Deprecate gt in favor of lt

DESCRIPTION

@@ -43,7 +43,7 @@ Imports:
     data.table,
     dplyr,
     gsDesign,
-    gt,
+    lt,
     methods,
     mvtnorm,
     npsurvSS (>= 1.1.0),
@@ -67,5 +67,7 @@ VignetteBuilder:
     knitr
 LinkingTo:
     Rcpp
+Remotes:
+    yihui/lt
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
+Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -1,8 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(as_gt,fixed_design_summary)
-S3method(as_gt,gs_design_summary)
-S3method(as_gt,simtrial_gs_wlr)
+S3method(as_lt,fixed_design_summary)
+S3method(as_lt,gs_design_summary)
 S3method(as_rtf,fixed_design_summary)
 S3method(as_rtf,gs_design_summary)
 S3method(print,fixed_design)
@@ -13,7 +12,7 @@ S3method(to_integer,fixed_design)
 S3method(to_integer,gs_design)
 export(ahr)
 export(ahr_blinded)
-export(as_gt)
+export(as_lt)
 export(as_rtf)
 export(define_enroll_rate)
 export(define_fail_rate)

R/as_gt.R

@@ -16,258 +16,6 @@
 #  You should have received a copy of the GNU General Public License
 #  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-#' Convert summary table of a fixed or group sequential design object to a gt object
-#'
-#' @param x A summary object of a fixed or group sequential design.
-#' @param ... Additional arguments (not used).
-#'
-#' @return A `gt_tbl` object.
-#'
-#' @export
-as_gt <- function(x, ...) {
-  UseMethod("as_gt", x)
-}
-
-#' @rdname as_gt
-#'
-#' @export
-#'
-#' @examples
-#' # Fixed design examples ----
-#'
-#' # Enrollment rate
-#' enroll_rate <- define_enroll_rate(
-#'   duration = 18,
-#'   rate = 20
-#' )
-#'
-#' # Failure rates
-#' fail_rate <- define_fail_rate(
-#'   duration = c(4, 100),
-#'   fail_rate = log(2) / 12,
-#'   dropout_rate = .001,
-#'   hr = c(1, .6)
-#' )
-#'
-#' # Study duration in months
-#' study_duration <- 36
-#'
-#' # Experimental / Control randomization ratio
-#' ratio <- 1
-#'
-#' # 1-sided Type I error
-#' alpha <- 0.025
-#'
-#' # Type II error (1 - power)
-#' beta <- 0.1
-#'
-#' # Example 1 ----
-#' fixed_design_ahr(
-#'   alpha = alpha, power = 1 - beta,
-#'   enroll_rate = enroll_rate, fail_rate = fail_rate,
-#'   study_duration = study_duration, ratio = ratio
-#' ) |>
-#'   summary() |>
-#'   as_gt()
-#'
-#' # Example 2 ----
-#' fixed_design_fh(
-#'   alpha = alpha, power = 1 - beta,
-#'   enroll_rate = enroll_rate, fail_rate = fail_rate,
-#'   study_duration = study_duration, ratio = ratio
-#' ) |>
-#'   summary() |>
-#'   as_gt()
-as_gt.fixed_design_summary <- function(x, title = NULL, footnote = NULL, ...) {
-  if (is.null(title)) title <- attr(x, "title")
-  if (is.null(footnote)) footnote <- attr(x, "footnote")
-
-  ans <- gt::gt(x) |>
-    gt::tab_header(title = title)
-
-  if (!isFALSE(footnote)) {
-    ans <- ans |>
-      gt::tab_footnote(
-        footnote = footnote,
-        locations = gt::cells_title(group = "title")
-      )
-  }
-
-  return(ans)
-}
-
-#' @rdname as_gt
-#'
-#' @param title A string to specify the title of the gt table.
-#' @param subtitle A string to specify the subtitle of the gt table.
-#' @param colname_spanner A string to specify the spanner of the gt table.
-#' @param colname_spannersub A vector of strings to specify the spanner details
-#'   of the gt table.
-#' @param footnote A list containing `content`, `location`, and `attr`.
-#'   `content` is a vector of string to specify the footnote text; `location` is
-#'   a vector of string to specify the locations to put the superscript of the
-#'   footnote index; `attr` is a vector of string to specify the attributes of
-#'   the footnotes, for example, `c("colname", "title", "subtitle", "analysis",
-#'   "spanner")`; users can use the functions in the `gt` package to customize
-#'   the table. To disable footnotes, use `footnote = FALSE`.
-#' @param display_bound A vector of strings specifying the label of the bounds.
-#'   The default is `c("Efficacy", "Futility")`.
-#' @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.
-#'
-#' @export
-#'
-#' @examples
-#' \donttest{
-#' # Group sequential design examples ---
-#'
-#' # Example 1 ----
-#' # The default output
-#'
-#' gs_design_ahr() |>
-#'   summary() |>
-#'   as_gt()
-#'
-#' gs_power_ahr(lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.1)) |>
-#'   summary() |>
-#'   as_gt()
-#'
-#' gs_design_wlr() |>
-#'   summary() |>
-#'   as_gt()
-#'
-#' gs_power_wlr(lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.1)) |>
-#'   summary() |>
-#'   as_gt()
-#'
-#' gs_power_combo() |>
-#'   summary() |>
-#'   as_gt()
-#'
-#' gs_design_rd() |>
-#'   summary() |>
-#'   as_gt()
-#'
-#' gs_power_rd() |>
-#'   summary() |>
-#'   as_gt()
-#'
-#' # Example 2 ----
-#' # Usage of title = ..., subtitle = ...
-#' # to edit the title/subtitle
-#' gs_power_wlr(lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.1)) |>
-#'   summary() |>
-#'   as_gt(
-#'     title = "Bound Summary",
-#'     subtitle = "from gs_power_wlr"
-#'   )
-#'
-#' # Example 3 ----
-#' # Usage of colname_spanner = ..., colname_spannersub = ...
-#' # to edit the spanner and its sub-spanner
-#' gs_power_wlr(lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.1)) |>
-#'   summary() |>
-#'   as_gt(
-#'     colname_spanner = "Cumulative probability to cross boundaries",
-#'     colname_spannersub = c("under H1", "under H0")
-#'   )
-#'
-#' # Example 4 ----
-#' # Usage of footnote = ...
-#' # to edit the footnote
-#' gs_power_wlr(lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.1)) |>
-#'   summary() |>
-#'   as_gt(
-#'     footnote = list(
-#'       content = c(
-#'         "approximate weighted hazard ratio to cross bound.",
-#'         "wAHR is the weighted AHR.",
-#'         "the crossing probability.",
-#'         "this table is generated by gs_power_wlr."
-#'       ),
-#'       location = c("~wHR at bound", NA, NA, NA),
-#'       attr = c("colname", "analysis", "spanner", "title")
-#'     )
-#'   )
-#'
-#' # Example 5 ----
-#' # Usage of display_bound = ...
-#' # to either show efficacy bound or futility bound, or both(default)
-#' gs_power_wlr(lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.1)) |>
-#'   summary() |>
-#'   as_gt(display_bound = "Efficacy")
-#'
-#' # Example 6 ----
-#' # Usage of display_columns = ...
-#' # to select the columns to display in the summary table
-#' gs_power_wlr(lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.1)) |>
-#'   summary() |>
-#'   as_gt(display_columns = c("Analysis", "Bound", "Nominal p", "Z", "Probability"))
-#' }
-as_gt.gs_design_summary <- function(
-    x,
-    title = NULL,
-    subtitle = NULL,
-    colname_spanner = "Cumulative boundary crossing probability",
-    colname_spannersub = c("Alternate hypothesis", "Null hypothesis"),
-    footnote = NULL,
-    display_bound = c("Efficacy", "Futility"),
-    display_columns = NULL,
-    display_inf_bound = FALSE,
-    ...) {
-
-  x_old <- x
-  parts <- gsd_parts(
-    x, title, subtitle, colname_spannersub, footnote,
-    display_bound, display_columns, display_inf_bound
-  )
-
-  x <- parts$x |>
-    group_by(Analysis) |>
-    gt::gt() |>
-    gt::tab_spanner(
-      columns = all_of(colname_spannersub),
-      label = colname_spanner
-    ) |>
-    gt::tab_header(title = parts$title, subtitle = parts$subtitle)
-
-  # Add footnotes ----
-  add_footnote <- !isFALSE(footnote)
-  footnote <- parts$footnote
-  for (i in seq_along(footnote$content)) {
-    att <- footnote$attr[i]
-    loc <- if (att == "colname") {
-      # footnotes are added on the colnames
-      gt::cells_column_labels(columns = footnote$location[i])
-    } else if (att %in% c("title", "subtitle")) {
-      # on the title/subtitle
-      gt::cells_title(group = att)
-    } else if (att == "analysis") {
-      # on the analysis summary row, which is a grouping variable, i.e., Analysis
-      gt::cells_row_groups(groups = dplyr::starts_with("Analysis"))
-    } else if (att == "spanner") {
-      # on the column spanner
-      gt::cells_column_spanners(spanners = colname_spanner)
-    }
-    if (!is.null(loc))
-      x <- gt::tab_footnote(x, footnote = footnote$content[i], locations = loc)
-  }
-
-  # add footnote for non-binding design
-  footnote_nb <- if (add_footnote) gsd_footnote_nb(x_old, parts$alpha)
-  if (!is.null(footnote_nb)) x <- gt::tab_footnote(
-    x,
-    footnote = footnote_nb,
-    locations = gt::cells_body(
-      columns = colname_spannersub[2],
-      rows = gsd_footnote_row(parts$x, display_bound[1])
-    )
-  )
-
-  return(x)
-}
-
 # get different default columns to display
 gsd_columns <- function(columns, method, x) {
   # set different default columns to display
@@ -349,7 +97,7 @@ gsd_footnote_row <- function(x, bound) {
   i & x$Bound == bound
 }
 
-# a list of information for `as_[gt|rtf].gs_design()` methods: the transformed
+# a list of information for `as_[lt|rtf].gs_design()` methods: the transformed
 # data, title, and footnote, etc.
 gsd_parts <- function(
   x, title, subtitle, spannersub, footnote, bound, columns, inf_bound,
@@ -388,12 +136,3 @@ gsd_parts <- function(
     alpha = max(filter(x, Bound == bound[1])[["Null hypothesis"]])
   )
 }
-
-# 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, ...) {
-  f <- getFromNamespace("as_gt.simtrial_gs_wlr", "simtrial")
-  f(x, ...)
-}