Add some sdmTMBextra tests

pbs-assess · Feb 8, 2024 · af853ef · af853ef
1 parent 2db9fa6
commit af853ef
Showing 1 changed file with 60 additions and 40 deletions.
diff --git a/tests/testthat/test-5-residuals.R b/tests/testthat/test-5-residuals.R
@@ -294,43 +294,63 @@ test_that("MCMC residuals throw error as needed", {
   }, regexp = "mcmc")
 })
 
-# test_that("MCMC residuals work with sdmTMBextra", {
-#   skip_on_cran()
-#   skip_if_not_installed("INLA")
-#   skip_if_not_installed("sdmTMBextra")
-#   skip_if_not_installed("rstan")
-#   d <- pcod_2011
-#   set.seed(1)
-#   d$offset <- rnorm(nrow(d))
-#   fit_dg <- sdmTMB(
-#     density ~ 1,
-#     data = d,
-#     mesh = pcod_mesh_2011,
-#     offset = d$offset,
-#     family = delta_gamma()
-#   )
-#   set.seed(1)
-#   p0 <- sdmTMBextra::predict_mle_mcmc(fit_dg, mcmc_iter = 11, mcmc_warmup = 10)
-#   set.seed(1)
-#   p1 <- sdmTMBextra::predict_mle_mcmc(fit_dg,
-#     mcmc_iter = 11, mcmc_warmup = 10,
-#     model = 1
-#   )
-#   set.seed(1)
-#   p2 <- sdmTMBextra::predict_mle_mcmc(fit_dg,
-#     mcmc_iter = 11, mcmc_warmup = 10,
-#     model = 2
-#   )
-#   expect_equal(p0, p1)
-#   set.seed(1)
-#   r1 <- residuals(fit_dg, type = "mle-mcmc", mcmc_samples = p1)
-#   set.seed(1)
-#   r2 <- residuals(fit_dg, type = "mle-mcmc", mcmc_samples = p2)
-#   qqnorm(r1)
-#   qqnorm(r2)
-#   expect_false(identical(r1, r2))
-#   expect_true(max(r1) < 5)
-#   expect_true(min(r1) > -5)
-#   expect_true(max(r2) < 5)
-#   expect_true(min(r2) > -5)
-# })
+test_that("MCMC residuals work with sdmTMBextra", {
+  skip_on_cran()
+  skip_if_not_installed("sdmTMBextra")
+  skip_if_not_installed("rstan")
+  skip_on_ci()
+  d <- pcod_2011
+  set.seed(1)
+  d$offset <- rnorm(nrow(d))
+  fit_dg <- sdmTMB(
+    density ~ 1,
+    data = d,
+    mesh = pcod_mesh_2011,
+    offset = d$offset,
+    family = delta_gamma()
+  )
+  set.seed(1)
+  p0 <- sdmTMBextra::predict_mle_mcmc(fit_dg, mcmc_iter = 11, mcmc_warmup = 10)
+  set.seed(1)
+  p1 <- sdmTMBextra::predict_mle_mcmc(fit_dg,
+    mcmc_iter = 11, mcmc_warmup = 10,
+    model = 1
+  )
+  set.seed(1)
+  p2 <- sdmTMBextra::predict_mle_mcmc(fit_dg,
+    mcmc_iter = 11, mcmc_warmup = 10,
+    model = 2
+  )
+  expect_equal(p0, p1)
+  set.seed(1)
+  r1 <- residuals(fit_dg, type = "mle-mcmc", mcmc_samples = p1)
+  set.seed(1)
+  r2 <- residuals(fit_dg, type = "mle-mcmc", mcmc_samples = p2)
+  qqnorm(r1)
+  qqnorm(r2)
+  expect_false(identical(r1, r2))
+  expect_true(max(r1) < 5)
+  expect_true(min(r1) > -5)
+  expect_true(max(r2) < 5)
+  expect_true(min(r2) > -5)
+})
+
+test_that("predict_mle_mcmc() works with extra_time #297", {
+  skip_on_cran()
+  skip_if_not_installed("sdmTMBextra")
+  skip_if_not_installed("rstan")
+  skip_on_ci()
+  fit <- sdmTMB(
+    density ~ 0 + as.factor(year),
+    time = "year",
+    spatiotemporal = "off",
+    spatial = "on",
+    mesh = pcod_mesh_2011,
+    data = pcod_2011,
+    family = tweedie(link = "log"),
+    extra_time = c(2012, 2014, 2016)
+  )
+  set.seed(123)
+  samps <- sdmTMBextra::predict_mle_mcmc(fit, mcmc_iter = 11, mcmc_warmup = 10)
+  expect_true(nrow(samps) == 972L)
+})