From e6b11ed3c6651fb45b26e3be6803559d831c0b4c Mon Sep 17 00:00:00 2001
From: Ilse <55379552+iaugusty@users.noreply.github.com>
Date: Wed, 20 Nov 2024 09:33:33 +0100
Subject: [PATCH 1/2] 1301 feature request add confidence intervals for
 quantiles in surv time (#1306)

# Pull Request
Fixes #1301
@melkiades
I'm not sure about the impact of adding new stats to an analyze function
on the remainder of the code/packages.
Could you review and share your thoughts?
This is the first function for which we'd like to add extra stats, there
will be more functions for which we'd like to combine the stat and it's
confidence interval into 1 line.
Once we know the approach we can follow, more of these types of updates
might follow.

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: Davide Garolini <davide.garolini@roche.com>
Co-authored-by: Joe Zhu <joe.zhu@roche.com>
Co-authored-by: shajoezhu <sha.joe.zhu@gmail.com>
---
 NEWS.md                                       |   5 +
 R/analyze_variables.R                         |  11 +
 R/survival_coxph_pairwise.R                   |   8 +-
 R/survival_time.R                             |  50 ++++-
 R/survival_timepoint.R                        |  20 +-
 R/utils_default_stats_formats_labels.R        |  38 +++-
 man/analyze_variables.Rd                      |   2 +-
 man/compare_variables.Rd                      |   2 +-
 man/summarize_change.Rd                       |   2 +-
 man/survival_time.Rd                          |   5 +-
 man/survival_timepoint.Rd                     |   4 +-
 tests/testthat/_snaps/analyze_variables.md    | 198 +++++++++++++-----
 tests/testthat/_snaps/compare_variables.md    |  12 +-
 tests/testthat/_snaps/summarize_change.md     |  72 +++++++
 .../_snaps/survival_coxph_pairwise.md         |  20 ++
 tests/testthat/_snaps/survival_time.md        |  68 ++++--
 tests/testthat/_snaps/survival_timepoint.md   |  25 +++
 .../utils_default_stats_formats_labels.md     |  50 +++--
 tests/testthat/test-utils_rtables.R           |   1 +
 19 files changed, 482 insertions(+), 111 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 7e8b78f29d..ead9eb614e 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -20,6 +20,11 @@
 # tern 0.9.6
 
 ### Enhancements
+* Added `median_ci_3d` to `s_summary` which includes estimate and confidence interval in one statistic.
+* Added `median_ci_3d`, `quantiles_lower` and `quantiles_upper` to `s_surv_time` which includes estimate and confidence interval in one statistic.
+* Added `hr_ci_3d` to `s_coxph_pairwise` which includes estimate and confidence interval in one statistic.
+* Added `event_free_rate_3d` to `s_surv_timepoint` which includes estimate and confidence interval in one statistic.
+* Added `rate_diff_ci_3d` to `s_surv_timepoint_diff` which includes estimate and confidence interval in one statistic.
 * Added `errorbar_width` and `linetype` parameters to `g_lineplot`.
 * Added the `.formats` argument to `tabulate_rsp_subgroups` and `tabulate_survival_subgroups` to allow users to specify formats.
 * Added the `riskdiff` argument to `tabulate_rsp_subgroups` and `tabulate_survival_subgroups` to allow users to add a risk difference table column, and function `control_riskdiff` to specify settings for the risk difference column.
diff --git a/R/analyze_variables.R b/R/analyze_variables.R
index 5af2961f10..392a253f18 100644
--- a/R/analyze_variables.R
+++ b/R/analyze_variables.R
@@ -190,6 +190,8 @@ s_summary.numeric <- function(x,
   mean_sdi <- y$mean[[1]] + c(-1, 1) * stats::sd(x, na.rm = FALSE)
   names(mean_sdi) <- c("mean_sdi_lwr", "mean_sdi_upr")
   y$mean_sdi <- formatters::with_label(mean_sdi, "Mean -/+ 1xSD")
+  mean_ci_3d <- c(y$mean, y$mean_ci)
+  y$mean_ci_3d <- formatters::with_label(mean_ci_3d, paste0("Mean (", f_conf_level(control$conf_level), ")"))
 
   mean_pval <- stat_mean_pval(x, test_mean = control$test_mean, na.rm = FALSE, n_min = 2)
   y$mean_pval <- formatters::with_label(mean_pval, paste("Mean", f_pval(control$test_mean)))
@@ -201,6 +203,9 @@ s_summary.numeric <- function(x,
   median_ci <- stat_median_ci(x, conf_level = control$conf_level, na.rm = FALSE, gg_helper = FALSE)
   y$median_ci <- formatters::with_label(median_ci, paste("Median", f_conf_level(control$conf_level)))
 
+  median_ci_3d <- c(y$median, median_ci)
+  y$median_ci_3d <- formatters::with_label(median_ci_3d, paste0("Median (", f_conf_level(control$conf_level), ")"))
+
   q <- control$quantiles
   if (any(is.na(x))) {
     qnts <- rep(NA_real_, length(q))
@@ -233,6 +238,12 @@ s_summary.numeric <- function(x,
 
   y$geom_cv <- c("geom_cv" = sqrt(exp(stats::sd(log(x_no_negative_vals), na.rm = FALSE) ^ 2) - 1) * 100) # styler: off
 
+  geom_mean_ci_3d <- c(y$geom_mean, y$geom_mean_ci)
+  y$geom_mean_ci_3d <- formatters::with_label(
+    geom_mean_ci_3d,
+    paste0("Geometric Mean (", f_conf_level(control$conf_level), ")")
+  )
+
   y
 }
 
diff --git a/R/survival_coxph_pairwise.R b/R/survival_coxph_pairwise.R
index 823c159379..f8cf696bf5 100644
--- a/R/survival_coxph_pairwise.R
+++ b/R/survival_coxph_pairwise.R
@@ -66,6 +66,7 @@ s_coxph_pairwise <- function(df,
         pvalue = formatters::with_label("", paste0("p-value (", pval_method, ")")),
         hr = formatters::with_label("", "Hazard Ratio"),
         hr_ci = formatters::with_label("", f_conf_level(conf_level)),
+        hr_ci_3d = formatters::with_label("", paste0("Hazard Ratio (", f_conf_level(conf_level), ")")),
         n_tot = formatters::with_label("", "Total n"),
         n_tot_events = formatters::with_label("", "Total events")
       )
@@ -112,6 +113,10 @@ s_coxph_pairwise <- function(df,
     pvalue = formatters::with_label(unname(pval), paste0("p-value (", pval_method, ")")),
     hr = formatters::with_label(sum_cox$conf.int[1, 1], "Hazard Ratio"),
     hr_ci = formatters::with_label(unname(sum_cox$conf.int[1, 3:4]), f_conf_level(conf_level)),
+    hr_ci_3d = formatters::with_label(
+      c(sum_cox$conf.int[1, 1], unname(sum_cox$conf.int[1, 3:4])),
+      paste0("Hazard Ratio (", f_conf_level(conf_level), ")")
+    ),
     n_tot = formatters::with_label(sum_cox$n, "Total n"),
     n_tot_events = formatters::with_label(sum_cox$nevent, "Total events")
   )
@@ -125,11 +130,12 @@ s_coxph_pairwise <- function(df,
 #' @keywords internal
 a_coxph_pairwise <- make_afun(
   s_coxph_pairwise,
-  .indent_mods = c(pvalue = 0L, hr = 0L, hr_ci = 1L, n_tot = 0L, n_tot_events = 0L),
+  .indent_mods = c(pvalue = 0L, hr = 0L, hr_ci = 1L, n_tot = 0L, n_tot_events = 0L, hr_ci_3d = 0L),
   .formats = c(
     pvalue = "x.xxxx | (<0.0001)",
     hr = "xx.xx",
     hr_ci = "(xx.xx, xx.xx)",
+    hr_ci_3d = "xx.xx (xx.xx - xx.xx)",
     n_tot = "xx.xx",
     n_tot_events = "xx.xx"
   )
diff --git a/R/survival_time.R b/R/survival_time.R
index de12ff681d..6d1d2d5ee9 100644
--- a/R/survival_time.R
+++ b/R/survival_time.R
@@ -44,7 +44,10 @@ NULL
 #' * `s_surv_time()` returns the statistics:
 #'   * `median`: Median survival time.
 #'   * `median_ci`: Confidence interval for median time.
+#'   * `median_ci_3d`: Median with confidence interval for median time.
 #'   * `quantiles`: Survival time for two specified quantiles.
+#'   * `quantiles_lower`: quantile with confidence interval for the first specified quantile.
+#'   * `quantiles_upper`: quantile with confidence interval for the second specified quantile.
 #'   * `range_censor`: Survival time range for censored observations.
 #'   * `range_event`: Survival time range for observations with events.
 #'   * `range`: Survival time range for all observations.
@@ -71,10 +74,24 @@ s_surv_time <- function(df,
     conf.type = conf_type
   )
   srv_tab <- summary(srv_fit, extend = TRUE)$table
-  srv_qt_tab <- stats::quantile(srv_fit, probs = quantiles)$quantile
+  srv_qt_tab_pre <- stats::quantile(srv_fit, probs = quantiles)
+  srv_qt_tab <- srv_qt_tab_pre$quantile
   range_censor <- range_noinf(df[[.var]][!df[[is_event]]], na.rm = TRUE)
   range_event <- range_noinf(df[[.var]][df[[is_event]]], na.rm = TRUE)
   range <- range_noinf(df[[.var]], na.rm = TRUE)
+
+  names(quantiles) <- as.character(100 * quantiles)
+  srv_qt_tab_pre <- unlist(srv_qt_tab_pre)
+  srv_qt_ci <- lapply(quantiles, function(x) {
+    name <- as.character(100 * x)
+
+    c(
+      srv_qt_tab_pre[[paste0("quantile.", name)]],
+      srv_qt_tab_pre[[paste0("lower.", name)]],
+      srv_qt_tab_pre[[paste0("upper.", name)]]
+    )
+  })
+
   list(
     median = formatters::with_label(unname(srv_tab["median"]), "Median"),
     median_ci = formatters::with_label(
@@ -85,7 +102,20 @@ s_surv_time <- function(df,
     ),
     range_censor = formatters::with_label(range_censor, "Range (censored)"),
     range_event = formatters::with_label(range_event, "Range (event)"),
-    range = formatters::with_label(range, "Range")
+    range = formatters::with_label(range, "Range"),
+    median_ci_3d = formatters::with_label(
+      c(
+        unname(srv_tab["median"]),
+        unname(srv_tab[paste0(srv_fit$conf.int, c("LCL", "UCL"))])
+      ),
+      paste0("Median (", f_conf_level(conf_level), ")")
+    ),
+    quantiles_lower = formatters::with_label(
+      unname(srv_qt_ci[[1]]), paste0(quantiles[1] * 100, "%-ile (", f_conf_level(conf_level), ")")
+    ),
+    quantiles_upper = formatters::with_label(
+      unname(srv_qt_ci[[2]]), paste0(quantiles[2] * 100, "%-ile (", f_conf_level(conf_level), ")")
+    )
   )
 }
 
@@ -122,8 +152,17 @@ a_surv_time <- function(df,
   rng_censor_upr <- x_stats[["range_censor"]][2]
 
   # Use method-specific defaults
-  fmts <- c(median_ci = "(xx.x, xx.x)", quantiles = "xx.x, xx.x", range = "xx.x to xx.x")
-  lbls <- c(median_ci = "95% CI", range = "Range", range_censor = "Range (censored)", range_event = "Range (event)")
+  fmts <- c(
+    median_ci = "(xx.x, xx.x)", quantiles = "xx.x, xx.x", range = "xx.x to xx.x",
+    median_ci_3d = "xx.x (xx.x - xx.x)",
+    quantiles_lower = "xx.x (xx.x - xx.x)", quantiles_upper = "xx.x (xx.x - xx.x)"
+  )
+  lbls <- c(
+    median_ci = "95% CI", range = "Range", range_censor = "Range (censored)", range_event = "Range (event)",
+    median_ci_3d = "Median (95% CI)",
+    quantiles_lower = "25%-ile (95% CI)",
+    quantiles_upper = "75%-ile (95% CI)"
+  )
   lbls_custom <- .labels
   .formats <- c(.formats, fmts[setdiff(names(fmts), names(.formats))])
   .labels <- c(.labels, lbls[setdiff(names(lbls), names(lbls_custom))])
@@ -156,7 +195,6 @@ a_surv_time <- function(df,
     .names = .labels,
     .labels = .labels,
     .indent_mods = .indent_mods,
-    .format_na_strs = na_str,
     .cell_footnotes = cell_fns
   )
 }
@@ -199,7 +237,7 @@ surv_time <- function(lyt,
                       .labels = NULL,
                       .indent_mods = c(median_ci = 1L)) {
   extra_args <- list(
-    .stats = .stats, .formats = .formats, .labels = .labels, .indent_mods = .indent_mods, na_str = na_str,
+    .stats = .stats, .formats = .formats, .labels = .labels, .indent_mods = .indent_mods,
     is_event = is_event, control = control, ref_fn_censor = ref_fn_censor, ...
   )
 
diff --git a/R/survival_timepoint.R b/R/survival_timepoint.R
index 0bbb0e2248..9a95784504 100644
--- a/R/survival_timepoint.R
+++ b/R/survival_timepoint.R
@@ -40,6 +40,7 @@ NULL
 #'   * `event_free_rate`: Event-free rate (%).
 #'   * `rate_se`: Standard error of event free rate.
 #'   * `rate_ci`: Confidence interval for event free rate.
+#'   * `event_free_rate_3d`: Event-free rate (%) with Confidence interval.
 #'
 #' @keywords internal
 s_surv_timepoint <- function(df,
@@ -74,11 +75,15 @@ s_surv_timepoint <- function(df,
     rate_se <- df_srv_fit$std.err
     rate_ci <- c(df_srv_fit$lower, df_srv_fit$upper)
   }
+  event_free_rate_3d <- c(event_free_rate, rate_ci)
   list(
     pt_at_risk = formatters::with_label(pt_at_risk, "Patients remaining at risk"),
     event_free_rate = formatters::with_label(event_free_rate * 100, "Event Free Rate (%)"),
     rate_se = formatters::with_label(rate_se * 100, "Standard Error of Event Free Rate"),
-    rate_ci = formatters::with_label(rate_ci * 100, f_conf_level(conf_level))
+    rate_ci = formatters::with_label(rate_ci * 100, f_conf_level(conf_level)),
+    event_free_rate_3d = formatters::with_label(
+      event_free_rate_3d * 100, paste0("Event Free Rate (", f_conf_level(conf_level), ")")
+    )
   )
 }
 
@@ -111,6 +116,7 @@ a_surv_timepoint <- make_afun(
 #' * `s_surv_timepoint_diff()` returns the statistics:
 #'   * `rate_diff`: Event-free rate difference between two groups.
 #'   * `rate_diff_ci`: Confidence interval for the difference.
+#'   * `rate_diff_ci_3d`: Event-free rate difference and confidence interval between two groups.
 #'   * `ztest_pval`: p-value to test the difference is 0.
 #'
 #' @keywords internal
@@ -126,6 +132,9 @@ s_surv_timepoint_diff <- function(df,
       list(
         rate_diff = formatters::with_label("", "Difference in Event Free Rate"),
         rate_diff_ci = formatters::with_label("", f_conf_level(control$conf_level)),
+        rate_diff_ci_3d = formatters::with_label(
+          "", paste0("Difference in Event Free Rate", f_conf_level(control$conf_level))
+        ),
         ztest_pval = formatters::with_label("", "p-value (Z-test)")
       )
     )
@@ -143,6 +152,7 @@ s_surv_timepoint_diff <- function(df,
 
   qs <- c(-1, 1) * stats::qnorm(1 - (1 - control$conf_level) / 2)
   rate_diff_ci <- rate_diff + qs * se_diff
+  rate_diff_ci_3d <- c(rate_diff, rate_diff_ci)
   ztest_pval <- if (is.na(rate_diff)) {
     NA
   } else {
@@ -151,6 +161,9 @@ s_surv_timepoint_diff <- function(df,
   list(
     rate_diff = formatters::with_label(rate_diff, "Difference in Event Free Rate"),
     rate_diff_ci = formatters::with_label(rate_diff_ci, f_conf_level(control$conf_level)),
+    rate_diff_ci_3d = formatters::with_label(
+      rate_diff_ci_3d, paste0("Difference in Event Free Rate", f_conf_level(control$conf_level))
+    ),
     ztest_pval = formatters::with_label(ztest_pval, "p-value (Z-test)")
   )
 }
@@ -167,6 +180,7 @@ a_surv_timepoint_diff <- make_afun(
   .formats = c(
     rate_diff = "xx.xx",
     rate_diff_ci = "(xx.xx, xx.xx)",
+    rate_diff_ci_3d = format_xx("xx.xx (xx.xx, xx.xx)"),
     ztest_pval = "x.xxxx | (<0.0001)"
   )
 )
@@ -260,8 +274,8 @@ surv_timepoint <- function(lyt,
   extra_args <- list(time_point = time_point, is_event = is_event, control = control, ...)
 
   f <- list(
-    surv = c("pt_at_risk", "event_free_rate", "rate_se", "rate_ci"),
-    surv_diff = c("rate_diff", "rate_diff_ci", "ztest_pval")
+    surv = c("pt_at_risk", "event_free_rate", "rate_se", "rate_ci", "event_free_rate_3d"),
+    surv_diff = c("rate_diff", "rate_diff_ci", "ztest_pval", "rate_diff_ci_3d")
   )
   .stats <- h_split_param(.stats, .stats, f = f)
   .formats <- h_split_param(.formats, names(.formats), f = f)
diff --git a/R/utils_default_stats_formats_labels.R b/R/utils_default_stats_formats_labels.R
index b97acf4a08..64a041b715 100644
--- a/R/utils_default_stats_formats_labels.R
+++ b/R/utils_default_stats_formats_labels.R
@@ -395,6 +395,20 @@ labels_use_control <- function(labels_default, control, labels_custom = NULL) {
       labels_default["quantiles"]
     )
   }
+  if ("quantiles" %in% names(control) && "quantiles_lower" %in% names(labels_default) &&
+    !"quantiles_lower" %in% names(labels_custom)) { # nolint
+    labels_default["quantiles_lower"] <- gsub(
+      "[0-9]+%-ile", paste0(control[["quantiles"]][1] * 100, "%-ile", ""),
+      labels_default["quantiles_lower"]
+    )
+  }
+  if ("quantiles" %in% names(control) && "quantiles_upper" %in% names(labels_default) &&
+    !"quantiles_upper" %in% names(labels_custom)) { # nolint
+    labels_default["quantiles_upper"] <- gsub(
+      "[0-9]+%-ile", paste0(control[["quantiles"]][2] * 100, "%-ile", ""),
+      labels_default["quantiles_upper"]
+    )
+  }
   if ("test_mean" %in% names(control) && "mean_pval" %in% names(labels_default) &&
     !"mean_pval" %in% names(labels_custom)) { # nolint
     labels_default["mean_pval"] <- gsub(
@@ -423,7 +437,9 @@ tern_default_stats <- list(
   analyze_vars_numeric = c(
     "n", "sum", "mean", "sd", "se", "mean_sd", "mean_se", "mean_ci", "mean_sei", "mean_sdi", "mean_pval",
     "median", "mad", "median_ci", "quantiles", "iqr", "range", "min", "max", "median_range", "cv",
-    "geom_mean", "geom_mean_ci", "geom_cv"
+    "geom_mean", "geom_mean_ci", "geom_cv",
+    "median_ci_3d",
+    "mean_ci_3d", "geom_mean_ci_3d"
   ),
   count_cumulative = c("count_fraction", "count_fraction_fixed_dp"),
   count_missed_doses = c("n", "count_fraction", "count_fraction_fixed_dp"),
@@ -443,8 +459,14 @@ tern_default_stats <- list(
   summarize_glm_count = c("n", "rate", "rate_ci", "rate_ratio", "rate_ratio_ci", "pval"),
   summarize_num_patients = c("unique", "nonunique", "unique_count"),
   summarize_patients_events_in_cols = c("unique", "all"),
-  surv_time = c("median", "median_ci", "quantiles", "range_censor", "range_event", "range"),
-  surv_timepoint = c("pt_at_risk", "event_free_rate", "rate_se", "rate_ci", "rate_diff", "rate_diff_ci", "ztest_pval"),
+  surv_time = c(
+    "median", "median_ci", "median_ci_3d", "quantiles",
+    "quantiles_lower", "quantiles_upper", "range_censor", "range_event", "range"
+  ),
+  surv_timepoint = c(
+    "pt_at_risk", "event_free_rate", "rate_se", "rate_ci", "rate_diff", "rate_diff_ci", "ztest_pval",
+    "event_free_rate_3d"
+  ),
   tabulate_rsp_biomarkers = c("n_tot", "n_rsp", "prop", "or", "ci", "pval"),
   tabulate_rsp_subgroups = c("n", "n_rsp", "prop", "n_tot", "or", "ci", "pval"),
   tabulate_survival_biomarkers = c("n_tot", "n_tot_events", "median", "hr", "ci", "pval"),
@@ -479,10 +501,14 @@ tern_default_formats <- c(
   mean_sei = "(xx.xx, xx.xx)",
   mean_sdi = "(xx.xx, xx.xx)",
   mean_pval = "x.xxxx | (<0.0001)",
+  mean_ci_3d = "xx.xx (xx.xx - xx.xx)",
   median = "xx.x",
   mad = "xx.x",
   median_ci = "(xx.xx, xx.xx)",
+  median_ci_3d = "xx.xx (xx.xx - xx.xx)",
   quantiles = "xx.x - xx.x",
+  quantiles_lower = "xx.xx (xx.xx - xx.xx)",
+  quantiles_upper = "xx.xx (xx.xx - xx.xx)",
   iqr = "xx.x",
   range = "xx.x - xx.x",
   min = "xx.x",
@@ -491,6 +517,7 @@ tern_default_formats <- c(
   cv = "xx.x",
   geom_mean = "xx.x",
   geom_mean_ci = "(xx.xx, xx.xx)",
+  geom_mean_ci_3d = "xx.xx (xx.xx - xx.xx)",
   geom_cv = "xx.x",
   pval = "x.xxxx | (<0.0001)",
   pval_counts = "x.xxxx | (<0.0001)",
@@ -528,10 +555,14 @@ tern_default_labels <- c(
   mean_sei = "Mean -/+ 1xSE",
   mean_sdi = "Mean -/+ 1xSD",
   mean_pval = "Mean p-value (H0: mean = 0)",
+  mean_ci_3d = "Mean (95% CI)",
   median = "Median",
   mad = "Median Absolute Deviation",
   median_ci = "Median 95% CI",
+  median_ci_3d = "Median (95% CI)",
   quantiles = "25% and 75%-ile",
+  quantiles_lower = "25%-ile (95% CI)",
+  quantiles_upper = "75%-ile (95% CI)",
   iqr = "IQR",
   range = "Min - Max",
   min = "Minimum",
@@ -540,6 +571,7 @@ tern_default_labels <- c(
   cv = "CV (%)",
   geom_mean = "Geometric Mean",
   geom_mean_ci = "Geometric Mean 95% CI",
+  geom_mean_ci_3d = "Geometric Mean (95% CI)",
   geom_cv = "CV % Geometric Mean",
   pval = "p-value (t-test)", # Default for numeric
   pval_counts = "p-value (chi-squared test)", # Default for counts
diff --git a/man/analyze_variables.Rd b/man/analyze_variables.Rd
index 18a6b603dc..ba567bd1ae 100644
--- a/man/analyze_variables.Rd
+++ b/man/analyze_variables.Rd
@@ -115,7 +115,7 @@ defined by this split instruction, or \code{NA_character_} (the default) for no
 
 \item{.stats}{(\code{character})\cr statistics to select for the table.
 
-Options for numeric variables are: \verb{'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv'}
+Options for numeric variables are: \verb{'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv', 'median_ci_3d', 'mean_ci_3d', 'geom_mean_ci_3d'}
 
 Options for non-numeric variables are: \verb{'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction', 'n_blq'}}
 
diff --git a/man/compare_variables.Rd b/man/compare_variables.Rd
index 5f9d0cd1f7..b5b611ffd9 100644
--- a/man/compare_variables.Rd
+++ b/man/compare_variables.Rd
@@ -73,7 +73,7 @@ defined by this split instruction, or \code{NA_character_} (the default) for no
 
 \item{.stats}{(\code{character})\cr statistics to select for the table.
 
-Options for numeric variables are: \verb{'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv', 'pval'}
+Options for numeric variables are: \verb{'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv', 'median_ci_3d', 'mean_ci_3d', 'geom_mean_ci_3d', 'pval'}
 
 Options for non-numeric variables are: \verb{'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction', 'n_blq', 'pval_counts'}}
 
diff --git a/man/summarize_change.Rd b/man/summarize_change.Rd
index b37cdd761c..f324348b6a 100644
--- a/man/summarize_change.Rd
+++ b/man/summarize_change.Rd
@@ -65,7 +65,7 @@ defined by this split instruction, or \code{NA_character_} (the default) for no
 
 \item{.stats}{(\code{character})\cr statistics to select for the table.
 
-Options are: \verb{'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv'}}
+Options are: \verb{'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv', 'median_ci_3d', 'mean_ci_3d', 'geom_mean_ci_3d'}}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/survival_time.Rd b/man/survival_time.Rd
index 4a150208da..3961d4e1e3 100644
--- a/man/survival_time.Rd
+++ b/man/survival_time.Rd
@@ -78,7 +78,7 @@ times, to avoid warnings from \code{rtables}.}
 
 \item{.stats}{(\code{character})\cr statistics to select for the table.
 
-Options are: \verb{'median', 'median_ci', 'quantiles', 'range_censor', 'range_event', 'range'}}
+Options are: \verb{'median', 'median_ci', 'median_ci_3d', 'quantiles', 'quantiles_lower', 'quantiles_upper', 'range_censor', 'range_event', 'range'}}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
@@ -112,7 +112,10 @@ the statistics from \code{s_surv_time()} to the table layout.
 \itemize{
 \item \code{median}: Median survival time.
 \item \code{median_ci}: Confidence interval for median time.
+\item \code{median_ci_3d}: Median with confidence interval for median time.
 \item \code{quantiles}: Survival time for two specified quantiles.
+\item \code{quantiles_lower}: quantile with confidence interval for the first specified quantile.
+\item \code{quantiles_upper}: quantile with confidence interval for the second specified quantile.
 \item \code{range_censor}: Survival time range for censored observations.
 \item \code{range_event}: Survival time range for observations with events.
 \item \code{range}: Survival time range for all observations.
diff --git a/man/survival_timepoint.Rd b/man/survival_timepoint.Rd
index 2420718a1b..f3d96c5d2b 100644
--- a/man/survival_timepoint.Rd
+++ b/man/survival_timepoint.Rd
@@ -107,7 +107,7 @@ avoid warnings from duplicate table names.}
 
 \item{.stats}{(\code{character})\cr statistics to select for the table.
 
-Options are: \verb{'pt_at_risk', 'event_free_rate', 'rate_se', 'rate_ci', 'rate_diff', 'rate_diff_ci', 'ztest_pval'}}
+Options are: \verb{'pt_at_risk', 'event_free_rate', 'rate_se', 'rate_ci', 'rate_diff', 'rate_diff_ci', 'ztest_pval', 'event_free_rate_3d'}}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
@@ -142,6 +142,7 @@ the value of \code{method}.
 \item \code{event_free_rate}: Event-free rate (\%).
 \item \code{rate_se}: Standard error of event free rate.
 \item \code{rate_ci}: Confidence interval for event free rate.
+\item \code{event_free_rate_3d}: Event-free rate (\%) with Confidence interval.
 }
 }
 
@@ -154,6 +155,7 @@ the value of \code{method}.
 \itemize{
 \item \code{rate_diff}: Event-free rate difference between two groups.
 \item \code{rate_diff_ci}: Confidence interval for the difference.
+\item \code{rate_diff_ci_3d}: Event-free rate difference and confidence interval between two groups.
 \item \code{ztest_pval}: p-value to test the difference is 0.
 }
 }
diff --git a/tests/testthat/_snaps/analyze_variables.md b/tests/testthat/_snaps/analyze_variables.md
index f367f7e1ad..021a9756f7 100644
--- a/tests/testthat/_snaps/analyze_variables.md
+++ b/tests/testthat/_snaps/analyze_variables.md
@@ -49,6 +49,12 @@
       attr(,"label")
       [1] "Mean -/+ 1xSD"
       
+      $mean_ci_3d
+             mean mean_ci_lwr mean_ci_upr 
+               NA          NA          NA 
+      attr(,"label")
+      [1] "Mean (95% CI)"
+      
       $mean_pval
       p_value 
            NA 
@@ -71,6 +77,12 @@
       attr(,"label")
       [1] "Median 95% CI"
       
+      $median_ci_3d
+             median median_ci_lwr median_ci_upr 
+                 NA            NA            NA 
+      attr(,"label")
+      [1] "Median (95% CI)"
+      
       $quantiles
       quantile_0.25 quantile_0.75 
                  NA            NA 
@@ -117,6 +129,12 @@
       geom_cv 
            NA 
       
+      $geom_mean_ci_3d
+        geom_mean mean_ci_lwr mean_ci_upr 
+              NaN          NA          NA 
+      attr(,"label")
+      [1] "Geometric Mean (95% CI)"
+      
 
 # s_summary handles NA
 
@@ -169,6 +187,12 @@
       attr(,"label")
       [1] "Mean -/+ 1xSD"
       
+      $mean_ci_3d
+             mean mean_ci_lwr mean_ci_upr 
+                1          NA          NA 
+      attr(,"label")
+      [1] "Mean (95% CI)"
+      
       $mean_pval
       p_value 
            NA 
@@ -191,6 +215,12 @@
       attr(,"label")
       [1] "Median 95% CI"
       
+      $median_ci_3d
+             median median_ci_lwr median_ci_upr 
+                  1            NA            NA 
+      attr(,"label")
+      [1] "Median (95% CI)"
+      
       $quantiles
       quantile_0.25 quantile_0.75 
                   1             1 
@@ -237,6 +267,12 @@
       geom_cv 
            NA 
       
+      $geom_mean_ci_3d
+        geom_mean mean_ci_lwr mean_ci_upr 
+                1          NA          NA 
+      attr(,"label")
+      [1] "Geometric Mean (95% CI)"
+      
 
 ---
 
@@ -289,6 +325,12 @@
       attr(,"label")
       [1] "Mean -/+ 1xSD"
       
+      $mean_ci_3d
+             mean mean_ci_lwr mean_ci_upr 
+               NA          NA          NA 
+      attr(,"label")
+      [1] "Mean (95% CI)"
+      
       $mean_pval
       p_value 
            NA 
@@ -311,6 +353,12 @@
       attr(,"label")
       [1] "Median 95% CI"
       
+      $median_ci_3d
+             median median_ci_lwr median_ci_upr 
+                 NA            NA            NA 
+      attr(,"label")
+      [1] "Median (95% CI)"
+      
       $quantiles
       quantile_0.25 quantile_0.75 
                  NA            NA 
@@ -357,6 +405,12 @@
       geom_cv 
            NA 
       
+      $geom_mean_ci_3d
+        geom_mean mean_ci_lwr mean_ci_upr 
+               NA          NA          NA 
+      attr(,"label")
+      [1] "Geometric Mean (95% CI)"
+      
 
 # s_summary returns right results for n = 2
 
@@ -409,6 +463,12 @@
       attr(,"label")
       [1] "Mean -/+ 1xSD"
       
+      $mean_ci_3d
+             mean mean_ci_lwr mean_ci_upr 
+         1.500000   -4.853102    7.853102 
+      attr(,"label")
+      [1] "Mean (95% CI)"
+      
       $mean_pval
         p_value 
       0.2048328 
@@ -431,6 +491,12 @@
       attr(,"label")
       [1] "Median 95% CI"
       
+      $median_ci_3d
+             median median_ci_lwr median_ci_upr 
+                1.5            NA            NA 
+      attr(,"label")
+      [1] "Median (95% CI)"
+      
       $quantiles
       quantile_0.25 quantile_0.75 
                   1             2 
@@ -477,6 +543,12 @@
        geom_cv 
       52.10922 
       
+      $geom_mean_ci_3d
+         geom_mean  mean_ci_lwr  mean_ci_upr 
+        1.41421356   0.01729978 115.60839614 
+      attr(,"label")
+      [1] "Geometric Mean (95% CI)"
+      
 
 # s_summary returns right results for n = 8
 
@@ -529,6 +601,12 @@
       attr(,"label")
       [1] "Mean -/+ 1xSD"
       
+      $mean_ci_3d
+             mean mean_ci_lwr mean_ci_upr 
+         6.000000    3.318768    8.681232 
+      attr(,"label")
+      [1] "Mean (95% CI)"
+      
       $mean_pval
           p_value 
       0.001133783 
@@ -551,6 +629,12 @@
       attr(,"label")
       [1] "Median 95% CI"
       
+      $median_ci_3d
+             median median_ci_lwr median_ci_upr 
+                6.5           1.0          10.0 
+      attr(,"label")
+      [1] "Median (95% CI)"
+      
       $quantiles
       quantile_0.25 quantile_0.75 
                 3.5           8.5 
@@ -597,6 +681,12 @@
        geom_cv 
       96.61307 
       
+      $geom_mean_ci_3d
+        geom_mean mean_ci_lwr mean_ci_upr 
+         4.842534    2.456211    9.547283 
+      attr(,"label")
+      [1] "Geometric Mean (95% CI)"
+      
 
 # s_summary works with factors
 
@@ -1033,31 +1123,34 @@
     Output
       RowsVerticalSection (in_rows) object print method:
       ----------------------------
-             row_name   formatted_cell indent_mod                   row_label
-      1             n               10          0                           n
-      2           sum              1.3          0                         Sum
-      3          mean              0.1          0                        Mean
-      4            sd              0.8          0                          SD
-      5            se              0.2          0                          SE
-      6       mean_sd        0.1 (0.8)          0                   Mean (SD)
-      7       mean_se        0.1 (0.2)          0                   Mean (SE)
-      8       mean_ci    (-0.43, 0.69)          0                 Mean 95% CI
-      9      mean_sei    (-0.11, 0.38)          0               Mean -/+ 1xSE
-      10     mean_sdi    (-0.65, 0.91)          0               Mean -/+ 1xSD
-      11    mean_pval           0.6052          0 Mean p-value (H0: mean = 0)
-      12       median              0.3          0                      Median
-      13          mad             -0.0          0   Median Absolute Deviation
-      14    median_ci    (-0.82, 0.74)          0               Median 95% CI
-      15    quantiles       -0.6 - 0.6          0             25% and 75%-ile
-      16          iqr              1.2          0                         IQR
-      17        range       -0.8 - 1.6          0                   Min - Max
-      18          min             -0.8          0                     Minimum
-      19          max              1.6          0                     Maximum
-      20 median_range 0.3 (-0.8 - 1.6)          0          Median (Min - Max)
-      21           cv            590.4          0                      CV (%)
-      22    geom_mean               NA          0              Geometric Mean
-      23 geom_mean_ci               NA          0       Geometric Mean 95% CI
-      24      geom_cv               NA          0         CV % Geometric Mean
+                row_name      formatted_cell indent_mod                   row_label
+      1                n                  10          0                           n
+      2              sum                 1.3          0                         Sum
+      3             mean                 0.1          0                        Mean
+      4               sd                 0.8          0                          SD
+      5               se                 0.2          0                          SE
+      6          mean_sd           0.1 (0.8)          0                   Mean (SD)
+      7          mean_se           0.1 (0.2)          0                   Mean (SE)
+      8          mean_ci       (-0.43, 0.69)          0                 Mean 95% CI
+      9         mean_sei       (-0.11, 0.38)          0               Mean -/+ 1xSE
+      10        mean_sdi       (-0.65, 0.91)          0               Mean -/+ 1xSD
+      11       mean_pval              0.6052          0 Mean p-value (H0: mean = 0)
+      12          median                 0.3          0                      Median
+      13             mad                -0.0          0   Median Absolute Deviation
+      14       median_ci       (-0.82, 0.74)          0               Median 95% CI
+      15       quantiles          -0.6 - 0.6          0             25% and 75%-ile
+      16             iqr                 1.2          0                         IQR
+      17           range          -0.8 - 1.6          0                   Min - Max
+      18             min                -0.8          0                     Minimum
+      19             max                 1.6          0                     Maximum
+      20    median_range    0.3 (-0.8 - 1.6)          0          Median (Min - Max)
+      21              cv               590.4          0                      CV (%)
+      22       geom_mean                  NA          0              Geometric Mean
+      23    geom_mean_ci                  NA          0       Geometric Mean 95% CI
+      24         geom_cv                  NA          0         CV % Geometric Mean
+      25    median_ci_3d 0.26 (-0.82 - 0.74)          0             Median (95% CI)
+      26      mean_ci_3d 0.13 (-0.43 - 0.69)          0               Mean (95% CI)
+      27 geom_mean_ci_3d                  NA          0     Geometric Mean (95% CI)
 
 ---
 
@@ -1165,32 +1258,35 @@
     Output
       RowsVerticalSection (in_rows) object print method:
       ----------------------------
-             row_name  formatted_cell indent_mod                   row_label
-      1             n              10          0                           n
-      2           sum            51.3          0                         Sum
-      3          mean             5.1          0                        Mean
-      4            sd             0.8          0                          SD
-      5            se             0.2          0                          SE
-      6       mean_sd       5.1 (0.8)          0                   Mean (SD)
-      7       mean_se       5.1 (0.2)          0                   Mean (SE)
-      8       mean_ci    (4.57, 5.69)          0                 Mean 95% CI
-      9      mean_sei    (4.89, 5.38)          0               Mean -/+ 1xSE
-      10     mean_sdi    (4.35, 5.91)          0               Mean -/+ 1xSD
-      11    mean_pval         <0.0001          0 Mean p-value (H0: mean = 0)
-      12       median             5.3          0                      Median
-      13          mad            -0.0          0   Median Absolute Deviation
-      14    median_ci    (4.18, 5.74)          0               Median 95% CI
-      15    quantiles       4.4 - 5.6          0             25% and 75%-ile
-      16          iqr             1.2          0                         IQR
-      17        range       4.2 - 6.6          0                   Min - Max
-      18          min             4.2          0                     Minimum
-      19          max             6.6          0                     Maximum
-      20 median_range 5.3 (4.2 - 6.6)          0          Median (Min - Max)
-      21           cv            15.2          0                      CV (%)
-      22    geom_mean             5.1          0              Geometric Mean
-      23 geom_mean_ci    (4.56, 5.66)          0       Geometric Mean 95% CI
-      24      geom_cv            15.2          0         CV % Geometric Mean
-      25         pval         <0.0001          0            p-value (t-test)
+                row_name     formatted_cell indent_mod                   row_label
+      1                n                 10          0                           n
+      2              sum               51.3          0                         Sum
+      3             mean                5.1          0                        Mean
+      4               sd                0.8          0                          SD
+      5               se                0.2          0                          SE
+      6          mean_sd          5.1 (0.8)          0                   Mean (SD)
+      7          mean_se          5.1 (0.2)          0                   Mean (SE)
+      8          mean_ci       (4.57, 5.69)          0                 Mean 95% CI
+      9         mean_sei       (4.89, 5.38)          0               Mean -/+ 1xSE
+      10        mean_sdi       (4.35, 5.91)          0               Mean -/+ 1xSD
+      11       mean_pval            <0.0001          0 Mean p-value (H0: mean = 0)
+      12          median                5.3          0                      Median
+      13             mad               -0.0          0   Median Absolute Deviation
+      14       median_ci       (4.18, 5.74)          0               Median 95% CI
+      15       quantiles          4.4 - 5.6          0             25% and 75%-ile
+      16             iqr                1.2          0                         IQR
+      17           range          4.2 - 6.6          0                   Min - Max
+      18             min                4.2          0                     Minimum
+      19             max                6.6          0                     Maximum
+      20    median_range    5.3 (4.2 - 6.6)          0          Median (Min - Max)
+      21              cv               15.2          0                      CV (%)
+      22       geom_mean                5.1          0              Geometric Mean
+      23    geom_mean_ci       (4.56, 5.66)          0       Geometric Mean 95% CI
+      24         geom_cv               15.2          0         CV % Geometric Mean
+      25    median_ci_3d 5.26 (4.18 - 5.74)          0             Median (95% CI)
+      26      mean_ci_3d 5.13 (4.57 - 5.69)          0               Mean (95% CI)
+      27 geom_mean_ci_3d 5.08 (4.56 - 5.66)          0     Geometric Mean (95% CI)
+      28            pval            <0.0001          0            p-value (t-test)
 
 ---
 
diff --git a/tests/testthat/_snaps/compare_variables.md b/tests/testthat/_snaps/compare_variables.md
index 493db5697c..6c98b121bb 100644
--- a/tests/testthat/_snaps/compare_variables.md
+++ b/tests/testthat/_snaps/compare_variables.md
@@ -3,11 +3,13 @@
     Code
       res
     Output
-       [1] "n"            "sum"          "mean"         "sd"           "se"          
-       [6] "mean_sd"      "mean_se"      "mean_ci"      "mean_sei"     "mean_sdi"    
-      [11] "mean_pval"    "median"       "mad"          "median_ci"    "quantiles"   
-      [16] "iqr"          "range"        "min"          "max"          "median_range"
-      [21] "cv"           "geom_mean"    "geom_mean_ci" "geom_cv"      "pval"        
+       [1] "n"               "sum"             "mean"            "sd"             
+       [5] "se"              "mean_sd"         "mean_se"         "mean_ci"        
+       [9] "mean_sei"        "mean_sdi"        "mean_ci_3d"      "mean_pval"      
+      [13] "median"          "mad"             "median_ci"       "median_ci_3d"   
+      [17] "quantiles"       "iqr"             "range"           "min"            
+      [21] "max"             "median_range"    "cv"              "geom_mean"      
+      [25] "geom_mean_ci"    "geom_cv"         "geom_mean_ci_3d" "pval"           
 
 # s_compare for numeric does not give p-value when not at least 2 values in each group
 
diff --git a/tests/testthat/_snaps/summarize_change.md b/tests/testthat/_snaps/summarize_change.md
index 9752712464..520ff1d99d 100644
--- a/tests/testthat/_snaps/summarize_change.md
+++ b/tests/testthat/_snaps/summarize_change.md
@@ -49,6 +49,12 @@
       attr(,"label")
       [1] "Mean -/+ 1xSD"
       
+      $mean_ci_3d
+             mean mean_ci_lwr mean_ci_upr 
+               NA          NA          NA 
+      attr(,"label")
+      [1] "Mean (95% CI)"
+      
       $mean_pval
       p_value 
            NA 
@@ -71,6 +77,12 @@
       attr(,"label")
       [1] "Median 95% CI"
       
+      $median_ci_3d
+             median median_ci_lwr median_ci_upr 
+                 NA            NA            NA 
+      attr(,"label")
+      [1] "Median (95% CI)"
+      
       $quantiles
       quantile_0.25 quantile_0.75 
                  NA            NA 
@@ -117,6 +129,12 @@
       geom_cv 
            NA 
       
+      $geom_mean_ci_3d
+        geom_mean mean_ci_lwr mean_ci_upr 
+              NaN          NA          NA 
+      attr(,"label")
+      [1] "Geometric Mean (95% CI)"
+      
 
 # s_change_from_baseline handles NA in baseline values
 
@@ -169,6 +187,12 @@
       attr(,"label")
       [1] "Mean -/+ 1xSD"
       
+      $mean_ci_3d
+             mean mean_ci_lwr mean_ci_upr 
+         3.000000   -4.452413   10.452413 
+      attr(,"label")
+      [1] "Mean (95% CI)"
+      
       $mean_pval
         p_value 
       0.2254033 
@@ -191,6 +215,12 @@
       attr(,"label")
       [1] "Median 95% CI"
       
+      $median_ci_3d
+             median median_ci_lwr median_ci_upr 
+                  3            NA            NA 
+      attr(,"label")
+      [1] "Median (95% CI)"
+      
       $quantiles
       quantile_0.25 quantile_0.75 
                   0             6 
@@ -237,6 +267,12 @@
       geom_cv 
            NA 
       
+      $geom_mean_ci_3d
+        geom_mean mean_ci_lwr mean_ci_upr 
+               NA          NA          NA 
+      attr(,"label")
+      [1] "Geometric Mean (95% CI)"
+      
 
 # s_change_from_baseline handles baseline substitution
 
@@ -290,6 +326,12 @@
       attr(,"label")
       [1] "Mean -/+ 1xSD"
       
+      $`FALSE`$mean_ci_3d
+             mean mean_ci_lwr mean_ci_upr 
+         1.500000   -4.853102    7.853102 
+      attr(,"label")
+      [1] "Mean (95% CI)"
+      
       $`FALSE`$mean_pval
         p_value 
       0.2048328 
@@ -312,6 +354,12 @@
       attr(,"label")
       [1] "Median 95% CI"
       
+      $`FALSE`$median_ci_3d
+             median median_ci_lwr median_ci_upr 
+                1.5            NA            NA 
+      attr(,"label")
+      [1] "Median (95% CI)"
+      
       $`FALSE`$quantiles
       quantile_0.25 quantile_0.75 
                   1             2 
@@ -358,6 +406,12 @@
        geom_cv 
       52.10922 
       
+      $`FALSE`$geom_mean_ci_3d
+         geom_mean  mean_ci_lwr  mean_ci_upr 
+        1.41421356   0.01729978 115.60839614 
+      attr(,"label")
+      [1] "Geometric Mean (95% CI)"
+      
       
       $`TRUE`
       $`TRUE`$n
@@ -406,6 +460,12 @@
       attr(,"label")
       [1] "Mean -/+ 1xSD"
       
+      $`TRUE`$mean_ci_3d
+             mean mean_ci_lwr mean_ci_upr 
+          2.50000   -16.55931    21.55931 
+      attr(,"label")
+      [1] "Mean (95% CI)"
+      
       $`TRUE`$mean_pval
         p_value 
       0.3440417 
@@ -428,6 +488,12 @@
       attr(,"label")
       [1] "Median 95% CI"
       
+      $`TRUE`$median_ci_3d
+             median median_ci_lwr median_ci_upr 
+                2.5            NA            NA 
+      attr(,"label")
+      [1] "Median (95% CI)"
+      
       $`TRUE`$quantiles
       quantile_0.25 quantile_0.75 
                   1             4 
@@ -474,6 +540,12 @@
        geom_cv 
       127.0458 
       
+      $`TRUE`$geom_mean_ci_3d
+         geom_mean  mean_ci_lwr  mean_ci_upr 
+      2.000000e+00 2.992824e-04 1.336530e+04 
+      attr(,"label")
+      [1] "Geometric Mean (95% CI)"
+      
       
 
 # summarize_change works as expected
diff --git a/tests/testthat/_snaps/survival_coxph_pairwise.md b/tests/testthat/_snaps/survival_coxph_pairwise.md
index 282ac2e850..a309f01b0a 100644
--- a/tests/testthat/_snaps/survival_coxph_pairwise.md
+++ b/tests/testthat/_snaps/survival_coxph_pairwise.md
@@ -18,6 +18,11 @@
       attr(,"label")
       [1] "95% CI"
       
+      $hr_ci_3d
+      [1] 0.7108557 0.4779138 1.0573368
+      attr(,"label")
+      [1] "Hazard Ratio (95% CI)"
+      
       $n_tot
       [1] 142
       attr(,"label")
@@ -49,6 +54,11 @@
       attr(,"label")
       [1] "90% CI"
       
+      $hr_ci_3d
+      [1] 0.7108557 0.5094153 0.9919525
+      attr(,"label")
+      [1] "Hazard Ratio (90% CI)"
+      
       $n_tot
       [1] 142
       attr(,"label")
@@ -80,6 +90,11 @@
       attr(,"label")
       [1] "95% CI"
       
+      $hr_ci_3d
+      [1] 0.6251817 0.4014842 0.9735181
+      attr(,"label")
+      [1] "Hazard Ratio (95% CI)"
+      
       $n_tot
       [1] 142
       attr(,"label")
@@ -111,6 +126,11 @@
       attr(,"label")
       [1] "90% CI"
       
+      $hr_ci_3d
+      [1] 0.6251817 0.4311132 0.9066115
+      attr(,"label")
+      [1] "Hazard Ratio (90% CI)"
+      
       $n_tot
       [1] 142
       attr(,"label")
diff --git a/tests/testthat/_snaps/survival_time.md b/tests/testthat/_snaps/survival_time.md
index b3779dd04d..10d0453dce 100644
--- a/tests/testthat/_snaps/survival_time.md
+++ b/tests/testthat/_snaps/survival_time.md
@@ -33,6 +33,21 @@
       attr(,"label")
       [1] "Range"
       
+      $median_ci_3d
+      [1] 23.91143 18.25878 32.85945
+      attr(,"label")
+      [1] "Median (95% CI)"
+      
+      $quantiles_lower
+      [1]  9.822926  5.628823 16.690121
+      attr(,"label")
+      [1] "25%-ile (95% CI)"
+      
+      $quantiles_upper
+      [1] 41.98181 32.85945 53.41445
+      attr(,"label")
+      [1] "75%-ile (95% CI)"
+      
 
 # s_surv_time works with customized arguments
 
@@ -69,6 +84,21 @@
       attr(,"label")
       [1] "Range"
       
+      $median_ci_3d
+      [1] 23.91143 13.59124 37.97055
+      attr(,"label")
+      [1] "Median (99% CI)"
+      
+      $quantiles_lower
+      [1]  6.649204  1.887860 12.771697
+      attr(,"label")
+      [1] "20%-ile (99% CI)"
+      
+      $quantiles_upper
+      [1] 51.09487 37.97055       NA
+      attr(,"label")
+      [1] "80%-ile (99% CI)"
+      
 
 # a_surv_time works with default arguments
 
@@ -77,13 +107,16 @@
     Output
       RowsVerticalSection (in_rows) object print method:
       ----------------------------
-                row_name formatted_cell indent_mod        row_label
-      1           Median           24.8          0           Median
-      2           95% CI   (21.1, 31.3)          0           95% CI
-      3  25% and 75%-ile     10.8, 47.6          0  25% and 75%-ile
-      4 Range (censored)    0.8 to 78.9          0 Range (censored)
-      5    Range (event)   0.1 to 155.5          0    Range (event)
-      6            Range   0.1 to 155.5          0            Range
+                row_name     formatted_cell indent_mod        row_label
+      1           Median               24.8          0           Median
+      2           95% CI       (21.1, 31.3)          0           95% CI
+      3  Median (95% CI) 24.8 (21.1 - 31.3)          0  Median (95% CI)
+      4  25% and 75%-ile         10.8, 47.6          0  25% and 75%-ile
+      5 25%-ile (95% CI)  10.8 (6.6 - 13.4)          0 25%-ile (95% CI)
+      6 75%-ile (95% CI) 47.6 (39.3 - 57.8)          0 75%-ile (95% CI)
+      7 Range (censored)        0.8 to 78.9          0 Range (censored)
+      8    Range (event)       0.1 to 155.5          0    Range (event)
+      9            Range       0.1 to 155.5          0            Range
 
 # a_surv_time works with customized arguments
 
@@ -115,15 +148,18 @@
     Code
       res
     Output
-                                  ARM A          ARM B          ARM C    
-      ———————————————————————————————————————————————————————————————————
-      Survival Time (Months)                                             
-        Median                     32.0           23.9           20.8    
-          90% CI               (25.6, 49.3)   (18.9, 32.1)   (13.0, 26.0)
-        40% and 60%-ile         25.6, 46.5     18.3, 29.2     13.0, 25.7 
-        Range (censored)       0.8 to 63.5    6.2 to 78.9    3.4 to 52.4 
-        Range (event)          0.3 to 155.5   0.1 to 154.1   0.6 to 80.7 
-        Range                  0.3 to 155.5   0.1 to 154.1   0.6 to 80.7 
+                                     ARM A                ARM B                ARM C       
+      —————————————————————————————————————————————————————————————————————————————————————
+      Survival Time (Months)                                                               
+        Median                        32.0                 23.9                 20.8       
+          90% CI                  (25.6, 49.3)         (18.9, 32.1)         (13.0, 26.0)   
+        Median (90% CI)        32.0 (25.6 - 49.3)   23.9 (18.9 - 32.1)   20.8 (13.0 - 26.0)
+        40% and 60%-ile            25.6, 46.5           18.3, 29.2           13.0, 25.7    
+        40%-ile (90% CI)       25.6 (20.7 - 33.4)   18.3 (12.8 - 23.9)   13.0 (10.1 - 24.8)
+        60%-ile (90% CI)       46.5 (32.0 - 57.8)   29.2 (23.9 - 41.3)   25.7 (20.8 - 37.1)
+        Range (censored)          0.8 to 63.5          6.2 to 78.9          3.4 to 52.4    
+        Range (event)             0.3 to 155.5         0.1 to 154.1         0.6 to 80.7    
+        Range                     0.3 to 155.5         0.1 to 154.1         0.6 to 80.7    
 
 # surv_time works with referential footnotes
 
diff --git a/tests/testthat/_snaps/survival_timepoint.md b/tests/testthat/_snaps/survival_timepoint.md
index 8c2a7691af..18e7f1f433 100644
--- a/tests/testthat/_snaps/survival_timepoint.md
+++ b/tests/testthat/_snaps/survival_timepoint.md
@@ -23,6 +23,11 @@
       attr(,"label")
       [1] "95% CI"
       
+      $event_free_rate_3d
+      [1] 82.19178 73.41549 90.96807
+      attr(,"label")
+      [1] "Event Free Rate (95% CI)"
+      
 
 # s_surv_timepoint works with customized arguments
 
@@ -49,6 +54,11 @@
       attr(,"label")
       [1] "99% CI"
       
+      $event_free_rate_3d
+      [1] 75.49797 62.15793 91.70097
+      attr(,"label")
+      [1] "Event Free Rate (99% CI)"
+      
 
 # s_surv_timepoint also works when there are 0 patients at risk
 
@@ -75,6 +85,11 @@
       attr(,"label")
       [1] "95% CI"
       
+      $event_free_rate_3d
+      [1] NA NA NA
+      attr(,"label")
+      [1] "Event Free Rate (95% CI)"
+      
 
 # surv_timepoint works with default arguments
 
@@ -115,6 +130,11 @@
       attr(,"label")
       [1] "95% CI"
       
+      $rate_diff_ci_3d
+      [1]  4.269100 -7.767371 16.305570
+      attr(,"label")
+      [1] "Difference in Event Free Rate95% CI"
+      
       $ztest_pval
       [1] 0.4869546
       attr(,"label")
@@ -136,6 +156,11 @@
       attr(,"label")
       [1] "90% CI"
       
+      $rate_diff_ci_3d
+      [1]  9.640872 -1.404177 20.685921
+      attr(,"label")
+      [1] "Difference in Event Free Rate90% CI"
+      
       $ztest_pval
       [1] 0.1510762
       attr(,"label")
diff --git a/tests/testthat/_snaps/utils_default_stats_formats_labels.md b/tests/testthat/_snaps/utils_default_stats_formats_labels.md
index 774a14a31d..aa5850acc1 100644
--- a/tests/testthat/_snaps/utils_default_stats_formats_labels.md
+++ b/tests/testthat/_snaps/utils_default_stats_formats_labels.md
@@ -27,11 +27,13 @@
     Code
       res
     Output
-       [1] "n"            "sum"          "mean"         "sd"           "se"          
-       [6] "mean_sd"      "mean_se"      "mean_ci"      "mean_sei"     "mean_sdi"    
-      [11] "mean_pval"    "median"       "mad"          "median_ci"    "quantiles"   
-      [16] "iqr"          "range"        "min"          "max"          "median_range"
-      [21] "cv"           "geom_mean"    "geom_mean_ci" "geom_cv"     
+       [1] "n"               "sum"             "mean"            "sd"             
+       [5] "se"              "mean_sd"         "mean_se"         "mean_ci"        
+       [9] "mean_sei"        "mean_sdi"        "mean_pval"       "median"         
+      [13] "mad"             "median_ci"       "quantiles"       "iqr"            
+      [17] "range"           "min"             "max"             "median_range"   
+      [21] "cv"              "geom_mean"       "geom_mean_ci"    "geom_cv"        
+      [25] "median_ci_3d"    "mean_ci_3d"      "geom_mean_ci_3d"
 
 # get_labels_from_stats works as expected
 
@@ -82,22 +84,24 @@
     Code
       res
     Output
-                         n                  sum                 mean 
-                     "xx."               "xx.x"               "xx.x" 
-                        sd                   se              mean_sd 
-                    "xx.x"               "xx.x"        "xx.x (xx.x)" 
-                   mean_se              mean_ci             mean_sei 
-             "xx.x (xx.x)"     "(xx.xx, xx.xx)"     "(xx.xx, xx.xx)" 
-                  mean_sdi            mean_pval               median 
-          "(xx.xx, xx.xx)" "x.xxxx | (<0.0001)"               "xx.x" 
-                       mad            median_ci            quantiles 
-                    "xx.x"     "(xx.xx, xx.xx)"        "xx.x - xx.x" 
-                       iqr                range                  min 
-                    "xx.x"        "xx.x - xx.x"               "xx.x" 
-                       max         median_range                   cv 
-                    "xx.x" "xx.x (xx.x - xx.x)"               "xx.x" 
-                 geom_mean         geom_mean_ci              geom_cv 
-                    "xx.x"     "(xx.xx, xx.xx)"               "xx.x" 
+                            n                     sum                    mean 
+                        "xx."                  "xx.x"                  "xx.x" 
+                           sd                      se                 mean_sd 
+                       "xx.x"                  "xx.x"           "xx.x (xx.x)" 
+                      mean_se                 mean_ci                mean_sei 
+                "xx.x (xx.x)"        "(xx.xx, xx.xx)"        "(xx.xx, xx.xx)" 
+                     mean_sdi               mean_pval                  median 
+             "(xx.xx, xx.xx)"    "x.xxxx | (<0.0001)"                  "xx.x" 
+                          mad               median_ci               quantiles 
+                       "xx.x"        "(xx.xx, xx.xx)"           "xx.x - xx.x" 
+                          iqr                   range                     min 
+                       "xx.x"           "xx.x - xx.x"                  "xx.x" 
+                          max            median_range                      cv 
+                       "xx.x"    "xx.x (xx.x - xx.x)"                  "xx.x" 
+                    geom_mean            geom_mean_ci                 geom_cv 
+                       "xx.x"        "(xx.xx, xx.xx)"                  "xx.x" 
+                 median_ci_3d              mean_ci_3d         geom_mean_ci_3d 
+      "xx.xx (xx.xx - xx.xx)" "xx.xx (xx.xx - xx.xx)" "xx.xx (xx.xx - xx.xx)" 
 
 # summary_labels works as expected
 
@@ -128,6 +132,10 @@
                            "CV (%)"              "Geometric Mean" 
                        geom_mean_ci                       geom_cv 
             "Geometric Mean 95% CI"         "CV % Geometric Mean" 
+                       median_ci_3d                    mean_ci_3d 
+                  "Median (95% CI)"               "Mean (95% CI)" 
+                    geom_mean_ci_3d 
+          "Geometric Mean (95% CI)" 
 
 ---
 
diff --git a/tests/testthat/test-utils_rtables.R b/tests/testthat/test-utils_rtables.R
index 3e482c9a39..fbeb9e337c 100644
--- a/tests/testthat/test-utils_rtables.R
+++ b/tests/testthat/test-utils_rtables.R
@@ -291,4 +291,5 @@ testthat::test_that("default na_str works properly", {
     analyze_vars(vars = "VAR", .stats = c("n", "mean")) %>%
     build_table(dt)
   testthat::expect_identical(matrix_form(tbl)$strings[-1, 2], c("0", "<no-value>"))
+  set_default_na_str(NULL)
 })

From 7f8a165066bb8c63b440a8eda7bd02d1615f5652 Mon Sep 17 00:00:00 2001
From: Melkiades <Melkiades@users.noreply.github.com>
Date: Wed, 20 Nov 2024 08:34:51 +0000
Subject: [PATCH 2/2] [skip actions] Bump version to 0.9.6.9016

---
 DESCRIPTION | 4 ++--
 NEWS.md     | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8d8b2bbe06..d12a525cd6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: tern
 Title: Create Common TLGs Used in Clinical Trials
-Version: 0.9.6.9015
-Date: 2024-11-07
+Version: 0.9.6.9016
+Date: 2024-11-20
 Authors@R: c(
     person("Joe", "Zhu", , "joe.zhu@roche.com", role = c("aut", "cre")),
     person("Daniel", "Sabanés Bové", , "daniel.sabanes_bove@roche.com", role = "aut"),
diff --git a/NEWS.md b/NEWS.md
index ead9eb614e..1fb0cc7b09 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# tern 0.9.6.9015
+# tern 0.9.6.9016
 
 ### Enhancements
 * Added the `denom` parameter to `s_count_cumulative()`, `s_count_missed_doses()`, and `s_count_occurrences_by_grade()`.