Remove stray triple colons

openpharma · Jul 11, 2024 · 057d92c · 057d92c
1 parent 786bb10
commit 057d92c
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Showing 7 changed files with 9 additions and 60 deletions.
diff --git a/R/adjust_weights.R b/R/adjust_weights.R
@@ -131,7 +131,7 @@ adjust_weights_parametric <- function(matrix_weights,
 #' matrix_intersections <- weighting_strategy[, seq_len(num_hyps)]
 #' matrix_weights <- weighting_strategy[, -seq_len(num_hyps)]
 #'
-#' graphicalMCP:::adjust_weights_simes(
+#' adjust_weights_simes(
 #'   matrix_weights = matrix_weights,
 #'   p = p,
 #'   test_groups = list(1:4)

diff --git a/R/test_values.R b/R/test_values.R
@@ -38,19 +38,6 @@
 #'   for weighted parametric multiple test procedures.
 #'   \emph{Biometrical Journal}, 59(5), 918-931.
 #'
-#' @examples
-#' alpha <- 0.025
-#' hypotheses <- c(H1 = 0.5, H2 = 0.5, H3 = 0, H4 = 0)
-#' p <- c(0.018, 0.01, 0.105, 0.006)
-#'
-#' graphicalMCP:::test_values_bonferroni(p, hypotheses, alpha)
-#' graphicalMCP:::test_values_parametric(
-#'   p,
-#'   hypotheses,
-#'   alpha,
-#'   test_corr = diag(4)
-#' )
-#' graphicalMCP:::test_values_simes(p, hypotheses, alpha)
 test_values_bonferroni <- function(p, hypotheses, alpha, intersection = NA) {
   if (length(p) == 0) {
     NULL

diff --git a/man/adjust_weights.Rd b/man/adjust_weights.Rd
diff --git a/man/graph_test_fast.Rd b/man/graph_test_fast.Rd
diff --git a/man/test_values.Rd b/man/test_values.Rd
diff --git a/misc/testing-basics.Rmd b/misc/testing-basics.Rmd
@@ -180,12 +180,12 @@ inter_h <- gw[, seq_len(m)]
 gw_bonf <- ifelse(inter_h, gw[, seq_len(m) + m], NA)
 
 gw_para <-
-  graphicalMCP:::adjust_weights_parametric(gw_bonf, diag(m), .05, list(1:m))
+  adjust_weights_parametric(gw_bonf, diag(m), .05, list(1:m))
 
 p <- runif(m, .0001, .03)
 sim_corr <- diag(m)
 
-gw_simes <- graphicalMCP:::adjust_weights_simes(gw_bonf, p, list(1:m))
+gw_simes <- adjust_weights_simes(gw_bonf, p, list(1:m))
 groups <- list(1:floor(m / 2), (floor(m / 2) + 1):m)
 
 h <- as.integer(rep(0, m))
@@ -219,7 +219,7 @@ simes_bench <- bench::mark(
     graphicalMCP:::graph_test_closure_fast(
       p,
       .05,
-      graphicalMCP:::adjust_weights_simes(gw_bonf, p, list(1:m)),
+      adjust_weights_simes(gw_bonf, p, list(1:m)),
       inter_h
     ),
   `gMCP::gMCP` =

diff --git a/tests/testthat/test-power_tests.R b/tests/testthat/test-power_tests.R
@@ -10,13 +10,13 @@ test_that("vectorized testing matches standard testing (single-group)", {
 
   groups1 <- list(seq_len(m))
 
-  gw_compact_simes <- graphicalMCP:::adjust_weights_simes(
+  gw_compact_simes <- adjust_weights_simes(
     gw_weights,
     p,
     groups1
   )
 
-  gw_compact_parametric <- graphicalMCP:::adjust_weights_parametric(
+  gw_compact_parametric <- adjust_weights_parametric(
     gw_weights,
     gw_h,
     diag(m),
@@ -73,13 +73,13 @@ test_that("vectorized testing matches standard testing (multi-group)", {
   simes_groups_reduce <- list(1:2)
   para_groups <- list(5:m)
 
-  adjusted_weights_simes <- graphicalMCP:::adjust_weights_simes(
+  adjusted_weights_simes <- adjust_weights_simes(
     gw_weights[, unlist(simes_groups)],
     p[unlist(simes_groups)],
     simes_groups_reduce
   )
 
-  adjusted_weights_para <- graphicalMCP:::adjust_weights_parametric(
+  adjusted_weights_para <- adjust_weights_parametric(
     gw_weights,
     gw_h,
     diag(m),