tests/testthat/test-07-dynamic_stability_drake_plan.R

In ha0ye/portalDS: Compute Dynamic Stability for Rodents at Portal

context("Check functions to build plans for dynamic stability workflow")

options(drake_make_menu = FALSE, 
        drake_clean_recovery_msg = FALSE)

test_that("check full dynamic stability plan using block_3sp example data", {
  skip_on_covr()
  # setup
  data("block_3sp", package = "rEDM")
  block <- setNames(block_3sp[, c("time", "x_t", "y_t", "z_t")],
                    c("time", "x", "y", "z"))
  targets <- c(
    "simplex_results",
    "ccm_results", "ccm_links",
    "smap_coeffs", "smap_matrices",
    "eigen_decomp", "eigenvalues", "eigenvectors", 
    "svd_decomp", "volume_contraction", "total_variance"
  )
  
  # check plan
  expect_error(my_plan <- build_dynamic_stability_plan(id_var = "time", 
                                                       E_list = 3:5,
                                                       surrogate_method = "random_shuffle",
                                                       num_surr = 4,
                                                       lib_sizes = seq(10, 100, 10),
                                                       num_samples = 10), 
               NA)
  expect_is(my_plan, c("drake_plan", "tbl_df"))
  expect_equal(vapply(targets, function(patt) {
    grep(patt, my_plan$target)
  }, 0),
  seq_along(targets),
  check.names = FALSE
  )
  expect_known_hash(as.character(my_plan$command), "d23bb11bbf")
})

test_that("running full dynamic stability plan using block_3sp example data", {
  data("block_3sp", package = "rEDM")
  block <- setNames(block_3sp[, c("time", "x_t", "y_t", "z_t")],
                    c("time", "x", "y", "z")
  )
  targets <- c(
    "simplex_results",
    "ccm_results", "ccm_links",
    "smap_coeffs", "smap_matrices",
    "eigen_decomp", "eigenvalues", "eigenvectors"
  )
  
  # check plan
  my_plan <- build_dynamic_stability_plan(id_var = "time", 
                                          E_list = 3:5,
                                          surrogate_method = "random_shuffle",
                                          num_surr = 4,
                                          lib_sizes = seq(10, 100, 10),
                                          num_samples = 10)
  
  # run plan
  future::plan(future.callr::callr)
  drake::clean(destroy = TRUE)
  expect_error(drake::make(my_plan, seed = 42), NA)
  
  # inspect targets and check seed
  expect_error(drake::loadd(), NA)
  expect_true(all(targets %in% ls()))
  expect_equal(drake::diagnose(simplex_results)$seed, 616382247)
  
  # check targets
  simplex_results$simplex_out <- lapply(simplex_results$simplex_out, round, 4)
  expect_known_hash(simplex_results, "b00009fc2d")
  expect_known_hash(
    dplyr::mutate_at(ccm_results, c("rho", "mae", "rmse"), round, 4),
    "40a8eb1668"
  )
  expect_known_hash(ccm_links, "70474772ed")
  expect_known_hash(lapply(smap_coeffs, round, 4), "c86a8cb782")
  expect_known_hash(lapply(smap_matrices, round, 4), "1eeb9778c0")
  expect_known_hash(lapply(eigenvalues, round, 4), "1988c00e57")
  expect_known_hash(which(is.na(eigenvectors)), "bf89101447")
  expect_error(ev <- eigenvectors[!is.na(eigenvectors)], NA)
  expect_known_hash(
    lapply(ev, function(x) {
      s <- ifelse(Re(x[1, ]) == 0, 1, sign(Re(x[1, ])))
      s <- matrix(s, nrow = nrow(x), ncol = ncol(x), byrow = TRUE)
      round(s * x, 4)
    }),
    "9ec8d8efaf"
  )
})