Fix median annotation and update vignette

Author: larry-leon

R/baseline_table.R

@@ -435,11 +435,21 @@ create_baseline_table <- function(data,
       title = "Baseline Characteristics by Treatment Arm"
     )
 
-    gt_table <- gt::fmt_missing(
-      gt_table,
-      columns = gt::everything(),
-      missing_text = ""
-    )
+    # Check gt version and use appropriate function
+    # sub_missing was introduced in gt v0.6.0 to replace fmt_missing
+    if (utils::packageVersion("gt") >= "0.6.0") {
+      gt_table <- gt::sub_missing(
+        gt_table,
+        columns = gt::everything(),
+        missing_text = ""
+      )
+    } else {
+      gt_table <- gt::fmt_missing(
+        gt_table,
+        columns = gt::everything(),
+        missing_text = ""
+      )
+    }
 
     gt_table <- gt::tab_style(
       gt_table,

R/kmplotting_helpers.R

@@ -152,13 +152,12 @@ add_risk_table <- function(risk.points, rpoints0, rpoints1, col.0, col.1, risk.c
 #' @param med.digits Integer; number of digits to display for median and confidence interval.
 #' @param med.cex Numeric; text size for median annotation.
 #' @param med.font Integer; font for median annotation.
-#' @param xmed.fraction Numeric; fraction of the x-axis for annotation placement (e.g., 0.8 for 80\% to the right).
+#' @param xmed.fraction Numeric; fraction of the x-axis for annotation placement (e.g., 0.8 for 80\\% to the right).
 #' @param ymed.offset Numeric; offset from the top of the plot for annotation placement.
 #'
 #' @importFrom graphics text
 #' @return Invisibly returns NULL. Used for plotting side effects.
 #' @export
-
 add_median_annotation <- function(medians_df, med.digits, med.cex, med.font, xmed.fraction, ymed.offset) {
   medians_df$label <- paste0(
     format(medians_df$quantile, digits = med.digits), " [",
@@ -169,14 +168,13 @@ add_median_annotation <- function(medians_df, med.digits, med.cex, med.font, xme
     paste(medians_df$group, medians_df$label, sep = ": "),
     collapse = "\n"
   )
-
   usr <- par("usr")
   x_pos <- usr[2] * xmed.fraction
   y_pos <- usr[4] - ymed.offset
-
   text(x = x_pos, y = y_pos, labels = annotation_text, adj = c(0, 1), cex = med.cex, font = med.font)
 }
 
+
 #' Add legends to KM plot
 #'
 #' Adds legends for Cox model, log-rank test, and arms to a Kaplan-Meier plot.

man/add_median_annotation.Rd

@@ -461,7 +461,7 @@ baseline_table <- create_baseline_table(
   data = df_CTC,
   treat_var = "treat",
   vars_continuous = c("age", "pgr", "er", "nodes"),
-  vars_categorical = c("size","meno","chemo","er_negative"),
+  vars_categorical = c("size","meno","er_negative"),
   show_pvalue = TRUE,
   show_smd = TRUE
 )