1301 feature request add confidence intervals for quantiles in surv time

R/survival_time.R

@@ -70,10 +70,24 @@ 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$quantile
   range_censor <- range_noinf(df[[.var]][!df[[is_event]]], na.rm = TRUE)
   range_event <- range_noinf(df[[.var]][df[[is_event]]], na.rm = TRUE)
   range <- range_noinf(df[[.var]], na.rm = TRUE)
+
+  names(quantiles) <- as.character(100 * quantiles)
+  srv_qt_tab_pre <- unlist(srv_qt_tab_pre)
+  srv_qt_ci <- lapply(quantiles, function(x) {
+    name <- as.character(100 * x)
+
+    c(
+      srv_qt_tab_pre[[paste0("quantile.", name)]],
+      srv_qt_tab_pre[[paste0("lower.", name)]],
+      srv_qt_tab_pre[[paste0("upper.", name)]]
+    )
+  })
+
   list(
     median = formatters::with_label(unname(srv_tab["median"]), "Median"),
     median_ci = formatters::with_label(
@@ -84,7 +98,20 @@ s_surv_time <- function(df,
     ),
     range_censor = formatters::with_label(range_censor, "Range (censored)"),
     range_event = formatters::with_label(range_event, "Range (event)"),
-    range = formatters::with_label(range, "Range")
+    range = formatters::with_label(range, "Range"),
+    median_ci_1_line = formatters::with_label(
+      c(
+        unname(srv_tab["median"]),
+        unname(srv_tab[paste0(srv_fit$conf.int, c("LCL", "UCL"))])
+      ),
+      paste0("Median ", f_conf_level(conf_level))
+    ),
+    quantiles_ci_1 = formatters::with_label(
+      unname(srv_qt_ci[[1]]), paste0(quantiles[1] * 100, "%-ile with ", f_conf_level(conf_level))
+    ),
+    quantiles_ci_2 = formatters::with_label(
+      unname(srv_qt_ci[[2]]), paste0(quantiles[2] * 100, "%-ile with ", f_conf_level(conf_level))
+    )
   )
 }
 
@@ -121,8 +148,17 @@ 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_1_line = "xx.x (xx.x - xx.x)",
+    quantiles_ci_1 = "xx.x (xx.x - xx.x)", quantiles_ci_2 = "xx.x (xx.x - xx.x)"
+  )
+  lbls <- c(
+    median_ci = "95% CI", range = "Range", range_censor = "Range (censored)", range_event = "Range (event)",
+    median_ci_1_line = "Median 95% CI",
+    quantiles_ci_1 = "25%-ile with 95% CI",
+    quantiles_ci_2 = "75%-ile with 95% CI"
+  )
   lbls_custom <- .labels
   .formats <- c(.formats, fmts[setdiff(names(fmts), names(.formats))])
   .labels <- c(.labels, lbls[setdiff(names(lbls), names(lbls_custom))])
@@ -209,7 +245,6 @@ surv_time <- function(lyt,
     var_labels = var_labels,
     show_labels = show_labels,
     table_names = table_names,
-    na_str = na_str,
     nested = nested,
     extra_args = extra_args
   )

R/utils_default_stats_formats_labels.R

@@ -344,6 +344,20 @@ labels_use_control <- function(labels_default, control, labels_custom = NULL) {
       labels_default["quantiles"]
     )
   }
+  if ("quantiles" %in% names(control) && "quantiles_ci_1" %in% names(labels_default) &&
+    !"quantiles_ci_1" %in% names(labels_custom)) { # nolint
+    labels_default["quantiles_ci_1"] <- gsub(
+      "[0-9]+%-ile", paste0(control[["quantiles"]][1] * 100, "%-ile", ""),
+      labels_default["quantiles_ci_1"]
+    )
+  }
+  if ("quantiles" %in% names(control) && "quantiles_ci_2" %in% names(labels_default) &&
+    !"quantiles_ci_2" %in% names(labels_custom)) { # nolint
+    labels_default["quantiles_ci_2"] <- gsub(
+      "[0-9]+%-ile", paste0(control[["quantiles"]][2] * 100, "%-ile", ""),
+      labels_default["quantiles_ci_2"]
+    )
+  }
   if ("test_mean" %in% names(control) && "mean_pval" %in% names(labels_default) &&
     !"mean_pval" %in% names(labels_custom)) { # nolint
     labels_default["mean_pval"] <- gsub(
@@ -392,7 +406,10 @@ 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_time = c(
+    "median", "median_ci", "median_ci_1_line", "quantiles",
+    "quantiles_ci_1", "quantiles_ci_2", "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"),
   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"),
@@ -431,7 +448,10 @@ tern_default_formats <- c(
   median = "xx.x",
   mad = "xx.x",
   median_ci = "(xx.xx, xx.xx)",
+  median_ci_1_line = "xx.xx (xx.xx, xx.xx)",
   quantiles = "xx.x - xx.x",
+  quantiles_ci_1 = "xx.xx (xx.xx, xx.xx)",
+  quantiles_ci_2 = "xx.xx (xx.xx, xx.xx)",
   iqr = "xx.x",
   range = "xx.x - xx.x",
   min = "xx.x",
@@ -480,7 +500,10 @@ tern_default_labels <- c(
   median = "Median",
   mad = "Median Absolute Deviation",
   median_ci = "Median 95% CI",
+  median_ci_1_line = "Median 95% CI",
   quantiles = "25% and 75%-ile",
+  quantiles_ci_1 = "25%-ile 95% CI",
+  quantiles_ci_2 = "75%-ile 95% CI",
   iqr = "IQR",
   range = "Min - Max",
   min = "Minimum",

tests/testthat/_snaps/survival_time.md

@@ -33,6 +33,21 @@
       attr(,"label")
       [1] "Range"
 
+      $median_ci_1_line
+      [1] 23.91143 18.25878 32.85945
+      attr(,"label")
+      [1] "Median 95% CI"
+
+      $quantiles_ci_1
+      [1]  9.822926  5.628823 16.690121
+      attr(,"label")
+      [1] "25%-ile with 95% CI"
+
+      $quantiles_ci_2
+      [1] 41.98181 32.85945 53.41445
+      attr(,"label")
+      [1] "75%-ile with 95% CI"
+
 
 # s_surv_time works with customized arguments
 
@@ -69,6 +84,21 @@
       attr(,"label")
       [1] "Range"
 
+      $median_ci_1_line
+      [1] 23.91143 13.59124 37.97055
+      attr(,"label")
+      [1] "Median 99% CI"
+
+      $quantiles_ci_1
+      [1]  6.649204  1.887860 12.771697
+      attr(,"label")
+      [1] "20%-ile with 99% CI"
+
+      $quantiles_ci_2
+      [1] 51.09487 37.97055       NA
+      attr(,"label")
+      [1] "80%-ile with 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 with 95% CI  10.8 (6.6 - 13.4)          0 25%-ile with 95% CI
+      6 75%-ile with 95% CI 47.6 (39.3 - 57.8)          0 75%-ile with 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 with 90% CI    25.6 (20.7 - 33.4)   18.3 (12.8 - 23.9)   13.0 (10.1 - 24.8)
+        60%-ile with 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