lint

Author: yoshidk6

R/dev_ermod_emax.R

@@ -26,7 +26,7 @@
 #'
 #' @return An object of class `ermod_emax`.or `ermod_bin_emax`.
 #'
-#' @examplesIf BayesERtools:::.if_run_plot_er()
+#' @examplesIf BayesERtools:::.if_run_ex_plot_er()
 #' \donttest{
 #' data_er_cont <- rstanemax::exposure.response.sample
 #'
@@ -178,7 +178,7 @@ dev_ermod_emax_exp_sel <- function(
 
 #' @export
 #' @rdname dev_ermod_emax
-#' @examplesIf BayesERtools:::.if_run_plot_er()
+#' @examplesIf BayesERtools:::.if_run_ex_plot_er()
 #' \donttest{
 #' data_er_bin <- rstanemax::exposure.response.sample.binary
 #'

R/dev_ermod_lin.R

@@ -749,4 +749,3 @@ capture_selected_args <- function(arg_names, env) {
 .if_run_ex_covsel <- function() {
   requireNamespace("projpred", quietly = TRUE)
 }
-

man/dev_ermod_emax.Rd

@@ -34,10 +34,11 @@ if (.if_run_ex_coveff()) {
 
   coveffsim1 <- sim_coveff(ermod_bin, spec_coveff = spec_coveff_new)
   coveffsim2 <- sim_coveff(ermod_bin, spec_coveff = spec_coveff_no_keep_ref)
-  coveffsim3 <- sim_coveff(ermod_bin, spec_coveff = spec_coveff_no_keep_ref_race)
+  coveffsim3 <-
+    sim_coveff(ermod_bin, spec_coveff = spec_coveff_no_keep_ref_race)
 
 
-  # Tests -----------------------------------------------------------------------
+  # Tests ---------------------------------------------------------------------
   test_that("input col & row error", {
     expect_error(replace_spec_coveff(
       spec_coveff, spec_new_bgluc |> dplyr::select(-value_cont)

tests/testthat/test-build_spec_coveff.R

@@ -9,7 +9,7 @@ if (.if_run_ex_coveff()) {
 
   var_resp <- "AEFLAG"
 
-  # develop models --------------------------------------------------------------
+  # develop models ------------------------------------------------------------
   set.seed(1234)
   ermod_bin <- dev_ermod_bin(
     data = df_er_ae_hgly2,
@@ -25,7 +25,7 @@ if (.if_run_ex_coveff()) {
   coveffsim <- sim_coveff(ermod_bin)
   coveffsim_2 <- sim_coveff(ermod_bin, spec_coveff = spec_coveff)
 
-  # Tests -----------------------------------------------------------------------
+  # Tests ---------------------------------------------------------------------
   test_that("sim_coveff", {
     expect_equal(coveffsim, coveffsim_2)
     expect_equal(dim(coveffsim), c(14, 12))
@@ -73,8 +73,8 @@ if (.if_run_ex_coveff()) {
     expect_equal(
       spec_coveff$value_label,
       c(
-        "0.824", "2.31", "4.80", "6.01", "8.19", "10.3", "4.42", "6.09", "7.28",
-        "White", "Asian", "Black", "No", "Yes"
+        "0.824", "2.31", "4.80", "6.01", "8.19", "10.3", "4.42", "6.09",
+        "7.28", "White", "Asian", "Black", "No", "Yes"
       )
     )
   })

tests/testthat/test-coveff.R

@@ -196,7 +196,9 @@ test_that("plot_ermod_bin_emax", {
 })
 
 test_that("Convert factor as response variable into number", {
-  plot_er_gof(mod_mtcars_emax, n_bins = 4) |>
-    expect_error("The breaks for the binned probability ")
-  plot_er_gof(mod_mtcars_emax, n_bins = 2) |> expect_silent()
+  if (.if_run_ex_plot_er()) {
+    plot_er_gof(mod_mtcars_emax, n_bins = 4) |>
+      expect_error("The breaks for the binned probability ")
+    plot_er_gof(mod_mtcars_emax, n_bins = 2) |> expect_silent()
+  }
 })

tests/testthat/test-dev_ermod_emax.R

@@ -372,12 +372,14 @@ test_that("print.ermod_exp_sel prints correct information", {
 })
 
 test_that("print.ermod_cov_sel prints correct information", {
-  out <- cli::cli_fmt({
-    print(ermod_bin_cov_sel_kfold_dummy)
-  })
-  expect_true(any(grepl("Binary ER model", out)))
-  expect_true(any(grepl("& covariate selection", out)))
-  expect_true(any(grepl("Use \\`plot_submod_performance\\(\\)\\`", out)))
+  if (requireNamespace("projpred")) {
+    out <- cli::cli_fmt({
+      print(ermod_bin_cov_sel_kfold_dummy)
+    })
+    expect_true(any(grepl("Binary ER model", out)))
+    expect_true(any(grepl("& covariate selection", out)))
+    expect_true(any(grepl("Use \\`plot_submod_performance\\(\\)\\`", out)))
+  }
 })
 
 # plot.ermod_exp_sel

tests/testthat/test-dev_ermod_lin.R

@@ -1,4 +1,4 @@
-if (.if_run_ex_covsel()){
+if (.if_run_ex_covsel()) {
   d_sim_binom_cov <- d_sim_binom_cov
 
   id_to_sample <- seq(1, max(d_sim_binom_cov$ID), by = 5)
@@ -15,7 +15,7 @@ if (.if_run_ex_covsel()){
     )
 
 
-  # Create  ermod_bin objects for testing ---------------------------------------
+  # Create  ermod_bin objects for testing -------------------------------------
   set.seed(1234)
   ermod_bin <- dev_ermod_bin(
     data = df_er_ae_covsel_test,

tests/testthat/test-p_direction.R

@@ -134,8 +134,10 @@ test_that("plot_er.ersim", {
 
   expect_silent(plot(g1))
 
-  plot_er(ersim_curve_2_med_qi, show_orig_data = TRUE) |>
-    expect_warning("Model has covariate\\(s\\), and only one covariate data")
+  if (requireNamespace("xgxr")) {
+    plot_er(ersim_curve_2_med_qi, show_orig_data = TRUE) |>
+      expect_warning("Model has covariate\\(s\\), and only one covariate data")
+  }
   plot_er(ersim_curve_3_med_qi) |>
     expect_error("Model has covariate\\(s\\) and multiple covariate data rows")
 })