tests/testthat/test-checks.R
In ncsu-landscape-dynamics/rpops: Pest or Pathogen Spread Model
context("test-checks")
test_that("Initial raster checks report correct errors and return a raster", {
infected_file <- ""
infected <- initial_raster_checks(infected_file)
expect_equal(infected$checks_passed, FALSE)
expect_equal(infected$failed_check, PoPS:::file_exists_error)
infected_file <-
system.file("extdata", "simple2x2", "infected.csv", package = "PoPS")
infected <- initial_raster_checks(infected_file)
expect_equal(infected$checks_passed, FALSE)
expect_equal(infected$failed_check, PoPS:::raster_type_error)
infected_file <-
system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
infected <- initial_raster_checks(infected_file)
expect_equal(infected$checks_passed, TRUE)
expect_equal(infected$raster[], terra::rast(infected_file)[])
})
test_that("Secondary raster checks report correct errors and return a raster", {
infected_file <-
system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
infected <- terra::rast(infected_file)
host_file <- ""
host <- secondary_raster_checks(host_file, infected)
expect_equal(host$checks_passed, FALSE)
expect_equal(host$failed_check, PoPS:::file_exists_error)
host_file <-
system.file("extdata", "simple2x2", "infected.csv", package = "PoPS")
host <- secondary_raster_checks(host_file, infected)
expect_equal(host$checks_passed, FALSE)
expect_equal(host$failed_check, PoPS:::raster_type_error)
host_file <-
system.file("extdata", "simple5x5", "total_plants.tif", package = "PoPS")
host <- secondary_raster_checks(host_file, infected)
expect_equal(host$checks_passed, FALSE)
expect_equal(host$failed_check, PoPS:::extent_error)
host_file <-
system.file("extdata", "simple2x2", "total_plants_diff_res.tif",
package = "PoPS")
host <- secondary_raster_checks(host_file, infected)
expect_equal(host$checks_passed, FALSE)
expect_equal(host$failed_check, PoPS:::resolution_error)
host_file <-
system.file("extdata", "simple2x2", "total_plants_diff_xres.tif",
package = "PoPS")
host <- secondary_raster_checks(host_file, infected)
expect_equal(host$checks_passed, FALSE)
expect_equal(host$failed_check, PoPS:::resolution_error)
host_file <- system.file("extdata", "simple2x2", "total_plants_diff_yres.tif", package = "PoPS")
host <- secondary_raster_checks(host_file, infected)
expect_equal(host$checks_passed, FALSE)
expect_equal(host$failed_check, PoPS:::resolution_error)
host_file <-
system.file("extdata", "simple2x2", "critical_temp_diff_crs.tif", package = "PoPS")
host <- secondary_raster_checks(host_file, infected)
expect_equal(host$checks_passed, FALSE)
expect_equal(host$failed_check, PoPS:::crs_error)
host_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
host <- secondary_raster_checks(host_file, infected)
expect_equal(host$checks_passed, TRUE)
expect_equal(host$raster[], terra::rast(host_file)[])
})
test_that(
"Treatment checks report correct errors and return a matrices of treatments if all checks pass", {
treatments_file <-
system.file("extdata", "simple2x2", "treatments.tif", package = "PoPS")
treatment_stack <- terra::rast(treatments_file)
pesticide_duration <- c(60)
treatment_dates <- c("2016-01-01", "2016-03-15")
pesticide_efficacy <- 1.0
treatment_check <-
treatment_checks(treatment_stack,
treatments_file,
pesticide_duration,
treatment_dates,
pesticide_efficacy)
expect_equal(treatment_check$checks_passed, FALSE)
expect_equal(treatment_check$failed_check, treatment_length_error)
treatments_file <- system.file("extdata", "simple2x2", "treatments.tif", package = "PoPS")
treatment_stack <- terra::rast(treatments_file)
pesticide_duration <- c(60, 45, 60)
treatment_dates <- c("2016-01-01")
pesticide_efficacy <- 1.0
treatment_check <-
treatment_checks(treatment_stack,
treatments_file,
pesticide_duration,
treatment_dates,
pesticide_efficacy)
expect_equal(treatment_check$checks_passed, FALSE)
expect_equal(treatment_check$failed_check, pesticide_length_error)
treatments_file <- system.file("extdata", "simple2x2", "treatments.tif", package = "PoPS")
treatment_stack <- terra::rast(treatments_file)
pesticide_duration <- c(60)
treatment_dates <- c("2016-01-01")
pesticide_efficacy <- 1.0
treatment_check <-
treatment_checks(treatment_stack,
treatments_file,
pesticide_duration,
treatment_dates,
pesticide_efficacy)
expect_equal(treatment_check$checks_passed, TRUE)
expect_equal(treatment_check$treatment_maps[[1]],
terra::as.matrix(treatment_stack[[1]], wide = TRUE))
treatments_file <-
c(system.file("extdata", "simple2x2", "treatments.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "treatments.tif", package = "PoPS"))
treatment_stack <- terra::rast(treatments_file)
pesticide_duration <- c(60, 45)
treatment_dates <- c("2016-01-01", "2016-10-02")
pesticide_efficacy <- 1.0
treatment_check <-
treatment_checks(treatment_stack,
treatments_file,
pesticide_duration,
treatment_dates,
pesticide_efficacy)
expect_equal(treatment_check$checks_passed, TRUE)
expect_equal(treatment_check$treatment_maps[[1]],
terra::as.matrix(treatment_stack[[1]], wide = TRUE))
})
test_that("Treatment method checks report correct errors and TRUE otherwise", {
treatment_method <- "Test"
methods_check <- treatment_metric_checks(treatment_method)
expect_equal(methods_check$checks_passed, FALSE)
expect_equal(methods_check$failed_check, treatment_option_error)
treatment_method <- "ratio"
methods_check <- treatment_metric_checks(treatment_method)
expect_equal(methods_check$checks_passed, TRUE)
treatment_method <- "all infected"
methods_check <- treatment_metric_checks(treatment_method)
expect_equal(methods_check$checks_passed, TRUE)
})
test_that(
"Time checks report correct errors and return number of time steps, number of
years, and number of outputs otherwise", {
end_date <- 2017
start_date <- 2016
time_step <- "hour"
output_frequency <- "week"
output_frequency_n <- 1
time_check <- time_checks(end_date, start_date, time_step, output_frequency, output_frequency_n)
expect_equal(time_check$checks_passed, FALSE)
expect_equal(time_check$failed_check, time_step_error)
end_date <- 2017
start_date <- 2016
time_step <- "week"
output_frequency <- "week"
time_check <- time_checks(end_date, start_date, time_step, output_frequency, output_frequency_n)
expect_equal(time_check$checks_passed, FALSE)
expect_equal(time_check$failed_check, date_format_error)
end_date <- "2017-01-01"
start_date <- "2016-01-01"
time_step <- "month"
output_frequency <- "hour"
time_check <- time_checks(end_date, start_date, time_step, output_frequency, output_frequency_n)
expect_equal(time_check$checks_passed, FALSE)
expect_equal(time_check$failed_check, frequency_error)
time_step <- "month"
output_frequency <- "week"
time_check <- time_checks(end_date, start_date, time_step, output_frequency, output_frequency_n)
expect_equal(time_check$checks_passed, FALSE)
expect_equal(time_check$failed_check, output_frequency_error)
time_step <- "week"
output_frequency <- "week"
time_check <- time_checks(end_date, start_date, time_step, output_frequency, output_frequency_n)
expect_equal(time_check$checks_passed, TRUE)
expect_equal(time_check$number_of_time_steps, 53)
expect_equal(time_check$number_of_years, 1)
expect_equal(time_check$number_of_outputs, 53)
time_step <- "week"
output_frequency <- "month"
time_check <- time_checks(end_date, start_date, time_step, output_frequency, output_frequency_n)
expect_equal(time_check$checks_passed, TRUE)
expect_equal(time_check$number_of_time_steps, 53)
expect_equal(time_check$number_of_years, 1)
expect_equal(time_check$number_of_outputs, 12)
time_step <- "week"
output_frequency <- "year"
time_check <- time_checks(end_date, start_date, time_step, output_frequency, output_frequency_n)
expect_equal(time_check$checks_passed, TRUE)
expect_equal(time_check$number_of_time_steps, 53)
expect_equal(time_check$number_of_years, 1)
expect_equal(time_check$number_of_outputs, 1)
end_date <- "2016-02-01"
start_date <- "2016-01-01"
time_step <- "week"
output_frequency <- "week"
time_check <- time_checks(end_date, start_date, time_step, output_frequency, output_frequency_n)
expect_equal(time_check$checks_passed, TRUE)
expect_equal(time_check$number_of_time_steps, 5)
expect_equal(time_check$number_of_years, 1)
expect_equal(time_check$number_of_outputs, 5)
end_date <- "2016-02-01"
start_date <- "2016-01-01"
time_step <- "week"
output_frequency <- "time_step"
time_check <- time_checks(end_date, start_date, time_step, output_frequency, output_frequency_n)
expect_equal(time_check$checks_passed, TRUE)
expect_equal(time_check$number_of_time_steps, 5)
expect_equal(time_check$number_of_years, 1)
expect_equal(time_check$number_of_outputs, 5)
})
test_that("Bayesian MNN checks work properly", {
prior_means <- c(0.2, 23)
prior_cov_matrix <- matrix(c(1, 1, 1, 1), ncol = 2, nrow = 2)
calibrated_means <- c(0.3, 21)
calibrated_cov_matrix <- matrix(c(1, 2, 1, 1), ncol = 2, nrow = 2)
prior_weight <- 0.05
weight <- 1 - prior_weight
mnn_check <-
bayesian_mnn_checks(prior_means,
prior_cov_matrix,
calibrated_means,
calibrated_cov_matrix,
prior_weight,
weight)
expect_equal(mnn_check$checks_passed, TRUE)
expect_equal(mnn_check$posterior_means, c(0.295, 21.1))
expect_equal(mnn_check$posterior_cov_matrix, matrix(c(1, 1.95, 1, 1), ncol = 2, nrow = 2))
prior_means <- c(0.2, 23)
prior_cov_matrix <- matrix(c(1, 1, 1, 1), ncol = 2, nrow = 2)
calibrated_means <- c(0.3, 21)
calibrated_cov_matrix <- matrix(c(1, 2), ncol = 1, nrow = 2)
prior_weight <- 0.05
weight <- 1 - prior_weight
mnn_check <-
bayesian_mnn_checks(prior_means,
prior_cov_matrix,
calibrated_means,
calibrated_cov_matrix,
prior_weight,
weight)
expect_equal(mnn_check$checks_passed, FALSE)
expect_equal(mnn_check$failed_check, prior_cov_matrix_error)
prior_means <- c(0.2, 23)
prior_cov_matrix <- matrix(c(1, 1, 1, 1), ncol = 2, nrow = 2)
calibrated_means <- c(0.3)
calibrated_cov_matrix <- matrix(c(1, 2, 1, 1), ncol = 2, nrow = 2)
prior_weight <- 0.05
weight <- 1 - prior_weight
mnn_check <-
bayesian_mnn_checks(prior_means,
prior_cov_matrix,
calibrated_means,
calibrated_cov_matrix,
prior_weight,
weight)
expect_equal(mnn_check$checks_passed, FALSE)
expect_equal(mnn_check$failed_check, prior_means_error)
})
test_that("Movements checks return errors when present and correct outputs", {
rast <- terra::rast(system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS"))
start_date <- "2009-01-01"
end_date <- "2009-12-31"
movements_file <- system.file("extdata", "simple20x20", "movements.csv", package = "PoPS")
x <- movements_file
check_moves <- movement_checks(movements_file, rast, start_date, end_date)
expect_equal(length(check_moves$movements), 2)
expect_equal(length(check_moves$movements_dates), 2)
expect_equal(nrow(check_moves$movements_r), 2)
expect_equal(ncol(check_moves$movements_r), 6)
})
test_that("Multispecies checks return erros if any of the inputs aren't the same length", {
infected_files <- c("", "")
host_file <- c("", "")
total_populations_file <- c("", "")
parameter_means <- c("", "")
parameter_cov_matrix <- c("", "")
temp <- c(FALSE, FALSE)
temperature_coefficient_file <- c("", "")
precip <- c(FALSE, FALSE)
precipitation_coefficient_file <- c("", "")
model_type <- c("SI", "SI")
latency_period <- c(0, 0)
time_step <- c("month", "month")
season_month_start <- c(1, 1)
season_month_end <- c(12, 12)
use_lethal_temperature <- c(FALSE, FALSE)
temperature_file <- c("", "")
lethal_temperature <- c(1, 1)
lethal_temperature_month <- c(1, 1)
mortality_on <- c(FALSE, FALSE)
mortality_rate <- c(0.05, 0.05)
mortality_time_lag <- c(1, 1)
natural_kernel_type <- c("cauchy", "cauchy")
anthropogenic_kernel_type <- c("cauchy", "cauchy")
natural_dir <- c("NONE", "NONE")
anthropogenic_dir <- c("NONE", "NONE")
movements_file <- c("", "")
use_movements <- c(FALSE, FALSE)
start_exposed <- c(TRUE, TRUE)
quarantine_areas_file <- c("", "")
use_quarantine <- c(TRUE, TRUE)
use_spreadrates <- c(TRUE, TRUE)
species <- c("species1", "species2")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, TRUE)
infected_files <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(multispecies_check$failed_check, PoPS:::species_length_error)
infected_files <- c("", "")
host_file <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(multispecies_check$failed_check, PoPS:::host_file_length_error)
host_file <- c("", "")
total_populations_file <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(multispecies_check$failed_check, PoPS:::total_population_length_error)
total_populations_file <- c("", "")
parameter_means <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::parameter_length_error)
parameter_means <- c("", "")
parameter_cov_matrix <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::cov_matrix_length_error)
parameter_cov_matrix <- c("", "")
temp <- c(FALSE)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(multispecies_check$failed_check, PoPS:::temp_length_error)
temp <- c(FALSE, FALSE)
temperature_coefficient_file <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(multispecies_check$failed_check, PoPS:::temperature_coefficient_length_error)
temperature_coefficient_file <- c("", "")
precip <- c(FALSE)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(multispecies_check$failed_check, PoPS:::precip_length_error)
precip <- c(FALSE, FALSE)
precipitation_coefficient_file <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::precipitation_coefficient_length_error)
precipitation_coefficient_file <- c("", "")
model_type <- c("SI")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(multispecies_check$failed_check, PoPS:::model_type_length_error)
model_type <- c("SI", "SI")
latency_period <- c(0)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::latency_period_length_error)
latency_period <- c(0, 0)
time_step <- c("month")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(multispecies_check$failed_check, PoPS:::time_step_length_error)
time_step <- c("month", "month")
season_month_start <- c(1)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::season_month_start_length_error)
season_month_start <- c(1, 1)
season_month_end <- c(12)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::season_month_end_length_error)
season_month_end <- c(12, 12)
use_lethal_temperature <- c(FALSE)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::use_lethal_length_error)
use_lethal_temperature <- c(FALSE, FALSE)
temperature_file <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::temperature_file_length_error)
temperature_file <- c("", "")
lethal_temperature <- c(1)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::lethal_temperature_length_error)
lethal_temperature <- c(1, 1)
lethal_temperature_month <- c(1)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::lethal_temperature_month_length_error)
lethal_temperature_month <- c(1, 1)
mortality_on <- c(FALSE)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::mortality_on_length_error)
mortality_on <- c(FALSE, FALSE)
mortality_rate <- c(0.05)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::mortality_rate_length_error)
mortality_rate <- c(0.05, 0.05)
mortality_time_lag <- c(1)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::mortality_time_lag_length_error)
mortality_time_lag <- c(1, 1)
natural_kernel_type <- c("cauchy")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::natural_kernel_length_error)
natural_kernel_type <- c("cauchy", "cauchy")
anthropogenic_kernel_type <- c("cauchy")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::anthropogenic_kernel_length_error)
anthropogenic_kernel_type <- c("cauchy", "cauchy")
natural_dir <- c("NONE")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::natural_dir_length_error)
natural_dir <- c("NONE", "NONE")
anthropogenic_dir <- c("NONE")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::anthropogenic_dir_length_error)
anthropogenic_dir <- c("NONE", "NONE")
movements_file <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::movements_file_length_error)
movements_file <- c("", "")
use_movements <- c(FALSE)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::use_movements_length_error)
use_movements <- c(FALSE, FALSE)
start_exposed <- c(TRUE)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::start_exposed_length_error)
start_exposed <- c(TRUE, TRUE)
quarantine_areas_file <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::quarantine_areas_length_error)
quarantine_areas_file <- c("", "")
use_quarantine <- c(TRUE)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::use_quarantine_length_error)
use_quarantine <- c(TRUE, TRUE)
use_spreadrates <- c(TRUE)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::use_spreadrates_length_error)
use_spreadrates <- c(TRUE, TRUE)
species <- c("species1")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(multispecies_check$failed_check, PoPS:::species_length_error)
})
test_that("Multiple random seed draws and checks work", {
randoms_file <- "NULL.fs"
randoms <- random_seeds_file_checks(randoms_file)
expect_equal(randoms$checks_passed, FALSE)
expect_equal(randoms$failed_check, PoPS:::file_exists_error)
randoms_file <-
system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
randoms <- random_seeds_file_checks(randoms_file)
expect_equal(randoms$checks_passed, FALSE)
expect_equal(randoms$failed_check, PoPS:::file_type_error)
randoms_file <-
system.file("extdata", "simple2x2", "randoms.csv", package = "PoPS")
randoms <- random_seeds_file_checks(randoms_file)
expect_equal(randoms$checks_passed, TRUE)
})
ncsu-landscape-dynamics/rpops documentation built on May 1, 2024, 10:21 a.m.
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context("test-checks")
test_that("Initial raster checks report correct errors and return a raster", {
infected_file <- ""
infected <- initial_raster_checks(infected_file)
expect_equal(infected$checks_passed, FALSE)
expect_equal(infected$failed_check, PoPS:::file_exists_error)
infected_file <-
system.file("extdata", "simple2x2", "infected.csv", package = "PoPS")
infected <- initial_raster_checks(infected_file)
expect_equal(infected$checks_passed, FALSE)
expect_equal(infected$failed_check, PoPS:::raster_type_error)
infected_file <-
system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
infected <- initial_raster_checks(infected_file)
expect_equal(infected$checks_passed, TRUE)
expect_equal(infected$raster[], terra::rast(infected_file)[])
})
test_that("Secondary raster checks report correct errors and return a raster", {
infected_file <-
system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
infected <- terra::rast(infected_file)
host_file <- ""
host <- secondary_raster_checks(host_file, infected)
expect_equal(host$checks_passed, FALSE)
expect_equal(host$failed_check, PoPS:::file_exists_error)
host_file <-
system.file("extdata", "simple2x2", "infected.csv", package = "PoPS")
host <- secondary_raster_checks(host_file, infected)
expect_equal(host$checks_passed, FALSE)
expect_equal(host$failed_check, PoPS:::raster_type_error)
host_file <-
system.file("extdata", "simple5x5", "total_plants.tif", package = "PoPS")
host <- secondary_raster_checks(host_file, infected)
expect_equal(host$checks_passed, FALSE)
expect_equal(host$failed_check, PoPS:::extent_error)
host_file <-
system.file("extdata", "simple2x2", "total_plants_diff_res.tif",
package = "PoPS")
host <- secondary_raster_checks(host_file, infected)
expect_equal(host$checks_passed, FALSE)
expect_equal(host$failed_check, PoPS:::resolution_error)
host_file <-
system.file("extdata", "simple2x2", "total_plants_diff_xres.tif",
package = "PoPS")
host <- secondary_raster_checks(host_file, infected)
expect_equal(host$checks_passed, FALSE)
expect_equal(host$failed_check, PoPS:::resolution_error)
host_file <- system.file("extdata", "simple2x2", "total_plants_diff_yres.tif", package = "PoPS")
host <- secondary_raster_checks(host_file, infected)
expect_equal(host$checks_passed, FALSE)
expect_equal(host$failed_check, PoPS:::resolution_error)
host_file <-
system.file("extdata", "simple2x2", "critical_temp_diff_crs.tif", package = "PoPS")
host <- secondary_raster_checks(host_file, infected)
expect_equal(host$checks_passed, FALSE)
expect_equal(host$failed_check, PoPS:::crs_error)
host_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
host <- secondary_raster_checks(host_file, infected)
expect_equal(host$checks_passed, TRUE)
expect_equal(host$raster[], terra::rast(host_file)[])
})
test_that(
"Treatment checks report correct errors and return a matrices of treatments if all checks pass", {
treatments_file <-
system.file("extdata", "simple2x2", "treatments.tif", package = "PoPS")
treatment_stack <- terra::rast(treatments_file)
pesticide_duration <- c(60)
treatment_dates <- c("2016-01-01", "2016-03-15")
pesticide_efficacy <- 1.0
treatment_check <-
treatment_checks(treatment_stack,
treatments_file,
pesticide_duration,
treatment_dates,
pesticide_efficacy)
expect_equal(treatment_check$checks_passed, FALSE)
expect_equal(treatment_check$failed_check, treatment_length_error)
treatments_file <- system.file("extdata", "simple2x2", "treatments.tif", package = "PoPS")
treatment_stack <- terra::rast(treatments_file)
pesticide_duration <- c(60, 45, 60)
treatment_dates <- c("2016-01-01")
pesticide_efficacy <- 1.0
treatment_check <-
treatment_checks(treatment_stack,
treatments_file,
pesticide_duration,
treatment_dates,
pesticide_efficacy)
expect_equal(treatment_check$checks_passed, FALSE)
expect_equal(treatment_check$failed_check, pesticide_length_error)
treatments_file <- system.file("extdata", "simple2x2", "treatments.tif", package = "PoPS")
treatment_stack <- terra::rast(treatments_file)
pesticide_duration <- c(60)
treatment_dates <- c("2016-01-01")
pesticide_efficacy <- 1.0
treatment_check <-
treatment_checks(treatment_stack,
treatments_file,
pesticide_duration,
treatment_dates,
pesticide_efficacy)
expect_equal(treatment_check$checks_passed, TRUE)
expect_equal(treatment_check$treatment_maps[[1]],
terra::as.matrix(treatment_stack[[1]], wide = TRUE))
treatments_file <-
c(system.file("extdata", "simple2x2", "treatments.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "treatments.tif", package = "PoPS"))
treatment_stack <- terra::rast(treatments_file)
pesticide_duration <- c(60, 45)
treatment_dates <- c("2016-01-01", "2016-10-02")
pesticide_efficacy <- 1.0
treatment_check <-
treatment_checks(treatment_stack,
treatments_file,
pesticide_duration,
treatment_dates,
pesticide_efficacy)
expect_equal(treatment_check$checks_passed, TRUE)
expect_equal(treatment_check$treatment_maps[[1]],
terra::as.matrix(treatment_stack[[1]], wide = TRUE))
})
test_that("Treatment method checks report correct errors and TRUE otherwise", {
treatment_method <- "Test"
methods_check <- treatment_metric_checks(treatment_method)
expect_equal(methods_check$checks_passed, FALSE)
expect_equal(methods_check$failed_check, treatment_option_error)
treatment_method <- "ratio"
methods_check <- treatment_metric_checks(treatment_method)
expect_equal(methods_check$checks_passed, TRUE)
treatment_method <- "all infected"
methods_check <- treatment_metric_checks(treatment_method)
expect_equal(methods_check$checks_passed, TRUE)
})
test_that(
"Time checks report correct errors and return number of time steps, number of
years, and number of outputs otherwise", {
end_date <- 2017
start_date <- 2016
time_step <- "hour"
output_frequency <- "week"
output_frequency_n <- 1
time_check <- time_checks(end_date, start_date, time_step, output_frequency, output_frequency_n)
expect_equal(time_check$checks_passed, FALSE)
expect_equal(time_check$failed_check, time_step_error)
end_date <- 2017
start_date <- 2016
time_step <- "week"
output_frequency <- "week"
time_check <- time_checks(end_date, start_date, time_step, output_frequency, output_frequency_n)
expect_equal(time_check$checks_passed, FALSE)
expect_equal(time_check$failed_check, date_format_error)
end_date <- "2017-01-01"
start_date <- "2016-01-01"
time_step <- "month"
output_frequency <- "hour"
time_check <- time_checks(end_date, start_date, time_step, output_frequency, output_frequency_n)
expect_equal(time_check$checks_passed, FALSE)
expect_equal(time_check$failed_check, frequency_error)
time_step <- "month"
output_frequency <- "week"
time_check <- time_checks(end_date, start_date, time_step, output_frequency, output_frequency_n)
expect_equal(time_check$checks_passed, FALSE)
expect_equal(time_check$failed_check, output_frequency_error)
time_step <- "week"
output_frequency <- "week"
time_check <- time_checks(end_date, start_date, time_step, output_frequency, output_frequency_n)
expect_equal(time_check$checks_passed, TRUE)
expect_equal(time_check$number_of_time_steps, 53)
expect_equal(time_check$number_of_years, 1)
expect_equal(time_check$number_of_outputs, 53)
time_step <- "week"
output_frequency <- "month"
time_check <- time_checks(end_date, start_date, time_step, output_frequency, output_frequency_n)
expect_equal(time_check$checks_passed, TRUE)
expect_equal(time_check$number_of_time_steps, 53)
expect_equal(time_check$number_of_years, 1)
expect_equal(time_check$number_of_outputs, 12)
time_step <- "week"
output_frequency <- "year"
time_check <- time_checks(end_date, start_date, time_step, output_frequency, output_frequency_n)
expect_equal(time_check$checks_passed, TRUE)
expect_equal(time_check$number_of_time_steps, 53)
expect_equal(time_check$number_of_years, 1)
expect_equal(time_check$number_of_outputs, 1)
end_date <- "2016-02-01"
start_date <- "2016-01-01"
time_step <- "week"
output_frequency <- "week"
time_check <- time_checks(end_date, start_date, time_step, output_frequency, output_frequency_n)
expect_equal(time_check$checks_passed, TRUE)
expect_equal(time_check$number_of_time_steps, 5)
expect_equal(time_check$number_of_years, 1)
expect_equal(time_check$number_of_outputs, 5)
end_date <- "2016-02-01"
start_date <- "2016-01-01"
time_step <- "week"
output_frequency <- "time_step"
time_check <- time_checks(end_date, start_date, time_step, output_frequency, output_frequency_n)
expect_equal(time_check$checks_passed, TRUE)
expect_equal(time_check$number_of_time_steps, 5)
expect_equal(time_check$number_of_years, 1)
expect_equal(time_check$number_of_outputs, 5)
})
test_that("Bayesian MNN checks work properly", {
prior_means <- c(0.2, 23)
prior_cov_matrix <- matrix(c(1, 1, 1, 1), ncol = 2, nrow = 2)
calibrated_means <- c(0.3, 21)
calibrated_cov_matrix <- matrix(c(1, 2, 1, 1), ncol = 2, nrow = 2)
prior_weight <- 0.05
weight <- 1 - prior_weight
mnn_check <-
bayesian_mnn_checks(prior_means,
prior_cov_matrix,
calibrated_means,
calibrated_cov_matrix,
prior_weight,
weight)
expect_equal(mnn_check$checks_passed, TRUE)
expect_equal(mnn_check$posterior_means, c(0.295, 21.1))
expect_equal(mnn_check$posterior_cov_matrix, matrix(c(1, 1.95, 1, 1), ncol = 2, nrow = 2))
prior_means <- c(0.2, 23)
prior_cov_matrix <- matrix(c(1, 1, 1, 1), ncol = 2, nrow = 2)
calibrated_means <- c(0.3, 21)
calibrated_cov_matrix <- matrix(c(1, 2), ncol = 1, nrow = 2)
prior_weight <- 0.05
weight <- 1 - prior_weight
mnn_check <-
bayesian_mnn_checks(prior_means,
prior_cov_matrix,
calibrated_means,
calibrated_cov_matrix,
prior_weight,
weight)
expect_equal(mnn_check$checks_passed, FALSE)
expect_equal(mnn_check$failed_check, prior_cov_matrix_error)
prior_means <- c(0.2, 23)
prior_cov_matrix <- matrix(c(1, 1, 1, 1), ncol = 2, nrow = 2)
calibrated_means <- c(0.3)
calibrated_cov_matrix <- matrix(c(1, 2, 1, 1), ncol = 2, nrow = 2)
prior_weight <- 0.05
weight <- 1 - prior_weight
mnn_check <-
bayesian_mnn_checks(prior_means,
prior_cov_matrix,
calibrated_means,
calibrated_cov_matrix,
prior_weight,
weight)
expect_equal(mnn_check$checks_passed, FALSE)
expect_equal(mnn_check$failed_check, prior_means_error)
})
test_that("Movements checks return errors when present and correct outputs", {
rast <- terra::rast(system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS"))
start_date <- "2009-01-01"
end_date <- "2009-12-31"
movements_file <- system.file("extdata", "simple20x20", "movements.csv", package = "PoPS")
x <- movements_file
check_moves <- movement_checks(movements_file, rast, start_date, end_date)
expect_equal(length(check_moves$movements), 2)
expect_equal(length(check_moves$movements_dates), 2)
expect_equal(nrow(check_moves$movements_r), 2)
expect_equal(ncol(check_moves$movements_r), 6)
})
test_that("Multispecies checks return erros if any of the inputs aren't the same length", {
infected_files <- c("", "")
host_file <- c("", "")
total_populations_file <- c("", "")
parameter_means <- c("", "")
parameter_cov_matrix <- c("", "")
temp <- c(FALSE, FALSE)
temperature_coefficient_file <- c("", "")
precip <- c(FALSE, FALSE)
precipitation_coefficient_file <- c("", "")
model_type <- c("SI", "SI")
latency_period <- c(0, 0)
time_step <- c("month", "month")
season_month_start <- c(1, 1)
season_month_end <- c(12, 12)
use_lethal_temperature <- c(FALSE, FALSE)
temperature_file <- c("", "")
lethal_temperature <- c(1, 1)
lethal_temperature_month <- c(1, 1)
mortality_on <- c(FALSE, FALSE)
mortality_rate <- c(0.05, 0.05)
mortality_time_lag <- c(1, 1)
natural_kernel_type <- c("cauchy", "cauchy")
anthropogenic_kernel_type <- c("cauchy", "cauchy")
natural_dir <- c("NONE", "NONE")
anthropogenic_dir <- c("NONE", "NONE")
movements_file <- c("", "")
use_movements <- c(FALSE, FALSE)
start_exposed <- c(TRUE, TRUE)
quarantine_areas_file <- c("", "")
use_quarantine <- c(TRUE, TRUE)
use_spreadrates <- c(TRUE, TRUE)
species <- c("species1", "species2")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, TRUE)
infected_files <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(multispecies_check$failed_check, PoPS:::species_length_error)
infected_files <- c("", "")
host_file <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(multispecies_check$failed_check, PoPS:::host_file_length_error)
host_file <- c("", "")
total_populations_file <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(multispecies_check$failed_check, PoPS:::total_population_length_error)
total_populations_file <- c("", "")
parameter_means <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::parameter_length_error)
parameter_means <- c("", "")
parameter_cov_matrix <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::cov_matrix_length_error)
parameter_cov_matrix <- c("", "")
temp <- c(FALSE)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(multispecies_check$failed_check, PoPS:::temp_length_error)
temp <- c(FALSE, FALSE)
temperature_coefficient_file <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(multispecies_check$failed_check, PoPS:::temperature_coefficient_length_error)
temperature_coefficient_file <- c("", "")
precip <- c(FALSE)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(multispecies_check$failed_check, PoPS:::precip_length_error)
precip <- c(FALSE, FALSE)
precipitation_coefficient_file <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::precipitation_coefficient_length_error)
precipitation_coefficient_file <- c("", "")
model_type <- c("SI")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(multispecies_check$failed_check, PoPS:::model_type_length_error)
model_type <- c("SI", "SI")
latency_period <- c(0)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::latency_period_length_error)
latency_period <- c(0, 0)
time_step <- c("month")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(multispecies_check$failed_check, PoPS:::time_step_length_error)
time_step <- c("month", "month")
season_month_start <- c(1)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::season_month_start_length_error)
season_month_start <- c(1, 1)
season_month_end <- c(12)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::season_month_end_length_error)
season_month_end <- c(12, 12)
use_lethal_temperature <- c(FALSE)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::use_lethal_length_error)
use_lethal_temperature <- c(FALSE, FALSE)
temperature_file <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::temperature_file_length_error)
temperature_file <- c("", "")
lethal_temperature <- c(1)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::lethal_temperature_length_error)
lethal_temperature <- c(1, 1)
lethal_temperature_month <- c(1)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::lethal_temperature_month_length_error)
lethal_temperature_month <- c(1, 1)
mortality_on <- c(FALSE)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::mortality_on_length_error)
mortality_on <- c(FALSE, FALSE)
mortality_rate <- c(0.05)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::mortality_rate_length_error)
mortality_rate <- c(0.05, 0.05)
mortality_time_lag <- c(1)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::mortality_time_lag_length_error)
mortality_time_lag <- c(1, 1)
natural_kernel_type <- c("cauchy")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::natural_kernel_length_error)
natural_kernel_type <- c("cauchy", "cauchy")
anthropogenic_kernel_type <- c("cauchy")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::anthropogenic_kernel_length_error)
anthropogenic_kernel_type <- c("cauchy", "cauchy")
natural_dir <- c("NONE")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::natural_dir_length_error)
natural_dir <- c("NONE", "NONE")
anthropogenic_dir <- c("NONE")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::anthropogenic_dir_length_error)
anthropogenic_dir <- c("NONE", "NONE")
movements_file <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::movements_file_length_error)
movements_file <- c("", "")
use_movements <- c(FALSE)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::use_movements_length_error)
use_movements <- c(FALSE, FALSE)
start_exposed <- c(TRUE)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::start_exposed_length_error)
start_exposed <- c(TRUE, TRUE)
quarantine_areas_file <- c("")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::quarantine_areas_length_error)
quarantine_areas_file <- c("", "")
use_quarantine <- c(TRUE)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::use_quarantine_length_error)
use_quarantine <- c(TRUE, TRUE)
use_spreadrates <- c(TRUE)
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(
multispecies_check$failed_check, PoPS:::use_spreadrates_length_error)
use_spreadrates <- c(TRUE, TRUE)
species <- c("species1")
multispecies_check <-
multispecies_checks(species,
infected_files,
parameter_means,
parameter_cov_matrix,
natural_kernel_type,
anthropogenic_kernel_type,
natural_dir,
anthropogenic_dir,
model_type,
host_file,
total_populations_file,
temp,
temperature_coefficient_file,
precip,
precipitation_coefficient_file,
latency_period,
time_step,
season_month_start,
season_month_end,
use_lethal_temperature,
temperature_file,
lethal_temperature,
lethal_temperature_month,
mortality_on,
mortality_rate,
mortality_time_lag,
movements_file,
use_movements,
start_exposed,
quarantine_areas_file,
use_quarantine,
use_spreadrates)
expect_equal(multispecies_check$checks_passed, FALSE)
expect_equal(multispecies_check$failed_check, PoPS:::species_length_error)
})
test_that("Multiple random seed draws and checks work", {
randoms_file <- "NULL.fs"
randoms <- random_seeds_file_checks(randoms_file)
expect_equal(randoms$checks_passed, FALSE)
expect_equal(randoms$failed_check, PoPS:::file_exists_error)
randoms_file <-
system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
randoms <- random_seeds_file_checks(randoms_file)
expect_equal(randoms$checks_passed, FALSE)
expect_equal(randoms$failed_check, PoPS:::file_type_error)
randoms_file <-
system.file("extdata", "simple2x2", "randoms.csv", package = "PoPS")
randoms <- random_seeds_file_checks(randoms_file)
expect_equal(randoms$checks_passed, TRUE)
})
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