update name of new stats according to suggestion median_long into med…

…ian_ci_3d

R/analyze_variables.R

@@ -188,8 +188,8 @@ 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_long <- c(y$mean, y$mean_ci)
-  y$mean_long <- formatters::with_label(mean_long, paste0("Mean (", f_conf_level(control$conf_level), ")"))
+  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$test_mean)))
@@ -201,8 +201,8 @@ s_summary.numeric <- function(x,
   median_ci <- stat_median_ci(x, conf_level = control$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_long <- c(y$median, median_ci)
-  y$median_long <- formatters::with_label(median_long, paste0("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))) {
@@ -236,8 +236,8 @@ 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_long <- c(y$geom_mean, y$geom_mean_ci)
-  y$geom_mean_long <- formatters::with_label(geom_mean_long, paste0("Geometric Mean (", f_conf_level(control$conf_level), ")"))
+  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
 }

R/survival_coxph_pairwise.R

@@ -65,7 +65,7 @@ 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_long = formatters::with_label("", paste0("Hazard Ratio (", 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")
       )
@@ -112,7 +112,7 @@ 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_long = formatters::with_label(
+    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), ")")
     ),
@@ -129,12 +129,12 @@ 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, hr_long = 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_long = "xx.xx (xx.xx - xx.xx)",
+    hr_ci_3d = "xx.xx (xx.xx - xx.xx)",
     n_tot = "xx.xx",
     n_tot_events = "xx.xx"
   )

R/survival_time.R

@@ -43,7 +43,7 @@ NULL
 #' * `s_surv_time()` returns the statistics:
 #'   * `median`: Median survival time.
 #'   * `median_ci`: Confidence interval for median time.
-#'   * `median_long`: Median with 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.
@@ -102,7 +102,7 @@ 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"),
-    median_long = formatters::with_label(
+    median_ci_3d = formatters::with_label(
       c(
         unname(srv_tab["median"]),
         unname(srv_tab[paste0(srv_fit$conf.int, c("LCL", "UCL"))])
@@ -153,12 +153,12 @@ a_surv_time <- function(df,
   # Use method-specific defaults
   fmts <- c(
     median_ci = "(xx.x, xx.x)", quantiles = "xx.x, xx.x", range = "xx.x to xx.x",
-    median_long = "xx.x (xx.x - 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_long = "Median (95% CI)",
+    median_ci_3d = "Median (95% CI)",
     quantiles_lower = "25%-ile (95% CI)",
     quantiles_upper = "75%-ile (95% CI)"
   )

R/survival_timepoint.R

@@ -39,7 +39,7 @@ 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_long`: Event-free rate (%) with Confidence interval.
+#'   * `event_free_rate_3d`: Event-free rate (%) with Confidence interval.
 #'
 #' @keywords internal
 s_surv_timepoint <- function(df,
@@ -74,14 +74,14 @@ s_surv_timepoint <- function(df,
     rate_se <- df_srv_fit$std.err
     rate_ci <- c(df_srv_fit$lower, df_srv_fit$upper)
   }
-  event_free_rate_long <- c(event_free_rate, rate_ci)
+  event_free_rate_3d <- c(event_free_rate, rate_ci)
   list(
     pt_at_risk = formatters::with_label(pt_at_risk, "Patients remaining at risk"),
     event_free_rate = formatters::with_label(event_free_rate * 100, "Event Free Rate (%)"),
     rate_se = formatters::with_label(rate_se * 100, "Standard Error of Event Free Rate"),
     rate_ci = formatters::with_label(rate_ci * 100, f_conf_level(conf_level)),
-    event_free_rate_long = formatters::with_label(
-      event_free_rate_long * 100, paste0("Event Free Rate (", f_conf_level(conf_level), ")")
+    event_free_rate_3d = formatters::with_label(
+      event_free_rate_3d * 100, paste0("Event Free Rate (", f_conf_level(conf_level), ")")
     )
   )
 }
@@ -115,7 +115,7 @@ a_surv_timepoint <- make_afun(
 #' * `s_surv_timepoint_diff()` returns the statistics:
 #'   * `rate_diff`: Event-free rate difference between two groups.
 #'   * `rate_diff_ci`: Confidence interval for the difference.
-#'   * `rate_diff_long`: Event-free rate difference and confidence interval between two groups.
+#'   * `rate_diff_ci_3d`: Event-free rate difference and confidence interval between two groups.
 #'   * `ztest_pval`: p-value to test the difference is 0.
 #'
 #' @keywords internal
@@ -131,7 +131,7 @@ s_surv_timepoint_diff <- function(df,
       list(
         rate_diff = formatters::with_label("", "Difference in Event Free Rate"),
         rate_diff_ci = formatters::with_label("", f_conf_level(control$conf_level)),
-        rate_diff_long = formatters::with_label(
+        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)")
@@ -151,7 +151,7 @@ s_surv_timepoint_diff <- function(df,
 
   qs <- c(-1, 1) * stats::qnorm(1 - (1 - control$conf_level) / 2)
   rate_diff_ci <- rate_diff + qs * se_diff
-  rate_diff_long <- c(rate_diff, rate_diff_ci)
+  rate_diff_ci_3d <- c(rate_diff, rate_diff_ci)
   ztest_pval <- if (is.na(rate_diff)) {
     NA
   } else {
@@ -160,8 +160,8 @@ s_surv_timepoint_diff <- function(df,
   list(
     rate_diff = formatters::with_label(rate_diff, "Difference in Event Free Rate"),
     rate_diff_ci = formatters::with_label(rate_diff_ci, f_conf_level(control$conf_level)),
-    rate_diff_long = formatters::with_label(
-      rate_diff_long, paste0("Difference in Event Free Rate", 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)")
   )
@@ -179,7 +179,7 @@ a_surv_timepoint_diff <- make_afun(
   .formats = c(
     rate_diff = "xx.xx",
     rate_diff_ci = "(xx.xx, xx.xx)",
-    rate_diff_long = format_xx("xx.xx (xx.xx, xx.xx)"),
+    rate_diff_ci_3d = format_xx("xx.xx (xx.xx, xx.xx)"),
     ztest_pval = "x.xxxx | (<0.0001)"
   )
 )
@@ -273,8 +273,8 @@ 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", "event_free_rate_long"),
-    surv_diff = c("rate_diff", "rate_diff_ci", "ztest_pval", "rate_diff_long")
+    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)

R/utils_default_stats_formats_labels.R

@@ -387,8 +387,8 @@ tern_default_stats <- list(
     "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_long",
-    "mean_long", "geom_mean_long"
+    "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"),
@@ -409,12 +409,12 @@ tern_default_stats <- list(
   summarize_num_patients = c("unique", "nonunique", "unique_count"),
   summarize_patients_events_in_cols = c("unique", "all"),
   surv_time = c(
-    "median", "median_ci", "median_long", "quantiles",
+    "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_long"
+    "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"),
@@ -450,11 +450,11 @@ tern_default_formats <- c(
   mean_sei = "(xx.xx, xx.xx)",
   mean_sdi = "(xx.xx, xx.xx)",
   mean_pval = "x.xxxx | (<0.0001)",
-  mean_long = "xx.xx (xx.xx - xx.xx)",
+  mean_ci_3d = "xx.xx (xx.xx - xx.xx)",
   median = "xx.x",
   mad = "xx.x",
   median_ci = "(xx.xx, xx.xx)",
-  median_long = "xx.xx (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)",
@@ -466,7 +466,7 @@ tern_default_formats <- c(
   cv = "xx.x",
   geom_mean = "xx.x",
   geom_mean_ci = "(xx.xx, xx.xx)",
-  geom_mean_long = "xx.xx (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)",
@@ -504,11 +504,11 @@ tern_default_labels <- c(
   mean_sei = "Mean -/+ 1xSE",
   mean_sdi = "Mean -/+ 1xSD",
   mean_pval = "Mean p-value (H0: mean = 0)",
-  mean_long = "Mean (95% CI)",
+  mean_ci_3d = "Mean (95% CI)",
   median = "Median",
   mad = "Median Absolute Deviation",
   median_ci = "Median 95% CI",
-  median_long = "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)",
@@ -520,7 +520,7 @@ tern_default_labels <- c(
   cv = "CV (%)",
   geom_mean = "Geometric Mean",
   geom_mean_ci = "Geometric Mean 95% CI",
-  geom_mean_long = "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

tests/testthat/_snaps/analyze_variables.md

@@ -49,7 +49,7 @@
       attr(,"label")
       [1] "Mean -/+ 1xSD"
       
-      $mean_long
+      $mean_ci_3d
              mean mean_ci_lwr mean_ci_upr 
                NA          NA          NA 
       attr(,"label")
@@ -77,7 +77,7 @@
       attr(,"label")
       [1] "Median 95% CI"
       
-      $median_long
+      $median_ci_3d
              median median_ci_lwr median_ci_upr 
                  NA            NA            NA 
       attr(,"label")
@@ -129,7 +129,7 @@
       geom_cv 
            NA 
       
-      $geom_mean_long
+      $geom_mean_ci_3d
         geom_mean mean_ci_lwr mean_ci_upr 
               NaN          NA          NA 
       attr(,"label")
@@ -187,7 +187,7 @@
       attr(,"label")
       [1] "Mean -/+ 1xSD"
       
-      $mean_long
+      $mean_ci_3d
              mean mean_ci_lwr mean_ci_upr 
                 1          NA          NA 
       attr(,"label")
@@ -215,7 +215,7 @@
       attr(,"label")
       [1] "Median 95% CI"
       
-      $median_long
+      $median_ci_3d
              median median_ci_lwr median_ci_upr 
                   1            NA            NA 
       attr(,"label")
@@ -267,7 +267,7 @@
       geom_cv 
            NA 
       
-      $geom_mean_long
+      $geom_mean_ci_3d
         geom_mean mean_ci_lwr mean_ci_upr 
                 1          NA          NA 
       attr(,"label")
@@ -325,7 +325,7 @@
       attr(,"label")
       [1] "Mean -/+ 1xSD"
       
-      $mean_long
+      $mean_ci_3d
              mean mean_ci_lwr mean_ci_upr 
                NA          NA          NA 
       attr(,"label")
@@ -353,7 +353,7 @@
       attr(,"label")
       [1] "Median 95% CI"
       
-      $median_long
+      $median_ci_3d
              median median_ci_lwr median_ci_upr 
                  NA            NA            NA 
       attr(,"label")
@@ -405,7 +405,7 @@
       geom_cv 
            NA 
       
-      $geom_mean_long
+      $geom_mean_ci_3d
         geom_mean mean_ci_lwr mean_ci_upr 
                NA          NA          NA 
       attr(,"label")
@@ -463,7 +463,7 @@
       attr(,"label")
       [1] "Mean -/+ 1xSD"
       
-      $mean_long
+      $mean_ci_3d
              mean mean_ci_lwr mean_ci_upr 
          1.500000   -4.853102    7.853102 
       attr(,"label")
@@ -491,7 +491,7 @@
       attr(,"label")
       [1] "Median 95% CI"
       
-      $median_long
+      $median_ci_3d
              median median_ci_lwr median_ci_upr 
                 1.5            NA            NA 
       attr(,"label")
@@ -543,7 +543,7 @@
        geom_cv 
       52.10922 
       
-      $geom_mean_long
+      $geom_mean_ci_3d
          geom_mean  mean_ci_lwr  mean_ci_upr 
         1.41421356   0.01729978 115.60839614 
       attr(,"label")
@@ -601,7 +601,7 @@
       attr(,"label")
       [1] "Mean -/+ 1xSD"
       
-      $mean_long
+      $mean_ci_3d
              mean mean_ci_lwr mean_ci_upr 
          6.000000    3.318768    8.681232 
       attr(,"label")
@@ -629,7 +629,7 @@
       attr(,"label")
       [1] "Median 95% CI"
       
-      $median_long
+      $median_ci_3d
              median median_ci_lwr median_ci_upr 
                 6.5           1.0          10.0 
       attr(,"label")
@@ -681,7 +681,7 @@
        geom_cv 
       96.61307 
       
-      $geom_mean_long
+      $geom_mean_ci_3d
         geom_mean mean_ci_lwr mean_ci_upr 
          4.842534    2.456211    9.547283 
       attr(,"label")