number_of_cores <- 2
model_type <- "SEI"
latency_period <- 2
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
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
output_frequency_n <- 1
use_spreadrates <- TRUE
mask <- system.file("extdata", "simple20x20", "mask.tif", package = "PoPS")
use_survival_rates <- FALSE
survival_rate_month <- 3
survival_rate_day <- 15
survival_rates_file <- ""
network_movement <- "walk"
network_movement <- "walk"
use_overpopulation_movements <- FALSE
overpopulation_percentage <- 0
leaving_percentage <- 0
leaving_scale_coefficient <- 1
exposed_file_list <- ""
write_outputs <- "all_simulations"
output_folder_path <- tempdir()
network_filename <- ""
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 <- TRUE
file_random_seeds <- NULL
use_soils <- FALSE
soil_starting_pest_file <- ""
start_with_soil_populations <- FALSE
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
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,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
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,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement,
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)
expect_equal(length(data), 18)
expect_equal(terra::as.matrix(data$median_run[[1]], wide = TRUE),
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(data$number_infecteds[[1]], 1)
expect_equal(data$number_infecteds[[2]], 0)
expect_equal(data$infected_areas[[1]], 10000)
expect_equal(data$infected_areas[[2]], 0)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
})
ncsu-landscape-dynamics/rpops documentation built on May 1, 2024, 10:21 a.m.
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context("test-pops-multirun")
test_that("Model stops if files don't exist or aren't the correct extension", {
infected_file_list <-
system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
expect_error(pops_multirun(infected_file_list = "",
host_file_list = host_file_list,
total_populations_file = host_file_list,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
file_exists_error)
expect_error(pops_multirun(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
mask = ""),
file_exists_error)
})
test_that("Multirun model outputs work", {
skip_on_os("windows")
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
temperature_file <- ""
temperature_coefficient_file <- ""
precipitation_coefficient_file <- ""
use_lethal_temperature <- FALSE
temp <- FALSE
precip <- FALSE
season_month_start <- 5
season_month_end <- 11
time_step <- "month"
start_date <- "2019-01-01"
end_date <- "2019-12-31"
lethal_temperature <- -35
lethal_temperature_month <- 1
random_seed <- 42
treatments_file <- ""
treatment_dates <- c("2019-11-01")
treatment_method <- "ratio"
management <- FALSE
mortality_frequency <- "Year"
mortality_frequency_n <- 1
natural_kernel_type <- "cauchy"
anthropogenic_kernel_type <- "cauchy"
natural_dir <- "NONE"
anthropogenic_dir <- "NONE"
pesticide_duration <- c(0)
pesticide_efficacy <- 1.0
random_seed <- NULL
output_frequency <- "year"
movements_file <- ""
use_movements <- FALSE
number_of_iterations <- 2
number_of_cores <- 2
model_type <- "SI"
latency_period <- 0
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
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
output_frequency_n <- 1
use_spreadrates <- TRUE
use_overpopulation_movements <- FALSE
overpopulation_percentage <- 0
leaving_percentage <- 0
leaving_scale_coefficient <- 1
exposed_file_list <- ""
mask <- NULL
write_outputs <- "None"
output_folder_path <- tempdir()
network_filename <- ""
use_survival_rates <- FALSE
survival_rate_month <- 3
survival_rate_day <- 15
survival_rates_file <- ""
network_movement <- "walk"
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
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
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,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
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,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement,
use_initial_condition_uncertainty,
use_host_uncertainty)
expect_equal(length(data), 18)
expect_equal(terra::as.matrix(data$median_run[[1]], wide = TRUE),
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
# expect_equal(terra::as.matrix(data$susceptible_run[[1]], wide = TRUE),
# matrix(c(10, 6, 14, 15), nrow = 2, ncol = 2))
expect_equal(terra::as.matrix(data$probability[[1]], wide = TRUE),
matrix(c(100, 0, 0, 0), nrow = 2, ncol = 2))
expect_equal(data$number_infecteds[[1]], 5)
expect_equal(data$number_infecteds[[2]], 0)
expect_equal(data$infected_areas[[1]], 900)
expect_equal(data$infected_areas[[2]], 0)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
output_frequency <- "month"
write_outputs <- "None"
output_folder_path <- ""
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
model_type,
latency_period,
time_step,
season_month_start,
season_month_end,
start_date,
end_date,
use_survival_rates,
survival_rate_month,
survival_rate_day,
survival_rates_file,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_frequency,
mortality_frequency_n,
management,
treatment_dates,
treatments_file,
treatment_method,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
output_frequency,
output_frequency_n,
movements_file,
use_movements,
start_exposed,
generate_stochasticity,
establishment_stochasticity,
movement_stochasticity,
dispersal_stochasticity,
establishment_probability,
dispersal_percentage,
quarantine_areas_file,
use_quarantine,
use_spreadrates,
use_overpopulation_movements,
overpopulation_percentage,
leaving_percentage,
leaving_scale_coefficient,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement,
use_initial_condition_uncertainty = FALSE,
use_host_uncertainty = FALSE,
weather_type = "deterministic",
temperature_coefficient_sd_file = "",
precipitation_coefficient_sd_file = "",
dispersers_to_soils_percentage = 0,
quarantine_directions = "",
multiple_random_seeds = FALSE,
file_random_seeds = NULL,
use_soils = FALSE,
soil_starting_pest_file = "",
start_with_soil_populations = FALSE)
expect_equal(length(data), 18)
expect_equal(terra::as.matrix(data$median_run[[1]], wide = TRUE),
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
# expect_equal(terra::as.matrix(data$susceptible_run[[1]], wide = TRUE),
# matrix(c(10, 6, 14, 15), nrow = 2, ncol = 2))
expect_equal(terra::as.matrix(data$probability[[1]], wide = TRUE),
matrix(c(100, 0, 0, 0), nrow = 2, ncol = 2))
expect_equal(data$number_infecteds[[1]], 5)
expect_equal(data$number_infecteds[[2]], 0)
expect_equal(data$infected_areas[[1]], 900)
expect_equal(data$infected_areas[[2]], 0)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
output_frequency <- "year"
quarantine_areas_file <-
system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
use_quarantine <- TRUE
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
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,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
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,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement)
expect_equal(length(data), 18)
expect_equal(terra::as.matrix(data$median_run[[1]], wide = TRUE),
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
# expect_equal(terra::as.matrix(data$susceptible_run[[1]], wide = TRUE),
# matrix(c(10, 6, 14, 15), nrow = 2, ncol = 2))
expect_equal(terra::as.matrix(data$probability[[1]], wide = TRUE),
matrix(c(100, 0, 0, 0), nrow = 2, ncol = 2))
expect_equal(data$number_infecteds[[1]], 5)
expect_equal(data$number_infecteds[[2]], 0)
expect_equal(data$infected_areas[[1]], 900)
expect_equal(data$infected_areas[[2]], 0)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
output_frequency <- "month"
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
model_type,
latency_period,
time_step,
season_month_start,
season_month_end,
start_date,
end_date,
use_survival_rates,
survival_rate_month,
survival_rate_day,
survival_rates_file,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_frequency,
mortality_frequency_n,
management,
treatment_dates,
treatments_file,
treatment_method,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
output_frequency,
output_frequency_n,
movements_file,
use_movements,
start_exposed,
generate_stochasticity,
establishment_stochasticity,
movement_stochasticity,
dispersal_stochasticity,
establishment_probability,
dispersal_percentage,
quarantine_areas_file,
use_quarantine,
use_spreadrates,
use_overpopulation_movements,
overpopulation_percentage,
leaving_percentage,
leaving_scale_coefficient,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement)
expect_equal(length(data), 18)
expect_equal(terra::as.matrix(data$median_run[[1]], wide = TRUE),
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
# expect_equal(terra::as.matrix(data$susceptible_run[[1]], wide = TRUE),
# matrix(c(10, 6, 14, 15), nrow = 2, ncol = 2))
expect_equal(terra::as.matrix(data$probability[[1]], wide = TRUE),
matrix(c(100, 0, 0, 0), nrow = 2, ncol = 2))
expect_equal(data$number_infecteds[[1]], 5)
expect_equal(data$number_infecteds[[2]], 0)
expect_equal(data$infected_areas[[1]], 900)
expect_equal(data$infected_areas[[2]], 0)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
})
test_that("Multirun model outputs work with mask", {
skip_on_os("windows")
infected_file_list <-
system.file("extdata", "simple20x20", "initial_infection.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple20x20", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
temperature_file <- ""
temperature_coefficient_file <- ""
precipitation_coefficient_file <- ""
use_lethal_temperature <- FALSE
temp <- FALSE
precip <- FALSE
season_month_start <- 5
season_month_end <- 11
time_step <- "month"
start_date <- "2019-01-01"
end_date <- "2019-12-31"
lethal_temperature <- -35
lethal_temperature_month <- 1
random_seed <- NA
treatments_file <- ""
treatment_dates <- c("2019-11-01")
treatment_method <- "ratio"
management <- FALSE
mortality_frequency <- "Year"
mortality_frequency_n <- 1
natural_kernel_type <- "cauchy"
anthropogenic_kernel_type <- "cauchy"
natural_dir <- "NONE"
anthropogenic_dir <- "NONE"
pesticide_duration <- c(0)
pesticide_efficacy <- 1.0
random_seed <- NULL
output_frequency <- "year"
movements_file <- ""
use_movements <- FALSE
number_of_iterations <- 2
number_of_cores <- 2
model_type <- "SI"
latency_period <- 0
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
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
output_frequency_n <- 1
use_spreadrates <- TRUE
mask <- system.file("extdata", "simple20x20", "mask.tif", package = "PoPS")
use_survival_rates <- FALSE
survival_rate_month <- 3
survival_rate_day <- 15
survival_rates_file <- ""
network_movement <- "walk"
use_overpopulation_movements <- FALSE
overpopulation_percentage <- 0
leaving_percentage <- 0
leaving_scale_coefficient <- 1
exposed_file_list <- ""
write_outputs <- "None"
output_folder_path <- tempdir()
network_filename <- ""
quarantine_directions <- ""
multiple_random_seeds <- TRUE
file_random_seeds <- NULL
use_soils <- FALSE
soil_starting_pest_file <- ""
start_with_soil_populations <- FALSE
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
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
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,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
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,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement,
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)
expect_equal(length(data), 18)
expect_equal(terra::as.matrix(data$median_run[[1]], wide = TRUE),
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(data$number_infecteds[[1]], 1)
expect_equal(data$number_infecteds[[2]], 0)
expect_equal(data$infected_areas[[1]], 10000)
expect_equal(data$infected_areas[[2]], 0)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
use_initial_condition_uncertainty <- TRUE
use_host_uncertainty <- TRUE
infected_file_list <-
system.file("extdata", "simple20x20", "infected_wsd.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple20x20", "host_w_sd2.tif", package = "PoPS")
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
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,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
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,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement,
use_initial_condition_uncertainty,
use_host_uncertainty,
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)
expect_equal(length(data), 18)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
use_initial_condition_uncertainty <- TRUE
use_host_uncertainty <- FALSE
infected_file_list <-
system.file("extdata", "simple20x20", "infected_wsd.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple20x20", "host_w_sd2.tif", package = "PoPS")
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
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,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
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,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement,
use_initial_condition_uncertainty,
use_host_uncertainty,
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)
expect_equal(length(data), 18)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
use_initial_condition_uncertainty <- FALSE
use_host_uncertainty <- TRUE
infected_file_list <-
system.file("extdata", "simple20x20", "infected_wsd.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple20x20", "host_w_sd2.tif", package = "PoPS")
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
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,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
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,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement,
use_initial_condition_uncertainty,
use_host_uncertainty,
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)
expect_equal(length(data), 18)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
use_initial_condition_uncertainty <- FALSE
use_host_uncertainty <- FALSE
infected_file_list <-
system.file("extdata", "simple20x20", "infected_wsd.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple20x20", "host_w_sd2.tif", package = "PoPS")
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
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,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
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,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement,
use_initial_condition_uncertainty,
use_host_uncertainty,
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)
expect_equal(length(data), 18)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
})
test_that("Multirun model outputs work with writing all simulations and random seeds", {
skip_on_os("windows")
infected_file_list <-
system.file("extdata", "simple20x20", "initial_infection.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple20x20", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
temperature_file <- ""
temperature_coefficient_file <- ""
precipitation_coefficient_file <- ""
use_lethal_temperature <- FALSE
temp <- FALSE
precip <- FALSE
season_month_start <- 5
season_month_end <- 11
time_step <- "month"
start_date <- "2019-01-01"
end_date <- "2019-12-31"
lethal_temperature <- -35
lethal_temperature_month <- 1
random_seed <- 42
treatments_file <- ""
treatment_dates <- c("2019-11-01")
treatment_method <- "ratio"
management <- FALSE
mortality_frequency <- "Year"
mortality_frequency_n <- 1
natural_kernel_type <- "cauchy"
anthropogenic_kernel_type <- "cauchy"
natural_dir <- "NONE"
anthropogenic_dir <- "NONE"
pesticide_duration <- c(0)
pesticide_efficacy <- 1.0
random_seed <- NULL
output_frequency <- "year"
movements_file <- ""
use_movements <- FALSE
number_of_iterations <- 2
number_of_cores <- 2
model_type <- "SEI"
latency_period <- 2
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
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
output_frequency_n <- 1
use_spreadrates <- TRUE
mask <- system.file("extdata", "simple20x20", "mask.tif", package = "PoPS")
use_survival_rates <- FALSE
survival_rate_month <- 3
survival_rate_day <- 15
survival_rates_file <- ""
network_movement <- "walk"
network_movement <- "walk"
use_overpopulation_movements <- FALSE
overpopulation_percentage <- 0
leaving_percentage <- 0
leaving_scale_coefficient <- 1
exposed_file_list <- ""
write_outputs <- "all_simulations"
output_folder_path <- tempdir()
network_filename <- ""
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 <- TRUE
file_random_seeds <- NULL
use_soils <- FALSE
soil_starting_pest_file <- ""
start_with_soil_populations <- FALSE
data <- pops_multirun(infected_file_list,
host_file_list,
total_populations_file,
parameter_means,
parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
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,
anthropogenic_dir,
number_of_iterations,
number_of_cores,
pesticide_duration,
pesticide_efficacy,
random_seed,
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,
exposed_file_list,
mask,
write_outputs,
output_folder_path,
network_filename,
network_movement,
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)
expect_equal(length(data), 18)
expect_equal(terra::as.matrix(data$median_run[[1]], wide = TRUE),
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(data$number_infecteds[[1]], 1)
expect_equal(data$number_infecteds[[2]], 0)
expect_equal(data$infected_areas[[1]], 10000)
expect_equal(data$infected_areas[[2]], 0)
expect_equal(data$west_rate[[1]], 0)
expect_equal(data$west_rate[[2]], 0)
expect_equal(data$east_rate[[1]], 0)
expect_equal(data$east_rate[[2]], 0)
expect_equal(data$south_rate[[1]], 0)
expect_equal(data$south_rate[[2]], 0)
expect_equal(data$north_rate[[1]], 0)
expect_equal(data$north_rate[[2]], 0)
})
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