Revert "cleaned tests"

This reverts commit 7a398ee.

tests/testthat/setup.R

@@ -1,5 +1,5 @@
 library(bayesnec)
-library(brms)
+library(dplyr)
 library(testthat)
 
 random_filename <- function(nchar) {
@@ -16,14 +16,15 @@ add_na <- function(x, n = 3) {
 data(nec_data)
 other_data <- nec_data
 colnames(other_data) <- c("a", "b")
-nec_data$count <- as.integer(round(nec_data$y * 20))
-nec_data$trials <- as.integer(20)
-nec_data$log_x <- log(nec_data$x)
+nec_data <- nec_data %>% 
+  mutate(count = as.integer(round(y * 20)),
+         trials = as.integer(20),
+         log_x = log(x))
 
 data(manec_example)
-nec4param <- pull_out(manec_example, model = "nec4param") |>
-  suppressMessages() |>
-  suppressWarnings()
-ecx4param <- pull_out(manec_example, model = "ecx4param") |>
-  suppressMessages() |>
-  suppressWarnings()
+nec4param <- pull_out(manec_example, model = "nec4param") %>%
+  suppressMessages %>%
+  suppressWarnings
+ecx4param <- pull_out(manec_example, model = "ecx4param") %>%
+  suppressMessages %>%
+  suppressWarnings

tests/testthat/test-amend.R

@@ -1,9 +1,10 @@
 library(bayesnec)
+library(dplyr)
+
+data(manec_example)
 
 test_that("input checks work correctly and return appropriate messages", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
+  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."
@@ -14,27 +15,27 @@ test_that("input checks work correctly and return appropriate messages", {
   m_3 <- paste0("No new LOO fitting/weighting arguments have been specified;",
                 " ignoring argument loo_controls.")
   expect_message(amend(manec_example), general_error)
-  amend(manec_example, drop = "nec3param") |>
-    expect_message(general_error) |>
+  amend(manec_example, drop = "nec3param") %>%
+    expect_message(general_error) %>%
     expect_message(m_1)
   m_4 <- "loo_controls list names are incorrect. See ?bnec"
-  manec_example |>
-    amend(loo_controls = list(method = "somethingwrong")) |>
-    expect_message(m_4) |>
-    expect_error()
-  expect_message(amend(manec_example, drop = "nec4param")) |>
-    suppressWarnings()
-  amend(manec_example, add = "nec3param") |>
-    expect_message() |>
-    expect_message("Fitted models are: nec4param ecx4param") |>
-    suppressWarnings()
+  manec_example %>%
+    amend(loo_controls = list(method = "somethingwrong")) %>%
+    expect_message(m_4) %>%
+    expect_error
+  expect_message(amend(manec_example, drop = "nec4param")) %>%
+    suppressWarnings
+  amend(manec_example, add = "nec3param") %>%
+    expect_message %>%
+    expect_message("Fitted models are: nec4param ecx4param") %>%
+    suppressWarnings
   amend(manec_example, add = "nec4param",
-        loo_controls = list(weights = list(method = "pseudobma"))) |>
-    expect_message(general_error) |>
-    expect_message(m_1) |>
+        loo_controls = list(weights = list(method = "pseudobma"))) %>%
+    expect_message(general_error) %>%
+    expect_message(m_1) %>%
     expect_message(m_3)
   amend(manec_example,
-        loo_controls = list(weights = list(method = "pseudobma"))) |>
-    expect_message(general_error) |>
+        loo_controls = list(weights = list(method = "pseudobma"))) %>%
+    expect_message(general_error) %>%
     expect_message(m_3)
 })

tests/testthat/test-bayesmanec_methods.R

@@ -1,13 +1,14 @@
 library(bayesnec)
+library(brms)
+
+data(manec_example)
 
 test_that("predict is silent", {
   expect_silent(predict(manec_example))
 })
 
 test_that("predict/fitted is a matrix of appropriately name elements", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
+  skip_on_cran()
   pred_p <- predict(manec_example)
   expect_equal(class(pred_p), c("matrix", "array"))
   expect_equal(dim(pred_p), c(100, 4))
@@ -19,18 +20,14 @@ test_that("predict/fitted is a matrix of appropriately name elements", {
 })
 
 test_that("plot returns null, is invisible, and is silent", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
+  skip_on_cran()
   expect_null(plot(manec_example))
   expect_silent(plot(manec_example))
   expect_invisible(plot(manec_example))
 })
 
 test_that("rhat behaves as expected", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
+  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))
@@ -39,9 +36,7 @@ test_that("rhat behaves as expected", {
 })
 
 test_that("summary behaves as expected", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
+  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",
@@ -51,9 +46,7 @@ test_that("summary behaves as expected", {
 })
 
 test_that("formula behaves as expected", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
+  skip_on_cran()
   expect_error(formula(manec_example))
   expect_s3_class(formula(manec_example, "nec4param"), "bayesnecformula")
   expect_s3_class(formula(manec_example, model = "nec4param"),
@@ -64,9 +57,7 @@ test_that("formula behaves as expected", {
 })
 
 test_that("model.frame behaves as expected", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
+  skip_on_cran()
   expect_error(model.frame(manec_example))
   expect_s3_class(model.frame(manec_example, "nec4param"),
                   "data.frame")

tests/testthat/test-bayesnec_methods.R

@@ -1,4 +1,5 @@
 library(bayesnec)
+library(brms)
 
 test_that("predict is silent", {
   expect_silent(predict(nec4param))

tests/testthat/test-bnec.R

@@ -1,11 +1,12 @@
 library(bayesnec)
+library(dplyr)
 
 test_that("Check for data when using formula syntax", {
   expect_error(bnec(y ~ crf(x, "ecxlin")), "argument \"data\" is missing")
 })
 
 test_that("Check models inappropriate for negative x are dropped", {
- bnec(y ~ crf(log_x, "nechorme4pwr"), data = nec_data) |>
-    expect_message("Dropping the model\\(s\\) nechorme4pwr as they are not valid for data with negative predictor \\(x\\) values\\.") |>
+ bnec(y ~ crf(log_x, "nechorme4pwr"), data = nec_data) %>% 
+    expect_message("Dropping the model\\(s\\) nechorme4pwr as they are not valid for data with negative predictor \\(x\\) values\\.") %>%
     expect_error("No valid models have been supplied for this data type.")
 })

tests/testthat/test-check_chains.R

@@ -1,19 +1,16 @@
 library(bayesnec)
+library(dplyr)
+
+data(manec_example)
 
 test_that("returns null", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
   expect_null(check_chains(nec4param))
 })
 
 test_that("returns pdf for bayesmanec objects with filename argument", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
   filename <- random_filename(15)
-  check_chains(manec_example, filename = filename) |>
-    expect_invisible() |>
-    expect_message()
+  check_chains(manec_example, filename = filename) %>%
+    expect_invisible %>%
+    expect_message
   on.exit(file.remove(paste(filename, ".pdf", sep = "")))
 })

tests/testthat/test-check_formula.R

@@ -1,4 +1,5 @@
 library(bayesnec)
+library(dplyr)
 
 nec3param <- function(beta, nec, top, x) {
   top * exp(-exp(beta) * (x - nec) *
@@ -33,14 +34,14 @@ test_that("Parameter checks", {
   f_2 <- y | trials(tr) ~ crf(x, "nec") + (nec + bot | group_1)
   expect_s3_class(check_formula(bnf(f_2), data, run_par_checks = FALSE),
                   "bayesnecformula")
-  check_formula(bnf(f_2), data, run_par_checks = TRUE) |>
-    expect_message("Performing single parameter checks on all models...") |>
-    expect_message("\"bot\" not valid parameters") |>
-    expect_message("\"bot\" not valid parameters") |>
-    expect_message("\"bot\" not valid parameters") |>
-    expect_message("\"bot\" not valid parameters") |>
-    expect_message("\"bot\" not valid parameters") |>
-    expect_message("\"bot\" not valid parameters") |>
+  check_formula(bnf(f_2), data, run_par_checks = TRUE) %>%
+    expect_message("Performing single parameter checks on all models...") %>%
+    expect_message("\"bot\" not valid parameters") %>%
+    expect_message("\"bot\" not valid parameters") %>%
+    expect_message("\"bot\" not valid parameters") %>%
+    expect_message("\"bot\" not valid parameters") %>%
+    expect_message("\"bot\" not valid parameters") %>%
+    expect_message("\"bot\" not valid parameters") %>%
     expect_message("\"bot\" not valid parameters")
   f_3 <- "log(y) | trials(tr) ~ crf(sqrt(x), \"nec3param\")"
   expect_s3_class(check_formula(bnf(f_3), data), "bayesnecformula")

tests/testthat/test-check_priors.R

@@ -1,19 +1,16 @@
 library(bayesnec)
+library(ggplot2)
+
+data(manec_example)
 
 test_that("returns ggplot for bayesnecfit objects", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
   p <- check_priors(nec4param)
   expect_error(print(p), NA)
   expect_silent(check_priors(nec4param))
   expect_equal(class(p), c("gg", "ggplot"))
 })
 
 test_that("returns pdf for bayesmanecfit objects", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
   filename <- random_filename(15)
   expect_invisible(check_priors(manec_example, filename = filename))
   on.exit(file.remove(paste(filename, ".pdf", sep = "")))

tests/testthat/test-data.R

@@ -1,4 +1,5 @@
 library(bayesnec)
+data("nec_data")
 
 test_that("nec_data are as expected", {
   expect_equal(class(nec_data), "data.frame")

tests/testthat/test-define_prior.R

@@ -1,4 +1,5 @@
 library(bayesnec)
+library(brms)
 
 pred_a <- rnorm(100)
 pred_na <- add_na(pred_a)
@@ -7,6 +8,8 @@ resp_na <- add_na(resp_a)
 pred_b <- pred_a[-1]
 resp_b <- resp_a[-1]
 
+data(manec_example)
+
 test_that("model is always properly specified as character", {
   p_a <- define_prior(model = "nec3param", family = gaussian(),
                       predictor = pred_a, response = resp_a)

tests/testthat/test-dispersion.R

@@ -1,4 +1,5 @@
 library(bayesnec)
+data(manec_example)
 
 test_that("dispersion fails because family is gaussian", {
   expect_length(dispersion(ecx4param), 0)

tests/testthat/test-ecx.R

@@ -1,9 +1,10 @@
 library(bayesnec)
+library(brms)
+
+data(manec_example)
 
 test_that("prob_vals warnings behave as expected", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
+  skip_on_cran()
   ecx(manec_example, prob_vals = c(0.6, 0.1, 0.9), precision = 10,
       type = "relative") |>
     expect_length(3) |>
@@ -26,9 +27,7 @@ test_that("prob_vals warnings behave as expected", {
 })
 
 test_that("ecx_val warnings behave as expected", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
+  skip_on_cran()
   expect_error(
     ecx(manec_example, ecx_val = 0.9, type = "relative", precision = 10)
   ) |>
@@ -39,9 +38,7 @@ test_that("ecx_val warnings behave as expected", {
 })
 
 test_that("ecx returns expected object types and arguments pass correctly", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
+  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",
@@ -67,52 +64,40 @@ test_that("ecx returns expected object types and arguments pass correctly", {
 })
 
 test_that("works for bayesnecfit", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
+  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", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
+  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", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
+  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", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
+  skip_on_cran()
   ecx3 <- ecx(ecx4param, posterior = TRUE, precision = 10)
   expect_equal(length(ecx3), 100)
 })
 
 test_that("prob_vals passes correctly", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
+  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", {
-  if (Sys.getenv("NOT_CRAN") == "") {
-    skip_on_cran()
-  }
+  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"))