tests/testthat/test-run_robustness.R

In xieshu95/robustness: Test the Robustness of DAISIE to Geodynamics

context("run_robustness")

test_that("run_robustness gives error when save_output = TRUE as it
          only runs when folder structure is in place, an therefore
          test not run unless required", {
  if (1 == 2) {
    expect_error(run_robustness(
      param_space_name = "oceanic_ontogeny",
      param_set = 2,
      replicates = 2,
      save_output = TRUE))
  }
})

test_that("run_robustness output is correct when save_output = FALSE and
          it passes sim_constraints", {
  skip("temp skip to pass on travis")
  if (Sys.getenv("TRAVIS") != "" || Sys.getenv("APPVEYOR") != "") {
    errors <- run_robustness(
      param_space_name = "oceanic_ontogeny",
      param_set = 2,
      replicates = 2,
      save_output = FALSE)
    expect_length(errors, 12)
    expect_equal(errors$spec_error, list(nltt = c(14.60200218911491,
                                                  21.13234531729715),
                                         num_spec_error = c(6, 18),
                                         num_col_error = c(1, 2)))
    expect_equal(errors$endemic_error, list(nltt = c(12.19399299074907,
                                                     20.13397293941591)))
    expect_equal(errors$nonendemic_error, list(nltt = c(4.105857769709307,
                                                        9.843170592071163)))
    expect_equal(errors$spec_baseline_error, list(nltt = c(5.36978441221806,
                                                           20.12382130303635),
                                                  num_spec_error = c(2, 6),
                                                  num_col_error = c(8, 3)))
    expect_equal(errors$endemic_baseline_error,
                 list(nltt = c(2.479620682470331,
                               13.987840695971366)))
    expect_equal(errors$nonendemic_baseline_error,
                 list(nltt = c(5.065599417345626,
                               8.150210879922227)))
    expect_equal(errors$error_metrics,
                 list(num_spec_mean_diff = 8,
                      num_spec_sd_diff = 5.65685424949238,
                      num_col_mean_diff = 4,
                      num_col_sd_diff = 2.82842712474619,
                      spec_nltt_mean_diff = 5.120370895578827,
                      endemic_nltt_mean_diff = 7.930252275861640,
                      nonendemic_nltt_mean_diff = 0.3666090322563083,
                      spec_nltt_sd_diff = 5.81502962596146,
                      endemic_nltt_sd_diff = 2.523126746745787,
                      nonendemic_nltt_sd_diff = 1.875743119966929,
                      spec_nltt_ks_dist = 0.1979939251300001,
                      endemic_nltt_ks_dist = 0.226619434409659,
                      nonendemic_nltt_ks_dist = 0.0889512124304479))
    expect_length(errors$geodynamic_sim, 2)
    expect_length(errors$geodynamic_sim[[1]][[1]], 12)
    expect_equal(errors$geodynamic_sim[[1]][[1]][[1]]$island_age, 2.55)
    expect_equal(errors$geodynamic_sim[[1]][[1]][[1]]$not_present, 989)
    expect_equal(nrow(errors$geodynamic_sim[[1]][[1]][[1]]$stt_all), 137)
    expect_equal(ncol(errors$geodynamic_sim[[1]][[1]][[1]]$stt_all), 5)
    expect_equal(errors$geodynamic_sim[[1]][[1]][[2]]$branching_times,
                 c(2.55, 0.16583840374981))
    expect_equal(errors$geodynamic_sim[[1]][[1]][[2]]$stac, 4)
    expect_equal(errors$geodynamic_sim[[1]][[1]][[2]]$missing_species, 0)
    expect_length(errors$geodynamic_sim[[2]][[1]], 18)
    expect_equal(errors$geodynamic_sim[[2]][[1]][[1]]$island_age, 2.55)
    expect_equal(errors$geodynamic_sim[[2]][[1]][[1]]$not_present, 983)
    expect_equal(nrow(errors$geodynamic_sim[[2]][[1]][[1]]$stt_all), 198)
    expect_equal(ncol(errors$geodynamic_sim[[2]][[1]][[1]]$stt_all), 5)
    expect_equal(errors$geodynamic_sim[[2]][[1]][[2]]$branching_times,
                 c(2.55, 0.54060034565628, 0.33472010537022,
                   0.32340948469476, 0.27463199550981, 0.16866730824241,
                   0.11526339338235))
    expect_equal(errors$geodynamic_sim[[2]][[1]][[2]]$stac, 2)
    expect_equal(errors$geodynamic_sim[[2]][[1]][[2]]$missing_species, 0)
    expect_equal(errors$geodynamic_ml,
                 list(data.frame("lambda_c" = 0.9516893216529831,
                                 "mu" = 0.4371724756929532,
                                 "K" = 26.45933105611771,
                                 "gamma" = 0.005832693735317008,
                                 "lambda_a" = 1.91311658602524,
                                 "loglik" = -93.6464134227662,
                                 "df" = 5,
                                 "conv" = 0),
                      data.frame("lambda_c" = 1.17346081209476,
                                 "mu" = 0.9780652536369839,
                                 "K" = 1.798109468901113,
                                 "gamma" = 0.01258190594811776,
                                 "lambda_a" = 0.8917175650839453,
                                 "loglik" = -133.3346436904723,
                                 "df" = 5,
                                 "conv" = 0)))
  } else {
    skip("Run only on TRAVIS or AppVeyor")
  }
})

test_that("run_robustness output is correct when save_output = FALSE and
          it fails sim_constraints", {
  if (Sys.getenv("TRAVIS") != "" || Sys.getenv("APPVEYOR") != "") {
    errors <- run_robustness(
      param_space_name = "oceanic_ontogeny",
      param_set = 1,
      replicates = 2,
      save_output = FALSE)
    expect_length(errors, 1)
    expect_length(errors$geodynamic_sim, 2)
    expect_length(errors$geodynamic_sim[[1]][[1]], 11)
    expect_equal(errors$geodynamic_sim[[1]][[1]][[1]]$island_age, 2.55)
    expect_equal(errors$geodynamic_sim[[1]][[1]][[1]]$not_present, 990)
    expect_equal(nrow(errors$geodynamic_sim[[1]][[1]][[1]]$stt_all), 92)
    expect_equal(ncol(errors$geodynamic_sim[[1]][[1]][[1]]$stt_all), 5)
    expect_equal(errors$geodynamic_sim[[1]][[1]][[2]]$branching_times,
                 c(2.55, 0.16583840374981))
    expect_equal(errors$geodynamic_sim[[1]][[1]][[2]]$stac, 4)
    expect_equal(errors$geodynamic_sim[[1]][[1]][[2]]$missing_species, 0)
    expect_length(errors$geodynamic_sim[[2]][[1]], 19)
    expect_equal(errors$geodynamic_sim[[2]][[1]][[1]]$island_age, 2.55)
    expect_equal(errors$geodynamic_sim[[2]][[1]][[1]]$not_present, 982)
    expect_equal(nrow(errors$geodynamic_sim[[2]][[1]][[1]]$stt_all), 132)
    expect_equal(ncol(errors$geodynamic_sim[[2]][[1]][[1]]$stt_all), 5)
    expect_equal(errors$geodynamic_sim[[2]][[1]][[2]]$branching_times,
                 c(2.55, 1.29032111838460, 0.80903212943811, 0.31633454531757))
    expect_equal(errors$geodynamic_sim[[2]][[1]][[2]]$stac, 2)
    expect_equal(errors$geodynamic_sim[[2]][[1]][[2]]$missing_species, 0)
  } else {
    skip("Run only on TRAVIS or AppVeyor")
  }
})

test_that("run_robustness output is correct when save_output = FALSE and
          it fails ml_constraints", {
  skip("cannot find parameter set that fails ml_constraints")
  if (Sys.getenv("TRAVIS") != "" || Sys.getenv("APPVEYOR") != "") {
    error <- run_robustness(
      param_space_name = "oceanic_ontogeny",
      param_set = 1,
      replicates = 2)
    expect_length(errors, 4)
    expect_length(errors$geodynamic_sim, 2)
    expect_length(errors$geodynamic_sim[[1]][[1]], 12)
    expect_equal(errors$geodynamic_sim[[1]][[1]][[1]]$island_age, 2.55)
    expect_equal(errors$geodynamic_sim[[1]][[1]][[1]]$not_present, 989)
    expect_equal(nrow(errors$geodynamic_sim[[1]][[1]][[1]]$stt_all), 92)
    expect_equal(ncol(errors$geodynamic_sim[[1]][[1]][[1]]$stt_all), 5)
    expect_equal(errors$geodynamic_sim[[1]][[1]][[2]]$branching_times,
                 c(2.55, 0.16583840374981))
    expect_equal(errors$geodynamic_sim[[1]][[1]][[2]]$stac, 4)
    expect_equal(errors$geodynamic_sim[[1]][[1]][[2]]$missing_species, 0)
    expect_length(errors$geodynamic_sim[[2]][[1]], 19)
    expect_equal(errors$geodynamic_sim[[2]][[1]][[1]]$island_age, 2.55)
    expect_equal(errors$geodynamic_sim[[2]][[1]][[1]]$not_present, 982)
    expect_equal(nrow(errors$geodynamic_sim[[2]][[1]][[1]]$stt_all), 132)
    expect_equal(ncol(errors$geodynamic_sim[[2]][[1]][[1]]$stt_all), 5)
    expect_equal(errors$geodynamic_sim[[2]][[1]][[2]]$branching_times,
                 c(2.55, 1.29032111838460, 0.80903212943811, 0.31633454531757))
    expect_equal(errors$geodynamic_sim[[2]][[1]][[2]]$stac, 2)
    expect_equal(errors$geodynamic_sim[[2]][[1]][[2]]$missing_species, 0)
    expect_equal(error$geodynamic_ml,
                 list(data.frame("lambda_c" = 0.9516893216529831,
                                 "mu" = 0.4371724756929532,
                                 "K" = 26.45933105611771,
                                 "gamma" = 0.005832693735317008,
                                 "lambda_a" = 1.91311658602524,
                                 "loglik" = -93.6464134227662,
                                 "df" = 5,
                                 "conv" = 0),
                      data.frame("lambda_c" = 1.17346081209476,
                                 "mu" = 0.9780652536369839,
                                 "K" = 1.798109468901113,
                                 "gamma" = 0.01258190594811776,
                                 "lambda_a" = 0.8917175650839453,
                                 "loglik" = -133.3346436904723,
                                 "df" = 5,
                                 "conv" = 0)))
    expect_length(oceanic_sim, 2)
    expect_length(oceanic_sim[[1]][[1]], 13)
    expect_equal(oceanic_sim[[1]][[1]][[1]]$island_age, 2.55)
    expect_equal(oceanic_sim[[1]][[1]][[1]]$not_present, 988)
    expect_equal(nrow(oceanic_sim[[1]][[1]][[1]]$stt_all), 35)
    expect_equal(ncol(oceanic_sim[[1]][[1]][[1]]$stt_all), 5)
    expect_equal(oceanic_sim[[1]][[1]][[2]]$branching_times,
                 c(2.55, 2.15575062694003, 1.54615286277701))
    expect_equal(oceanic_sim[[1]][[1]][[2]]$stac, 2)
    expect_equal(oceanic_sim[[1]][[1]][[2]]$missing_species, 0)
    expect_length(oceanic_sim[[2]][[1]], 21)
    expect_equal(oceanic_sim[[2]][[1]][[1]]$island_age, 2.55)
    expect_equal(oceanic_sim[[2]][[1]][[1]]$not_present, 980)
    expect_equal(nrow(oceanic_sim[[2]][[1]][[1]]$stt_all), 84)
    expect_equal(ncol(oceanic_sim[[2]][[1]][[1]]$stt_all), 5)
    expect_equal(oceanic_sim[[2]][[1]][[2]]$branching_times,
                 c(2.55, 0.0134786754538898))
    expect_equal(oceanic_sim[[2]][[1]][[2]]$stac, 4)
    expect_equal(oceanic_sim[[2]][[1]][[2]]$missing_species, 0)
    expect_equal(error$oceanic_ml,
                 list(data.frame("lambda_c" = 0.9516893216529831,
                                 "mu" = 0.4371724756929532,
                                 "K" = 26.45933105611771,
                                 "gamma" = 0.005832693735317008,
                                 "lambda_a" = 1.91311658602524,
                                 "loglik" = -93.6464134227662,
                                 "df" = 5,
                                 "conv" = 0),
                      data.frame("lambda_c" = 1.17346081209476,
                                 "mu" = 0.9780652536369839,
                                 "K" = 1.798109468901113,
                                 "gamma" = 0.01258190594811776,
                                 "lambda_a" = 0.8917175650839453,
                                 "loglik" = -133.3346436904723,
                                 "df" = 5,
                                 "conv" = 0)))
  } else {
    skip("Run only on TRAVIS or AppVeyor")
  }
})

test_that("abuse param_set", {
  expect_error(run_robustness(
    param_space_name = "oceanic_ontogeny",
    param_set = 0,
    replicates = 2))

  expect_error(run_robustness(
    param_space_name = "oceanic_ontogeny",
    param_set = 1000000,
    replicates = 2))

  expect_error(run_robustness(
    param_space_name = "oceanic_sea_level",
    param_set = 0,
    replicates = 2))

  expect_error(run_robustness(
    param_space_name = "oceanic_sea_level",
    param_set = 1000000,
    replicates = 2))

  expect_error(run_robustness(
    param_space_name = "oceanic_ontogeny_sea_level",
    param_set = 0,
    replicates = 2))

  expect_error(run_robustness(
    param_space_name = "oceanic_ontogeny_sea_level",
    param_set = 1000000,
    replicates = 2))

  expect_error(run_robustness(
    param_space_name = "nonoceanic",
    param_set = 0,
    replicates = 2))

  expect_error(run_robustness(
    param_space_name = "nonoceanic",
    param_set = 1000000,
    replicates = 2))

  expect_error(run_robustness(
    param_space_name = "nonoceanic_sea_level",
    param_set = 0,
    replicates = 2))

  expect_error(run_robustness(
    param_space_name = "nonoceanic_sea_level",
    param_set = 1000000,
    replicates = 2))

  expect_error(run_robustness(
    param_space_name = "nonoceanic_land_bridge",
    param_set = 0,
    replicates = 2))

  expect_error(run_robustness(
    param_space_name = "nonoceanic_land_bridge",
    param_set = 1000000,
    replicates = 2))
})

test_that("abuse replicates", {
  expect_error(run_robustness(
    param_space_name = "oceanic_ontogeny",
    param_set = 1,
    replicates = 0))

  expect_error(run_robustness(
    param_space_name = "oceanic_sea_level",
    param_set = 1,
    replicates = 0))

  expect_error(run_robustness(
    param_space_name = "oceanic_ontogeny_sea_level",
    param_set = 1,
    replicates = 0))

  expect_error(run_robustness(
    param_space_name = "nonoceanic",
    param_set = 1,
    replicates = 0))

  expect_error(run_robustness(
    param_space_name = "nonoceanic_sea_level",
    param_set = 1,
    replicates = 0))

  expect_error(run_robustness(
    param_space_name = "nonoceanic_land_bridge",
    param_set = 1,
    replicates = 0))
})