change all emplate

.gitignore

@@ -44,3 +44,4 @@ cache
 *_data
 *_files
 figures
+*.tar.gz

DESCRIPTION

@@ -43,17 +43,18 @@ Depends:
     gtsummary (>= 2.5.1),
     R (>= 4.2)
 Imports:
-    dplyr (>= 1.2.1)
-Suggests:
     cowplot (>= 1.2.0),
-    crane (>= 0.3.1),
-    forcats (>= 1.0.1),
+    dplyr (>= 1.2.1),
     ggplot2 (>= 4.0),
     ggsurvfit (>= 1.2.0),
+    lubridate (>= 1.9),
+    rlistings
+Suggests:
+    crane (>= 0.3.1),
+    forcats (>= 1.0.1),
     gt (>= 1.3.0),
     knitr (>= 1.50),
     labelled (>= 2.16.0),
-    lubridate (>= 1.9),
     pharmaverseadam (>= 1.3.0),
     purrr (>= 1.2),
     random.cdisc.data (>= 0.3.16),

NAMESPACE

@@ -1,15 +1,116 @@
 # Generated by roxygen2: do not edit by hand
 
+export(make_fig_01)
+export(make_fig_02)
+export(make_fig_03)
+export(make_fig_14)
 export(make_table_02)
+export(make_table_03)
+export(make_table_04)
+export(make_table_05)
+export(make_table_06)
+export(make_table_07)
+export(make_table_08)
+export(make_table_09)
+export(make_table_10)
+export(make_table_11)
+export(make_table_12)
+export(make_table_13)
+export(make_table_14)
+export(make_table_15)
+export(make_table_16)
+export(make_table_17)
+export(make_table_18)
+export(make_table_20)
+export(make_table_21)
+export(make_table_22)
+export(make_table_29)
+export(make_table_32)
+export(make_table_33)
+export(make_table_34)
+export(make_table_35)
+export(make_table_36)
+export(make_table_37)
+export(make_table_38)
+export(make_table_43)
+export(make_table_44)
+export(make_table_45)
+export(make_table_50)
+export(make_table_51)
+export(make_table_roche_lbt01)
+importFrom(cards,ard_categorical)
 importFrom(cards,ard_continuous)
+importFrom(cards,ard_hierarchical)
+importFrom(cards,ard_stack_hierarchical)
+importFrom(cards,ard_tabulate)
+importFrom(cards,ard_tabulate_value)
+importFrom(cards,bind_ard)
+importFrom(cards,tidy_ard_row_order)
 importFrom(cardx,ard_continuous_ci)
+importFrom(cowplot,get_plot_component)
+importFrom(cowplot,plot_grid)
 importFrom(dplyr,.data)
+importFrom(dplyr,across)
 importFrom(dplyr,all_of)
+importFrom(dplyr,arrange)
+importFrom(dplyr,case_when)
+importFrom(dplyr,distinct)
 importFrom(dplyr,everything)
 importFrom(dplyr,filter)
+importFrom(dplyr,group_by)
+importFrom(dplyr,left_join)
+importFrom(dplyr,mutate)
+importFrom(dplyr,rowwise)
+importFrom(dplyr,select)
+importFrom(dplyr,slice_head)
+importFrom(dplyr,slice_max)
+importFrom(dplyr,slice_min)
+importFrom(dplyr,summarise)
+importFrom(dplyr,sym)
+importFrom(dplyr,ungroup)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,annotate)
+importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_rect)
+importFrom(ggplot2,element_text)
+importFrom(ggplot2,geom_errorbar)
+importFrom(ggplot2,geom_line)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,ggplot_build)
+importFrom(ggplot2,labs)
+importFrom(ggplot2,position_dodge)
+importFrom(ggplot2,scale_color_manual)
+importFrom(ggplot2,scale_x_continuous)
+importFrom(ggplot2,scale_y_continuous)
+importFrom(ggplot2,theme)
+importFrom(ggplot2,unit)
+importFrom(ggsurvfit,Surv)
+importFrom(ggsurvfit,ggsurvfit)
+importFrom(ggsurvfit,survfit2)
 importFrom(gtsummary,add_overall)
 importFrom(gtsummary,all_categorical)
 importFrom(gtsummary,all_continuous)
+importFrom(gtsummary,all_stat_cols)
 importFrom(gtsummary,gather_ard)
+importFrom(gtsummary,modify_bold)
+importFrom(gtsummary,modify_column_indent)
+importFrom(gtsummary,modify_footnote_header)
+importFrom(gtsummary,modify_header)
+importFrom(gtsummary,modify_indent)
+importFrom(gtsummary,modify_post_fmt_fun)
+importFrom(gtsummary,modify_spanning_header)
+importFrom(gtsummary,modify_table_body)
 importFrom(gtsummary,remove_footnote_header)
+importFrom(gtsummary,tbl_ard_hierarchical)
+importFrom(gtsummary,tbl_ard_summary)
+importFrom(gtsummary,tbl_hierarchical)
+importFrom(gtsummary,tbl_merge)
+importFrom(gtsummary,tbl_stack)
+importFrom(gtsummary,tbl_strata_nested_stack)
 importFrom(gtsummary,tbl_summary)
+importFrom(lubridate,days)
+importFrom(lubridate,interval)
+importFrom(lubridate,ymd_hms)
+importFrom(rlistings,as_listing)
+importFrom(tidyr,pivot_wider)

NEWS.md

@@ -1,5 +1,8 @@
 # cardinal 0.2.0.9001
 
+
+# cardinal 0.2.0
+
 * Initial release.
 * Added `make_table_02()` to produce FDA Table 2 (Baseline Demographic and Clinical Characteristics, Safety Population). The function filters for the safety population, builds a `gtsummary` table with continuous (mean/SD, median/range) and categorical (n/%) summaries by treatment arm, and optionally returns the intermediate ARD (`return_ard = TRUE`).
 * Moved `dplyr` from `Suggests` to `Imports` to support `make_table_02()`.

R/fda-fig_01.R

@@ -0,0 +1,157 @@
+#' FDA Figure 1: Time to Permanent Discontinuation of Study Drug, Safety Population, Pooled Analyses
+#'
+#' @description
+#' Creates FDA Figure 1 showing time to permanent discontinuation of study drug for the safety
+#' population, with an optional "Number of Patients" table below the plot.
+#'
+#' @param df (`data.frame`)\cr dataset (typically ADSL) required to build the figure.
+#' @param arm_var (`character`)\cr name of the treatment arm variable used to split figure into lines.
+#'   Defaults to `"TRT01A"`.
+#' @param id_var (`character`)\cr name of the subject identifier variable. Defaults to `"USUBJID"`.
+#' @param saffl_var (`character`)\cr name of the safety flag variable. Defaults to `"SAFFL"`.
+#' @param trtsdtm_var (`character`)\cr name of the treatment start datetime variable.
+#'   Defaults to `"TRTSDTM"`.
+#' @param trtedtm_var (`character`)\cr name of the treatment end datetime variable.
+#'   Defaults to `"TRTEDTM"`.
+#' @param u_trtdur (`character`)\cr unit for treatment duration. One of `"days"`, `"weeks"`,
+#'   `"months"`, or `"years"`. Defaults to `"days"`.
+#' @param x_lab (`character`)\cr x-axis label. Defaults to `"Time from first dose (<u_trtdur>)"`.
+#' @param y_lab (`character`)\cr y-axis label. Defaults to `"Percent of Patients (%)"`.
+#' @param xticks (`numeric` or `NA`)\cr x-axis tick mark positions. Defaults to `NA` (auto).
+#' @param ggtheme (`ggplot2::theme` or `NULL`)\cr ggplot2 theme to apply. Defaults to `NULL`.
+#' @param add_table (`flag`)\cr whether to add a "Number of Patients" table below the plot.
+#'   Defaults to `TRUE`.
+#' @param annotations (named `list` of `character`)\cr list of annotations to add to the figure.
+#'   Valid types are `title`, `subtitles`, and `caption`.
+#'
+#' @details
+#' * `df` must contain the variables specified by `arm_var`, `id_var`, `saffl_var`, `trtsdtm_var`,
+#'   and `trtedtm_var`.
+#' * Flag variables (i.e. `XXXFL`) are expected to have two levels: `"Y"` (true) and `"N"` (false).
+#'   Missing values in flag variables are treated as `"N"`.
+#' * Records with missing treatment start and/or end datetime are excluded from all calculations.
+#' * Values in the "Number of Patients" table are the number of patients with treatment duration
+#'   equal to or greater than the given time.
+#'
+#' @return A `ggplot2` object.
+#'
+#' @examplesIf requireNamespace("pharmaverseadam", quietly = TRUE)
+#' library(dplyr)
+#'
+#' adsl <- pharmaverseadam::adsl |>
+#'   filter(TRT01A != "Screen Failure")
+#'
+#' fig <- make_fig_01(df = adsl)
+#' fig
+#'
+#' @importFrom dplyr filter mutate select distinct arrange all_of
+#' @importFrom lubridate interval ymd_hms
+#' @importFrom ggplot2 ggplot aes geom_line labs theme element_blank
+#' @importFrom ggplot2 scale_x_continuous ggplot_build annotate unit element_rect
+#' @importFrom cowplot get_plot_component plot_grid
+#' @export
+make_fig_01 <- function(df,
+                        arm_var = "TRT01A",
+                        id_var = "USUBJID",
+                        saffl_var = "SAFFL",
+                        trtsdtm_var = "TRTSDTM",
+                        trtedtm_var = "TRTEDTM",
+                        u_trtdur = "days",
+                        x_lab = paste0("Time from first dose (", u_trtdur, ")"),
+                        y_lab = "Percent of Patients (%)",
+                        xticks = NA,
+                        ggtheme = NULL,
+                        add_table = TRUE,
+                        annotations = NULL) {
+  stopifnot(is.data.frame(df))
+  stopifnot(all(c(arm_var, id_var, saffl_var, trtsdtm_var, trtedtm_var) %in% names(df)))
+  stopifnot(u_trtdur %in% c("days", "weeks", "months", "years"))
+
+  df <- df |>
+    dplyr::filter(.data[[saffl_var]] == "Y") |>
+    dplyr::mutate(
+      TRTDUR = as.numeric(
+        lubridate::interval(
+          lubridate::ymd_hms(.data[[trtsdtm_var]]),
+          lubridate::ymd_hms(.data[[trtedtm_var]])
+        ),
+        u_trtdur
+      )
+    ) |>
+    dplyr::filter(!is.na(TRTDUR)) |>
+    dplyr::select(dplyr::all_of(c(id_var, arm_var)), TRTDUR) |>
+    dplyr::distinct() |>
+    dplyr::arrange(desc(TRTDUR))
+
+  df$PT_PCT <- seq_len(nrow(df)) / nrow(df) * 100
+  max_time <- max(df$TRTDUR)
+
+  g <- ggplot2::ggplot(
+    data = df,
+    ggplot2::aes(x = TRTDUR, y = PT_PCT, group = .data[[arm_var]], color = .data[[arm_var]])
+  ) +
+    ggplot2::geom_line() +
+    ggplot2::labs(
+      title = annotations[["title"]],
+      subtitle = annotations[["subtitles"]],
+      caption = annotations[["caption"]],
+      x = x_lab,
+      y = y_lab
+    ) +
+    ggplot2::theme(
+      legend.position = "bottom",
+      legend.title = ggplot2::element_blank(),
+      plot.margin = ggplot2::unit(c(0.05, 0.05, 0, 0.025), "npc")
+    )
+
+  if (any(!is.na(xticks))) {
+    g <- g + ggplot2::scale_x_continuous(
+      breaks = xticks,
+      limits = c(min(xticks), max(c(xticks, max_time)))
+    )
+  }
+
+  if (!is.null(ggtheme)) g <- g + ggtheme
+
+  if (add_table) {
+    legend_pos <- paste0("guide-box-", ifelse(is.null(ggtheme), "bottom", ggtheme$legend.position))
+    g_legend <- cowplot::get_plot_component(g, legend_pos, return_all = TRUE)
+
+    g <- g + ggplot2::theme(legend.position = "none")
+
+    xtick_lbls <- ggplot2::ggplot_build(g)$layout$panel_params[[1]]$x$breaks
+    xtick_lbls <- xtick_lbls[!is.na(xtick_lbls)]
+    xlims <- ggplot2::ggplot_build(g)$layout$panel_params[[1]]$x$limits
+
+    tbl_n <- expand.grid(x = xtick_lbls, arm = rev(levels(df[[arm_var]])), n = 0)
+
+    g_tbl <- ggplot2::ggplot(tbl_n, ggplot2::aes(x = x, y = arm)) +
+      ggplot2::theme(
+        axis.title.x = ggplot2::element_blank(),
+        axis.title.y = ggplot2::element_blank(),
+        axis.ticks.x = ggplot2::element_blank(),
+        axis.ticks.y = ggplot2::element_blank(),
+        panel.background = ggplot2::element_blank(),
+        axis.text.x = ggplot2::element_blank(),
+        panel.border = ggplot2::element_rect(color = "black", fill = NA, linewidth = 0.5),
+        plot.margin = ggplot2::unit(c(0.1, 0.05, 0, 0.025), "npc")
+      ) +
+      ggplot2::labs(title = "Number of Patients") +
+      ggplot2::scale_x_continuous(
+        breaks = xtick_lbls,
+        limits = c(min(xlims, xtick_lbls), max(xlims, xtick_lbls))
+      )
+
+    for (i in seq_len(nrow(tbl_n))) {
+      tbl_n$n[i] <- sum(df[[arm_var]] == tbl_n$arm[i] & df$TRTDUR >= tbl_n$x[i])
+      g_tbl <- g_tbl +
+        ggplot2::annotate("text", label = as.character(tbl_n$n[i]), x = tbl_n$x[i], y = tbl_n$arm[i])
+    }
+
+    if (!is.null(ggtheme)) g_tbl <- g_tbl + ggtheme
+
+    cowplot::plot_grid(g, g_tbl, g_legend, align = "v", axis = "l", ncol = 1, rel_heights = c(0.7, 0.25, 0.1))
+  } else {
+    g
+  }
+}