tests/testthat/test-ts-ancestors-descendants.R

In bodkan/slendr: A Simulation Framework for Spatiotemporal Population Genetics

skip_if(!is_slendr_env_present())

pop <- population("POP", time = 1, N = 100)

model <- compile_model(populations = pop, generation_time = 1, simulation_length = 200)

ts_file <- normalizePath(tempfile(fileext = ".trees"), winslash = "/", mustWork = FALSE)
slim(model, sequence_length = 1000000, recombination_rate = 0, random_seed = 42) %>% ts_write(ts_file)

ts <- ts_read(ts_file, model) %>% ts_recapitate(Ne = 100, recombination_rate = 0, random_seed = 42) %>%
  ts_simplify(simplify_to = paste0("POP_", seq(1, 10)))

# library(ggtree)
# tree <- ts_phylo(ts, 0)
# labels <- ts_nodes(tree) %>% dplyr::select(node = phylo_id, tskit_id = node_id)
# ggtree(tree, branch.length="none") %<+% labels +
#   geom_label(aes(label = tskit_id))
# ts_draw(ts_tree(ts, 0))

test_that("any node ID or individual given to ts_ancestors must be present", {
  expect_error(ts_ancestors(ts, "qweasdzxc"), "The given individual")
  expect_error(ts_ancestors(ts, -123), "The given node")
})

test_that("reconstructed ancestral relationships match what is seen in a tree", {
  expect_true(all(ts_ancestors(ts, 0, complete = TRUE)$parent_id == c(22, 32, 36, 37)))
  expect_true(all(ts_ancestors(ts, 1, complete = TRUE)$parent_id == c(27, 31, 34, 35)))
  expect_error(ts_ancestors(ts, 38, complete = TRUE), "The given node")
  expect_true(all(ts_ancestors(ts, 37, complete = FALSE)$parent_id == 38))
  expect_true(all(ts_ancestors(ts, 20, complete = TRUE)$parent_id == c(25, 29, 32, 36, 37)))

  expect_true(all(ts_ancestors(ts, 0, complete = FALSE)$parent_id == c(22, 32, 36, 37, 38)))
  expect_true(all(ts_ancestors(ts, 15, complete = FALSE)$parent_id == c(22, 32, 36, 37, 38)))
  expect_true(all(ts_ancestors(ts, 37, complete = FALSE)$parent_id == 38))
  expect_true(all(ts_ancestors(ts, 34, complete = FALSE)$parent_id == c(35, 38)))
})

test_that("any node ID or individual given to ts_descendants must be present", {
  expect_error(ts_descendants(ts, "qweasdzxc"), "The given individual")
  expect_error(ts_descendants(ts, -123), "The given node")
})

test_that("reconstructed descendant relationships match what is seen in a tree", {
  root_id <- ts_nodes(ts) %>% .[.$time == min(.$time), ] %>% .$node_id

  expect_true(all(sort(ts_descendants(ts, 29, complete = TRUE)$child_id) == c(3, 4, 5, 13, 17, 19, 20, 25, 26, 28)))
  expect_true(all(sort(ts_descendants(ts, 26, complete = TRUE)$child_id) == c(4, 5)))
  expect_true(all(sort(ts_descendants(ts, 30, complete = TRUE)$child_id) == c(7, 9, 14, 21)))

  expect_true(all(sort(ts_descendants(ts, root_id, complete = FALSE)$child_id) == sort(setdiff(ts_nodes(ts)$node_id, root_id))))
  expect_true(all(sort(ts_descendants(ts, 32, complete = FALSE)$child_id) == sort(c(0, 15, 3, 17, 19, 4, 5, 13, 22, 20, 25, 29, 26, 28))))
  expect_true(all(sort(ts_descendants(ts, 26, complete = FALSE)$child_id) == c(4, 5)))
  expect_true(all(sort(ts_descendants(ts, 30, complete = FALSE)$child_id) == c(7, 9, 14, 21)))
})