skip_on_cran() added to heavy tests

tests/testthat/test-amend.R

@@ -4,6 +4,7 @@ library(dplyr)
 data(manec_example)
 
 test_that("input checks work correctly and return appropriate messages", {
+  skip_on_cran()
   general_error <- paste(
     "Nothing to amend, please specify a proper model to either add or drop, or",
     "changes to loo_controls;\n Returning original model set."

tests/testthat/test-bayesmanec_methods.R

@@ -8,6 +8,7 @@ test_that("predict is silent", {
 })
 
 test_that("predict/fitted is a matrix of appropriately name elements", {
+  skip_on_cran()
   pred_p <- predict(manec_example)
   expect_equal(class(pred_p), c("matrix", "array"))
   expect_equal(dim(pred_p), c(100, 4))
@@ -19,12 +20,14 @@ test_that("predict/fitted is a matrix of appropriately name elements", {
 })
 
 test_that("plot returns null, is invisible, and is silent", {
+  skip_on_cran()
   expect_null(plot(manec_example))
   expect_silent(plot(manec_example))
   expect_invisible(plot(manec_example))
 })
 
 test_that("rhat behaves as expected", {
+  skip_on_cran()
   rhat_p <- suppressMessages(rhat(manec_example))
   rhat2_p <-  rhat(manec_example, rhat_cutoff = 1)
   expect_message(rhat(manec_example, rhat_cutoff = 1))
@@ -33,6 +36,7 @@ test_that("rhat behaves as expected", {
 })
 
 test_that("summary behaves as expected", {
+  skip_on_cran()
   summary.p <- suppressWarnings(summary(manec_example))
   expect_equal(class(summary.p), "manecsummary")
   expect_equal(names(summary.p), c("models", "family", "sample_size",
@@ -42,6 +46,7 @@ test_that("summary behaves as expected", {
 })
 
 test_that("formula behaves as expected", {
+  skip_on_cran()
   expect_error(formula(manec_example))
   expect_s3_class(formula(manec_example, "nec4param"), "bayesnecformula")
   expect_s3_class(formula(manec_example, model = "nec4param"),
@@ -52,6 +57,7 @@ test_that("formula behaves as expected", {
 })
 
 test_that("model.frame behaves as expected", {
+  skip_on_cran()
   expect_error(model.frame(manec_example))
   expect_s3_class(model.frame(manec_example, "nec4param"),
                   "data.frame")

tests/testthat/test-ecx.R

@@ -1,37 +1,44 @@
 library(bayesnec)
-library(dplyr)
 library(brms)
 
 data(manec_example)
 
 test_that("prob_vals warnings behave as expected", {
-  ecx(manec_example, prob_vals = c(0.6, 0.1, 0.9),
-      type = "relative") %>%
-    expect_length(3) %>%
-    suppressWarnings
-  ecx(manec_example, prob_vals = 0.9, type = "relative") %>%
-    expect_error %>%
-    suppressWarnings
-  ecx(manec_example, prob_vals = c(0.6, 0.9, 0.1),
-      type = "relative") %>%
-    expect_error %>%
-    suppressWarnings
-  ecx(nec4param, prob_vals = c(0.6, 0.1, 0.9),
-      type = "relative") %>%
-    expect_length(3) %>%
-    suppressWarnings
-  expect_error(ecx(nec4param, prob_vals = 0.9, type = "relative"))
-  expect_error(ecx(nec4param, prob_vals = c(0.6, 0.9, 0.1),
+  skip_on_cran()
+  ecx(manec_example, prob_vals = c(0.6, 0.1, 0.9), precision = 10,
+      type = "relative") |>
+    expect_length(3) |>
+    suppressWarnings()
+  ecx(manec_example, prob_vals = 0.9, precision = 10, type = "relative") |>
+    expect_error() |>
+    suppressWarnings()
+  ecx(manec_example, prob_vals = c(0.6, 0.9, 0.1), precision = 10,
+      type = "relative") |>
+    expect_error() |>
+    suppressWarnings()
+  ecx(nec4param, prob_vals = c(0.6, 0.1, 0.9), precision = 10,
+      type = "relative") |>
+    expect_length(3) |>
+    suppressWarnings()
+  expect_error(ecx(nec4param, prob_vals = 0.9, type = "relative",
+                   precision = 10))
+  expect_error(ecx(nec4param, prob_vals = c(0.6, 0.9, 0.1), precision = 10,
                    type = "relative"))
 })
 
 test_that("ecx_val warnings behave as expected", {
-  expect_error(ecx(manec_example, ecx_val = 0.9, type = "relative")) %>%
-    suppressWarnings
-  expect_error(ecx(nec4param, ecx_val = 0.9, type = "relative"))
+  skip_on_cran()
+  expect_error(
+    ecx(manec_example, ecx_val = 0.9, type = "relative", precision = 10)
+  ) |>
+    suppressWarnings()
+  expect_error(
+    ecx(nec4param, ecx_val = 0.9, type = "relative", precision = 10)
+  )
 })
 
 test_that("ecx returns expected object types and arguments pass correctly", {
+  skip_on_cran()
   ec50_summary <- ecx(manec_example, ecx_val = 50, type = "relative",
                       precision = 50)
   ec50_summary2 <- ecx(manec_example, ecx_val = 50, type = "relative",
@@ -57,34 +64,41 @@ test_that("ecx returns expected object types and arguments pass correctly", {
 })
 
 test_that("works for bayesnecfit", {
-  ecx1 <- ecx(ecx4param)
+  skip_on_cran()
+  ecx1 <- ecx(ecx4param, precision = 10)
   expect_equal(length(ecx1), 3)
   expect_equal(names(ecx1), c("Q50", "Q2.5", "Q97.5"))
 })
 
 test_that("works for bayesmanecfit", {
-  ecx1 <- ecx(manec_example)
+  skip_on_cran()
+  ecx1 <- ecx(manec_example, precision = 10)
   expect_equal(length(ecx1), 3)
   expect_equal(names(ecx1), c("Q50", "Q2.5", "Q97.5"))
 })
 
 test_that("xform passes correctly", {
-  ecx1 <- ecx(ecx4param)
-  ecx2 <- ecx(ecx4param, xform = exp)
+  skip_on_cran()
+  ecx1 <- ecx(ecx4param, precision = 10)
+  ecx2 <- ecx(ecx4param, xform = exp, precision = 10)
   expect_gt(ecx2[1], ecx1[2])
 })
 
 test_that("posterior passes correctly", {
-  ecx3 <- ecx(ecx4param, posterior = TRUE)
+  skip_on_cran()
+  ecx3 <- ecx(ecx4param, posterior = TRUE, precision = 10)
   expect_equal(length(ecx3), 100)
 })
 
 test_that("prob_vals passes correctly", {
-  ecx4 <- ecx(ecx4param, prob_vals = c(0.5, 0.3, 0.7))
+  skip_on_cran()
+  ecx4 <- ecx(ecx4param, prob_vals = c(0.5, 0.3, 0.7), precision = 10)
   expect_equal(names(ecx4), c("Q50", "Q30", "Q70"))
 })
 
 test_that("ecx_val passes correctly", {
-  ecx4 <- ecx(ecx4param, prob_vals = c(0.5, 0.3, 0.7), ecx_val = 20)
+  skip_on_cran()
+  ecx4 <- ecx(ecx4param, prob_vals = c(0.5, 0.3, 0.7), ecx_val = 20,
+              precision = 10)
   expect_equal(names(ecx4), c("Q50", "Q30", "Q70"))
 })

tests/testthat/test-expand_classes.R

@@ -5,6 +5,7 @@ fit1 <- manec_example$mod_fits[["nec4param"]]
 fit2 <- manec_example$mod_fits[["ecx4param"]]
 
 test_that("expand_nec defaults work for nec model", {
+  skip_on_cran()
   nec_fit <- expand_nec(fit1, fit1$bayesnecformula, model = "nec4param") %>%
     suppressWarnings
   expect_equal(names(nec_fit), c("fit", "model", "init", "bayesnecformula",
@@ -20,6 +21,7 @@ test_that("expand_nec defaults work for nec model", {
 })
 
 test_that("expand_nec arguments work for nec model", {
+  skip_on_cran()
   nec_fit <- expand_nec(fit1, fit1$bayesnecformula, model = "nec4param",
                         x_range = c(0.01, 4), precision = 20) %>%
     suppressWarnings
@@ -36,6 +38,7 @@ test_that("expand_nec arguments work for nec model", {
 })
 
 test_that("expand_ecx defaults work for ecx model", {
+  skip_on_cran()
   ecx_fit <- expand_nec(fit2, fit2$bayesnecformula, model = "ecx4param") %>%
     suppressWarnings
   expect_equal(names(ecx_fit), c("fit", "model", "init", "bayesnecformula",
@@ -51,6 +54,7 @@ test_that("expand_ecx defaults work for ecx model", {
 })
 
 test_that("expand_ecx arguments work for ecx model", {
+  skip_on_cran()
   ecx_fit <- expand_nec(fit2, fit2$bayesnecformula, model = "ecx4param",
                         x_range = c(0.01, 4), precision = 20) %>%
     suppressWarnings
@@ -67,6 +71,7 @@ test_that("expand_ecx arguments work for ecx model", {
 })
 
 test_that("expand_ecx sig_val argument work for ecx model", {
+  skip_on_cran()
   ecx_fit_a <- expand_nec(fit2, fit2$bayesnecformula, model = "ecx4param") %>%
     suppressWarnings
   ecx_fit_b <- expand_nec(fit2, fit2$bayesnecformula, model = "ecx4param",
@@ -81,6 +86,7 @@ test_null <- NULL
 tt2 <- tt1["nec4param"]
 
 test_that("expand_manec warnings work correctly", {
+  skip_on_cran()
   expect_error(expand_manec(test_null))
   expect_message(expand_manec(tt2, formulas[["nec4param"]]),
                  "Only nec4param is fitted, no model averaging done.")
@@ -90,6 +96,7 @@ test_that("expand_manec warnings work correctly", {
 })
 
 test_that("expand_manec defaults work correctly", {
+  skip_on_cran()
   tt3 <- expand_manec(tt1, formulas) %>%
     suppressMessages %>%
     suppressWarnings
@@ -99,6 +106,7 @@ test_that("expand_manec defaults work correctly", {
 })
 
 test_that("expand_manec defaults work correctly", {
+  skip_on_cran()
   tt4 <- expand_manec(tt1, formulas, x_range = c(0.01, 4), precision = 20) %>%
     suppressMessages %>%
     suppressWarnings
@@ -111,6 +119,7 @@ test_that("new loo_controls are incorporated", {
   get_new_method <- function(x) {
     attributes(x$mod_stats$wi)$method
   }
+  skip_on_cran()
   expand_manec(tt1, formulas) %>%
     get_new_method %>%
     expect_null %>%

tests/testthat/test-nsec.R

@@ -1,38 +1,49 @@
 library(bayesnec)
+library(dplyr)
 library(brms)
 
 data(manec_example)
 
 test_that("prob_vals warnings behave as expected", {
-  expect_length(nsec(manec_example, prob_vals = c(0.6, 0.1, 0.9)), 3) %>%
-    suppressWarnings
-  expect_error(nsec(manec_example, prob_vals = 0.9)) %>%
-    suppressWarnings
-  expect_error(nsec(manec_example, prob_vals = c(0.6, 0.9, 0.1))) %>%
-    suppressWarnings
-  expect_length(nsec(nec4param, prob_vals = c(0.6, 0.1, 0.9)), 3)
-  expect_error(nsec(nec4param, prob_vals = 0.9))
-  expect_error(nsec(nec4param, prob_vals = c(0.6, 0.9, 0.1)))
+  skip_on_cran()
+  expect_length(
+    nsec(manec_example, prob_vals = c(0.6, 0.1, 0.9), precision = 10), 3
+  ) |>
+    suppressWarnings()
+  expect_error(
+    nsec(manec_example, prob_vals = 0.9, precision = 10)
+  ) |>
+    suppressWarnings()
+  expect_error(
+    nsec(manec_example, prob_vals = c(0.6, 0.9, 0.1), precision = 10)
+  ) |>
+    suppressWarnings()
+  expect_length(
+    nsec(nec4param, prob_vals = c(0.6, 0.1, 0.9), precision = 10), 3
+  )
+  expect_error(nsec(nec4param, prob_vals = 0.9, precision = 10))
+  expect_error(nsec(nec4param, prob_vals = c(0.6, 0.9, 0.1), precision = 10))
 })
 
 test_that(paste0("nsec returns expected object types and precision is",
                  " passing correctly"), {
-  nsec_summary <- nsec(manec_example, sig_val = 0.01, precision = 50) %>%
-    suppressWarnings
+  skip_on_cran()
+  nsec_summary <- nsec(manec_example, sig_val = 0.01, precision = 50) |>
+    suppressWarnings()
   nsec_summary2 <- nsec(manec_example, sig_val = 0.01, precision = 50,
-                        xform = exp) %>%
-    suppressWarnings
+                        xform = exp) |>
+    suppressWarnings()
   nsec_posterior <- nsec(manec_example, sig_val = 0.01,
-                         posterior = TRUE, precision = 50) %>%
-    suppressWarnings
-  nsecn_summary <- nsec(nec4param, sig_val = 0.01, precision = 50) %>%
-    suppressWarnings
+                         posterior = TRUE, precision = 50) |>
+    suppressWarnings()
+  nsecn_summary <- nsec(nec4param, sig_val = 0.01, precision = 50) |>
+    suppressWarnings()
   nsecn_summary2 <- nsec(nec4param, sig_val = 0.01, precision = 50,
-                         xform = exp) %>%
-    suppressWarnings
+                         xform = exp) |>
+    suppressWarnings()
   nsecn_posterior <- nsec(nec4param, sig_val = 0.01,
-                          posterior = TRUE, precision = 50) %>%
-    suppressWarnings
+                          posterior = TRUE, precision = 50) |>
+    suppressWarnings()
   expect_equal(length(nsec_summary), 3)
   expect_gt(length(nsec_posterior), 3)
   expect_equal(length(nsecn_summary), 3)
@@ -44,35 +55,42 @@ test_that(paste0("nsec returns expected object types and precision is",
 })
 
 test_that("works for bayesnecfit", {
-  nsec1 <- nsec(ecx4param)
+  skip_on_cran()
+  nsec1 <- nsec(ecx4param, precision = 10)
   expect_equal(length(nsec1), 3)
   expect_equal(names(nsec1), c("Q50", "Q2.5", "Q97.5"))
 })
 
 test_that("works for bayesmanecfit", {
-  nsec1 <- nsec(manec_example) %>%
-    suppressWarnings
+  skip_on_cran()
+  nsec1 <- nsec(manec_example, precision = 10) |>
+    suppressWarnings()
   expect_equal(length(nsec1), 3)
   expect_equal(names(nsec1), c("Q50", "Q2.5", "Q97.5"))
 })
 
 test_that("xform passes correctly", {
-  nsec1 <- nsec(ecx4param)
-  nsec2 <- nsec(ecx4param, xform = exp)
+  skip_on_cran()
+  nsec1 <- nsec(ecx4param, precision = 10)
+  nsec2 <- nsec(ecx4param, xform = exp, precision = 10)
   expect_gt(nsec2[1], nsec1[2])
 })
 
 test_that("posterior passes correctly", {
-  nsec3 <- nsec(ecx4param, posterior = TRUE)
+  skip_on_cran()
+  nsec3 <- nsec(ecx4param, posterior = TRUE, precision = 10)
   expect_equal(length(nsec3), 100)
 })
 
 test_that("prob_vals passes correctly", {
-  nsec4 <- nsec(ecx4param, prob_vals = c(0.5, 0.3, 0.7))
+  skip_on_cran()
+  nsec4 <- nsec(ecx4param, prob_vals = c(0.5, 0.3, 0.7), precision = 10)
   expect_equal(names(nsec4), c("Q50", "Q30", "Q70"))
 })
 
 test_that("sig_val passes correctly", {
-  nsec4 <- nsec(ecx4param, prob_vals = c(0.5, 0.3, 0.7), sig_val = 0.05)
+  skip_on_cran()
+  nsec4 <- nsec(ecx4param, prob_vals = c(0.5, 0.3, 0.7), sig_val = 0.05,
+                precision = 10)
   expect_equal(names(nsec4), c("Q50", "Q30", "Q70"))
 })