tests/testthat/test-pops.r
In ncsu-landscape-dynamics/rpops: Pest or Pathogen Spread Model
context("test-pops")
test_that("Model stops if files don't exist or aren't the correct extension", {
infected_file_list <- c("")
host_file_list <- c(system.file("extdata", "simple2x2", "host.tif", package = "PoPS"))
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
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.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table))
infected_file_list <- system.file("extdata", "simple2x2", "infected.csv", package = "PoPS")
expect_error(pops(
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),
raster_type_error, fixed = TRUE)
host_file_list <- ""
infected_file_list <- c(system.file("extdata", "simple2x2", "infected.tif", package = "PoPS"))
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table))
host_file_list <- c(system.file("extdata", "simple2x2", "infected.csv", package = "PoPS"))
expect_error(pops(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),
raster_type_error, fixed = TRUE)
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <- ""
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
detailed_file_exists_error(total_populations_file))
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file =
system.file("extdata", "simple2x2", "infected.csv", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
raster_type_error, fixed = TRUE)
temperature_file <- ""
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
use_lethal_temperature = TRUE,
temperature_file = temperature_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
detailed_file_exists_error(temperature_file))
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
use_lethal_temperature = TRUE,
temperature_file =
system.file("extdata", "simple2x2", "infected.csv", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
raster_type_error, fixed = TRUE)
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
temperature_coefficient_file <- ""
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
temp = TRUE,
temperature_coefficient_file = temperature_coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
detailed_file_exists_error(temperature_coefficient_file))
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2", "infected.csv", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
raster_type_error, fixed = TRUE)
precipitation_coefficient_file <- ""
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
precip = TRUE,
precipitation_coefficient_file = "",
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
detailed_file_exists_error(precipitation_coefficient_file))
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2", "infected.csv", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
raster_type_error, fixed = TRUE)
treatments_file <- ""
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
management = TRUE,
treatments_file = treatments_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
detailed_file_exists_error(treatments_file))
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
management = TRUE,
treatments_file =
system.file("extdata", "simple2x2", "infected.csv", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
raster_type_error, fixed = TRUE)
exposed_file_list <- ""
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
model_type = "SEI",
exposed_file_list = exposed_file_list,
latency_period = 2,
start_exposed = TRUE,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table))
quarantine_areas_file <- ""
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
quarantine_areas_file = quarantine_areas_file,
use_quarantine = TRUE,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
detailed_file_exists_error(quarantine_areas_file))
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
parameter_means = c(0, 0, 0, 0),
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
paramter_means_error, fixed = TRUE)
expect_error(pops(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 = matrix(0, nrow = 5, ncol = 6),
pest_host_table = pest_host_table,
competency_table = competency_table),
covariance_mat_error, fixed = TRUE)
})
test_that("Model stops if treatments don't have correct dimenisions", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
treatments_file <- system.file("extdata", "simple2x2", "treatments.tif", package = "PoPS")
treatment_dates <- c("2008-01-01", "2008-05-01")
pest_host_table <- system.file("extdata", "pest_host_table_singlehost.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
expect_error(pops(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,
management = TRUE,
treatments_file = treatments_file,
treatment_dates = treatment_dates),
treatment_length_error, fixed = TRUE)
})
test_that("Model stops if time and date parameters are of the wrong type and/or dimension", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
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.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
time_step = "two",
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
time_step_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
end_date = "two",
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
date_format_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
end_date = 156,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
date_format_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
start_date = "five",
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
date_format_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
start_date = 19,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
date_format_error, fixed = TRUE)
})
test_that("Model stops if kernel is of the wrong type and/or dimension", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <- system.file("extdata", "simple2x2",
"critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
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.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
expect_error(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
natural_kernel_type = "none",
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
natural_kernel_error, fixed = TRUE)
expect_error(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
anthropogenic_kernel_type = "none",
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
anthropogenic_kernel_error, fixed = TRUE)
})
test_that("Input raster resolutions, extents, and crs all match", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
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.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
expect_error(pops(infected_file_list = infected_file_list,
host_file_list =
system.file("extdata", "simple5x5", "total_plants.tif", package = "PoPS"),
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
extent_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file =
system.file("extdata", "simple5x5", "total_plants.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
extent_error, fixed = TRUE)
expect_error(pops(infected_file_list =
system.file("extdata", "simple5x5", "total_plants.tif", package = "PoPS"),
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
extent_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
temperature_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_extent.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
extent_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_extent.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
extent_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_extent.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
extent_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2", "critical_temp.tif", package = "PoPS"),
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_extent.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
extent_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatments_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_extent.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
extent_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list =
system.file("extdata", "simple2x2",
"total_plants_diff_res.tif", package = "PoPS"),
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list =
system.file("extdata", "simple2x2",
"total_plants_diff_xres.tif", package = "PoPS"),
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list =
system.file("extdata", "simple2x2",
"total_plants_diff_yres.tif", package = "PoPS"),
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file =
system.file("extdata", "simple2x2",
"total_plants_diff_res.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file =
system.file("extdata", "simple2x2",
"total_plants_diff_xres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file =
system.file("extdata", "simple2x2",
"total_plants_diff_yres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list =
system.file("extdata", "simple2x2",
"total_plants_diff_res.tif", package = "PoPS"),
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list =
system.file("extdata", "simple2x2",
"total_plants_diff_xres.tif", package = "PoPS"),
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list =
system.file("extdata", "simple2x2",
"total_plants_diff_yres.tif", package = "PoPS"),
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
temperature_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_res.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
temperature_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_xres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
temperature_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_yres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_res.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_xres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_yres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_res.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_xres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_yres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2", "critical_temp.tif", package = "PoPS"),
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_res.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2", "critical_temp.tif", package = "PoPS"),
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_xres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2", "critical_temp.tif", package = "PoPS"),
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_yres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatments_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_res.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatments_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_xres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatments_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_yres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list =
system.file("extdata", "simple2x2",
"critical_temp_diff_crs.tif", package = "PoPS"),
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
crs_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_crs.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
crs_error, fixed = TRUE)
expect_error(pops(infected_file_list =
system.file("extdata", "simple2x2",
"critical_temp_diff_crs.tif", package = "PoPS"),
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
crs_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
temperature_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_crs.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
crs_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_crs.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
crs_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_crs.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
crs_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2", "critical_temp.tif",
package = "PoPS"),
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_crs.tif",
package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
crs_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatments_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_crs.tif",
package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
crs_error, fixed = TRUE)
})
test_that("Infected results return initial infected if reproductive rate is set to 0", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
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_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
lethal_temperature = -16,
lethal_temperature_month = 1,
temperature_file =
system.file("extdata", "simple2x2", "critical_temp.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
temp = TRUE,
temperature_coefficient_file = coefficient_file)$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
precip = TRUE,
precipitation_coefficient_file =
coefficient_file)$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
precip = TRUE,
precipitation_coefficient_file =
coefficient_file)$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
use_lethal_temperature = TRUE,
lethal_temperature = -16,
lethal_temperature_month = 1,
temperature_file =
system.file("extdata", "simple2x2", "critical_temp.tif", package = "PoPS"),
temp = TRUE,
temperature_coefficient_file = coefficient_file,
precip = TRUE,
precipitation_coefficient_file =
coefficient_file)$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_weeks.tif", package = "PoPS"),
time_step = "week")$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_weeks.tif", package = "PoPS"),
time_step = "week")$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_weeks.tif", package = "PoPS"),
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_weeks.tif", package = "PoPS"),
time_step = "week")$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
use_lethal_temperature = TRUE,
lethal_temperature = -16,
lethal_temperature_month = 1,
temperature_file =
system.file("extdata", "simple2x2", "critical_temp.tif",
package = "PoPS"),
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_weeks.tif", package = "PoPS"),
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_weeks.tif", package = "PoPS"),
time_step = "week")$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
temp = TRUE,
time_step = "day",
temperature_coefficient_file =
system.file("extdata", "simple2x2", "temperature_coefficient_days.tif",
package = "PoPS"))$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_days.tif", package = "PoPS"),
time_step = "day")$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_days.tif", package = "PoPS"),
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_days.tif", package = "PoPS"),
time_step = "day")$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
use_lethal_temperature = TRUE,
lethal_temperature = -16,
lethal_temperature_month = 1,
temperature_file =
system.file("extdata", "simple2x2", "critical_temp.tif", package = "PoPS"),
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_days.tif", package = "PoPS"),
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_days.tif", package = "PoPS"),
time_step = "day")$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
})
test_that(
"Infected results returns all 0's if minimum temp drops below lethal temperature", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
parameter_means <- c(1, 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_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
temperature_file = temperature_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
matrix(0, ncol = 2, nrow = 2))
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
temperature_file = temperature_file,
precip = TRUE,
precipitation_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
matrix(0, ncol = 2, nrow = 2))
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
temperature_file = temperature_file,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
matrix(0, ncol = 2, nrow = 2))
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
temperature_file = temperature_file,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
precip = TRUE,
precipitation_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
matrix(0, ncol = 2, nrow = 2))
})
test_that(
"Infected results returns less infection after survival rates than before", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
survival_rates_file <-
system.file("extdata", "simple2x2", "survival_rates.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
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")
reduced_inf <- matrix(0, ncol = 2, nrow = 2)
reduced_inf[1, 1] <- 3
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_survival_rates = TRUE,
survival_rates_file = survival_rates_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
reduced_inf)
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_survival_rates = TRUE,
survival_rates_file = survival_rates_file,
precip = TRUE,
precipitation_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
reduced_inf)
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_survival_rates = TRUE,
survival_rates_file = survival_rates_file,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
reduced_inf)
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_survival_rates = TRUE,
survival_rates_file = survival_rates_file,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
precip = TRUE,
precipitation_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
reduced_inf)
})
test_that("Infected and Susceptible results return all 0's if treatments file is all 1's but
leaves a proportion of susceptibles if treatment method is ratio", {
infected_file_list <-
system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif",
package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
treatments_file <- system.file("extdata", "simple2x2", "treatments.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")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatment_dates = c("2008-12-01"),
treatments_file = treatments_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(data$host_pools[[1]]$infected[[1]], matrix(0, ncol = 2, nrow = 2))
expect_equal(data$host_pools[[1]]$susceptible[[1]], matrix(0, ncol = 2, nrow = 2))
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
treatment_method = "all infected",
total_populations_file = total_populations_file,
management = TRUE,
treatment_dates = c("2008-12-01"),
treatments_file = treatments_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(data$host_pools[[1]]$infected[[1]], matrix(0, ncol = 2, nrow = 2))
expect_equal(data$host_pools[[1]]$susceptible[[1]], matrix(0, ncol = 2, nrow = 2))
treatments_file <-
system.file("extdata", "simple2x2", "treatmentshalf.tif", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
treatment_method = "ratio",
total_populations_file = total_populations_file,
management = TRUE,
treatment_dates = c("2008-12-01"),
treatments_file = treatments_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(data$host_pools[[1]]$infected[[1]],
matrix(c(2, 0, 0, 0), ncol = 2, nrow = 2))
expect_equal(data$host_pools[[1]]$susceptible[[1]],
matrix(c(6, 7, 3, 7), ncol = 2, nrow = 2))
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
treatment_method = "all infected",
total_populations_file = total_populations_file,
management = TRUE,
treatment_dates = c("2008-12-01"),
treatments_file = treatments_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(data$host_pools[[1]]$infected[[1]],
matrix(c(0, 0, 0, 0), ncol = 2, nrow = 2))
expect_equal(data$host_pools[[1]]$susceptible[[1]],
matrix(c(6, 7, 3, 7), ncol = 2, nrow = 2))
})
test_that("Infected results are greater than initial infected", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
parameter_means <- c(1, 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_equal(all(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table
)$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
expect_equal(all(
pops(infected_file_list = infected_file_list,
host_file_list =
system.file("extdata", "simple2x2",
"total_plants_host_greater_than_infected.tif", package = "PoPS"),
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
})
test_that("All kernel types lead to spread", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-12-31"
time_step <- "month"
parameter_means <- c(4.0, 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")
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = time_step,
natural_kernel_type = "exponential")
infecteds <- data$host_pools[[1]]$infected[[1]]
expect_equal(all(infecteds >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
expect_gt(infecteds[1, 2] + infecteds[2, 1] + infecteds[2, 2], 0)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
natural_kernel_type = "cauchy")
infecteds <- data$host_pools[[1]]$infected[[1]]
expect_equal(all(infecteds >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
expect_gt(infecteds[1, 2] + infecteds[2, 1] + infecteds[2, 2], 0)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
natural_kernel_type = "uniform")
infecteds <- data$host_pools[[1]]$infected[[1]]
expect_equal(all(infecteds >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
expect_gt(infecteds[1, 2] + infecteds[2, 1] + infecteds[2, 2], 0)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
natural_kernel_type = "hyperbolic secant")
infecteds <- data$host_pools[[1]]$infected[[1]]
expect_equal(all(infecteds >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
expect_gt(infecteds[1, 2] + infecteds[2, 1] + infecteds[2, 2], 0)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
natural_kernel_type = "weibull")
infecteds <- data$host_pools[[1]]$infected[[1]]
expect_equal(all(infecteds >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
expect_gt(infecteds[1, 2] + infecteds[2, 1] + infecteds[2, 2], 0)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
natural_kernel_type = "logistic")
infecteds <- data$host_pools[[1]]$infected[[1]]
expect_equal(all(infecteds >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
expect_gt(infecteds[1, 2] + infecteds[2, 1] + infecteds[2, 2], 0)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
natural_kernel_type = "gamma")
infecteds <- data$host_pools[[1]]$infected[[1]]
expect_equal(all(infecteds >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
expect_gt(infecteds[1, 2] + infecteds[2, 1] + infecteds[2, 2], 0)
parameter_means <- c(0.4, 2, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
natural_kernel_type = "power law")
infecteds <- data$host_pools[[1]]$infected[[1]]
expect_equal(all(infecteds >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
expect_gte(infecteds[1, 2] + infecteds[2, 1] + infecteds[2, 2], 0)
## currently not working
# doesn't disperse outside of originally infected cell
# parameter_means <- c(0.4, 1000, 1, 500, 0, 0, 0, 0)
# parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
# data <- pops(infected_file_list = infected_file_list,
# host_file_list = host_file_list,
# total_populations_file = total_populations_file,
# parameter_means = parameter_means,
# parameter_cov_matrix = parameter_cov_matrix,
# pest_host_table = pest_host_table,
# competency_table = competency_table,
# natural_kernel_type = "exponential-power")
# infecteds <- data$host_pools[[1]]$infected[[1]]
# expect_equal(all(infecteds >=
# terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)),
# TRUE)
# expect_gt(infecteds[1,2] + infecteds[2,1] + infecteds[2,2], 0)
#
# # bad array when icdf is available
# data <- pops(infected_file_list = infected_file_list,
# host_file_list = host_file_list,
# total_populations_file = total_populations_file,
# parameter_means = parameter_means,
# parameter_cov_matrix = parameter_cov_matrix,
# pest_host_table = pest_host_table,
# competency_table = competency_table,
# natural_kernel_type = "log normal")
# infecteds <- data$host_pools[[1]]$infected[[1]]
# expect_equal(all(infecteds >=
# terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)),
# TRUE)
# expect_gt(infecteds[1,2] + infecteds[2,1] + infecteds[2,2], 0)
# checks for anthropogenic kernel type
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
anthropogenic_kernel_type = "exponential")
expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
anthropogenic_kernel_type = "cauchy")
expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
anthropogenic_kernel_type = "uniform")
expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
anthropogenic_kernel_type = "hyperbolic secant")
expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
anthropogenic_kernel_type = "logistic")
expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
anthropogenic_kernel_type = "weibull")
expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
anthropogenic_kernel_type = "power law")
expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
anthropogenic_kernel_type = "gamma")
expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
#
# data <- pops(infected_file_list = infected_file_list,
# host_file_list = host_file_list,
# total_populations_file = total_populations_file,
# parameter_means = parameter_means,
# parameter_cov_matrix = parameter_cov_matrix,
# pest_host_table = pest_host_table,
# competency_table = competency_table,
# anthropogenic_kernel_type = "exponential-power")
# expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
# terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)),
# TRUE)
## currently not working
#
#
# data <- pops(infected_file_list = infected_file_list,
# host_file_list = host_file_list,
# total_populations_file = total_populations_file,
# parameter_means = parameter_means,
# parameter_cov_matrix = parameter_cov_matrix,
# pest_host_table = pest_host_table,
# competency_table = competency_table,
# anthropogenic_kernel_type = "log normal")
# expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
# terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)),
# TRUE)
})
test_that("Susceptibles are never negative", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
parameter_means <- c(0.4, 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")
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date)
expect_equal(all(data$host_pools[[1]]$susceptible[[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data$host_pools[[1]]$susceptible[[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data$host_pools[[1]]$susceptible[[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
parameter_means <- c(0.5, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
data <-
pops(infected_file_list = infected_file_list,
host_file_list =
system.file("extdata", "simple2x2",
"total_plants_host_greater_than_infected.tif", package = "PoPS"),
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date)
expect_equal(all(data$host_pools[[1]]$susceptible[[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data$host_pools[[1]]$susceptible[[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data$host_pools[[1]]$susceptible[[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
})
test_that("SEI model works as intended", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-12-31"
model_type <- "SI"
latency_period <- 2
time_step <- "month"
output_frequency <- "month"
treatment_dates <- "2008-02-25"
parameter_means <- c(0.4, 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")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date,
model_type = model_type,
latency_period = latency_period,
output_frequency = output_frequency,
time_step = time_step,
treatment_dates = treatment_dates)
model_type <- "SEI"
data2 <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date,
model_type = model_type,
latency_period = latency_period,
output_frequency = output_frequency,
time_step = time_step,
treatment_dates = treatment_dates)
expect_equal(all(data2$exposed[[1]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[1]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[1]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[2]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[2]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[2]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[3]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[3]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[3]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[4]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[4]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[4]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[5]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[5]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[5]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[6]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[6]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[6]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[7]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[7]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[7]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[8]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[8]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[8]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[9]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[9]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[9]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[10]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[10]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[10]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[11]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[11]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[11]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[12]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[12]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[12]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data$host_pools[[1]]$susceptible[[1]] <=
data2$host_pools[[1]]$susceptible[[1]]), TRUE)
expect_equal(all(data$host_pools[[1]]$susceptible[[2]] <=
data2$host_pools[[1]]$susceptible[[1]]), TRUE)
expect_equal(all(data$host_pools[[1]]$susceptible[[3]] <=
data2$host_pools[[1]]$susceptible[[1]]), TRUE)
expect_equal(all(data$host_pools[[1]]$infected[[1]] >= data2$host_pools[[1]]$infected[[1]]), TRUE)
expect_equal(all(data$infected[[2]] >= data2$host_pools[[1]]$infected[[1]]), TRUE)
expect_equal(all(data$infected[[3]] >= data2$host_pools[[1]]$infected[[1]]), TRUE)
start_exposed <- TRUE
exposed_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
model_type <- "SEI"
data3 <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date,
model_type = model_type,
latency_period = latency_period,
output_frequency = output_frequency,
time_step = time_step,
treatment_dates = treatment_dates,
start_exposed = start_exposed,
exposed_file_list = exposed_file_list)
expect_equal(all(data3$host_pools[[1]]$susceptible[[1]] <=
data2$host_pools[[1]]$susceptible[[1]]), TRUE)
expect_equal(all(data3$host_pools[[1]]$susceptible[[2]] <=
data2$host_pools[[1]]$susceptible[[1]]), TRUE)
expect_equal(all(data3$host_pools[[1]]$susceptible[[3]] <=
data2$host_pools[[1]]$susceptible[[1]]), TRUE)
expect_equal(all(data3$host_pools[[1]]$infected[[1]] >=
data2$host_pools[[1]]$infected[[1]]), TRUE)
expect_equal(all(data3$infected[[2]] >= data2$host_pools[[1]]$infected[[1]]), TRUE)
expect_equal(all(data3$infected[[3]] >= data2$host_pools[[1]]$infected[[1]]), TRUE)
})
test_that("Infected results with weather are less than those without weather", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
parameter_means <- c(3.0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
coefficient_sd_file <- system.file("extdata", "simple2x2", "coefficient_sd.tif", package = "PoPS")
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")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date)
data_temp <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date)
data_precip <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
precip = TRUE,
precipitation_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date)
data_weather <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
precip = TRUE,
precipitation_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date)
data_temp_wsd <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date,
weather_type = "probabilistic",
temperature_coefficient_sd_file = coefficient_sd_file)
data_precip_wsd <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
precip = TRUE,
precipitation_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date,
weather_type = "probabilistic",
precipitation_coefficient_sd_file = coefficient_sd_file)
data_weather_wsd <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
precip = TRUE,
precipitation_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date,
weather_type = "probabilistic",
temperature_coefficient_sd_file = coefficient_sd_file,
precipitation_coefficient_sd_file = coefficient_sd_file)
expect_gte(sum(data$host_pools[[1]]$infected[[1]]), sum(data_temp$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data$host_pools[[1]]$infected[[2]]), sum(data_temp$host_pools[[1]]$infected[[2]]))
expect_gte(sum(data$host_pools[[1]]$infected[[3]]), sum(data_temp$host_pools[[1]]$infected[[3]]))
expect_gte(sum(data$host_pools[[1]]$infected[[1]]),
sum(data_precip$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data$host_pools[[1]]$infected[[2]]),
sum(data_precip$host_pools[[1]]$infected[[2]]))
expect_gte(sum(data$host_pools[[1]]$infected[[3]]),
sum(data_precip$host_pools[[1]]$infected[[3]]))
expect_gte(sum(data$host_pools[[1]]$infected[[1]]),
sum(data_weather$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data$host_pools[[1]]$infected[[2]]),
sum(data_weather$host_pools[[1]]$infected[[2]]))
expect_gte(sum(data$host_pools[[1]]$infected[[3]]),
sum(data_weather$host_pools[[1]]$infected[[3]]))
expect_gte(sum(data$host_pools[[1]]$infected[[2]]),
sum(data_temp_wsd$host_pools[[1]]$infected[[2]]))
expect_gte(sum(data$host_pools[[1]]$infected[[3]]),
sum(data_temp_wsd$host_pools[[1]]$infected[[3]]))
expect_gte(sum(data$host_pools[[1]]$infected[[1]]),
sum(data_temp_wsd$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data$host_pools[[1]]$infected[[1]]),
sum(data_precip_wsd$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data$host_pools[[1]]$infected[[2]]),
sum(data_precip_wsd$host_pools[[1]]$infected[[2]]))
expect_gte(sum(data$host_pools[[1]]$infected[[3]]),
sum(data_precip_wsd$host_pools[[1]]$infected[[3]]))
expect_gte(sum(data$host_pools[[1]]$infected[[1]]),
sum(data_weather_wsd$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data$host_pools[[1]]$infected[[2]]),
sum(data_weather_wsd$host_pools[[1]]$infected[[2]]))
expect_gte(sum(data$host_pools[[1]]$infected[[3]]),
sum(data_weather_wsd$host_pools[[1]]$infected[[3]]))
})
test_that(
"Infected results are greater with same parameters for weekly spread vs. monthly", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
parameter_means <- c(0.2, 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")
data_week <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "week",
random_seed = 42,
start_date = start_date,
end_date = end_date)
data_month <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "month",
random_seed = 42,
start_date = start_date,
end_date = end_date)
expect_equal(all(data_week$host_pools[[1]]$infected[[1]] >=
data_month$host_pools[[1]]$infected[[1]]), TRUE)
expect_equal(all(data_week$host_pools[[1]]$infected[[2]] >=
data_month$host_pools[[1]]$infected[[2]]), TRUE)
})
test_that("Infected results are greater with same parameters for daily spread vs. monthly and
weekly", {
infected_file_list <-
system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif",
package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
parameter_means <- c(0.1, 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")
data_day <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "day",
random_seed = 42)
data_week <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "week",
random_seed = 42,
start_date = start_date,
end_date = end_date)
data_month <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "month",
random_seed = 42,
start_date = start_date,
end_date = end_date)
expect_equal(all(data_day$host_pools[[1]]$infected[[1]] >=
data_month$host_pools[[1]]$infected[[1]]), TRUE)
expect_equal(all(data_day$host_pools[[1]]$infected[[1]] >=
data_week$host_pools[[1]]$infected[[1]]), TRUE)
expect_equal(all(data_week$host_pools[[1]]$infected[[1]] >=
data_month$host_pools[[1]]$infected[[1]]), TRUE)
})
test_that(
"Infected results are greater without treatment than with treatment", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
treatments_file <- system.file("extdata", "simple2x2", "treatments_1_1.tif", package = "PoPS")
treatment_dates <- c("2008-03-05")
start_date <- "2008-01-01"
end_date <- "2009-12-31"
parameter_means <- c(0.8, 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")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date)
data_treat <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatment_dates = treatment_dates,
treatments_file = treatments_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date)
expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
data_treat$host_pools[[1]]$infected[[1]]), TRUE)
expect_equal(all(data$host_pools[[1]]$infected[[2]] >=
data_treat$host_pools[[1]]$infected[[2]]), TRUE)
})
test_that("Infected results are greater with higher reproductive rate", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
parameter_means <- c(4.0, 15, 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")
data_1 <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "month",
random_seed = 42,
start_date = start_date,
end_date = end_date)
parameter_means <- c(3.0, 15, 1, 500, 0, 0, 0, 0)
data_075 <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "month",
random_seed = 42,
start_date = start_date,
end_date = end_date)
parameter_means <- c(2.0, 15, 1, 500, 0, 0, 0, 0)
data_050 <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "month",
random_seed = 42,
start_date = start_date,
end_date = end_date)
parameter_means <- c(1.0, 15, 1, 500, 0, 0, 0, 0)
data_025 <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "month",
random_seed = 42,
start_date = start_date,
end_date = end_date)
parameter_means <- c(0.5, 15, 1, 500, 0, 0, 0, 0)
data_010 <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "month",
random_seed = 42,
start_date = start_date,
end_date = end_date)
expect_gte(sum(data_1$host_pools[[1]]$infected[[1]]), sum(data_075$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_1$host_pools[[1]]$infected[[1]]), sum(data_050$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_1$host_pools[[1]]$infected[[1]]), sum(data_025$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_1$host_pools[[1]]$infected[[1]]), sum(data_010$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_075$host_pools[[1]]$infected[[1]]),
sum(data_050$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_075$host_pools[[1]]$infected[[1]]),
sum(data_025$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_075$host_pools[[1]]$infected[[1]]),
sum(data_010$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_050$host_pools[[1]]$infected[[1]]),
sum(data_025$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_050$host_pools[[1]]$infected[[2]]),
sum(data_025$host_pools[[1]]$infected[[2]]))
expect_gte(sum(data_050$host_pools[[1]]$infected[[1]]),
sum(data_010$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_050$host_pools[[1]]$infected[[2]]),
sum(data_010$host_pools[[1]]$infected[[2]]))
expect_gte(sum(data_025$host_pools[[1]]$infected[[1]]),
sum(data_010$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_025$host_pools[[1]]$infected[[2]]),
sum(data_010$host_pools[[1]]$infected[[2]]))
})
test_that("Treatments apply no matter what time step", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2009-01-01"
end_date <- "2009-12-31"
treatments_file <- system.file("extdata", "simple2x2", "treatments.tif", package = "PoPS")
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
dates <- seq.Date(as.Date(start_date), as.Date(end_date), by = "days")
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")
for (i in seq_len(length(dates))) {
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatment_dates = c(as.character(dates[i])),
treatments_file = treatments_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(data$host_pools[[1]]$infected[[1]], matrix(0, ncol = 2, nrow = 2))
expect_equal(data$host_pools[[1]]$susceptible[[1]], matrix(0, ncol = 2, nrow = 2))
}
})
test_that("Pesticide treatments apply no matter what time step", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2009-01-01"
end_date <- "2009-12-31"
treatments_file <- system.file("extdata", "simple2x2", "treatments.tif", package = "PoPS")
pesticide_duration <- c(120)
pesticide_efficacy <- 1.0
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
dates <- seq.Date(as.Date(start_date), as.Date("2009-06-30"), by = "days")
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")
for (i in seq_len(length(dates))) {
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatment_dates = c(as.character(dates[i])),
treatments_file = treatments_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
pesticide_duration = pesticide_duration,
pesticide_efficacy = pesticide_efficacy)
expect_equal(data$host_pools[[1]]$infected[[1]], matrix(0, ncol = 2, nrow = 2))
expect_equal(data$host_pools[[1]]$susceptible[[1]],
terra::as.matrix(terra::rast(host_file_list), wide = TRUE))
}
pesticide_duration <- c(120)
pesticide_efficacy <- 0.5
for (i in seq_len(length(dates))) {
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatment_dates = c(as.character(dates[i])),
treatments_file = treatments_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
pesticide_duration = pesticide_duration,
pesticide_efficacy = pesticide_efficacy)
expect_equal(data$host_pools[[1]]$infected[[1]], matrix(c(3, 0, 0, 0), ncol = 2, nrow = 2))
expect_equal(data$host_pools[[1]]$susceptible[[1]],
matrix(c(14, 14, 6, 15), ncol = 2, nrow = 2))
}
})
test_that("Changing the output frequency returns the correct number of outputs and output
statistics", {
infected_file_list <-
system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2009-01-01"
end_date <- "2009-12-31"
treatment_dates <- c(start_date)
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")
data <-
pops(output_frequency = "year",
time_step = "month",
treatment_dates = treatment_dates,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 1)
data <-
pops(output_frequency = "year",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 1)
data <-
pops(output_frequency = "year",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 1)
data <-
pops(output_frequency = "month",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 12)
data <-
pops(output_frequency = "month",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 12)
data <-
pops(output_frequency = "week",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 52)
data <-
pops(output_frequency = "week",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 52)
expect_error(pops(output_frequency = "day",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date), output_frequency_error)
expect_error(pops(output_frequency = "day",
time_step = "month",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date), output_frequency_error)
expect_error(pops(output_frequency = "week",
time_step = "month",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date), output_frequency_error)
data <- pops(output_frequency = "day",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 364)
data <- pops(output_frequency = "every_n_steps",
output_frequency_n = 5,
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 72)
})
test_that(
"Outputs occur with non-full year date range for all time step output frequency combinations", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2009-05-01"
end_date <- "2009-10-29"
treatment_dates <- start_date
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")
data <- pops(output_frequency = "year",
time_step = "month",
treatment_dates = treatment_dates,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 1)
data <- pops(output_frequency = "year",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 1)
data <- pops(output_frequency = "year",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 1)
data <- pops(output_frequency = "month",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 5)
data <- pops(output_frequency = "month",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 5)
data <- pops(output_frequency = "week",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 26)
data <- pops(output_frequency = "week",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 26)
data <-
pops(output_frequency = "day"
, time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 182)
data <-
pops(output_frequency = "time_step",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 182)
})
test_that("Quarantine and spread rates work at all timings", {
infected_file_list <-
system.file("extdata", "simple20x20", "initial_infection.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
start_date <- "2009-01-01"
end_date <- "2009-12-31"
treatment_dates <- start_date
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
quarantine_areas_file <-
system.file("extdata", "simple20x20", "initial_infection.tif", package = "PoPS")
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")
data <- pops(output_frequency = "year",
time_step = "month",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_quarantine = TRUE,
use_spreadrates = TRUE,
quarantine_areas_file = quarantine_areas_file)
expect_equal(length(data$host_pools[[1]]$infected), 1)
expect_equal(length(data$quarantine_escape), 1)
expect_equal(length(data$quarantine_escape_distance), 1)
expect_equal(length(data$quarantine_escape_directions), 1)
expect_equal(length(data$rates), 1)
data <- pops(output_frequency = "year",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_quarantine = TRUE,
use_spreadrates = TRUE,
quarantine_areas_file = quarantine_areas_file)
expect_equal(length(data$host_pools[[1]]$infected), 1)
expect_equal(length(data$quarantine_escape), 1)
expect_equal(length(data$quarantine_escape_distance), 1)
expect_equal(length(data$quarantine_escape_directions), 1)
expect_equal(length(data$rates), 1)
data <- pops(output_frequency = "year",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_quarantine = TRUE,
use_spreadrates = TRUE,
quarantine_areas_file = quarantine_areas_file)
expect_equal(length(data$host_pools[[1]]$infected), 1)
expect_equal(length(data$quarantine_escape), 1)
expect_equal(length(data$quarantine_escape_distance), 1)
expect_equal(length(data$quarantine_escape_directions), 1)
expect_equal(length(data$rates), 1)
data <- pops(output_frequency = "month",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_quarantine = TRUE,
use_spreadrates = TRUE,
quarantine_areas_file = quarantine_areas_file)
expect_equal(length(data$host_pools[[1]]$infected), 12)
expect_equal(length(data$quarantine_escape), 12)
expect_equal(length(data$quarantine_escape_distance), 12)
expect_equal(length(data$quarantine_escape_directions), 12)
expect_equal(length(data$rates), 12)
data <- pops(output_frequency = "month",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_quarantine = TRUE,
use_spreadrates = TRUE,
quarantine_areas_file = quarantine_areas_file)
expect_equal(length(data$host_pools[[1]]$infected), 12)
expect_equal(length(data$quarantine_escape), 12)
expect_equal(length(data$quarantine_escape_distance), 12)
expect_equal(length(data$quarantine_escape_directions), 12)
expect_equal(length(data$rates), 12)
data <- pops(output_frequency = "week",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_quarantine = TRUE,
use_spreadrates = TRUE,
quarantine_areas_file = quarantine_areas_file)
expect_equal(length(data$host_pools[[1]]$infected), 52)
expect_equal(length(data$quarantine_escape), 52)
expect_equal(length(data$quarantine_escape_distance), 52)
expect_equal(length(data$quarantine_escape_directions), 52)
expect_equal(length(data$rates), 52)
data <- pops(output_frequency = "week",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_quarantine = TRUE,
use_spreadrates = TRUE,
quarantine_areas_file = quarantine_areas_file)
expect_equal(length(data$host_pools[[1]]$infected), 52)
expect_equal(length(data$quarantine_escape), 52)
expect_equal(length(data$quarantine_escape_distance), 52)
expect_equal(length(data$quarantine_escape_directions), 52)
expect_equal(length(data$rates), 52)
data <- pops(output_frequency = "day",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date, use_quarantine = TRUE,
use_spreadrates = TRUE,
quarantine_areas_file = quarantine_areas_file,
quarantine_directions = "N,E,S,W")
expect_equal(length(data$host_pools[[1]]$infected), 364)
expect_equal(length(data$quarantine_escape), 364)
expect_equal(length(data$quarantine_escape_distance), 364)
expect_equal(length(data$quarantine_escape_directions), 364)
expect_equal(length(data$rates), 364)
data <- pops(output_frequency = "time_step",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_quarantine = TRUE,
use_spreadrates = TRUE,
quarantine_areas_file = quarantine_areas_file,
quarantine_directions = "N")
expect_equal(length(data$host_pools[[1]]$infected), 364)
expect_equal(length(data$quarantine_escape), 364)
expect_equal(length(data$quarantine_escape_distance), 364)
expect_equal(length(data$quarantine_escape_directions), 364)
expect_equal(length(data$rates), 364)
})
test_that("Mortality works as expected with multiple ", {
infected_file_list <-
system.file("extdata", "simple20x20", "initial_infection.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
start_date <- "2009-01-01"
end_date <- "2009-12-31"
treatment_dates <- start_date
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.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
data <- pops(output_frequency = "month",
time_step = "month",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
mortality_frequency = "month",
mortality_frequency_n = 1)
expect_equal(length(data$host_pools[[1]]$mortality), 12)
expect_equal(data$host_pools[[1]]$mortality[[1]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[2]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[3]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
data <- pops(output_frequency = "week",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
mortality_frequency = "month",
mortality_frequency_n = 1)
expect_equal(length(data$host_pools[[1]]$mortality), 12)
expect_equal(data$host_pools[[1]]$mortality[[1]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[2]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[3]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
pest_host_table <- system.file("extdata", "pest_host_table_singlehost025.csv", package = "PoPS")
data <- pops(output_frequency = "week",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
mortality_frequency = "month",
mortality_frequency_n = 1)
expect_equal(length(data$host_pools[[1]]$mortality), 12)
expect_equal(data$host_pools[[1]]$mortality[[1]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[2]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[3]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[4]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[5]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost025tl3.csv", package = "PoPS")
data <- pops(output_frequency = "week",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
mortality_frequency = "month",
mortality_frequency_n = 1)
expect_equal(length(data$host_pools[[1]]$mortality), 12)
expect_equal(data$host_pools[[1]]$mortality[[1]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[2]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[3]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[4]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[5]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[6]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[7]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost010tl1.csv", package = "PoPS")
data <- pops(output_frequency = "week",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
mortality_frequency = "month",
mortality_frequency_n = 1)
expect_equal(length(data$host_pools[[1]]$mortality), 12)
expect_equal(data$host_pools[[1]]$mortality[[1]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[2]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[3]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[4]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[5]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[6]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[7]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[8]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[9]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[10]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[11]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
})
test_that("Movements works as expected", {
infected_file_list <-
system.file("extdata", "simple20x20", "initial_infection.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
start_date <- "2009-01-01"
end_date <- "2009-12-31"
treatment_dates <- start_date
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
use_movements <- TRUE
movements_file <- system.file("extdata", "simple20x20", "movements.tif", package = "PoPS")
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(output_frequency = "month",
time_step = "month",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_movements = use_movements,
movements_file = movements_file,
random_seed = 42),
detailed_file_exists_error(movements_file))
movements_file <- system.file("extdata", "simple20x20", "movements.csv", package = "PoPS")
data <- pops(output_frequency = "month",
time_step = "month",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_movements = use_movements,
movements_file = movements_file,
random_seed = 42)
expect_equal(length(data$host_pools[[1]]$infected), 12)
expect_equal(data$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(data$host_pools[[1]]$infected[[2]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(data$host_pools[[1]]$infected[[3]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(data$host_pools[[1]]$infected[[4]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
infected_move <- matrix(0, ncol = 20, nrow = 20)
infected_move[2, 1] <- 1
expect_equal(data$host_pools[[1]]$infected[[5]], infected_move)
sus <- terra::rast(host_file_list) - terra::rast(infected_file_list)
sus <- terra::as.matrix(sus, wide = TRUE)
sus5 <- sus
sus5[1, 1] <- sus5[1, 1] - 199
sus5[2, 1] <- sus5[2, 1] + 199
sus6 <- sus5
sus6[1, 2] <- sus6[1, 2] - 50
sus6[2, 2] <- sus6[2, 2] + 50
expect_equal(data$host_pools[[1]]$susceptible[[1]], sus)
expect_equal(data$host_pools[[1]]$susceptible[[2]], sus)
expect_equal(data$host_pools[[1]]$susceptible[[3]], sus)
expect_equal(data$host_pools[[1]]$susceptible[[4]], sus)
expect_equal(data$host_pools[[1]]$susceptible[[5]], sus5)
expect_equal(data$host_pools[[1]]$susceptible[[6]], sus6)
data <- pops(output_frequency = "month",
time_step = "month",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_movements = use_movements,
movements_file = movements_file,
random_seed = 45)
expect_equal(length(data$host_pools[[1]]$infected), 12)
expect_equal(data$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(data$host_pools[[1]]$infected[[2]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(data$host_pools[[1]]$infected[[3]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(data$host_pools[[1]]$infected[[4]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
infected_move <- matrix(0, ncol = 20, nrow = 20)
infected_move[2, 1] <- 1
expect_equal(data$host_pools[[1]]$infected[[5]], infected_move)
sus <- terra::rast(host_file_list) - terra::rast(infected_file_list)
sus <- terra::as.matrix(sus, wide = TRUE)
sus5 <- sus
sus5[1, 1] <- sus5[1, 1] - 199
sus5[2, 1] <- sus5[2, 1] + 199
sus6 <- sus5
sus6[1, 2] <- sus6[1, 2] - 50
sus6[2, 2] <- sus6[2, 2] + 50
expect_equal(data$host_pools[[1]]$susceptible[[1]], sus)
expect_equal(data$host_pools[[1]]$susceptible[[2]], sus)
expect_equal(data$host_pools[[1]]$susceptible[[3]], sus)
expect_equal(data$host_pools[[1]]$susceptible[[4]], sus)
expect_equal(data$host_pools[[1]]$susceptible[[5]], sus5)
expect_equal(data$host_pools[[1]]$susceptible[[6]], sus6)
})
test_that(
"Overpopulation dispersal works as expected with directionality to prevent dispersers from
leaving the simulated area", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-12-31"
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")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_overpopulation_movements = TRUE,
overpopulation_percentage = 0.2,
leaving_percentage = 0.5,
leaving_scale_coefficient = 0.5,
natural_dir = "SE")
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_lte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
})
test_that("Deterministic dispersal works as expected", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-12-31"
parameter_means <- c(2, 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")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
generate_stochasticity = FALSE,
establishment_stochasticity = FALSE,
movement_stochasticity = FALSE,
dispersal_stochasticity = TRUE)
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
})
test_that("Network dispersal works as expected", {
infected_file_list <-
system.file("extdata", "simple20x20", "initial_infection.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-03-31"
parameter_means <- c(2, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
network_filename <- system.file("extdata", "simple20x20", "segments.csv", package = "PoPS")
anthropogenic_kernel_type <- "network"
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")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
network_filename = network_filename)
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
})
test_that("uncertainty propogation works as expected", {
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")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-03-31"
parameter_means <- c(2, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
anthropogenic_kernel_type <- "cauchy"
use_initial_condition_uncertainty <- TRUE
use_host_uncertainty <- TRUE
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")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty)
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
infected_file_list <- system.file("extdata", "simple20x20", "infected_wsd.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
total_populations_file <- system.file("extdata", "simple20x20", "all_plants.tif",
package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-03-31"
parameter_means <- c(2, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
anthropogenic_kernel_type <- "cauchy"
use_initial_condition_uncertainty <- TRUE
use_host_uncertainty <- FALSE
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty)
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
infected_file_list <-
system.file("extdata", "simple20x20", "initial_infection.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple20x20", "host_w_sd2.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-03-31"
parameter_means <- c(2, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
anthropogenic_kernel_type <- "cauchy"
use_initial_condition_uncertainty <- FALSE
use_host_uncertainty <- TRUE
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")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty)
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
})
test_that("multiple_random seeds works and returns expected results", {
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")
start_date <- "2008-01-01"
end_date <- "2008-03-31"
parameter_means <- c(5, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
anthropogenic_kernel_type <- "cauchy"
multiple_random_seeds <- TRUE
file_random_seeds <- NULL
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")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
multiple_random_seeds = multiple_random_seeds,
file_random_seeds = file_random_seeds)
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
file_random_seeds <- system.file("extdata", "simple2x2", "randoms.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
multiple_random_seeds = multiple_random_seeds,
file_random_seeds = file_random_seeds)
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
})
test_that("Using soils returns expected results", {
infected_file_list <-
system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2009-12-31"
parameter_means <- c(5, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
use_soils <- TRUE
dispersers_to_soils_percentage <- 0.05
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
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")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
use_soils = use_soils,
dispersers_to_soils_percentage = dispersers_to_soils_percentage)
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
expect_equal(length(data$soil_reservoirs[[1]]), 20)
expect_equal(length(data$soil_reservoirs[[2]]), 20)
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
use_soils = use_soils,
dispersers_to_soils_percentage = dispersers_to_soils_percentage,
soil_starting_pest_file = infected_file_list,
start_with_soil_populations = TRUE)
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
expect_equal(length(data$soil_reservoirs[[1]]), 20)
expect_equal(length(data$soil_reservoirs[[2]]), 20)
})
test_that("Using multiple hosts works as expected", {
infected_file_list <-
c(system.file("extdata", "simple2x2", "infected_oak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "infected_tanoak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "infected_baylaurel.tif", package = "PoPS"))
host_file_list <-
c(system.file("extdata", "simple2x2", "host_oak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "host_tanoak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "host_baylaurel.tif", package = "PoPS"))
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2009-12-31"
parameter_means <- c(0, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
pest_host_table <-
system.file("extdata", "pest_host_table.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_multihost.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
temp = TRUE,
random_seed = 42,
temperature_coefficient_file = coefficient_file)
test_mat <- terra::as.matrix(terra::rast(infected_file_list[1]), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
test_mat <- terra::as.matrix(terra::rast(infected_file_list[2]), wide = TRUE)
expect_gte(data$host_pools[[2]]$infected[[1]][[1]] + data$host_pools[[2]]$infected[[1]][[1]],
test_mat[[1]])
expect_gte(data$host_pools[[2]]$infected[[1]][[2]] + data$host_pools[[2]]$infected[[1]][[2]],
test_mat[[2]])
expect_gte(data$host_pools[[2]]$infected[[1]][[3]] + data$host_pools[[2]]$infected[[1]][[3]],
test_mat[[3]])
expect_gte(data$host_pools[[2]]$infected[[1]][[4]] + data$host_pools[[2]]$infected[[1]][[4]],
test_mat[[4]])
infected_file_list <-
c(system.file("extdata", "simple2x2", "infected_oak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "infected_tanoak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "infected_baylaurel.tif", package = "PoPS"))
host_file_list <-
c(system.file("extdata", "simple2x2", "host_oak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "host_tanoak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "host_baylaurel.tif", package = "PoPS"))
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2009-12-31"
parameter_means <- c(5, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
pest_host_table <-
system.file("extdata", "pest_host_table.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_multihost.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
temp = TRUE,
random_seed = 42,
temperature_coefficient_file = coefficient_file)
test_mat <- terra::as.matrix(terra::rast(infected_file_list[1]), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
test_mat <- terra::as.matrix(terra::rast(infected_file_list[2]), wide = TRUE)
expect_gte(data$host_pools[[2]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[2]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[2]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[2]]$infected[[1]][[4]], test_mat[[4]])
infected_file_list <-
c(system.file("extdata", "simple2x2", "infected_oak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "infected_tanoak.tif", package = "PoPS"))
host_file_list <-
c(system.file("extdata", "simple2x2", "host_oak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "host_tanoak.tif", package = "PoPS"))
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2009-12-31"
parameter_means <- c(5, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
pest_host_table <-
system.file("extdata", "pest_host_table_2host.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_2host.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
temp = TRUE,
random_seed = 42,
temperature_coefficient_file = coefficient_file)
test_mat <- terra::as.matrix(terra::rast(infected_file_list[1]), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
test_mat <- terra::as.matrix(terra::rast(infected_file_list[2]), wide = TRUE)
expect_gte(data$host_pools[[2]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[2]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[2]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[2]]$infected[[1]][[4]], test_mat[[4]])
})
test_that("Using multiple hosts with uncertainty works as expected", {
infected_file_list <-
c(system.file("extdata", "simple2x2", "infected_oak_wsd.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "infected_tanoak_wsd.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "infected_baylaurel_wsd.tif", package = "PoPS"))
host_file_list <-
c(system.file("extdata", "simple2x2", "host_oak_wsd.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "host_tanoak_wsd.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "host_baylaurel_wsd.tif", package = "PoPS"))
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2009-12-31"
parameter_means <- c(0, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_multihost.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date,
use_host_uncertainty = TRUE)
test_mat <- terra::as.matrix(terra::rast(infected_file_list[1]), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
test_mat <- terra::as.matrix(terra::rast(infected_file_list[2]), wide = TRUE)
expect_gte(data$host_pools[[2]]$infected[[1]][[1]] + data$host_pools[[2]]$infected[[1]][[1]],
test_mat[[1]])
expect_gte(data$host_pools[[2]]$infected[[1]][[2]] + data$host_pools[[2]]$infected[[1]][[2]],
test_mat[[2]])
expect_gte(data$host_pools[[2]]$infected[[1]][[3]] + data$host_pools[[2]]$infected[[1]][[3]],
test_mat[[3]])
expect_gte(data$host_pools[[2]]$infected[[1]][[4]] + data$host_pools[[2]]$infected[[1]][[4]],
test_mat[[4]])
infected_file_list <-
c(system.file("extdata", "simple2x2", "infected_oak_wsd.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "infected_tanoak_wsd.tif", package = "PoPS"))
host_file_list <-
c(system.file("extdata", "simple2x2", "host_oak_wsd.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "host_tanoak_wsd.tif", package = "PoPS"))
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2009-12-31"
parameter_means <- c(5, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_2host.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_2host.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
random_seed = 42,
use_host_uncertainty = TRUE)
test_mat <- terra::as.matrix(terra::rast(infected_file_list[1]), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
test_mat <- terra::as.matrix(terra::rast(infected_file_list[2]), wide = TRUE)
expect_gte(data$host_pools[[2]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[2]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[2]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[2]]$infected[[1]][[4]], test_mat[[4]])
})
test_that("county level infection works as expected", {
infected_file_list <-
system.file("extdata", "simple20x20", "county_infected.gpkg", package = "PoPS")
host_file_list <- system.file("extdata", "simple20x20", "host_w_sd2.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-03-31"
parameter_means <- c(0, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
anthropogenic_kernel_type <- "cauchy"
use_initial_condition_uncertainty <- FALSE
use_host_uncertainty <- FALSE
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")
county_level_infection_data <- TRUE
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty,
county_level_infection_data = county_level_infection_data)
test_infected <- terra::vect(infected_file_list[[1]])
expect_equal(data$number_infected, sum(test_infected$infected_mean))
parameter_means <- c(2, 21, 1, 500, 0, 0, 100, 1000)
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty,
county_level_infection_data = county_level_infection_data)
test_infected <- terra::vect(infected_file_list[[1]])
expect_gte(data$number_infected, sum(test_infected$infected_mean))
use_initial_condition_uncertainty <- TRUE
use_host_uncertainty <- TRUE
parameter_means <- c(0, 21, 1, 500, 0, 0, 100, 1000)
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty,
county_level_infection_data = county_level_infection_data)
test_infected <- terra::vect(infected_file_list[[1]])
expect_gte(data$number_infected, 0)
use_initial_condition_uncertainty <- TRUE
use_host_uncertainty <- TRUE
parameter_means <- c(2, 21, 1, 500, 0, 0, 100, 1000)
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty,
county_level_infection_data = county_level_infection_data)
test_infected <- terra::vect(infected_file_list[[1]])
expect_gte(data$number_infected, 0)
use_initial_condition_uncertainty <- FALSE
use_host_uncertainty <- FALSE
parameter_means <- c(2, 21, 1, 500, 0, 0, 100, 1000)
exposed_file_list <-
system.file("extdata", "simple20x20", "county_infected.gpkg", package = "PoPS")
start_exposed <- TRUE
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty,
county_level_infection_data = county_level_infection_data,
model_type = "SEI",
exposed_file_list = exposed_file_list,
latency_period = 2,
start_exposed = start_exposed)
test_infected <- terra::vect(infected_file_list[[1]])
expect_gte(data$number_infected, 0)
expect_gte(sum(data$host_pools[[1]]$total_exposed[[1]]), 0)
parameter_means <- c(0, 21, 1, 500, 0, 0, 100, 1000)
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty,
county_level_infection_data = county_level_infection_data,
model_type = "SEI",
exposed_file_list = exposed_file_list,
latency_period = 5,
start_exposed = start_exposed)
test_infected <- terra::vect(infected_file_list[[1]])
expect_equal(data$number_infected, sum(test_infected$infected_mean))
expect_equal(sum(data$host_pools[[1]]$total_exposed[[1]]), sum(test_infected$infected_mean))
host_file_list <- system.file("extdata", "simple20x20", "host_fullzeropoly.tif", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty,
county_level_infection_data = county_level_infection_data,
model_type = "SEI",
exposed_file_list = exposed_file_list,
latency_period = 5,
start_exposed = start_exposed)
test_infected <- terra::vect(infected_file_list[[1]])
expect_equal(data$number_infected, sum(test_infected$infected_mean))
expect_equal(sum(data$host_pools[[1]]$total_exposed[[1]]), sum(test_infected$infected_mean))
})
ncsu-landscape-dynamics/rpops documentation built on May 1, 2024, 10:21 a.m.
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context("test-pops")
test_that("Model stops if files don't exist or aren't the correct extension", {
infected_file_list <- c("")
host_file_list <- c(system.file("extdata", "simple2x2", "host.tif", package = "PoPS"))
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
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.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table))
infected_file_list <- system.file("extdata", "simple2x2", "infected.csv", package = "PoPS")
expect_error(pops(
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),
raster_type_error, fixed = TRUE)
host_file_list <- ""
infected_file_list <- c(system.file("extdata", "simple2x2", "infected.tif", package = "PoPS"))
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table))
host_file_list <- c(system.file("extdata", "simple2x2", "infected.csv", package = "PoPS"))
expect_error(pops(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),
raster_type_error, fixed = TRUE)
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <- ""
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
detailed_file_exists_error(total_populations_file))
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file =
system.file("extdata", "simple2x2", "infected.csv", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
raster_type_error, fixed = TRUE)
temperature_file <- ""
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
use_lethal_temperature = TRUE,
temperature_file = temperature_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
detailed_file_exists_error(temperature_file))
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
use_lethal_temperature = TRUE,
temperature_file =
system.file("extdata", "simple2x2", "infected.csv", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
raster_type_error, fixed = TRUE)
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
temperature_coefficient_file <- ""
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
temp = TRUE,
temperature_coefficient_file = temperature_coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
detailed_file_exists_error(temperature_coefficient_file))
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2", "infected.csv", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
raster_type_error, fixed = TRUE)
precipitation_coefficient_file <- ""
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
precip = TRUE,
precipitation_coefficient_file = "",
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
detailed_file_exists_error(precipitation_coefficient_file))
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2", "infected.csv", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
raster_type_error, fixed = TRUE)
treatments_file <- ""
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
management = TRUE,
treatments_file = treatments_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
detailed_file_exists_error(treatments_file))
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
management = TRUE,
treatments_file =
system.file("extdata", "simple2x2", "infected.csv", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
raster_type_error, fixed = TRUE)
exposed_file_list <- ""
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
model_type = "SEI",
exposed_file_list = exposed_file_list,
latency_period = 2,
start_exposed = TRUE,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table))
quarantine_areas_file <- ""
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
quarantine_areas_file = quarantine_areas_file,
use_quarantine = TRUE,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
detailed_file_exists_error(quarantine_areas_file))
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = host_file_list,
parameter_means = c(0, 0, 0, 0),
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
paramter_means_error, fixed = TRUE)
expect_error(pops(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 = matrix(0, nrow = 5, ncol = 6),
pest_host_table = pest_host_table,
competency_table = competency_table),
covariance_mat_error, fixed = TRUE)
})
test_that("Model stops if treatments don't have correct dimenisions", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
treatments_file <- system.file("extdata", "simple2x2", "treatments.tif", package = "PoPS")
treatment_dates <- c("2008-01-01", "2008-05-01")
pest_host_table <- system.file("extdata", "pest_host_table_singlehost.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
expect_error(pops(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,
management = TRUE,
treatments_file = treatments_file,
treatment_dates = treatment_dates),
treatment_length_error, fixed = TRUE)
})
test_that("Model stops if time and date parameters are of the wrong type and/or dimension", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
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.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
time_step = "two",
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
time_step_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
end_date = "two",
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
date_format_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
end_date = 156,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
date_format_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
start_date = "five",
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
date_format_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
start_date = 19,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
date_format_error, fixed = TRUE)
})
test_that("Model stops if kernel is of the wrong type and/or dimension", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <- system.file("extdata", "simple2x2",
"critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
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.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
expect_error(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
natural_kernel_type = "none",
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
natural_kernel_error, fixed = TRUE)
expect_error(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
anthropogenic_kernel_type = "none",
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
anthropogenic_kernel_error, fixed = TRUE)
})
test_that("Input raster resolutions, extents, and crs all match", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
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.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
expect_error(pops(infected_file_list = infected_file_list,
host_file_list =
system.file("extdata", "simple5x5", "total_plants.tif", package = "PoPS"),
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
extent_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file =
system.file("extdata", "simple5x5", "total_plants.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
extent_error, fixed = TRUE)
expect_error(pops(infected_file_list =
system.file("extdata", "simple5x5", "total_plants.tif", package = "PoPS"),
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
extent_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
temperature_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_extent.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
extent_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_extent.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
extent_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_extent.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
extent_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2", "critical_temp.tif", package = "PoPS"),
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_extent.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
extent_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatments_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_extent.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
extent_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list =
system.file("extdata", "simple2x2",
"total_plants_diff_res.tif", package = "PoPS"),
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list =
system.file("extdata", "simple2x2",
"total_plants_diff_xres.tif", package = "PoPS"),
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list =
system.file("extdata", "simple2x2",
"total_plants_diff_yres.tif", package = "PoPS"),
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file =
system.file("extdata", "simple2x2",
"total_plants_diff_res.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file =
system.file("extdata", "simple2x2",
"total_plants_diff_xres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file =
system.file("extdata", "simple2x2",
"total_plants_diff_yres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list =
system.file("extdata", "simple2x2",
"total_plants_diff_res.tif", package = "PoPS"),
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list =
system.file("extdata", "simple2x2",
"total_plants_diff_xres.tif", package = "PoPS"),
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list =
system.file("extdata", "simple2x2",
"total_plants_diff_yres.tif", package = "PoPS"),
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
temperature_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_res.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
temperature_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_xres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
temperature_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_yres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_res.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_xres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_yres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_res.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_xres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_yres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2", "critical_temp.tif", package = "PoPS"),
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_res.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2", "critical_temp.tif", package = "PoPS"),
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_xres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2", "critical_temp.tif", package = "PoPS"),
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_yres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatments_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_res.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatments_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_xres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatments_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_yres.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
resolution_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list =
system.file("extdata", "simple2x2",
"critical_temp_diff_crs.tif", package = "PoPS"),
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
crs_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_crs.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
crs_error, fixed = TRUE)
expect_error(pops(infected_file_list =
system.file("extdata", "simple2x2",
"critical_temp_diff_crs.tif", package = "PoPS"),
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
crs_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
temperature_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_crs.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
crs_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_crs.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
crs_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_crs.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
crs_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2", "critical_temp.tif",
package = "PoPS"),
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_crs.tif",
package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
crs_error, fixed = TRUE)
expect_error(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatments_file =
system.file("extdata", "simple2x2",
"critical_temp_diff_crs.tif",
package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table),
crs_error, fixed = TRUE)
})
test_that("Infected results return initial infected if reproductive rate is set to 0", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
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_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
lethal_temperature = -16,
lethal_temperature_month = 1,
temperature_file =
system.file("extdata", "simple2x2", "critical_temp.tif", package = "PoPS"),
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
temp = TRUE,
temperature_coefficient_file = coefficient_file)$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
precip = TRUE,
precipitation_coefficient_file =
coefficient_file)$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
precip = TRUE,
precipitation_coefficient_file =
coefficient_file)$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
use_lethal_temperature = TRUE,
lethal_temperature = -16,
lethal_temperature_month = 1,
temperature_file =
system.file("extdata", "simple2x2", "critical_temp.tif", package = "PoPS"),
temp = TRUE,
temperature_coefficient_file = coefficient_file,
precip = TRUE,
precipitation_coefficient_file =
coefficient_file)$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_weeks.tif", package = "PoPS"),
time_step = "week")$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_weeks.tif", package = "PoPS"),
time_step = "week")$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_weeks.tif", package = "PoPS"),
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_weeks.tif", package = "PoPS"),
time_step = "week")$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
use_lethal_temperature = TRUE,
lethal_temperature = -16,
lethal_temperature_month = 1,
temperature_file =
system.file("extdata", "simple2x2", "critical_temp.tif",
package = "PoPS"),
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_weeks.tif", package = "PoPS"),
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_weeks.tif", package = "PoPS"),
time_step = "week")$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
temp = TRUE,
time_step = "day",
temperature_coefficient_file =
system.file("extdata", "simple2x2", "temperature_coefficient_days.tif",
package = "PoPS"))$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_days.tif", package = "PoPS"),
time_step = "day")$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_days.tif", package = "PoPS"),
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_days.tif", package = "PoPS"),
time_step = "day")$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
use_lethal_temperature = TRUE,
lethal_temperature = -16,
lethal_temperature_month = 1,
temperature_file =
system.file("extdata", "simple2x2", "critical_temp.tif", package = "PoPS"),
temp = TRUE,
temperature_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_days.tif", package = "PoPS"),
precip = TRUE,
precipitation_coefficient_file =
system.file("extdata", "simple2x2",
"temperature_coefficient_days.tif", package = "PoPS"),
time_step = "day")$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
})
test_that(
"Infected results returns all 0's if minimum temp drops below lethal temperature", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
parameter_means <- c(1, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
temperature_file = temperature_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
matrix(0, ncol = 2, nrow = 2))
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
temperature_file = temperature_file,
precip = TRUE,
precipitation_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
matrix(0, ncol = 2, nrow = 2))
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
temperature_file = temperature_file,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
matrix(0, ncol = 2, nrow = 2))
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_lethal_temperature = TRUE,
temperature_file = temperature_file,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
precip = TRUE,
precipitation_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
matrix(0, ncol = 2, nrow = 2))
})
test_that(
"Infected results returns less infection after survival rates than before", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
survival_rates_file <-
system.file("extdata", "simple2x2", "survival_rates.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
reduced_inf <- matrix(0, ncol = 2, nrow = 2)
reduced_inf[1, 1] <- 3
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_survival_rates = TRUE,
survival_rates_file = survival_rates_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
reduced_inf)
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_survival_rates = TRUE,
survival_rates_file = survival_rates_file,
precip = TRUE,
precipitation_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
reduced_inf)
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_survival_rates = TRUE,
survival_rates_file = survival_rates_file,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
reduced_inf)
expect_equal(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
use_survival_rates = TRUE,
survival_rates_file = survival_rates_file,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
precip = TRUE,
precipitation_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]],
reduced_inf)
})
test_that("Infected and Susceptible results return all 0's if treatments file is all 1's but
leaves a proportion of susceptibles if treatment method is ratio", {
infected_file_list <-
system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif",
package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
treatments_file <- system.file("extdata", "simple2x2", "treatments.tif",
package = "PoPS")
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <-
system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatment_dates = c("2008-12-01"),
treatments_file = treatments_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(data$host_pools[[1]]$infected[[1]], matrix(0, ncol = 2, nrow = 2))
expect_equal(data$host_pools[[1]]$susceptible[[1]], matrix(0, ncol = 2, nrow = 2))
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
treatment_method = "all infected",
total_populations_file = total_populations_file,
management = TRUE,
treatment_dates = c("2008-12-01"),
treatments_file = treatments_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(data$host_pools[[1]]$infected[[1]], matrix(0, ncol = 2, nrow = 2))
expect_equal(data$host_pools[[1]]$susceptible[[1]], matrix(0, ncol = 2, nrow = 2))
treatments_file <-
system.file("extdata", "simple2x2", "treatmentshalf.tif", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
treatment_method = "ratio",
total_populations_file = total_populations_file,
management = TRUE,
treatment_dates = c("2008-12-01"),
treatments_file = treatments_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(data$host_pools[[1]]$infected[[1]],
matrix(c(2, 0, 0, 0), ncol = 2, nrow = 2))
expect_equal(data$host_pools[[1]]$susceptible[[1]],
matrix(c(6, 7, 3, 7), ncol = 2, nrow = 2))
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
treatment_method = "all infected",
total_populations_file = total_populations_file,
management = TRUE,
treatment_dates = c("2008-12-01"),
treatments_file = treatments_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(data$host_pools[[1]]$infected[[1]],
matrix(c(0, 0, 0, 0), ncol = 2, nrow = 2))
expect_equal(data$host_pools[[1]]$susceptible[[1]],
matrix(c(6, 7, 3, 7), ncol = 2, nrow = 2))
})
test_that("Infected results are greater than initial infected", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
parameter_means <- c(1, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
expect_equal(all(pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table
)$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
expect_equal(all(
pops(infected_file_list = infected_file_list,
host_file_list =
system.file("extdata", "simple2x2",
"total_plants_host_greater_than_infected.tif", package = "PoPS"),
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table)$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
})
test_that("All kernel types lead to spread", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-12-31"
time_step <- "month"
parameter_means <- c(4.0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = time_step,
natural_kernel_type = "exponential")
infecteds <- data$host_pools[[1]]$infected[[1]]
expect_equal(all(infecteds >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
expect_gt(infecteds[1, 2] + infecteds[2, 1] + infecteds[2, 2], 0)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
natural_kernel_type = "cauchy")
infecteds <- data$host_pools[[1]]$infected[[1]]
expect_equal(all(infecteds >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
expect_gt(infecteds[1, 2] + infecteds[2, 1] + infecteds[2, 2], 0)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
natural_kernel_type = "uniform")
infecteds <- data$host_pools[[1]]$infected[[1]]
expect_equal(all(infecteds >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
expect_gt(infecteds[1, 2] + infecteds[2, 1] + infecteds[2, 2], 0)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
natural_kernel_type = "hyperbolic secant")
infecteds <- data$host_pools[[1]]$infected[[1]]
expect_equal(all(infecteds >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
expect_gt(infecteds[1, 2] + infecteds[2, 1] + infecteds[2, 2], 0)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
natural_kernel_type = "weibull")
infecteds <- data$host_pools[[1]]$infected[[1]]
expect_equal(all(infecteds >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
expect_gt(infecteds[1, 2] + infecteds[2, 1] + infecteds[2, 2], 0)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
natural_kernel_type = "logistic")
infecteds <- data$host_pools[[1]]$infected[[1]]
expect_equal(all(infecteds >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
expect_gt(infecteds[1, 2] + infecteds[2, 1] + infecteds[2, 2], 0)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
natural_kernel_type = "gamma")
infecteds <- data$host_pools[[1]]$infected[[1]]
expect_equal(all(infecteds >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
expect_gt(infecteds[1, 2] + infecteds[2, 1] + infecteds[2, 2], 0)
parameter_means <- c(0.4, 2, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
natural_kernel_type = "power law")
infecteds <- data$host_pools[[1]]$infected[[1]]
expect_equal(all(infecteds >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
expect_gte(infecteds[1, 2] + infecteds[2, 1] + infecteds[2, 2], 0)
## currently not working
# doesn't disperse outside of originally infected cell
# parameter_means <- c(0.4, 1000, 1, 500, 0, 0, 0, 0)
# parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
# data <- pops(infected_file_list = infected_file_list,
# host_file_list = host_file_list,
# total_populations_file = total_populations_file,
# parameter_means = parameter_means,
# parameter_cov_matrix = parameter_cov_matrix,
# pest_host_table = pest_host_table,
# competency_table = competency_table,
# natural_kernel_type = "exponential-power")
# infecteds <- data$host_pools[[1]]$infected[[1]]
# expect_equal(all(infecteds >=
# terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)),
# TRUE)
# expect_gt(infecteds[1,2] + infecteds[2,1] + infecteds[2,2], 0)
#
# # bad array when icdf is available
# data <- pops(infected_file_list = infected_file_list,
# host_file_list = host_file_list,
# total_populations_file = total_populations_file,
# parameter_means = parameter_means,
# parameter_cov_matrix = parameter_cov_matrix,
# pest_host_table = pest_host_table,
# competency_table = competency_table,
# natural_kernel_type = "log normal")
# infecteds <- data$host_pools[[1]]$infected[[1]]
# expect_equal(all(infecteds >=
# terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)),
# TRUE)
# expect_gt(infecteds[1,2] + infecteds[2,1] + infecteds[2,2], 0)
# checks for anthropogenic kernel type
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
anthropogenic_kernel_type = "exponential")
expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
anthropogenic_kernel_type = "cauchy")
expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
anthropogenic_kernel_type = "uniform")
expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
anthropogenic_kernel_type = "hyperbolic secant")
expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
anthropogenic_kernel_type = "logistic")
expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
anthropogenic_kernel_type = "weibull")
expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
anthropogenic_kernel_type = "power law")
expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
anthropogenic_kernel_type = "gamma")
expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)), TRUE)
#
# data <- pops(infected_file_list = infected_file_list,
# host_file_list = host_file_list,
# total_populations_file = total_populations_file,
# parameter_means = parameter_means,
# parameter_cov_matrix = parameter_cov_matrix,
# pest_host_table = pest_host_table,
# competency_table = competency_table,
# anthropogenic_kernel_type = "exponential-power")
# expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
# terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)),
# TRUE)
## currently not working
#
#
# data <- pops(infected_file_list = infected_file_list,
# host_file_list = host_file_list,
# total_populations_file = total_populations_file,
# parameter_means = parameter_means,
# parameter_cov_matrix = parameter_cov_matrix,
# pest_host_table = pest_host_table,
# competency_table = competency_table,
# anthropogenic_kernel_type = "log normal")
# expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
# terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)),
# TRUE)
})
test_that("Susceptibles are never negative", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
parameter_means <- c(0.4, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
data <- pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date)
expect_equal(all(data$host_pools[[1]]$susceptible[[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data$host_pools[[1]]$susceptible[[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data$host_pools[[1]]$susceptible[[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
parameter_means <- c(0.5, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
data <-
pops(infected_file_list = infected_file_list,
host_file_list =
system.file("extdata", "simple2x2",
"total_plants_host_greater_than_infected.tif", package = "PoPS"),
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date)
expect_equal(all(data$host_pools[[1]]$susceptible[[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data$host_pools[[1]]$susceptible[[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data$host_pools[[1]]$susceptible[[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
})
test_that("SEI model works as intended", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-12-31"
model_type <- "SI"
latency_period <- 2
time_step <- "month"
output_frequency <- "month"
treatment_dates <- "2008-02-25"
parameter_means <- c(0.4, 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")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date,
model_type = model_type,
latency_period = latency_period,
output_frequency = output_frequency,
time_step = time_step,
treatment_dates = treatment_dates)
model_type <- "SEI"
data2 <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date,
model_type = model_type,
latency_period = latency_period,
output_frequency = output_frequency,
time_step = time_step,
treatment_dates = treatment_dates)
expect_equal(all(data2$exposed[[1]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[1]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[1]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[2]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[2]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[2]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[3]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[3]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[3]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[4]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[4]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[4]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[5]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[5]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[5]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[6]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[6]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[6]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[7]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[7]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[7]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[8]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[8]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[8]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[9]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[9]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[9]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[10]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[10]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[10]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[11]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[11]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[11]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[12]][[1]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[12]][[2]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data2$exposed[[12]][[3]] >= matrix(0, ncol = 2, nrow = 2)), TRUE)
expect_equal(all(data$host_pools[[1]]$susceptible[[1]] <=
data2$host_pools[[1]]$susceptible[[1]]), TRUE)
expect_equal(all(data$host_pools[[1]]$susceptible[[2]] <=
data2$host_pools[[1]]$susceptible[[1]]), TRUE)
expect_equal(all(data$host_pools[[1]]$susceptible[[3]] <=
data2$host_pools[[1]]$susceptible[[1]]), TRUE)
expect_equal(all(data$host_pools[[1]]$infected[[1]] >= data2$host_pools[[1]]$infected[[1]]), TRUE)
expect_equal(all(data$infected[[2]] >= data2$host_pools[[1]]$infected[[1]]), TRUE)
expect_equal(all(data$infected[[3]] >= data2$host_pools[[1]]$infected[[1]]), TRUE)
start_exposed <- TRUE
exposed_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
model_type <- "SEI"
data3 <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date,
model_type = model_type,
latency_period = latency_period,
output_frequency = output_frequency,
time_step = time_step,
treatment_dates = treatment_dates,
start_exposed = start_exposed,
exposed_file_list = exposed_file_list)
expect_equal(all(data3$host_pools[[1]]$susceptible[[1]] <=
data2$host_pools[[1]]$susceptible[[1]]), TRUE)
expect_equal(all(data3$host_pools[[1]]$susceptible[[2]] <=
data2$host_pools[[1]]$susceptible[[1]]), TRUE)
expect_equal(all(data3$host_pools[[1]]$susceptible[[3]] <=
data2$host_pools[[1]]$susceptible[[1]]), TRUE)
expect_equal(all(data3$host_pools[[1]]$infected[[1]] >=
data2$host_pools[[1]]$infected[[1]]), TRUE)
expect_equal(all(data3$infected[[2]] >= data2$host_pools[[1]]$infected[[1]]), TRUE)
expect_equal(all(data3$infected[[3]] >= data2$host_pools[[1]]$infected[[1]]), TRUE)
})
test_that("Infected results with weather are less than those without weather", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
parameter_means <- c(3.0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
coefficient_sd_file <- system.file("extdata", "simple2x2", "coefficient_sd.tif", package = "PoPS")
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")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date)
data_temp <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date)
data_precip <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
precip = TRUE,
precipitation_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date)
data_weather <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
precip = TRUE,
precipitation_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date)
data_temp_wsd <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date,
weather_type = "probabilistic",
temperature_coefficient_sd_file = coefficient_sd_file)
data_precip_wsd <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
precip = TRUE,
precipitation_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date,
weather_type = "probabilistic",
precipitation_coefficient_sd_file = coefficient_sd_file)
data_weather_wsd <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
precip = TRUE,
precipitation_coefficient_file = coefficient_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date,
weather_type = "probabilistic",
temperature_coefficient_sd_file = coefficient_sd_file,
precipitation_coefficient_sd_file = coefficient_sd_file)
expect_gte(sum(data$host_pools[[1]]$infected[[1]]), sum(data_temp$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data$host_pools[[1]]$infected[[2]]), sum(data_temp$host_pools[[1]]$infected[[2]]))
expect_gte(sum(data$host_pools[[1]]$infected[[3]]), sum(data_temp$host_pools[[1]]$infected[[3]]))
expect_gte(sum(data$host_pools[[1]]$infected[[1]]),
sum(data_precip$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data$host_pools[[1]]$infected[[2]]),
sum(data_precip$host_pools[[1]]$infected[[2]]))
expect_gte(sum(data$host_pools[[1]]$infected[[3]]),
sum(data_precip$host_pools[[1]]$infected[[3]]))
expect_gte(sum(data$host_pools[[1]]$infected[[1]]),
sum(data_weather$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data$host_pools[[1]]$infected[[2]]),
sum(data_weather$host_pools[[1]]$infected[[2]]))
expect_gte(sum(data$host_pools[[1]]$infected[[3]]),
sum(data_weather$host_pools[[1]]$infected[[3]]))
expect_gte(sum(data$host_pools[[1]]$infected[[2]]),
sum(data_temp_wsd$host_pools[[1]]$infected[[2]]))
expect_gte(sum(data$host_pools[[1]]$infected[[3]]),
sum(data_temp_wsd$host_pools[[1]]$infected[[3]]))
expect_gte(sum(data$host_pools[[1]]$infected[[1]]),
sum(data_temp_wsd$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data$host_pools[[1]]$infected[[1]]),
sum(data_precip_wsd$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data$host_pools[[1]]$infected[[2]]),
sum(data_precip_wsd$host_pools[[1]]$infected[[2]]))
expect_gte(sum(data$host_pools[[1]]$infected[[3]]),
sum(data_precip_wsd$host_pools[[1]]$infected[[3]]))
expect_gte(sum(data$host_pools[[1]]$infected[[1]]),
sum(data_weather_wsd$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data$host_pools[[1]]$infected[[2]]),
sum(data_weather_wsd$host_pools[[1]]$infected[[2]]))
expect_gte(sum(data$host_pools[[1]]$infected[[3]]),
sum(data_weather_wsd$host_pools[[1]]$infected[[3]]))
})
test_that(
"Infected results are greater with same parameters for weekly spread vs. monthly", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
parameter_means <- c(0.2, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
data_week <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "week",
random_seed = 42,
start_date = start_date,
end_date = end_date)
data_month <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "month",
random_seed = 42,
start_date = start_date,
end_date = end_date)
expect_equal(all(data_week$host_pools[[1]]$infected[[1]] >=
data_month$host_pools[[1]]$infected[[1]]), TRUE)
expect_equal(all(data_week$host_pools[[1]]$infected[[2]] >=
data_month$host_pools[[1]]$infected[[2]]), TRUE)
})
test_that("Infected results are greater with same parameters for daily spread vs. monthly and
weekly", {
infected_file_list <-
system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif",
package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
parameter_means <- c(0.1, 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")
data_day <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "day",
random_seed = 42)
data_week <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "week",
random_seed = 42,
start_date = start_date,
end_date = end_date)
data_month <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "month",
random_seed = 42,
start_date = start_date,
end_date = end_date)
expect_equal(all(data_day$host_pools[[1]]$infected[[1]] >=
data_month$host_pools[[1]]$infected[[1]]), TRUE)
expect_equal(all(data_day$host_pools[[1]]$infected[[1]] >=
data_week$host_pools[[1]]$infected[[1]]), TRUE)
expect_equal(all(data_week$host_pools[[1]]$infected[[1]] >=
data_month$host_pools[[1]]$infected[[1]]), TRUE)
})
test_that(
"Infected results are greater without treatment than with treatment", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
treatments_file <- system.file("extdata", "simple2x2", "treatments_1_1.tif", package = "PoPS")
treatment_dates <- c("2008-03-05")
start_date <- "2008-01-01"
end_date <- "2009-12-31"
parameter_means <- c(0.8, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date)
data_treat <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatment_dates = treatment_dates,
treatments_file = treatments_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date)
expect_equal(all(data$host_pools[[1]]$infected[[1]] >=
data_treat$host_pools[[1]]$infected[[1]]), TRUE)
expect_equal(all(data$host_pools[[1]]$infected[[2]] >=
data_treat$host_pools[[1]]$infected[[2]]), TRUE)
})
test_that("Infected results are greater with higher reproductive rate", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2010-12-31"
parameter_means <- c(4.0, 15, 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")
data_1 <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "month",
random_seed = 42,
start_date = start_date,
end_date = end_date)
parameter_means <- c(3.0, 15, 1, 500, 0, 0, 0, 0)
data_075 <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "month",
random_seed = 42,
start_date = start_date,
end_date = end_date)
parameter_means <- c(2.0, 15, 1, 500, 0, 0, 0, 0)
data_050 <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "month",
random_seed = 42,
start_date = start_date,
end_date = end_date)
parameter_means <- c(1.0, 15, 1, 500, 0, 0, 0, 0)
data_025 <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "month",
random_seed = 42,
start_date = start_date,
end_date = end_date)
parameter_means <- c(0.5, 15, 1, 500, 0, 0, 0, 0)
data_010 <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
time_step = "month",
random_seed = 42,
start_date = start_date,
end_date = end_date)
expect_gte(sum(data_1$host_pools[[1]]$infected[[1]]), sum(data_075$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_1$host_pools[[1]]$infected[[1]]), sum(data_050$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_1$host_pools[[1]]$infected[[1]]), sum(data_025$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_1$host_pools[[1]]$infected[[1]]), sum(data_010$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_075$host_pools[[1]]$infected[[1]]),
sum(data_050$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_075$host_pools[[1]]$infected[[1]]),
sum(data_025$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_075$host_pools[[1]]$infected[[1]]),
sum(data_010$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_050$host_pools[[1]]$infected[[1]]),
sum(data_025$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_050$host_pools[[1]]$infected[[2]]),
sum(data_025$host_pools[[1]]$infected[[2]]))
expect_gte(sum(data_050$host_pools[[1]]$infected[[1]]),
sum(data_010$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_050$host_pools[[1]]$infected[[2]]),
sum(data_010$host_pools[[1]]$infected[[2]]))
expect_gte(sum(data_025$host_pools[[1]]$infected[[1]]),
sum(data_010$host_pools[[1]]$infected[[1]]))
expect_gte(sum(data_025$host_pools[[1]]$infected[[2]]),
sum(data_010$host_pools[[1]]$infected[[2]]))
})
test_that("Treatments apply no matter what time step", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2009-01-01"
end_date <- "2009-12-31"
treatments_file <- system.file("extdata", "simple2x2", "treatments.tif", package = "PoPS")
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
dates <- seq.Date(as.Date(start_date), as.Date(end_date), by = "days")
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
for (i in seq_len(length(dates))) {
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatment_dates = c(as.character(dates[i])),
treatments_file = treatments_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(data$host_pools[[1]]$infected[[1]], matrix(0, ncol = 2, nrow = 2))
expect_equal(data$host_pools[[1]]$susceptible[[1]], matrix(0, ncol = 2, nrow = 2))
}
})
test_that("Pesticide treatments apply no matter what time step", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
temperature_file <-
system.file("extdata", "simple2x2", "critical_temp_all_below_threshold.tif", package = "PoPS")
start_date <- "2009-01-01"
end_date <- "2009-12-31"
treatments_file <- system.file("extdata", "simple2x2", "treatments.tif", package = "PoPS")
pesticide_duration <- c(120)
pesticide_efficacy <- 1.0
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
dates <- seq.Date(as.Date(start_date), as.Date("2009-06-30"), by = "days")
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
for (i in seq_len(length(dates))) {
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatment_dates = c(as.character(dates[i])),
treatments_file = treatments_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
pesticide_duration = pesticide_duration,
pesticide_efficacy = pesticide_efficacy)
expect_equal(data$host_pools[[1]]$infected[[1]], matrix(0, ncol = 2, nrow = 2))
expect_equal(data$host_pools[[1]]$susceptible[[1]],
terra::as.matrix(terra::rast(host_file_list), wide = TRUE))
}
pesticide_duration <- c(120)
pesticide_efficacy <- 0.5
for (i in seq_len(length(dates))) {
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
management = TRUE,
treatment_dates = c(as.character(dates[i])),
treatments_file = treatments_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
pesticide_duration = pesticide_duration,
pesticide_efficacy = pesticide_efficacy)
expect_equal(data$host_pools[[1]]$infected[[1]], matrix(c(3, 0, 0, 0), ncol = 2, nrow = 2))
expect_equal(data$host_pools[[1]]$susceptible[[1]],
matrix(c(14, 14, 6, 15), ncol = 2, nrow = 2))
}
})
test_that("Changing the output frequency returns the correct number of outputs and output
statistics", {
infected_file_list <-
system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <-
system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2009-01-01"
end_date <- "2009-12-31"
treatment_dates <- c(start_date)
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <-
system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
data <-
pops(output_frequency = "year",
time_step = "month",
treatment_dates = treatment_dates,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 1)
data <-
pops(output_frequency = "year",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 1)
data <-
pops(output_frequency = "year",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 1)
data <-
pops(output_frequency = "month",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 12)
data <-
pops(output_frequency = "month",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 12)
data <-
pops(output_frequency = "week",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 52)
data <-
pops(output_frequency = "week",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 52)
expect_error(pops(output_frequency = "day",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date), output_frequency_error)
expect_error(pops(output_frequency = "day",
time_step = "month",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date), output_frequency_error)
expect_error(pops(output_frequency = "week",
time_step = "month",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date), output_frequency_error)
data <- pops(output_frequency = "day",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 364)
data <- pops(output_frequency = "every_n_steps",
output_frequency_n = 5,
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 72)
})
test_that(
"Outputs occur with non-full year date range for all time step output frequency combinations", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2009-05-01"
end_date <- "2009-10-29"
treatment_dates <- start_date
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
data <- pops(output_frequency = "year",
time_step = "month",
treatment_dates = treatment_dates,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 1)
data <- pops(output_frequency = "year",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 1)
data <- pops(output_frequency = "year",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 1)
data <- pops(output_frequency = "month",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 5)
data <- pops(output_frequency = "month",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 5)
data <- pops(output_frequency = "week",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 26)
data <- pops(output_frequency = "week",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 26)
data <-
pops(output_frequency = "day"
, time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 182)
data <-
pops(output_frequency = "time_step",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date)
expect_equal(length(data$host_pools[[1]]$infected), 182)
})
test_that("Quarantine and spread rates work at all timings", {
infected_file_list <-
system.file("extdata", "simple20x20", "initial_infection.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
start_date <- "2009-01-01"
end_date <- "2009-12-31"
treatment_dates <- start_date
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
quarantine_areas_file <-
system.file("extdata", "simple20x20", "initial_infection.tif", package = "PoPS")
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
data <- pops(output_frequency = "year",
time_step = "month",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_quarantine = TRUE,
use_spreadrates = TRUE,
quarantine_areas_file = quarantine_areas_file)
expect_equal(length(data$host_pools[[1]]$infected), 1)
expect_equal(length(data$quarantine_escape), 1)
expect_equal(length(data$quarantine_escape_distance), 1)
expect_equal(length(data$quarantine_escape_directions), 1)
expect_equal(length(data$rates), 1)
data <- pops(output_frequency = "year",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_quarantine = TRUE,
use_spreadrates = TRUE,
quarantine_areas_file = quarantine_areas_file)
expect_equal(length(data$host_pools[[1]]$infected), 1)
expect_equal(length(data$quarantine_escape), 1)
expect_equal(length(data$quarantine_escape_distance), 1)
expect_equal(length(data$quarantine_escape_directions), 1)
expect_equal(length(data$rates), 1)
data <- pops(output_frequency = "year",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_quarantine = TRUE,
use_spreadrates = TRUE,
quarantine_areas_file = quarantine_areas_file)
expect_equal(length(data$host_pools[[1]]$infected), 1)
expect_equal(length(data$quarantine_escape), 1)
expect_equal(length(data$quarantine_escape_distance), 1)
expect_equal(length(data$quarantine_escape_directions), 1)
expect_equal(length(data$rates), 1)
data <- pops(output_frequency = "month",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_quarantine = TRUE,
use_spreadrates = TRUE,
quarantine_areas_file = quarantine_areas_file)
expect_equal(length(data$host_pools[[1]]$infected), 12)
expect_equal(length(data$quarantine_escape), 12)
expect_equal(length(data$quarantine_escape_distance), 12)
expect_equal(length(data$quarantine_escape_directions), 12)
expect_equal(length(data$rates), 12)
data <- pops(output_frequency = "month",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_quarantine = TRUE,
use_spreadrates = TRUE,
quarantine_areas_file = quarantine_areas_file)
expect_equal(length(data$host_pools[[1]]$infected), 12)
expect_equal(length(data$quarantine_escape), 12)
expect_equal(length(data$quarantine_escape_distance), 12)
expect_equal(length(data$quarantine_escape_directions), 12)
expect_equal(length(data$rates), 12)
data <- pops(output_frequency = "week",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_quarantine = TRUE,
use_spreadrates = TRUE,
quarantine_areas_file = quarantine_areas_file)
expect_equal(length(data$host_pools[[1]]$infected), 52)
expect_equal(length(data$quarantine_escape), 52)
expect_equal(length(data$quarantine_escape_distance), 52)
expect_equal(length(data$quarantine_escape_directions), 52)
expect_equal(length(data$rates), 52)
data <- pops(output_frequency = "week",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_quarantine = TRUE,
use_spreadrates = TRUE,
quarantine_areas_file = quarantine_areas_file)
expect_equal(length(data$host_pools[[1]]$infected), 52)
expect_equal(length(data$quarantine_escape), 52)
expect_equal(length(data$quarantine_escape_distance), 52)
expect_equal(length(data$quarantine_escape_directions), 52)
expect_equal(length(data$rates), 52)
data <- pops(output_frequency = "day",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date, use_quarantine = TRUE,
use_spreadrates = TRUE,
quarantine_areas_file = quarantine_areas_file,
quarantine_directions = "N,E,S,W")
expect_equal(length(data$host_pools[[1]]$infected), 364)
expect_equal(length(data$quarantine_escape), 364)
expect_equal(length(data$quarantine_escape_distance), 364)
expect_equal(length(data$quarantine_escape_directions), 364)
expect_equal(length(data$rates), 364)
data <- pops(output_frequency = "time_step",
time_step = "day",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_quarantine = TRUE,
use_spreadrates = TRUE,
quarantine_areas_file = quarantine_areas_file,
quarantine_directions = "N")
expect_equal(length(data$host_pools[[1]]$infected), 364)
expect_equal(length(data$quarantine_escape), 364)
expect_equal(length(data$quarantine_escape_distance), 364)
expect_equal(length(data$quarantine_escape_directions), 364)
expect_equal(length(data$rates), 364)
})
test_that("Mortality works as expected with multiple ", {
infected_file_list <-
system.file("extdata", "simple20x20", "initial_infection.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
start_date <- "2009-01-01"
end_date <- "2009-12-31"
treatment_dates <- start_date
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <- system.file("extdata", "pest_host_table_singlehost.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
data <- pops(output_frequency = "month",
time_step = "month",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
mortality_frequency = "month",
mortality_frequency_n = 1)
expect_equal(length(data$host_pools[[1]]$mortality), 12)
expect_equal(data$host_pools[[1]]$mortality[[1]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[2]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[3]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
data <- pops(output_frequency = "week",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
mortality_frequency = "month",
mortality_frequency_n = 1)
expect_equal(length(data$host_pools[[1]]$mortality), 12)
expect_equal(data$host_pools[[1]]$mortality[[1]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[2]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[3]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
pest_host_table <- system.file("extdata", "pest_host_table_singlehost025.csv", package = "PoPS")
data <- pops(output_frequency = "week",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
mortality_frequency = "month",
mortality_frequency_n = 1)
expect_equal(length(data$host_pools[[1]]$mortality), 12)
expect_equal(data$host_pools[[1]]$mortality[[1]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[2]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[3]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[4]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[5]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost025tl3.csv", package = "PoPS")
data <- pops(output_frequency = "week",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
mortality_frequency = "month",
mortality_frequency_n = 1)
expect_equal(length(data$host_pools[[1]]$mortality), 12)
expect_equal(data$host_pools[[1]]$mortality[[1]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[2]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[3]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[4]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[5]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[6]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[7]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost010tl1.csv", package = "PoPS")
data <- pops(output_frequency = "week",
time_step = "week",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
mortality_frequency = "month",
mortality_frequency_n = 1)
expect_equal(length(data$host_pools[[1]]$mortality), 12)
expect_equal(data$host_pools[[1]]$mortality[[1]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[2]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[3]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[4]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[5]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[6]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[7]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[8]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[9]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[10]], matrix(0, ncol = 20, nrow = 20))
expect_equal(data$host_pools[[1]]$mortality[[11]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
})
test_that("Movements works as expected", {
infected_file_list <-
system.file("extdata", "simple20x20", "initial_infection.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
start_date <- "2009-01-01"
end_date <- "2009-12-31"
treatment_dates <- start_date
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
use_movements <- TRUE
movements_file <- system.file("extdata", "simple20x20", "movements.tif", package = "PoPS")
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(output_frequency = "month",
time_step = "month",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_movements = use_movements,
movements_file = movements_file,
random_seed = 42),
detailed_file_exists_error(movements_file))
movements_file <- system.file("extdata", "simple20x20", "movements.csv", package = "PoPS")
data <- pops(output_frequency = "month",
time_step = "month",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_movements = use_movements,
movements_file = movements_file,
random_seed = 42)
expect_equal(length(data$host_pools[[1]]$infected), 12)
expect_equal(data$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(data$host_pools[[1]]$infected[[2]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(data$host_pools[[1]]$infected[[3]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(data$host_pools[[1]]$infected[[4]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
infected_move <- matrix(0, ncol = 20, nrow = 20)
infected_move[2, 1] <- 1
expect_equal(data$host_pools[[1]]$infected[[5]], infected_move)
sus <- terra::rast(host_file_list) - terra::rast(infected_file_list)
sus <- terra::as.matrix(sus, wide = TRUE)
sus5 <- sus
sus5[1, 1] <- sus5[1, 1] - 199
sus5[2, 1] <- sus5[2, 1] + 199
sus6 <- sus5
sus6[1, 2] <- sus6[1, 2] - 50
sus6[2, 2] <- sus6[2, 2] + 50
expect_equal(data$host_pools[[1]]$susceptible[[1]], sus)
expect_equal(data$host_pools[[1]]$susceptible[[2]], sus)
expect_equal(data$host_pools[[1]]$susceptible[[3]], sus)
expect_equal(data$host_pools[[1]]$susceptible[[4]], sus)
expect_equal(data$host_pools[[1]]$susceptible[[5]], sus5)
expect_equal(data$host_pools[[1]]$susceptible[[6]], sus6)
data <- pops(output_frequency = "month",
time_step = "month",
treatment_dates = start_date,
infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_movements = use_movements,
movements_file = movements_file,
random_seed = 45)
expect_equal(length(data$host_pools[[1]]$infected), 12)
expect_equal(data$host_pools[[1]]$infected[[1]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(data$host_pools[[1]]$infected[[2]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(data$host_pools[[1]]$infected[[3]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
expect_equal(data$host_pools[[1]]$infected[[4]],
terra::as.matrix(terra::rast(infected_file_list), wide = TRUE))
infected_move <- matrix(0, ncol = 20, nrow = 20)
infected_move[2, 1] <- 1
expect_equal(data$host_pools[[1]]$infected[[5]], infected_move)
sus <- terra::rast(host_file_list) - terra::rast(infected_file_list)
sus <- terra::as.matrix(sus, wide = TRUE)
sus5 <- sus
sus5[1, 1] <- sus5[1, 1] - 199
sus5[2, 1] <- sus5[2, 1] + 199
sus6 <- sus5
sus6[1, 2] <- sus6[1, 2] - 50
sus6[2, 2] <- sus6[2, 2] + 50
expect_equal(data$host_pools[[1]]$susceptible[[1]], sus)
expect_equal(data$host_pools[[1]]$susceptible[[2]], sus)
expect_equal(data$host_pools[[1]]$susceptible[[3]], sus)
expect_equal(data$host_pools[[1]]$susceptible[[4]], sus)
expect_equal(data$host_pools[[1]]$susceptible[[5]], sus5)
expect_equal(data$host_pools[[1]]$susceptible[[6]], sus6)
})
test_that(
"Overpopulation dispersal works as expected with directionality to prevent dispersers from
leaving the simulated area", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-12-31"
parameter_means <- c(0, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
use_overpopulation_movements = TRUE,
overpopulation_percentage = 0.2,
leaving_percentage = 0.5,
leaving_scale_coefficient = 0.5,
natural_dir = "SE")
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_lte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
})
test_that("Deterministic dispersal works as expected", {
infected_file_list <- system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-12-31"
parameter_means <- c(2, 21, 1, 500, 0, 0, 0, 0)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
generate_stochasticity = FALSE,
establishment_stochasticity = FALSE,
movement_stochasticity = FALSE,
dispersal_stochasticity = TRUE)
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
})
test_that("Network dispersal works as expected", {
infected_file_list <-
system.file("extdata", "simple20x20", "initial_infection.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-03-31"
parameter_means <- c(2, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
network_filename <- system.file("extdata", "simple20x20", "segments.csv", package = "PoPS")
anthropogenic_kernel_type <- "network"
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
network_filename = network_filename)
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
})
test_that("uncertainty propogation works as expected", {
infected_file_list <- system.file("extdata", "simple20x20", "infected_wsd.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple20x20", "host_w_sd2.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-03-31"
parameter_means <- c(2, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
anthropogenic_kernel_type <- "cauchy"
use_initial_condition_uncertainty <- TRUE
use_host_uncertainty <- TRUE
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty)
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
infected_file_list <- system.file("extdata", "simple20x20", "infected_wsd.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
total_populations_file <- system.file("extdata", "simple20x20", "all_plants.tif",
package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-03-31"
parameter_means <- c(2, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
anthropogenic_kernel_type <- "cauchy"
use_initial_condition_uncertainty <- TRUE
use_host_uncertainty <- FALSE
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty)
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
infected_file_list <-
system.file("extdata", "simple20x20", "initial_infection.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple20x20", "host_w_sd2.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-03-31"
parameter_means <- c(2, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
anthropogenic_kernel_type <- "cauchy"
use_initial_condition_uncertainty <- FALSE
use_host_uncertainty <- TRUE
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty)
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
})
test_that("multiple_random seeds works and returns expected results", {
infected_file_list <-
system.file("extdata", "simple20x20", "initial_infection.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple20x20", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-03-31"
parameter_means <- c(5, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
anthropogenic_kernel_type <- "cauchy"
multiple_random_seeds <- TRUE
file_random_seeds <- NULL
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
multiple_random_seeds = multiple_random_seeds,
file_random_seeds = file_random_seeds)
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
file_random_seeds <- system.file("extdata", "simple2x2", "randoms.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
multiple_random_seeds = multiple_random_seeds,
file_random_seeds = file_random_seeds)
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
})
test_that("Using soils returns expected results", {
infected_file_list <-
system.file("extdata", "simple2x2", "infected.tif", package = "PoPS")
host_file_list <- system.file("extdata", "simple2x2", "host.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2009-12-31"
parameter_means <- c(5, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
use_soils <- TRUE
dispersers_to_soils_percentage <- 0.05
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
use_soils = use_soils,
dispersers_to_soils_percentage = dispersers_to_soils_percentage)
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
expect_equal(length(data$soil_reservoirs[[1]]), 20)
expect_equal(length(data$soil_reservoirs[[2]]), 20)
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
temp = TRUE,
temperature_coefficient_file = coefficient_file,
use_soils = use_soils,
dispersers_to_soils_percentage = dispersers_to_soils_percentage,
soil_starting_pest_file = infected_file_list,
start_with_soil_populations = TRUE)
test_mat <- terra::as.matrix(terra::rast(infected_file_list), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
expect_equal(length(data$soil_reservoirs[[1]]), 20)
expect_equal(length(data$soil_reservoirs[[2]]), 20)
})
test_that("Using multiple hosts works as expected", {
infected_file_list <-
c(system.file("extdata", "simple2x2", "infected_oak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "infected_tanoak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "infected_baylaurel.tif", package = "PoPS"))
host_file_list <-
c(system.file("extdata", "simple2x2", "host_oak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "host_tanoak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "host_baylaurel.tif", package = "PoPS"))
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2009-12-31"
parameter_means <- c(0, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
pest_host_table <-
system.file("extdata", "pest_host_table.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_multihost.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
temp = TRUE,
random_seed = 42,
temperature_coefficient_file = coefficient_file)
test_mat <- terra::as.matrix(terra::rast(infected_file_list[1]), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
test_mat <- terra::as.matrix(terra::rast(infected_file_list[2]), wide = TRUE)
expect_gte(data$host_pools[[2]]$infected[[1]][[1]] + data$host_pools[[2]]$infected[[1]][[1]],
test_mat[[1]])
expect_gte(data$host_pools[[2]]$infected[[1]][[2]] + data$host_pools[[2]]$infected[[1]][[2]],
test_mat[[2]])
expect_gte(data$host_pools[[2]]$infected[[1]][[3]] + data$host_pools[[2]]$infected[[1]][[3]],
test_mat[[3]])
expect_gte(data$host_pools[[2]]$infected[[1]][[4]] + data$host_pools[[2]]$infected[[1]][[4]],
test_mat[[4]])
infected_file_list <-
c(system.file("extdata", "simple2x2", "infected_oak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "infected_tanoak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "infected_baylaurel.tif", package = "PoPS"))
host_file_list <-
c(system.file("extdata", "simple2x2", "host_oak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "host_tanoak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "host_baylaurel.tif", package = "PoPS"))
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2009-12-31"
parameter_means <- c(5, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
pest_host_table <-
system.file("extdata", "pest_host_table.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_multihost.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
temp = TRUE,
random_seed = 42,
temperature_coefficient_file = coefficient_file)
test_mat <- terra::as.matrix(terra::rast(infected_file_list[1]), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
test_mat <- terra::as.matrix(terra::rast(infected_file_list[2]), wide = TRUE)
expect_gte(data$host_pools[[2]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[2]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[2]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[2]]$infected[[1]][[4]], test_mat[[4]])
infected_file_list <-
c(system.file("extdata", "simple2x2", "infected_oak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "infected_tanoak.tif", package = "PoPS"))
host_file_list <-
c(system.file("extdata", "simple2x2", "host_oak.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "host_tanoak.tif", package = "PoPS"))
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2009-12-31"
parameter_means <- c(5, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
coefficient_file <-
system.file("extdata", "simple2x2", "temperature_coefficient.tif", package = "PoPS")
pest_host_table <-
system.file("extdata", "pest_host_table_2host.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_2host.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
temp = TRUE,
random_seed = 42,
temperature_coefficient_file = coefficient_file)
test_mat <- terra::as.matrix(terra::rast(infected_file_list[1]), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
test_mat <- terra::as.matrix(terra::rast(infected_file_list[2]), wide = TRUE)
expect_gte(data$host_pools[[2]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[2]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[2]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[2]]$infected[[1]][[4]], test_mat[[4]])
})
test_that("Using multiple hosts with uncertainty works as expected", {
infected_file_list <-
c(system.file("extdata", "simple2x2", "infected_oak_wsd.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "infected_tanoak_wsd.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "infected_baylaurel_wsd.tif", package = "PoPS"))
host_file_list <-
c(system.file("extdata", "simple2x2", "host_oak_wsd.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "host_tanoak_wsd.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "host_baylaurel_wsd.tif", package = "PoPS"))
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2009-12-31"
parameter_means <- c(0, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_multihost.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
random_seed = 42,
start_date = start_date,
end_date = end_date,
use_host_uncertainty = TRUE)
test_mat <- terra::as.matrix(terra::rast(infected_file_list[1]), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
test_mat <- terra::as.matrix(terra::rast(infected_file_list[2]), wide = TRUE)
expect_gte(data$host_pools[[2]]$infected[[1]][[1]] + data$host_pools[[2]]$infected[[1]][[1]],
test_mat[[1]])
expect_gte(data$host_pools[[2]]$infected[[1]][[2]] + data$host_pools[[2]]$infected[[1]][[2]],
test_mat[[2]])
expect_gte(data$host_pools[[2]]$infected[[1]][[3]] + data$host_pools[[2]]$infected[[1]][[3]],
test_mat[[3]])
expect_gte(data$host_pools[[2]]$infected[[1]][[4]] + data$host_pools[[2]]$infected[[1]][[4]],
test_mat[[4]])
infected_file_list <-
c(system.file("extdata", "simple2x2", "infected_oak_wsd.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "infected_tanoak_wsd.tif", package = "PoPS"))
host_file_list <-
c(system.file("extdata", "simple2x2", "host_oak_wsd.tif", package = "PoPS"),
system.file("extdata", "simple2x2", "host_tanoak_wsd.tif", package = "PoPS"))
total_populations_file <-
system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2009-12-31"
parameter_means <- c(5, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
pest_host_table <-
system.file("extdata", "pest_host_table_2host.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_2host.csv", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
random_seed = 42,
use_host_uncertainty = TRUE)
test_mat <- terra::as.matrix(terra::rast(infected_file_list[1]), wide = TRUE)
expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[1]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
test_mat <- terra::as.matrix(terra::rast(infected_file_list[2]), wide = TRUE)
expect_gte(data$host_pools[[2]]$infected[[1]][[1]], test_mat[[1]])
expect_gte(data$host_pools[[2]]$infected[[1]][[2]], test_mat[[2]])
expect_gte(data$host_pools[[2]]$infected[[1]][[3]], test_mat[[3]])
expect_gte(data$host_pools[[2]]$infected[[1]][[4]], test_mat[[4]])
})
test_that("county level infection works as expected", {
infected_file_list <-
system.file("extdata", "simple20x20", "county_infected.gpkg", package = "PoPS")
host_file_list <- system.file("extdata", "simple20x20", "host_w_sd2.tif", package = "PoPS")
total_populations_file <-
system.file("extdata", "simple20x20", "all_plants.tif", package = "PoPS")
start_date <- "2008-01-01"
end_date <- "2008-03-31"
parameter_means <- c(0, 21, 1, 500, 0, 0, 100, 1000)
parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
anthropogenic_kernel_type <- "cauchy"
use_initial_condition_uncertainty <- FALSE
use_host_uncertainty <- FALSE
pest_host_table <-
system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
competency_table <- system.file("extdata", "competency_table_singlehost.csv", package = "PoPS")
county_level_infection_data <- TRUE
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty,
county_level_infection_data = county_level_infection_data)
test_infected <- terra::vect(infected_file_list[[1]])
expect_equal(data$number_infected, sum(test_infected$infected_mean))
parameter_means <- c(2, 21, 1, 500, 0, 0, 100, 1000)
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty,
county_level_infection_data = county_level_infection_data)
test_infected <- terra::vect(infected_file_list[[1]])
expect_gte(data$number_infected, sum(test_infected$infected_mean))
use_initial_condition_uncertainty <- TRUE
use_host_uncertainty <- TRUE
parameter_means <- c(0, 21, 1, 500, 0, 0, 100, 1000)
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty,
county_level_infection_data = county_level_infection_data)
test_infected <- terra::vect(infected_file_list[[1]])
expect_gte(data$number_infected, 0)
use_initial_condition_uncertainty <- TRUE
use_host_uncertainty <- TRUE
parameter_means <- c(2, 21, 1, 500, 0, 0, 100, 1000)
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty,
county_level_infection_data = county_level_infection_data)
test_infected <- terra::vect(infected_file_list[[1]])
expect_gte(data$number_infected, 0)
use_initial_condition_uncertainty <- FALSE
use_host_uncertainty <- FALSE
parameter_means <- c(2, 21, 1, 500, 0, 0, 100, 1000)
exposed_file_list <-
system.file("extdata", "simple20x20", "county_infected.gpkg", package = "PoPS")
start_exposed <- TRUE
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty,
county_level_infection_data = county_level_infection_data,
model_type = "SEI",
exposed_file_list = exposed_file_list,
latency_period = 2,
start_exposed = start_exposed)
test_infected <- terra::vect(infected_file_list[[1]])
expect_gte(data$number_infected, 0)
expect_gte(sum(data$host_pools[[1]]$total_exposed[[1]]), 0)
parameter_means <- c(0, 21, 1, 500, 0, 0, 100, 1000)
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty,
county_level_infection_data = county_level_infection_data,
model_type = "SEI",
exposed_file_list = exposed_file_list,
latency_period = 5,
start_exposed = start_exposed)
test_infected <- terra::vect(infected_file_list[[1]])
expect_equal(data$number_infected, sum(test_infected$infected_mean))
expect_equal(sum(data$host_pools[[1]]$total_exposed[[1]]), sum(test_infected$infected_mean))
host_file_list <- system.file("extdata", "simple20x20", "host_fullzeropoly.tif", package = "PoPS")
data <-
pops(infected_file_list = infected_file_list,
host_file_list = host_file_list,
total_populations_file = total_populations_file,
parameter_means = parameter_means,
parameter_cov_matrix = parameter_cov_matrix,
pest_host_table = pest_host_table,
competency_table = competency_table,
start_date = start_date,
end_date = end_date,
anthropogenic_kernel_type = anthropogenic_kernel_type,
use_initial_condition_uncertainty = use_initial_condition_uncertainty,
use_host_uncertainty = use_host_uncertainty,
county_level_infection_data = county_level_infection_data,
model_type = "SEI",
exposed_file_list = exposed_file_list,
latency_period = 5,
start_exposed = start_exposed)
test_infected <- terra::vect(infected_file_list[[1]])
expect_equal(data$number_infected, sum(test_infected$infected_mean))
expect_equal(sum(data$host_pools[[1]]$total_exposed[[1]]), sum(test_infected$infected_mean))
})
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