Nothing
test_that("occupancy", {
library(raster)
# Ring Island example region
coordinates <- data.frame(x = rep(seq(-178.02, -178.06, -0.01), 5),
y = rep(seq(19.02, 19.06, 0.01), each = 5))
template_raster <- Region$new(coordinates = coordinates)$region_raster # full extent
sealevel_raster <- template_raster
template_raster[][c(7:9, 12:14, 17:19)] <- NA # make Ring Island
sealevel_raster[][c(7:9, 12:14, 17:18)] <- NA
raster_stack <- raster::stack(x = append(replicate(9, template_raster), sealevel_raster))
region <- PaleoRegion$new(template_raster = raster_stack)
# Model template
model_template <- PaleoPopModel$new(
region = region,
time_steps = 10,
years_per_step = 12, # years per generational time-step
standard_deviation = 0.1,
growth_rate_max = 0.6,
harvest = T,
harvest_max = 0.1,
harvest_z = 2,
harvest_g = 0.4,
harvest_max_n = 50,
human_density = array(rep(10), c(17,10)),
populations = region$region_cells,
initial_abundance = seq(9000, 0, -1000),
transition_rate = 1.0,
carrying_capacity = rep(1000, 17),
dispersal = (!diag(nrow = 17, ncol = 17))*0.05,
density_dependence = "logistic",
dispersal_target_k = 10,
occupancy_threshold = 1,
abundance_threshold = 10,
results_selection = c("abundance")
)
# Simulations
results <- paleopop_simulator(model_template)
# Results
results_model <- PaleoPopResults$new(results = results, region = region, time_steps = 10)
expect_true(all(!is.na(results_model$occupancy)))
expect_equal(results_model$occupancy[1:4,6:10], array(rep(0), c(4,5)))
})
test_that("extirpation", {
library(raster)
set.seed(567)
# Ring Island example region
coordinates <- data.frame(x = rep(seq(-178.02, -178.06, -0.01), 5),
y = rep(seq(19.02, 19.06, 0.01), each = 5))
template_raster <- Region$new(coordinates = coordinates)$region_raster # full extent
sealevel_raster <- template_raster
template_raster[][c(7:9, 12:14, 17:19)] <- NA # make Ring Island
sealevel_raster[][c(7:9, 12:14, 17:18)] <- NA
raster_stack <- raster::stack(x = append(replicate(9, template_raster), sealevel_raster))
region <- PaleoRegion$new(template_raster = raster_stack)
# Model template
model_template <- PaleoPopModel$new(
region = region,
time_steps = 10,
years_per_step = 12, # years per generational time-step
standard_deviation = 0.1,
growth_rate_max = 0.6,
harvest = T,
harvest_max = 0.1,
harvest_z = 2,
harvest_g = 0.4,
harvest_max_n = 50,
human_density = array(rep(10), c(17,10)),
populations = region$region_cells,
initial_abundance = seq(9000, 0, -1000),
transition_rate = 1.0,
carrying_capacity = rep(1000, 17),
dispersal = (!diag(nrow = 17, ncol = 17))*0.05,
density_dependence = "logistic",
dispersal_target_k = 10,
occupancy_threshold = 1,
abundance_threshold = 10,
results_selection = c("abundance")
)
# Simulations
results <- paleopop_simulator(model_template)
# Results
results_model <- PaleoPopResults$new(results = results, region = region, time_steps = 10)
expect_true(all(results_model$extirpation>=1))
expect_true(all(results_model$extirpation<7))
})
test_that("ema", {
inputs <- list(time_steps = 9, populations = 7, initial_abundance = seq(1000, 7000, 1000),
transition_rate = 1.0, sd = 0.005, carrying_capacity = rep(3000, 7),
harvest = T, harvest_max = 0.2, harvest_z = 1.5, harvest_g = 0.4, harvest_max_n = 50,
human_density = array(rep(10), c(7,9)),
results_selection = c("abundance"))
results <- paleopop_simulator(inputs)
results_model <- PaleoPopResults$new(results = results, time_steps = 9)
expect_true(all(results_model$abundance>=results_model$ema))
})
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