tests/testthat/test_sir.R

In antarctic-humpback-2019-assessment/HumpbackSIR: Use Sample-Importance-Resampling to Estimate Southern Humpback Abundance

context("SIR")

test_that("Example runs", {
  skip("Need new reference values")
  set.seed(48448)
  sir <- HUMPBACK.SIR(file_name = "test.N2005",
                      n_resamples = 100,
                      priors = make_prior_list(),
                      catch_multipliers = make_multiplier_list(),
                      target.Yr = 2005,
                      num.haplotypes = 0,
                      output.Yrs = c(2005, 2006),
                      abs.abundance = Abs.Abundance.2005,
                      rel.abundance = Rel.Abundance,
                      rel.abundance.key = TRUE,
                      count.data = Count.Data,
                      count.data.key = FALSE,
                      growth.rate.obs = c(0.074, 0.033, TRUE),
                      growth.rate.Yrs = c(1995, 1996, 1997, 1998),
                      catch.data = Catch.data,
                      control = sir_control(threshold = 1e-18,
                                            progress_bar = TRUE))
  resample_summary <- summary_sir(sir$resamples_output)
  trajectory_summary <- summary_sir(sir$resamples_trajectories)
  ## Results generated 2018-08-19
  ## Only using 100 samples so tests don't take forever
  ## Only checking a few of these; not clear which should be targeted for tests
  ## yet. Maybe use a fake data set for testing? At least this shows that the
  ## function runs?
  r_max_summ <- c(0.0747308365546679, 0.0785385308959521, 0.0325653742793947,
                  0.103600497766363, 0.0427498911390547, 0.101975065643247,
                  0.0246829054611735, 0.104749660704751, 100)
  expect_equal(resample_summary$output_summary$r_max, r_max_summ)
  K_summ <- c(24341.0440866569, 24013.5352974968, 22809.4671260726,
              27420.3612174263, 22881.3564593546, 26393.1754034563,
              22759.0720310569, 28434.3853907956, 100)
  expect_equal(resample_summary$output_summary$K, K_summ)
  Nmin_summ <- c(523.562366839516, 387.891026320824, 176.885416772425,
                 1724.51699097789, 183.140884857596, 1266.76707418949,
                 163.174008013952, 2201.98115521626, 100)
  expect_equal(resample_summary$output_summary$Nmin, Nmin_summ)
  ## make sure that relevant files are created (and then removed)
  wd <- getwd()
  outfiles <- c(paste0(wd, "/test.N2005_resamples_trajectories.csv"),
                paste0(wd, "/test.N2005_resamples_output.csv"))
  expect_true(file.exists(outfiles[1]))
  file.remove(outfiles[1])
  expect_true(file.exists(outfiles[2]))
  file.remove(outfiles[2])
})