New tests for DiseaseModel

NEWS.md

@@ -1,3 +1,22 @@
+# v 1.0.0 (27 Sep 2024)
+
+## Enhancements
+
+- A vignette has been added using `epizootic` to model house finch conjunctivitis.
+- Examples have been added to two of the functions.
+- `aspatial_siri` now runs much faster.
+- `check_aspatial_siri_inputs` now checks inputs much more thoroughly.
+- There are now unit tests to ensure that no dispersers are created or destroyed.
+- New tests have been added for `DiseaseModel`.
+
+## Bug fixes
+- Broken links to other packages have been fixed.
+- `siri_model` functions can now handle one active population.
+- `disease_simulator` no longer breaks when demographic rates are given as lists and masks are given as vectors.
+- Non-breeding season length is now calculated correctly.
+- `disease_dispersal` can now handle the case when dispersal does not change over time.
+- `disease_dispersal` was not working properly when there was density dependent dispersal and matrix-formatted dispersal data. This is now fixed.
+
 # v 0.2.1 (2 Apr 2024)
 
 - Important bug fix: the number of occupied indices now updates more frequently within the 

tests/testthat/test-DiseaseModel.R

@@ -1,9 +1,87 @@
-test_that("active get and set", {
-  region = Region$new(coordinates = array(c(1:4, 4:1), c(7, 2)))
-  disease_model <- DiseaseModel$new(time_steps = 10)
-  expect_null(disease_model$populations)
-  disease_model$initial_abundance <- seq(10, 60, by = 10)
-  expect_equal(disease_model$populations, 6)
-  disease_model$region <- region
-  expect_equal(disease_model$populations, 7)
+test_that("DiseaseModel initializes correctly", {
+  model <- DiseaseModel$new()
+  expect_true(inherits(model, "DiseaseModel"))
+  expect_true(inherits(model, "SimulationModel"))
+  expect_equal(model$seasons, 1)
+  expect_equal(model$results_breakdown, "segments")
+  expect_equal(model$stages, 1)
+  expect_equal(model$compartments, 1)
 })
+
+test_that("DiseaseModel sets and gets attributes correctly", {
+  model <- DiseaseModel$new()
+  model$populations <- 100
+  expect_equal(model$populations, 100)
+
+  model$initial_abundance <- matrix(1:100, nrow = 10)
+  expect_equal(model$initial_abundance, matrix(1:100, nrow = 10))
+
+  model$demographic_stochasticity <- FALSE
+  expect_false(model$demographic_stochasticity)
+
+  model$standard_deviation <- 0.1
+  expect_equal(model$standard_deviation, 0.1)
+
+  model$correlation <- list(type = "spatial", value = 0.5)
+  expect_equal(model$correlation, list(type = "spatial", value = 0.5))
+
+  model$stages <- 3
+  expect_equal(model$stages, 3)
+
+  model$compartments <- 2
+  expect_equal(model$compartments, 2)
+
+  model$results_breakdown <- "pooled"
+  expect_equal(model$results_breakdown, "pooled")
+
+  model$carrying_capacity <- matrix(1:100, nrow = 10)
+  expect_equal(model$carrying_capacity, matrix(1:100, nrow = 10))
+
+  model$density_dependence <- "logistic"
+  expect_equal(model$density_dependence, "logistic")
+
+  model$growth_rate_max <- 1.2
+  expect_equal(model$growth_rate_max, 1.2)
+
+  model$fecundity <- c(0.5, 0.6, 0.7)
+  expect_equal(model$fecundity, c(0.5, 0.6, 0.7))
+
+  model$density_stages <- c(1, 0.5, 0.2)
+  expect_equal(model$density_stages, c(1, 0.5, 0.2))
+
+  model$dispersal_source_n_k <- list(cutoff = 0.5, threshold = 0.2)
+  expect_equal(model$dispersal_source_n_k, list(cutoff = 0.5, threshold = 0.2))
+
+  model$dispersal_target_k <- 0.8
+  expect_equal(model$dispersal_target_k, 0.8)
+
+  model$dispersal_target_n <- list(threshold = 0.3, cutoff = 0.1)
+  expect_equal(model$dispersal_target_n, list(threshold = 0.3, cutoff = 0.1))
+
+  model$dispersal_target_n_k <- list(threshold = 0.4, cutoff = 0.2)
+  expect_equal(model$dispersal_target_n_k, list(threshold = 0.4, cutoff = 0.2))
+
+  model$abundance_threshold <- 10
+  expect_equal(model$abundance_threshold, 10)
+
+  model$seasons <- 4
+  expect_equal(model$seasons, 4)
+
+  model$results_selection <- c("abundance", "occupancy")
+  expect_equal(model$results_selection, c("abundance", "occupancy"))
+})
+
+test_that("DiseaseModel handles attribute aliases correctly", {
+  model <- DiseaseModel$new(attribute_aliases = list(dispersal_data = "dispersal"))
+  model$set_attributes(dispersal_data = list(strategy = "random", rate = 0.1))
+  expect_equal(model$dispersal, list(strategy = "random", rate = 0.1))
+})
+
+# Test set_sample_attributes method
+test_that("DiseaseModel set_sample_attributes works correctly", {
+  model <- DiseaseModel$new()
+
+  model$set_sample_attributes(params = list(populations = 100, seasons = 2))
+  expect_equal(model$populations, 100)
+  expect_equal(model$seasons, 2)
+})