Merge branch 'main' into 441-info-frac-driven-design-does-not-work-for-gs_design_wlr

Author: LittleBeannie

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: gsDesign2
 Title: Group Sequential Design with Non-Constant Effect
-Version: 1.1.2.22
+Version: 1.1.2.23
 Authors@R: c(
     person("Keaven", "Anderson", email = "keaven_anderson@merck.com", role = c("aut")),
     person("Yilong", "Zhang", email = "elong0527@gmail.com", role = c("aut")),

NAMESPACE

@@ -2,6 +2,7 @@
 
 S3method(as_gt,fixed_design)
 S3method(as_gt,gs_design)
+S3method(as_gt,simtrial_gs_wlr)
 S3method(as_rtf,fixed_design)
 S3method(as_rtf,gs_design)
 S3method(summary,fixed_design)
@@ -75,17 +76,17 @@ importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,one_of)
 importFrom(dplyr,rename)
+importFrom(dplyr,row_number)
 importFrom(dplyr,select)
 importFrom(dplyr,summarize)
 importFrom(dplyr,ungroup)
 importFrom(gsDesign,gsDesign)
 importFrom(gsDesign,sfLDOF)
-importFrom(mvtnorm,GenzBretz)
 importFrom(stats,pnorm)
 importFrom(stats,qnorm)
+importFrom(stats,setNames)
 importFrom(stats,stepfun)
 importFrom(stats,uniroot)
-importFrom(survival,Surv)
 importFrom(tibble,tibble)
 importFrom(utils,tail)
 useDynLib(gsDesign2, .registration = TRUE)

R/ahr.R

@@ -72,8 +72,6 @@
 #' }
 #' \if{html}{The contents of this section are shown in PDF user manual only.}
 #'
-#' @importFrom data.table setDF setDT
-#'
 #' @export
 #'
 #' @examples

R/ahr_blinded.R

@@ -60,9 +60,6 @@
 #' }
 #' \if{html}{The contents of this section are shown in PDF user manual only.}
 #'
-#' @importFrom tibble tibble
-#' @importFrom survival Surv
-#'
 #' @export
 #'
 #' @examples
@@ -91,7 +88,7 @@ ahr_blinded <- function(
     stop("'intervals' must be a vector of positive numbers.")
   }
   if (length(intervals) != length(hr)) {
-    stop("the piecewise model specified 'hr' and 'intervals' differ in length.")
+    stop("The piecewise model specified 'hr' and 'intervals' differ in length.")
   }
 
   # Set final element of "intervals" to Inf

R/as_gt.R

@@ -89,10 +89,11 @@ as_gt.fixed_design <- function(x, title = NULL, footnote = NULL, ...) {
   return(ans)
 }
 
+get_method <- function(x, methods) intersect(methods, class(x))[1]
+
 # get the fixed design method
 fd_method <- function(x) {
-  methods <- c("ahr", "fh", "mb", "lf", "rd", "maxcombo", "milestone", "rmst")
-  intersect(methods, class(x))[1]
+  get_method(x, c("ahr", "fh", "mb", "lf", "rd", "maxcombo", "milestone", "rmst"))
 }
 
 # get the default title
@@ -251,17 +252,16 @@ as_gt.gs_design <- function(
     ...) {
 
   x_old <- x
-  full_alpha <- attr(x, "full_alpha")
   parts <- gsd_parts(
     x, title, subtitle, colname_spannersub, footnote,
     display_bound, display_columns, display_inf_bound
   )
 
   x <- parts$x %>%
-    dplyr::group_by(Analysis) %>%
+    group_by(Analysis) %>%
     gt::gt() %>%
     gt::tab_spanner(
-      columns = dplyr::all_of(colname_spannersub),
+      columns = all_of(colname_spannersub),
       label = colname_spanner
     ) %>%
     gt::tab_header(title = parts$title, subtitle = parts$subtitle)
@@ -288,7 +288,7 @@ as_gt.gs_design <- function(
   }
 
   # add footnote for non-binding design
-  footnote_nb <- gsd_footnote_nb(x_old, parts$alpha, full_alpha)
+  footnote_nb <- gsd_footnote_nb(x_old, parts$alpha)
   if (!is.null(footnote_nb)) x <- gt::tab_footnote(
     x,
     footnote = footnote_nb,
@@ -348,7 +348,8 @@ gsd_footnote <- function(method, columns) {
 }
 
 # footnote for non-binding designs
-gsd_footnote_nb <- function(x, x_alpha, full_alpha) {
+gsd_footnote_nb <- function(x, x_alpha) {
+  full_alpha <- attr(x, "full_alpha")
   if (!inherits(x, "non_binding") || x_alpha >= full_alpha) return()
   a1 <- format(x_alpha, scientific = FALSE)
   a2 <- format(full_alpha, scientific = FALSE)
@@ -408,9 +409,17 @@ gsd_parts <- function(
   )
 
   list(
-    x = dplyr::arrange(x2, Analysis),
+    x = arrange(x2, Analysis),
     title = title, subtitle = subtitle,
     footnote = footnote %||% gsd_footnote(method, columns),
     alpha = max(filter(x, Bound == bound[1])[[alpha_column]])
   )
 }
+
+# Only purpose of the method below is to fix S3 redirection when gsDesign2 is
+# loaded after simtrial, which masks the as_gt() generic from simtrial
+
+#' @export
+as_gt.simtrial_gs_wlr <- function(x, ...) {
+  simtrial:::as_gt.simtrial_gs_wlr(x, ...)
+}

R/as_rtf.R

@@ -171,11 +171,6 @@ check_rel_width <- function(width, n_col) {
 #' @param display_columns A vector of strings specifying the variables to be
 #'   displayed in the summary table.
 #' @param display_inf_bound Logical, whether to display the +/-inf bound.
-#' @param full_alpha The full alpha used in the design, the default is 0.025.
-#    If the cumulative alpha for final analysis is less than the `full_alpha`
-#'   when the futility bound is non-binding, a footnote will be displayed, saying
-#'   the smaller value subtracts the probability of crossing a futility bound before
-#'   crossing an efficacy bound at a later analysis under the null hypothesis.
 #' @inheritParams r2rtf::rtf_page
 #' @inheritParams r2rtf::rtf_body
 #' @param file File path for the output.
@@ -283,7 +278,6 @@ as_rtf.gs_design <- function(
     display_bound = c("Efficacy", "Futility"),
     display_columns = NULL,
     display_inf_bound = TRUE,
-    full_alpha = 0.025,
     col_rel_width = NULL,
     orientation = c("portrait", "landscape"),
     text_font_size = 9,
@@ -368,7 +362,7 @@ as_rtf.gs_design <- function(
   }
 
   # add footnote for non-binding design
-  footnote_nb <- gsd_footnote_nb(x_old, parts$alpha, full_alpha)
+  footnote_nb <- gsd_footnote_nb(x_old, parts$alpha)
   if (!is.null(footnote_nb)) {
     mkr <- marker()
     i <- gsd_footnote_row(x, display_bound[1])

R/check_arg.R

@@ -255,7 +255,7 @@ check_enroll_rate_fail_rate <- function(enroll_rate, fail_rate) {
   if ("stratum" %in% colnames(enroll_rate) && "stratum" %in% colnames(fail_rate)) {
     strata_enroll <- unique(enroll_rate$stratum)
     strata_fail <- unique(fail_rate$stratum)
-    strata_common <- dplyr::intersect(strata_enroll, strata_fail)
+    strata_common <- intersect(strata_enroll, strata_fail)
 
     if (sum(strata_common %in% strata_enroll) != length(strata_enroll)) {
       stop("The `Strata` column in the input argument `enroll_rate` and `fail_rate` must be the same!")

R/define.R

@@ -54,7 +54,7 @@ define_enroll_rate <- function(
     duration,
     rate,
     stratum = "All") {
-  df <- tibble::tibble(
+  df <- tibble(
     stratum = stratum,
     duration = duration,
     rate = rate
@@ -117,7 +117,7 @@ define_fail_rate <- function(
     dropout_rate,
     hr = 1,
     stratum = "All") {
-  df <- tibble::tibble(
+  df <- tibble(
     stratum = stratum,
     duration = duration,
     fail_rate = fail_rate,

R/expected_accural.R

@@ -44,10 +44,6 @@
 #' }
 #' \if{html}{The contents of this section are shown in PDF user manual only.}
 #'
-#' @importFrom dplyr filter lead
-#' @importFrom tibble tibble
-#' @importFrom stats stepfun
-#'
 #' @export
 #'
 #' @examples

R/expected_time.R

@@ -45,8 +45,6 @@
 #'    }
 #'  }
 #'
-#' @importFrom stats uniroot
-#'
 #' @export
 #'
 #' @examples