Merge pull request #35 from Merck/test-style

Remove `library()` calls from tests
Merck · Feb 14, 2024 · bad5e0e · bad5e0e
2 parents 2a294bb + e83d268
commit bad5e0e
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Showing 3 changed files with 33 additions and 46 deletions.
diff --git a/tests/testthat.R b/tests/testthat.R
@@ -1,14 +1,4 @@
-# This file is part of the standard setup for testthat.
-# It is recommended that you do not modify it.
-#
-# Where should you do additional test configuration?
-# Learn more about the roles of various files in:
-# * https://r-pkgs.org/tests.html
-# * https://testthat.r-lib.org/reference/test_package.html#special-files
-
 library(testthat)
 library(wpgsd)
-library(tibble)
-library(dplyr)
 
 test_check("wpgsd")
diff --git a/tests/testthat/test-independent-closed_test.R b/tests/testthat/test-independent-closed_test.R
@@ -1,24 +1,23 @@
-p_obs <- bind_rows(
-  tibble(Analysis = 1, H1 = 0.001, H2 = 0.001),
-  tibble(Analysis = 2, H1 = 0.001, H2 = 0.001)
-)
-
-bound <- tribble(
-  ~Analysis, ~Hypotheses, ~H1, ~H2,
-  1, "H1", 0.02, NA,
-  1, "H1, H2", 0.0001, 0.00001,
-  1, "H2", NA, 0.003,
-  2, "H1", 0.02, NA,
-  2, "H1, H2", 0.02, 0.00001,
-  2, "H2", NA, 0.003
-)
+test_that("closed_test reject hypothesis as expected", {
+  p_obs <- dplyr::bind_rows(
+    tibble::tibble(Analysis = 1, H1 = 0.001, H2 = 0.001),
+    tibble::tibble(Analysis = 2, H1 = 0.001, H2 = 0.001)
+  )
 
-closed_test <- closed_test(bound, p_obs)
-closed_test_a1 <- closed_test %>% filter(Analysis == "Analysis 1")
-closed_test_a2 <- closed_test %>% filter(Analysis == "Analysis 2")
+  bound <- tibble::tribble(
+    ~Analysis, ~Hypotheses, ~H1, ~H2,
+    1, "H1", 0.02, NA,
+    1, "H1, H2", 0.0001, 0.00001,
+    1, "H2", NA, 0.003,
+    2, "H1", 0.02, NA,
+    2, "H1, H2", 0.02, 0.00001,
+    2, "H2", NA, 0.003
+  )
 
+  closed_test <- closed_test(bound, p_obs)
+  closed_test_a1 <- closed_test %>% dplyr::filter(Analysis == "Analysis 1")
+  closed_test_a2 <- closed_test %>% dplyr::filter(Analysis == "Analysis 2")
 
-test_that("closed_test reject hypothesis as expected", {
   expect_equal(closed_test_a1$H1, "Fail")
   expect_equal(closed_test_a1$H2, "Fail")
   expect_equal(closed_test_a2$H1, "Success")

diff --git a/tests/testthat/test-independent-generate_bounds.R b/tests/testthat/test-independent-generate_bounds.R
@@ -1,9 +1,3 @@
-library(gsDesign)
-library(gMCPLite)
-library(tibble)
-library(mvtnorm)
-library(dplyr)
-
 test_that("BH bounds replicate tables A3 and A4", {
   # Example 1 BH weighting results in Table A3 and A4
   set.seed(1234)
@@ -19,7 +13,7 @@ test_that("BH bounds replicate tables A3 and A4", {
   w <- c(0.3, 0.3, 0.4)
 
   # Event count of intersection of paired hypotheses - Table 1
-  event <- tribble(
+  event <- tibble::tribble(
     ~H1, ~H2, ~Analysis, ~Event,
     1, 1, 1, 100,
     2, 2, 1, 110,
@@ -43,35 +37,37 @@ test_that("BH bounds replicate tables A3 and A4", {
   # WPGSD bounds, spending method 3b
   bound_WPGSD <- generate_bounds(
     type = 2, k = 2, w = w, m = m, corr = corr, alpha = 0.025,
-    sf = sfHSD,
+    sf = gsDesign::sfHSD,
     sfparm = -4,
     t = c(min(100 / 200, 110 / 220, 225 / 450), 1)
   )
 
   # Bonferroni bounds
   bound_Bonf <- generate_bounds(
     type = 0, k = 2, w = w, m = m, corr = corr, alpha = 0.025,
-    sf = list(sfHSD, sfHSD, sfHSD),
+    sf = list(gsDesign::sfHSD, gsDesign::sfHSD, gsDesign::sfHSD),
     sfparm = list(-4, -4, -4),
     t = list(c(0.5, 1), c(0.5, 1), c(0.5, 1))
   )
 
   # Combine and back-calculate xi
-  bounds <- left_join(bound_Bonf, bound_WPGSD,
+  bounds <- dplyr::left_join(
+    bound_Bonf,
+    bound_WPGSD,
     by = c("Hypotheses", "Analysis"),
     suffix = c(".B", ".W")
   )
   bounds <- bounds %>%
-    rowwise() %>%
-    mutate(xi = sum(H1.W, H2.W, H3.W, na.rm = TRUE) /
+    dplyr::rowwise() %>%
+    dplyr::mutate(xi = sum(H1.W, H2.W, H3.W, na.rm = TRUE) /
       sum(H1.B, H2.B, H3.B, na.rm = TRUE))
   # Reorder for output
   bounds$order <- rep(c(5, 2, 1, 3, 6, 4, 7), 2)
-  bounds <- bounds %>% arrange(Analysis, order)
+  bounds <- bounds %>% dplyr::arrange(Analysis, order)
 
   # Z-statistics boundary, Table A4
   zbounds <- bounds %>%
-    mutate(
+    dplyr::mutate(
       zH1.B = -qnorm(H1.B),
       zH2.B = -qnorm(H2.B),
       zH3.B = -qnorm(H3.B),
@@ -234,7 +230,7 @@ test_that("BH bounds replicate tables A6 and A7", {
   w <- c(1 / 3, 1 / 3, 1 / 3)
 
   # Event count of intersection of paired hypotheses - Table 2
-  event <- tribble(
+  event <- tibble::tribble(
     ~H1, ~H2, ~Analysis, ~Event,
     1, 1, 1, 155,
     2, 2, 1, 160,
@@ -258,20 +254,22 @@ test_that("BH bounds replicate tables A6 and A7", {
   # WPGSD bounds, spending method 3c
   bound_WPGSD <- generate_bounds(
     type = 3, k = 2, w = w, m = m, corr = corr, alpha = 0.025,
-    sf = list(sfLDOF, sfLDOF, sfLDOF),
+    sf = list(gsDesign::sfLDOF, gsDesign::sfLDOF, gsDesign::sfLDOF),
     sfparm = list(0, 0, 0),
     t = list(c(155 / 305, 1), c(160 / 320, 1), c(165 / 335, 1))
   )
 
   # Bonferroni bounds
   bound_Bonf <- generate_bounds(
     type = 0, k = 2, w = w, m = m, corr = corr, alpha = 0.025,
-    sf = list(sfLDOF, sfLDOF, sfLDOF),
+    sf = list(gsDesign::sfLDOF, gsDesign::sfLDOF, gsDesign::sfLDOF),
     sfparm = list(0, 0, 0),
     t = list(c(155 / 305, 1), c(160 / 320, 1), c(165 / 335, 1))
   )
 
-  bounds <- left_join(bound_Bonf, bound_WPGSD,
+  bounds <- dplyr::left_join(
+    bound_Bonf,
+    bound_WPGSD,
     by = c("Hypotheses", "Analysis"),
     suffix = c(".B", ".W")
   )