tests/testthat/test-vr_vec.R

In jonesor/Rage: Life History Metrics from Matrix Population Models

test_that("vr_vec functions work correctly", {
  ### test vr_vec_U
  U1 <- rbind(
    c(0, 0, 0, 0),
    c(0.5, 0.2, 0.1, 0),
    c(0, 0.3, 0.3, 0.1),
    c(0, 0, 0.5, 0.6)
  )

  surv1 <- vr_vec_survival(U1)
  expect_type(surv1, "double")
  expect_length(surv1, 4)

  surv2 <- vr_vec_survival(U1, exclude_col = 4)
  expect_true(is.na(surv2[4]))

  surv3 <- vr_vec_survival(U1, exclude_col = c(FALSE, FALSE, FALSE, TRUE))
  expect_true(is.na(surv3[4]))

  grow1 <- vr_vec_growth(U1)
  expect_type(grow1, "double")
  expect_length(grow1, 4)

  grow2 <- vr_vec_growth(U1, posU = matrix(TRUE, nrow = 4, ncol = 4))
  expect_false(is.na(grow2[1]))

  grow3 <- vr_vec_growth(U1, surv_only_na = FALSE)
  expect_false(is.na(grow3[1]))

  shri1 <- vr_vec_shrinkage(U1)
  expect_type(shri1, "double")
  expect_length(shri1, 4)

  shri2 <- vr_vec_shrinkage(U1, exclude_row = 2)
  expect_true(is.na(shri2[3]))

  stas1 <- vr_vec_stasis(U1)
  expect_type(stas1, "double")
  expect_length(stas1, 4)

  stas2 <- vr_vec_stasis(U1, posU = matrix(TRUE, nrow = 4, ncol = 4))
  expect_identical(stas2[1], 0)

  dent1 <- vr_vec_dorm_enter(U1, dorm_stages = 4)
  expect_type(dent1, "double")
  expect_length(dent1, 4)
  expect_false(is.na(dent1[3]))

  dexi1 <- vr_vec_dorm_exit(U1, dorm_stages = 4)
  expect_type(dexi1, "double")
  expect_length(dexi1, 4)
  expect_false(is.na(dexi1[4]))


  R1 <- rbind(
    c(0, 0, 1.1, 1.6),
    c(0, 0, 0.8, 0.4),
    c(0, 0, 0, 0),
    c(0, 0, 0, 0)
  )

  fecu1 <- vr_vec_reproduction(U1, R1)
  expect_type(fecu1, "double")
  expect_length(fecu1, 4)
  expect_true(all(is.na(fecu1[1:2])))

  # weighting
  v <- popdemo::eigs(U1 + R1, what = "rv") # reproductive value
  fecu2 <- vr_vec_reproduction(U1, R1, weights_row = v)
  expect_true(fecu2[3] != fecu1[3])

  # no survival in a stage with reproduction
  U2 <- rbind(
    c(0, 0, 0, 0),
    c(0.5, 0.2, 0.1, 0),
    c(0, 0.3, 0.3, 0),
    c(0, 0, 0.5, 0)
  )

  fecu3 <- vr_vec_reproduction(U2, R1)
  expect_identical(fecu3[4], sum(R1[, 4]))
})


test_that("vr_vec functions warn and fail gracefully", {
  expect_error(vr_vec_survival(mat_u_na))
  expect_error(vr_vec_growth(mat_u_na))
  expect_error(vr_vec_shrinkage(mat_u_na))
  expect_error(vr_vec_stasis(mat_u_na))
  expect_error(vr_vec_reproduction(mat_u_na))
})