inst/tinytest/test-entity_tools.R

In epiworldR: Fast Agent-Based Epi Models

entities <- data.frame(
  name = c("Pop 1", "Pop 2", "Pop 3"),
  size = rep(3e3, 3)
)

# Row-stochastic matrix (rowsums 1)
cmatrix <- c(
  c(0.9, 0.05, 0.05),
  c(0.1, 0.8, 0.1),
  c(0.1, 0.2, 0.7)
) |> matrix(byrow = TRUE, nrow = 3)

measles_model <- ModelSIRMixing(
  name              = "Flu",
  n                 = 9e3,
  prevalence        = 1 / 9e3,
  contact_rate      = 20,
  transmission_rate = 0.1,
  recovery_rate     = 1 / 7,
  contact_matrix    = cmatrix
)

# Should be a data.frame
expect_error({
  measles_model |>
    add_entities_from_dataframe(
      entities = character(),
      col_name = "name",
      col_number = "size",
      as_proportion = TRUE
    )
}, "data.frame")

# Failed columns
expect_error({
  measles_model |>
    add_entities_from_dataframe(
      entities = cbind(entities, txt = "text"),
      col_name = "name",
      col_number = "txt",
      as_proportion = TRUE
    )
}, "integer")

measles_model |>
  add_entities_from_dataframe(
    entities = entities,
    col_name = "name",
    col_number = "size",
    as_proportion = FALSE
  ) |>
  verbose_off()

# Running the model to get the entities
run(measles_model, ndays=10, seed=1)

entities_obj <- get_entities(measles_model)

# Getting the entity distribution
esizes <- sapply(entities_obj, \(e) nrow(entity_get_agents(e)))
expect_true(all(esizes == 3000))

# Should be unique distributions
lapply(entities_obj, \(e) entity_get_agents(e)[,1]) |>
  unlist(recursive = FALSE) |>
  unique() |>
  length() |>
  expect_equal(9000)

# Checking names
enames <- entities_obj |> sapply(get_entity_name)
expect_equal(enames, entities$name)