From 6fdc7579be8448cd7bf078c29bbaad7781081598 Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Tue, 12 Nov 2024 07:53:54 +0000
Subject: [PATCH] [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

---
 DESCRIPTION                 |   3 -
 man/analyze_variables.Rd    |  32 ++++-
 man/g_km.Rd                 | 262 ++++++++++--------------------------
 man/h_data_plot.Rd          |  42 +-----
 man/h_decompose_gg.Rd       |  47 +------
 man/h_g_ipp.Rd              |  45 +------
 man/h_ggkm.Rd               |  89 ++++--------
 man/h_grob_coxph.Rd         |  50 ++-----
 man/h_grob_median_surv.Rd   |  42 +-----
 man/h_grob_tbl_at_risk.Rd   |  72 +---------
 man/h_grob_y_annot.Rd       |  36 +----
 man/h_km_layout.Rd          |  55 ++------
 man/h_tbl_coxph_pairwise.Rd |  48 +++----
 man/h_tbl_median_surv.Rd    |  24 +---
 man/h_xticks.Rd             |  37 +----
 man/try_car_anova.Rd        |   4 +-
 16 files changed, 188 insertions(+), 700 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 466418b93a..8d8b2bbe06 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -144,8 +144,6 @@ Collate:
     'h_survival_duration_subgroups.R'
     'imputation_rule.R'
     'incidence_rate.R'
-    'individual_patient_plot.R'
-    'kaplan_meier_plot.R'
     'logistic_regression.R'
     'missing_data.R'
     'odds_ratio.R'
@@ -168,7 +166,6 @@ Collate:
     'summarize_glm_count.R'
     'summarize_num_patients.R'
     'summarize_patients_exposure_in_cols.R'
-    'summarize_variables.R'
     'survival_biomarkers_subgroups.R'
     'survival_coxph_pairwise.R'
     'survival_duration_subgroups.R'
diff --git a/man/analyze_variables.Rd b/man/analyze_variables.Rd
index 7c38e531ec..18a6b603dc 100644
--- a/man/analyze_variables.Rd
+++ b/man/analyze_variables.Rd
@@ -37,14 +37,14 @@ s_summary(x, na.rm = TRUE, denom, .N_row, .N_col, .var, ...)
   .N_row,
   .N_col,
   .var,
-  control = control_summarize_vars(),
+  control = control_analyze_vars(),
   ...
 )
 
 \method{s_summary}{factor}(
   x,
   na.rm = TRUE,
-  denom = c("n", "N_row", "N_col"),
+  denom = c("n", "N_col", "N_row"),
   .N_row,
   .N_col,
   ...
@@ -53,7 +53,7 @@ s_summary(x, na.rm = TRUE, denom, .N_row, .N_col, .var, ...)
 \method{s_summary}{character}(
   x,
   na.rm = TRUE,
-  denom = c("n", "N_row", "N_col"),
+  denom = c("n", "N_col", "N_row"),
   .N_row,
   .N_col,
   .var,
@@ -64,13 +64,29 @@ s_summary(x, na.rm = TRUE, denom, .N_row, .N_col, .var, ...)
 \method{s_summary}{logical}(
   x,
   na.rm = TRUE,
-  denom = c("n", "N_row", "N_col"),
+  denom = c("n", "N_col", "N_row"),
   .N_row,
   .N_col,
   ...
 )
 
-a_summary(x, ..., .N_row, .N_col, .var)
+a_summary(
+  x,
+  .N_col,
+  .N_row,
+  .var = NULL,
+  .df_row = NULL,
+  .ref_group = NULL,
+  .in_ref_col = FALSE,
+  compare = FALSE,
+  .stats = NULL,
+  .formats = NULL,
+  .labels = NULL,
+  .indent_mods = NULL,
+  na.rm = TRUE,
+  na_str = default_na_str(),
+  ...
+)
 }
 \arguments{
 \item{lyt}{(\code{PreDataTableLayouts})\cr layout that analyses will be added to.}
@@ -143,6 +159,12 @@ See more about \code{type} in \code{\link[stats:quantile]{stats::quantile()}}.
 \item{verbose}{(\code{flag})\cr defaults to \code{TRUE}, which prints out warnings and messages. It is mainly used
 to print out information about factor casting.}
 
+\item{.df_row}{(\code{data.frame})\cr data frame across all of the columns for the given row split.}
+
+\item{.ref_group}{(\code{data.frame} or \code{vector})\cr the data corresponding to the reference group.}
+
+\item{.in_ref_col}{(\code{flag})\cr \code{TRUE} when working with the reference level, \code{FALSE} otherwise.}
+
 \item{compare}{(\code{flag})\cr whether comparison statistics should be analyzed instead of summary statistics
 (\code{compare = TRUE} adds \code{pval} statistic comparing against reference group).}
 }
diff --git a/man/g_km.Rd b/man/g_km.Rd
index 4191e04b4a..c46349a96c 100644
--- a/man/g_km.Rd
+++ b/man/g_km.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/g_km.R, R/kaplan_meier_plot.R
+% Please edit documentation in R/g_km.R
 \name{g_km}
 \alias{g_km}
 \alias{kaplan_meier}
@@ -20,59 +20,34 @@ g_km(
   xlab = "Days",
   yval = c("Survival", "Failure"),
   ylab = paste(yval, "Probability"),
+  ylim = NULL,
   title = NULL,
   footnotes = NULL,
-  draw = TRUE,
-  newpage = TRUE,
-  gp = NULL,
-  vp = NULL,
-  name = NULL,
-  font_size = 12,
+  font_size = 10,
   ci_ribbon = FALSE,
-  ggtheme = nestcolor::theme_nest(),
   annot_at_risk = TRUE,
+  annot_at_risk_title = TRUE,
   annot_surv_med = TRUE,
   annot_coxph = FALSE,
   annot_stats = NULL,
   annot_stats_vlines = FALSE,
   control_coxph_pw = control_coxph(),
-  position_coxph = c(0, 0.05),
-  position_surv_med = c(0.9, 0.9)
-)
-
-g_km(
-  df,
-  variables,
-  control_surv = control_surv_timepoint(),
-  col = NULL,
-  lty = NULL,
-  lwd = 0.5,
-  censor_show = TRUE,
-  pch = 3,
-  size = 2,
-  max_time = NULL,
-  xticks = NULL,
-  xlab = "Days",
-  yval = c("Survival", "Failure"),
-  ylab = paste(yval, "Probability"),
-  title = NULL,
-  footnotes = NULL,
-  draw = TRUE,
-  newpage = TRUE,
-  gp = NULL,
-  vp = NULL,
-  name = NULL,
-  font_size = 12,
-  ci_ribbon = FALSE,
-  ggtheme = nestcolor::theme_nest(),
-  annot_at_risk = TRUE,
-  annot_surv_med = TRUE,
-  annot_coxph = FALSE,
-  annot_stats = NULL,
-  annot_stats_vlines = FALSE,
-  control_coxph_pw = control_coxph(),
-  position_coxph = c(0, 0.05),
-  position_surv_med = c(0.9, 0.9)
+  ref_group_coxph = NULL,
+  control_annot_surv_med = control_surv_med_annot(),
+  control_annot_coxph = control_coxph_annot(),
+  legend_pos = NULL,
+  rel_height_plot = 0.75,
+  ggtheme = NULL,
+  as_list = FALSE,
+  draw = lifecycle::deprecated(),
+  newpage = lifecycle::deprecated(),
+  gp = lifecycle::deprecated(),
+  vp = lifecycle::deprecated(),
+  name = lifecycle::deprecated(),
+  annot_coxph_ref_lbls = lifecycle::deprecated(),
+  position_coxph = lifecycle::deprecated(),
+  position_surv_med = lifecycle::deprecated(),
+  width_annots = lifecycle::deprecated()
 )
 }
 \arguments{
@@ -83,97 +58,84 @@ g_km(
 \item \code{tte} (\code{numeric})\cr variable indicating time-to-event duration values.
 \item \code{is_event} (\code{logical})\cr event variable. \code{TRUE} if event, \code{FALSE} if time to event is censored.
 \item \code{arm} (\code{factor})\cr the treatment group variable.
-\item \code{strat} (\code{character} or \code{NULL})\cr variable names indicating stratification factors.
+\item \code{strata} (\code{character} or \code{NULL})\cr variable names indicating stratification factors.
 }}
 
 \item{control_surv}{(\code{list})\cr parameters for comparison details, specified by using
 the helper function \code{\link[=control_surv_timepoint]{control_surv_timepoint()}}. Some possible parameter options are:
 \itemize{
 \item \code{conf_level} (\code{proportion})\cr confidence level of the interval for survival rate.
-\item \code{conf_type} (\code{string})\cr "plain" (default), "log", "log-log" for confidence interval type,
+\item \code{conf_type} (\code{string})\cr \code{"plain"} (default), \code{"log"}, \code{"log-log"} for confidence interval type,
 see more in \code{\link[survival:survfit]{survival::survfit()}}. Note that the option "none" is no longer supported.
 }}
 
 \item{col}{(\code{character})\cr lines colors. Length of a vector should be equal
 to number of strata from \code{\link[survival:survfit]{survival::survfit()}}.}
 
-\item{lty}{(\code{numeric})\cr line type. Length of a vector should be equal
-to number of strata from \code{\link[survival:survfit]{survival::survfit()}}.}
+\item{lty}{(\code{numeric})\cr line type. If a vector is given, its length should be equal to the number of strata from
+\code{\link[survival:survfit]{survival::survfit()}}.}
 
-\item{lwd}{(\code{numeric})\cr line width. Length of a vector should be equal
-to number of strata from \code{\link[survival:survfit]{survival::survfit()}}.}
+\item{lwd}{(\code{numeric})\cr line width. If a vector is given, its length should be equal to the number of strata from
+\code{\link[survival:survfit]{survival::survfit()}}.}
 
-\item{censor_show}{(\code{flag})\cr whether to show censored.}
+\item{censor_show}{(\code{flag})\cr whether to show censored observations.}
 
-\item{pch}{(\code{numeric}, \code{string})\cr value or character of points symbol to indicate censored cases.}
+\item{pch}{(\code{string})\cr name of symbol or character to use as point symbol to indicate censored cases.}
 
-\item{size}{(\code{numeric})\cr size of censored point, a class of \code{unit}.}
+\item{size}{(\code{numeric(1)})\cr size of censored point symbols.}
 
-\item{max_time}{(\code{numeric})\cr maximum value to show on X axis. Only data values less than or up to
+\item{max_time}{(\code{numeric(1)})\cr maximum value to show on x-axis. Only data values less than or up to
 this threshold value will be plotted (defaults to \code{NULL}).}
 
-\item{xticks}{(\code{numeric}, \code{number}, or \code{NULL})\cr numeric vector of ticks or single number with spacing
-between ticks on the x axis. If \code{NULL} (default), \code{\link[labeling:extended]{labeling::extended()}} is used to determine
-an optimal tick position on the x axis.}
+\item{xticks}{(\code{numeric} or \code{NULL})\cr numeric vector of tick positions or a single number with spacing
+between ticks on the x-axis. If \code{NULL} (default), \code{\link[labeling:extended]{labeling::extended()}} is used to determine
+optimal tick positions on the x-axis.}
 
-\item{xlab}{(\code{string})\cr label of x-axis.}
+\item{xlab}{(\code{string})\cr x-axis label.}
 
-\item{yval}{(\code{string})\cr value of y-axis. Options are \code{Survival} (default) and \code{Failure} probability.}
+\item{yval}{(\code{string})\cr type of plot, to be plotted on the y-axis. Options are \code{Survival} (default) and \code{Failure}
+probability.}
 
-\item{ylab}{(\code{string})\cr label of y-axis.}
+\item{ylab}{(\code{string})\cr y-axis label.}
 
-\item{title}{(\code{string})\cr title for plot.}
+\item{ylim}{(\code{numeric(2)})\cr vector containing lower and upper limits for the y-axis, respectively.
+If \code{NULL} (default), the default scale range is used.}
 
-\item{footnotes}{(\code{string})\cr footnotes for plot.}
+\item{title}{(\code{string})\cr plot title.}
 
-\item{draw}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} This function no longer generates \code{grob} objects.}
-
-\item{newpage}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} This function no longer generates \code{grob} objects.}
-
-\item{gp}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} This function no longer generates \code{grob} objects.}
-
-\item{vp}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} This function no longer generates \code{grob} objects.}
+\item{footnotes}{(\code{string})\cr plot footnotes.}
 
-\item{name}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} This function no longer generates \code{grob} objects.}
-
-\item{font_size}{(\code{number})\cr font size to be used.}
+\item{font_size}{(\code{numeric(1)})\cr font size to use for all text.}
 
-\item{ci_ribbon}{(\code{flag})\cr draw the confidence interval around the Kaplan-Meier curve.}
-
-\item{ggtheme}{(\code{theme})\cr a graphical theme as provided by \code{ggplot2} to control outlook of the Kaplan-Meier curve.}
+\item{ci_ribbon}{(\code{flag})\cr whether the confidence interval should be drawn around the Kaplan-Meier curve.}
 
 \item{annot_at_risk}{(\code{flag})\cr compute and add the annotation table reporting the number of patient at risk
 matching the main grid of the Kaplan-Meier curve.}
 
+\item{annot_at_risk_title}{(\code{flag})\cr whether the "Patients at Risk" title should be added above the \code{annot_at_risk}
+table. Has no effect if \code{annot_at_risk} is \code{FALSE}. Defaults to \code{TRUE}.}
+
 \item{annot_surv_med}{(\code{flag})\cr compute and add the annotation table on the Kaplan-Meier curve estimating the
 median survival time per group.}
 
-\item{annot_coxph}{(\code{flag})\cr add the annotation table from a \code{\link[survival:coxph]{survival::coxph()}} model.}
+\item{annot_coxph}{(\code{flag})\cr whether to add the annotation table from a \code{\link[survival:coxph]{survival::coxph()}} model.}
 
-\item{annot_stats}{(\code{string})\cr statistics annotations to add to the plot. Options are
+\item{annot_stats}{(\code{string} or \code{NULL})\cr statistics annotations to add to the plot. Options are
 \code{median} (median survival follow-up time) and \code{min} (minimum survival follow-up time).}
 
 \item{annot_stats_vlines}{(\code{flag})\cr add vertical lines corresponding to each of the statistics
 specified by \code{annot_stats}. If \code{annot_stats} is \code{NULL} no lines will be added.}
 
-\item{control_coxph_pw}{(\code{list})\cr parameters for comparison details, specified by using
-the helper function \code{\link[=control_coxph]{control_coxph()}}. Some possible parameter options are:
+\item{control_coxph_pw}{(\code{list})\cr parameters for comparison details, specified using the helper function
+\code{\link[=control_coxph]{control_coxph()}}. Some possible parameter options are:
 \itemize{
 \item \code{pval_method} (\code{string})\cr p-value method for testing hazard ratio = 1.
-Default method is "log-rank", can also be set to "wald" or "likelihood".
-\item \code{ties} (\code{string})\cr method for tie handling. Default is "efron",
-can also be set to "breslow" or "exact". See more in \code{\link[survival:coxph]{survival::coxph()}}
+Default method is \code{"log-rank"}, can also be set to \code{"wald"} or \code{"likelihood"}.
+\item \code{ties} (\code{string})\cr method for tie handling. Default is \code{"efron"},
+can also be set to \code{"breslow"} or \code{"exact"}. See more in \code{\link[survival:coxph]{survival::coxph()}}
 \item \code{conf_level} (\code{proportion})\cr confidence level of the interval for HR.
 }}
 
-\item{position_coxph}{(\code{numeric})\cr x and y positions for plotting \code{\link[survival:coxph]{survival::coxph()}} model.}
-
-\item{position_surv_med}{(\code{numeric})\cr x and y positions for plotting annotation table estimating median survival
-time per group.}
-
-\item{annot_at_risk_title}{(\code{flag})\cr whether the "Patients at Risk" title should be added above the \code{annot_at_risk}
-table. Has no effect if \code{annot_at_risk} is \code{FALSE}. Defaults to \code{TRUE}.}
-
 \item{ref_group_coxph}{(\code{string} or \code{NULL})\cr level of arm variable to use as reference group in calculations for
 \code{annot_coxph} table. If \code{NULL} (default), uses the first level of the arm variable.}
 
@@ -193,30 +155,40 @@ the plot, or the middle right of the plot if needed to prevent overlapping.}
 Relative height of patients at risk table is then \code{1 - rel_height_plot}. If \code{annot_at_risk = FALSE} or
 \code{as_list = TRUE}, this parameter is ignored.}
 
+\item{ggtheme}{(\code{theme})\cr a graphical theme as provided by \code{ggplot2} to format the Kaplan-Meier plot.}
+
 \item{as_list}{(\code{flag})\cr whether the two \code{ggplot} objects should be returned as a list when \code{annot_at_risk = TRUE}.
 If \code{TRUE}, a named list with two elements, \code{plot} and \code{table}, will be returned. If \code{FALSE} (default) the patients
 at risk table is printed below the plot via \code{\link[cowplot:plot_grid]{cowplot::plot_grid()}}.}
 
+\item{draw}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} This function no longer generates \code{grob} objects.}
+
+\item{newpage}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} This function no longer generates \code{grob} objects.}
+
+\item{gp}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} This function no longer generates \code{grob} objects.}
+
+\item{vp}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} This function no longer generates \code{grob} objects.}
+
+\item{name}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} This function no longer generates \code{grob} objects.}
+
 \item{annot_coxph_ref_lbls}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Please use the \code{ref_lbls} element of
 \code{control_annot_coxph} instead.}
 
+\item{position_coxph}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}  Please use the \code{x} and \code{y} elements of
+\code{control_annot_coxph} instead.}
+
+\item{position_surv_med}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Please use the \code{x} and \code{y} elements of
+\code{control_annot_surv_med} instead.}
+
 \item{width_annots}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Please use the \code{w} element of \code{control_annot_surv_med}
 (for \code{surv_med}) and \code{control_annot_coxph} (for \code{coxph})."}
 }
 \value{
 A \code{ggplot} Kaplan-Meier plot and (optionally) summary table.
-
-A \code{grob} of class \code{gTree}.
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
 
-From a survival model, a graphic is rendered along with tabulated annotation
-including the number of patient at risk at given time and the median survival
-per group.
-
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-
 From a survival model, a graphic is rendered along with tabulated annotation
 including the number of patient at risk at given time and the median survival
 per group.
@@ -261,96 +233,4 @@ g_km(
   control_annot_surv_med = control_surv_med_annot(x = 0.8, y = 0.9, w = 0.35)
 )
 
-\dontrun{
-library(dplyr)
-library(ggplot2)
-library(survival)
-library(grid)
-library(nestcolor)
-
-df <- tern_ex_adtte \%>\%
-  filter(PARAMCD == "OS") \%>\%
-  mutate(is_event = CNSR == 0)
-variables <- list(tte = "AVAL", is_event = "is_event", arm = "ARMCD")
-
-# 1. Example - basic option
-
-res <- g_km(df = df, variables = variables)
-res <- g_km(df = df, variables = variables, yval = "Failure")
-res <- g_km(
-  df = df,
-  variables = variables,
-  control_surv = control_surv_timepoint(conf_level = 0.9),
-  col = c("grey25", "grey50", "grey75")
-)
-res <- g_km(df = df, variables = variables, ggtheme = theme_minimal())
-res <- g_km(df = df, variables = variables, ggtheme = theme_minimal(), lty = 1:3)
-res <- g_km(df = df, variables = variables, max = 2000)
-res <- g_km(
-  df = df,
-  variables = variables,
-  annot_stats = c("min", "median"),
-  annot_stats_vlines = TRUE
-)
-
-# 2. Example - Arrange several KM curve on a single graph device
-
-# 2.1 Use case: A general graph on the top, a zoom on the bottom.
-grid.newpage()
-lyt <- grid.layout(nrow = 2, ncol = 1) \%>\%
-  viewport(layout = .) \%>\%
-  pushViewport()
-
-res <- g_km(
-  df = df, variables = variables, newpage = FALSE, annot_surv_med = FALSE,
-  vp = viewport(layout.pos.row = 1, layout.pos.col = 1)
-)
-res <- g_km(
-  df = df, variables = variables, max = 1000, newpage = FALSE, annot_surv_med = FALSE,
-  ggtheme = theme_dark(),
-  vp = viewport(layout.pos.row = 2, layout.pos.col = 1)
-)
-
-# 2.1 Use case: No annotations on top, annotated graph on bottom
-grid.newpage()
-lyt <- grid.layout(nrow = 2, ncol = 1) \%>\%
-  viewport(layout = .) \%>\%
-  pushViewport()
-
-res <- g_km(
-  df = df, variables = variables, newpage = FALSE,
-  annot_surv_med = FALSE, annot_at_risk = FALSE,
-  vp = viewport(layout.pos.row = 1, layout.pos.col = 1)
-)
-res <- g_km(
-  df = df, variables = variables, max = 2000, newpage = FALSE, annot_surv_med = FALSE,
-  annot_at_risk = TRUE,
-  ggtheme = theme_dark(),
-  vp = viewport(layout.pos.row = 2, layout.pos.col = 1)
-)
-
-# Add annotation from a pairwise coxph analysis
-g_km(
-  df = df, variables = variables,
-  annot_coxph = TRUE
-)
-
-g_km(
-  df = df, variables = c(variables, list(strat = "SEX")),
-  font_size = 15,
-  annot_coxph = TRUE,
-  control_coxph = control_coxph(pval_method = "wald", ties = "exact", conf_level = 0.99),
-  position_coxph = c(0.4, 0.5)
-)
-
-# Change position of the treatment group annotation table.
-g_km(
-  df = df, variables = c(variables, list(strat = "SEX")),
-  font_size = 15,
-  annot_coxph = TRUE,
-  control_coxph = control_coxph(pval_method = "wald", ties = "exact", conf_level = 0.99),
-  position_surv_med = c(1, 0.7)
-)
-}
-
 }
diff --git a/man/h_data_plot.Rd b/man/h_data_plot.Rd
index 7d6e393f01..82b02f5e2c 100644
--- a/man/h_data_plot.Rd
+++ b/man/h_data_plot.Rd
@@ -1,25 +1,20 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/h_km.R, R/kaplan_meier_plot.R
+% Please edit documentation in R/h_km.R
 \name{h_data_plot}
 \alias{h_data_plot}
 \title{Helper function to tidy survival fit data}
 \usage{
-h_data_plot(fit_km, armval = "All", max_time = NULL)
-
 h_data_plot(fit_km, armval = "All", max_time = NULL)
 }
 \arguments{
 \item{fit_km}{(\code{survfit})\cr result of \code{\link[survival:survfit]{survival::survfit()}}.}
 
-\item{armval}{(\code{string})\cr used as strata name when treatment arm variable only has one level. Default is "All".}
+\item{armval}{(\code{string})\cr used as strata name when treatment arm variable only has one level. Default is \code{"All"}.}
 
-\item{max_time}{(\code{numeric})\cr maximum value to show on X axis. Only data values less than or up to
+\item{max_time}{(\code{numeric(1)})\cr maximum value to show on x-axis. Only data values less than or up to
 this threshold value will be plotted (defaults to \code{NULL}).}
 }
 \value{
-A \code{tibble} with columns \code{time}, \code{n.risk}, \code{n.event}, \code{n.censor}, \code{estimate}, \code{std.error}, \code{conf.high},
-\code{conf.low}, \code{strata}, and \code{censor}.
-
 A \code{tibble} with columns \code{time}, \code{n.risk}, \code{n.event}, \code{n.censor}, \code{estimate}, \code{std.error}, \code{conf.high},
 \code{conf.low}, \code{strata}, and \code{censor}.
 }
@@ -29,20 +24,6 @@ A \code{tibble} with columns \code{time}, \code{n.risk}, \code{n.event}, \code{n
 Convert the survival fit data into a data frame designed for plotting
 within \code{g_km}.
 
-This starts from the \code{\link[broom:reexports]{broom::tidy()}} result, and then:
-\itemize{
-\item Post-processes the \code{strata} column into a factor.
-\item Extends each stratum by an additional first row with time 0 and probability 1 so that
-downstream plot lines start at those coordinates.
-\item Adds a \code{censor} column.
-\item Filters the rows before \code{max_time}.
-}
-
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-
-Convert the survival fit data into a data frame designed for plotting
-within \code{g_km}.
-
 This starts from the \code{\link[broom:reexports]{broom::tidy()}} result, and then:
 \itemize{
 \item Post-processes the \code{strata} column into a factor.
@@ -68,21 +49,4 @@ tern_ex_adtte \%>\%
   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) \%>\%
   h_data_plot(armval = "ARM B")
 
-\dontrun{
-library(dplyr)
-library(survival)
-
-# Test with multiple arms
-tern_ex_adtte \%>\%
-  filter(PARAMCD == "OS") \%>\%
-  survfit(form = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) \%>\%
-  h_data_plot()
-
-# Test with single arm
-tern_ex_adtte \%>\%
-  filter(PARAMCD == "OS", ARMCD == "ARM B") \%>\%
-  survfit(form = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) \%>\%
-  h_data_plot(armval = "ARM B")
-}
-
 }
diff --git a/man/h_decompose_gg.Rd b/man/h_decompose_gg.Rd
index 04944dc1f1..db05430261 100644
--- a/man/h_decompose_gg.Rd
+++ b/man/h_decompose_gg.Rd
@@ -1,27 +1,15 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/h_km.R, R/kaplan_meier_plot.R
+% Please edit documentation in R/h_km.R
 \name{h_decompose_gg}
 \alias{h_decompose_gg}
 \title{\code{ggplot} decomposition}
 \usage{
-h_decompose_gg(gg)
-
 h_decompose_gg(gg)
 }
 \arguments{
 \item{gg}{(\code{ggplot})\cr a graphic to decompose.}
 }
 \value{
-A named \code{list} with elements:
-\itemize{
-\item \code{panel}: The panel.
-\item \code{yaxis}: The y-axis.
-\item \code{xaxis}: The x-axis.
-\item \code{xlab}: The x-axis label.
-\item \code{ylab}: The y-axis label.
-\item \code{guide}: The legend.
-}
-
 A named \code{list} with elements:
 \itemize{
 \item \code{panel}: The panel.
@@ -35,10 +23,6 @@ A named \code{list} with elements:
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}
 
-The elements composing the \code{ggplot} are extracted and organized in a \code{list}.
-
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-
 The elements composing the \code{ggplot} are extracted and organized in a \code{list}.
 }
 \examples{
@@ -71,33 +55,4 @@ grid.rect(gp = grid::gpar(lty = 1, col = "royalblue", fill = "gray85", lwd = 5))
 grid::grid.draw(with(g_el, cbind(ylab, yaxis)))
 }
 
-\dontrun{
-library(dplyr)
-library(survival)
-library(grid)
-
-fit_km <- tern_ex_adtte \%>\%
-  filter(PARAMCD == "OS") \%>\%
-  survfit(form = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .)
-data_plot <- h_data_plot(fit_km = fit_km)
-xticks <- h_xticks(data = data_plot)
-gg <- h_ggkm(
-  data = data_plot,
-  yval = "Survival",
-  censor_show = TRUE,
-  xticks = xticks, xlab = "Days", ylab = "Survival Probability",
-  title = "tt",
-  footnotes = "ff"
-)
-
-g_el <- h_decompose_gg(gg)
-grid::grid.newpage()
-grid.rect(gp = grid::gpar(lty = 1, col = "red", fill = "gray85", lwd = 5))
-grid::grid.draw(g_el$panel)
-
-grid::grid.newpage()
-grid.rect(gp = grid::gpar(lty = 1, col = "royalblue", fill = "gray85", lwd = 5))
-grid::grid.draw(with(g_el, cbind(ylab, yaxis)))
-}
-
 }
diff --git a/man/h_g_ipp.Rd b/man/h_g_ipp.Rd
index 6b98016af0..b1c6e75110 100644
--- a/man/h_g_ipp.Rd
+++ b/man/h_g_ipp.Rd
@@ -1,25 +1,9 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/g_ipp.R, R/individual_patient_plot.R
+% Please edit documentation in R/g_ipp.R
 \name{h_g_ipp}
 \alias{h_g_ipp}
 \title{Helper function to create simple line plot over time}
 \usage{
-h_g_ipp(
-  df,
-  xvar,
-  yvar,
-  xlab,
-  ylab,
-  id_var,
-  title = "Individual Patient Plots",
-  subtitle = "",
-  caption = NULL,
-  add_baseline_hline = FALSE,
-  yvar_baseline = "BASE",
-  ggtheme = nestcolor::theme_nest(),
-  col = NULL
-)
-
 h_g_ipp(
   df,
   xvar,
@@ -67,17 +51,11 @@ by \code{ggplot2} to control outlook of plot. Use \code{ggplot2::theme()} to twe
 \item{col}{(\code{character})\cr line colors.}
 }
 \value{
-A \code{ggplot} line plot.
-
 A \code{ggplot} line plot.
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
 
-Function that generates a simple line plot displaying parameter trends over time.
-
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-
 Function that generates a simple line plot displaying parameter trends over time.
 }
 \examples{
@@ -99,28 +77,7 @@ p <- h_g_ipp(
 )
 p
 
-library(dplyr)
-library(nestcolor)
-
-# Select a small sample of data to plot.
-adlb <- tern_ex_adlb \%>\%
-  filter(PARAMCD == "ALT", !(AVISIT \%in\% c("SCREENING", "BASELINE"))) \%>\%
-  slice(1:36)
-
-p <- h_g_ipp(
-  df = adlb,
-  xvar = "AVISIT",
-  yvar = "AVAL",
-  xlab = "Visit",
-  id_var = "USUBJID",
-  ylab = "SGOT/ALT (U/L)",
-  add_baseline_hline = TRUE
-)
-p
-
 }
 \seealso{
-\code{\link[=g_ipp]{g_ipp()}} which uses this function.
-
 \code{\link[=g_ipp]{g_ipp()}} which uses this function.
 }
diff --git a/man/h_ggkm.Rd b/man/h_ggkm.Rd
index 6fac344839..49abfe820d 100644
--- a/man/h_ggkm.Rd
+++ b/man/h_ggkm.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/h_km.R, R/kaplan_meier_plot.R
+% Please edit documentation in R/h_km.R
 \name{h_ggkm}
 \alias{h_ggkm}
 \title{Helper function to create a KM plot}
@@ -11,25 +11,7 @@ h_ggkm(
   censor_show,
   xlab,
   ylab,
-  title,
-  footnotes = NULL,
-  max_time = NULL,
-  lwd = 1,
-  lty = NULL,
-  pch = 3,
-  size = 2,
-  col = NULL,
-  ci_ribbon = FALSE,
-  ggtheme = nestcolor::theme_nest()
-)
-
-h_ggkm(
-  data,
-  xticks = NULL,
-  yval = "Survival",
-  censor_show,
-  xlab,
-  ylab,
+  ylim = NULL,
   title,
   footnotes = NULL,
   max_time = NULL,
@@ -45,54 +27,52 @@ h_ggkm(
 \arguments{
 \item{data}{(\code{data.frame})\cr survival data as pre-processed by \code{h_data_plot}.}
 
-\item{xticks}{(\code{numeric}, \code{number}, or \code{NULL})\cr numeric vector of ticks or single number with spacing
-between ticks on the x axis. If \code{NULL} (default), \code{\link[labeling:extended]{labeling::extended()}} is used to determine
-an optimal tick position on the x axis.}
+\item{xticks}{(\code{numeric} or \code{NULL})\cr numeric vector of tick positions or a single number with spacing
+between ticks on the x-axis. If \code{NULL} (default), \code{\link[labeling:extended]{labeling::extended()}} is used to determine
+optimal tick positions on the x-axis.}
+
+\item{yval}{(\code{string})\cr type of plot, to be plotted on the y-axis. Options are \code{Survival} (default) and \code{Failure}
+probability.}
 
-\item{yval}{(\code{string})\cr value of y-axis. Options are \code{Survival} (default) and \code{Failure} probability.}
+\item{censor_show}{(\code{flag})\cr whether to show censored observations.}
 
-\item{censor_show}{(\code{flag})\cr whether to show censored.}
+\item{xlab}{(\code{string})\cr x-axis label.}
 
-\item{xlab}{(\code{string})\cr label of x-axis.}
+\item{ylab}{(\code{string})\cr y-axis label.}
 
-\item{ylab}{(\code{string})\cr label of y-axis.}
+\item{ylim}{(\code{numeric(2)})\cr vector containing lower and upper limits for the y-axis, respectively.
+If \code{NULL} (default), the default scale range is used.}
 
-\item{title}{(\code{string})\cr title for plot.}
+\item{title}{(\code{string})\cr plot title.}
 
-\item{footnotes}{(\code{string})\cr footnotes for plot.}
+\item{footnotes}{(\code{string})\cr plot footnotes.}
 
-\item{max_time}{(\code{numeric})\cr maximum value to show on X axis. Only data values less than or up to
+\item{max_time}{(\code{numeric(1)})\cr maximum value to show on x-axis. Only data values less than or up to
 this threshold value will be plotted (defaults to \code{NULL}).}
 
-\item{lwd}{(\code{numeric})\cr line width. Length of a vector should be equal
-to number of strata from \code{\link[survival:survfit]{survival::survfit()}}.}
+\item{lwd}{(\code{numeric})\cr line width. If a vector is given, its length should be equal to the number of strata from
+\code{\link[survival:survfit]{survival::survfit()}}.}
 
-\item{lty}{(\code{numeric})\cr line type. Length of a vector should be equal
-to number of strata from \code{\link[survival:survfit]{survival::survfit()}}.}
+\item{lty}{(\code{numeric})\cr line type. If a vector is given, its length should be equal to the number of strata from
+\code{\link[survival:survfit]{survival::survfit()}}.}
 
-\item{pch}{(\code{numeric}, \code{string})\cr value or character of points symbol to indicate censored cases.}
+\item{pch}{(\code{string})\cr name of symbol or character to use as point symbol to indicate censored cases.}
 
-\item{size}{(\code{numeric})\cr size of censored point, a class of \code{unit}.}
+\item{size}{(\code{numeric(1)})\cr size of censored point symbols.}
 
 \item{col}{(\code{character})\cr lines colors. Length of a vector should be equal
 to number of strata from \code{\link[survival:survfit]{survival::survfit()}}.}
 
-\item{ci_ribbon}{(\code{flag})\cr draw the confidence interval around the Kaplan-Meier curve.}
+\item{ci_ribbon}{(\code{flag})\cr whether the confidence interval should be drawn around the Kaplan-Meier curve.}
 
-\item{ggtheme}{(\code{theme})\cr a graphical theme as provided by \code{ggplot2} to control outlook of the Kaplan-Meier curve.}
+\item{ggtheme}{(\code{theme})\cr a graphical theme as provided by \code{ggplot2} to format the Kaplan-Meier plot.}
 }
 \value{
-A \code{ggplot} object.
-
 A \code{ggplot} object.
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}
 
-Draw the Kaplan-Meier plot using \code{ggplot2}.
-
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-
 Draw the Kaplan-Meier plot using \code{ggplot2}.
 }
 \examples{
@@ -117,25 +97,4 @@ gg <- h_ggkm(
 gg
 }
 
-\dontrun{
-library(dplyr)
-library(survival)
-
-fit_km <- tern_ex_adtte \%>\%
-  filter(PARAMCD == "OS") \%>\%
-  survfit(form = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .)
-data_plot <- h_data_plot(fit_km = fit_km)
-xticks <- h_xticks(data = data_plot)
-gg <- h_ggkm(
-  data = data_plot,
-  censor_show = TRUE,
-  xticks = xticks,
-  xlab = "Days",
-  yval = "Survival",
-  ylab = "Survival Probability",
-  title = "Survival"
-)
-gg
-}
-
 }
diff --git a/man/h_grob_coxph.Rd b/man/h_grob_coxph.Rd
index 4b3da65c8e..739887e7ed 100644
--- a/man/h_grob_coxph.Rd
+++ b/man/h_grob_coxph.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/h_km.R, R/kaplan_meier_plot.R
+% Please edit documentation in R/h_km.R
 \name{h_grob_coxph}
 \alias{h_grob_coxph}
 \title{Helper function to create Cox-PH grobs}
@@ -8,43 +8,29 @@ h_grob_coxph(
   ...,
   x = 0,
   y = 0,
-  ttheme = gridExtra::ttheme_default(base_size = 12, padding = grid::unit(c(1, 0.5),
-    "lines"), core = list(bg_params = list(fill = c("grey95", "grey90"), alpha = 0.5)))
-)
-
-h_grob_coxph(
-  ...,
-  x = 0,
-  y = 0,
-  ttheme = gridExtra::ttheme_default(base_size = 12, padding = grid::unit(c(1, 0.5),
-    "lines"), core = list(bg_params = list(fill = c("grey95", "grey90"), alpha = 0.5)))
+  width = grid::unit(0.4, "npc"),
+  ttheme = gridExtra::ttheme_default(padding = grid::unit(c(1, 0.5), "lines"), core =
+    list(bg_params = list(fill = c("grey95", "grey90"), alpha = 0.5)))
 )
 }
 \arguments{
-\item{...}{arguments will be passed to \code{\link[=h_tbl_coxph_pairwise]{h_tbl_coxph_pairwise()}}.}
-
-\item{x}{(\code{numeric})\cr a value between 0 and 1 specifying x-location.}
+\item{...}{arguments to pass to \code{\link[=h_tbl_coxph_pairwise]{h_tbl_coxph_pairwise()}}.}
 
-\item{y}{(\code{numeric})\cr a value between 0 and 1 specifying y-location.}
+\item{x}{(\code{proportion})\cr a value between 0 and 1 specifying x-location.}
 
-\item{ttheme}{(\code{list})\cr see \code{\link[gridExtra:tableGrob]{gridExtra::ttheme_default()}}.}
+\item{y}{(\code{proportion})\cr a value between 0 and 1 specifying y-location.}
 
 \item{width}{(\code{grid::unit})\cr width (as a unit) to use when printing the grob.}
+
+\item{ttheme}{(\code{list})\cr see \code{\link[gridExtra:tableGrob]{gridExtra::ttheme_default()}}.}
 }
 \value{
-A \code{grob} of a table containing statistics \code{HR}, \verb{XX\% CI} (\code{XX} taken from \code{control_coxph_pw}),
-and \code{p-value (log-rank)}.
-
 A \code{grob} of a table containing statistics \code{HR}, \verb{XX\% CI} (\code{XX} taken from \code{control_coxph_pw}),
 and \code{p-value (log-rank)}.
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}
 
-Grob of \code{rtable} output from \code{\link[=h_tbl_coxph_pairwise]{h_tbl_coxph_pairwise()}}
-
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-
 Grob of \code{rtable} output from \code{\link[=h_tbl_coxph_pairwise]{h_tbl_coxph_pairwise()}}
 }
 \examples{
@@ -66,22 +52,4 @@ tbl_grob <- h_grob_coxph(
 grid::grid.draw(tbl_grob)
 }
 
-\dontrun{
-library(dplyr)
-library(survival)
-library(grid)
-
-grid::grid.newpage()
-grid.rect(gp = grid::gpar(lty = 1, col = "pink", fill = "gray85", lwd = 1))
-data <- tern_ex_adtte \%>\%
-  filter(PARAMCD == "OS") \%>\%
-  mutate(is_event = CNSR == 0)
-tbl_grob <- h_grob_coxph(
-  df = data,
-  variables = list(tte = "AVAL", is_event = "is_event", arm = "ARMCD"),
-  control_coxph_pw = control_coxph(conf_level = 0.9), x = 0.5, y = 0.5
-)
-grid::grid.draw(tbl_grob)
-}
-
 }
diff --git a/man/h_grob_median_surv.Rd b/man/h_grob_median_surv.Rd
index d72547c64f..b9bc0b4081 100644
--- a/man/h_grob_median_surv.Rd
+++ b/man/h_grob_median_surv.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/h_km.R, R/kaplan_meier_plot.R
+% Please edit documentation in R/h_km.R
 \name{h_grob_median_surv}
 \alias{h_grob_median_surv}
 \title{Helper function to create survival estimation grobs}
@@ -9,43 +9,29 @@ h_grob_median_surv(
   armval = "All",
   x = 0.9,
   y = 0.9,
-  ttheme = gridExtra::ttheme_default()
-)
-
-h_grob_median_surv(
-  fit_km,
-  armval = "All",
-  x = 0.9,
-  y = 0.9,
+  width = grid::unit(0.3, "npc"),
   ttheme = gridExtra::ttheme_default()
 )
 }
 \arguments{
 \item{fit_km}{(\code{survfit})\cr result of \code{\link[survival:survfit]{survival::survfit()}}.}
 
-\item{armval}{(\code{string})\cr used as strata name when treatment arm variable only has one level. Default is "All".}
+\item{armval}{(\code{string})\cr used as strata name when treatment arm variable only has one level. Default is \code{"All"}.}
 
-\item{x}{(\code{numeric})\cr a value between 0 and 1 specifying x-location.}
+\item{x}{(\code{proportion})\cr a value between 0 and 1 specifying x-location.}
 
-\item{y}{(\code{numeric})\cr a value between 0 and 1 specifying y-location.}
-
-\item{ttheme}{(\code{list})\cr see \code{\link[gridExtra:tableGrob]{gridExtra::ttheme_default()}}.}
+\item{y}{(\code{proportion})\cr a value between 0 and 1 specifying y-location.}
 
 \item{width}{(\code{grid::unit})\cr width (as a unit) to use when printing the grob.}
+
+\item{ttheme}{(\code{list})\cr see \code{\link[gridExtra:tableGrob]{gridExtra::ttheme_default()}}.}
 }
 \value{
-A \code{grob} of a table containing statistics \code{N}, \code{Median}, and \verb{XX\% CI} (\code{XX} taken from \code{fit_km}).
-
 A \code{grob} of a table containing statistics \code{N}, \code{Median}, and \verb{XX\% CI} (\code{XX} taken from \code{fit_km}).
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}
 
-The survival fit is transformed in a grob containing a table with groups in
-rows characterized by N, median and 95\% confidence interval.
-
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-
 The survival fit is transformed in a grob containing a table with groups in
 rows characterized by N, median and 95\% confidence interval.
 }
@@ -64,18 +50,4 @@ tern_ex_adtte \%>\%
   grid::grid.draw()
 }
 
-\dontrun{
-library(dplyr)
-library(survival)
-library(grid)
-
-grid::grid.newpage()
-grid.rect(gp = grid::gpar(lty = 1, col = "pink", fill = "gray85", lwd = 1))
-tern_ex_adtte \%>\%
-  filter(PARAMCD == "OS") \%>\%
-  survfit(form = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) \%>\%
-  h_grob_median_surv() \%>\%
-  grid::grid.draw()
-}
-
 }
diff --git a/man/h_grob_tbl_at_risk.Rd b/man/h_grob_tbl_at_risk.Rd
index eaee69fff4..49c301cf1c 100644
--- a/man/h_grob_tbl_at_risk.Rd
+++ b/man/h_grob_tbl_at_risk.Rd
@@ -1,12 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/h_km.R, R/kaplan_meier_plot.R
+% Please edit documentation in R/h_km.R
 \name{h_grob_tbl_at_risk}
 \alias{h_grob_tbl_at_risk}
 \title{Helper function to create patient-at-risk grobs}
 \usage{
-h_grob_tbl_at_risk(data, annot_tbl, xlim)
-
-h_grob_tbl_at_risk(data, annot_tbl, xlim)
+h_grob_tbl_at_risk(data, annot_tbl, xlim, title = TRUE)
 }
 \arguments{
 \item{data}{(\code{data.frame})\cr survival data as pre-processed by \code{h_data_plot}.}
@@ -14,8 +12,8 @@ h_grob_tbl_at_risk(data, annot_tbl, xlim)
 \item{annot_tbl}{(\code{data.frame})\cr annotation as prepared by \code{\link[survival:summary.survfit]{survival::summary.survfit()}} which
 includes the number of patients at risk at given time points.}
 
-\item{xlim}{(\code{numeric})\cr the maximum value on the x-axis (used to
-ensure the at risk table aligns with the KM graph).}
+\item{xlim}{(\code{numeric(1)})\cr the maximum value on the x-axis (used to ensure the at risk table aligns with the KM
+graph).}
 
 \item{title}{(\code{flag})\cr whether the "Patients at Risk" title should be added above the \code{annot_at_risk}
 table. Has no effect if \code{annot_at_risk} is \code{FALSE}. Defaults to \code{TRUE}.}
@@ -23,8 +21,6 @@ table. Has no effect if \code{annot_at_risk} is \code{FALSE}. Defaults to \code{
 \value{
 A named \code{list} of two \code{gTree} objects if \code{title = FALSE}: \code{at_risk} and \code{label}, or three
 \code{gTree} objects if \code{title = TRUE}: \code{at_risk}, \code{label}, and \code{title}.
-
-A named \code{list} of two \code{gTree} objects: \code{at_risk} and \code{label}.
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}
@@ -32,11 +28,6 @@ A named \code{list} of two \code{gTree} objects: \code{at_risk} and \code{label}
 Two graphical objects are obtained, one corresponding to row labeling and the second to the table of
 numbers of patients at risk. If \code{title = TRUE}, a third object corresponding to the table title is
 also obtained.
-
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-
-Two graphical objects are obtained, one corresponding to row labeling and
-the second to the number of patient at risk.
 }
 \examples{
 \donttest{
@@ -94,59 +85,4 @@ grid.rect(gp = grid::gpar(lty = 1, col = "green3", fill = "gray85", lwd = 1))
 grid::grid.draw(tbl$label)
 }
 
-\dontrun{
-library(dplyr)
-library(survival)
-library(grid)
-
-fit_km <- tern_ex_adtte \%>\%
-  filter(PARAMCD == "OS") \%>\%
-  survfit(form = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .)
-
-data_plot <- h_data_plot(fit_km = fit_km)
-
-xticks <- h_xticks(data = data_plot)
-
-gg <- h_ggkm(
-  data = data_plot,
-  censor_show = TRUE,
-  xticks = xticks, xlab = "Days", ylab = "Survival Probability",
-  title = "tt", footnotes = "ff", yval = "Survival"
-)
-
-# The annotation table reports the patient at risk for a given strata and
-# time (`xticks`).
-annot_tbl <- summary(fit_km, time = xticks)
-if (is.null(fit_km$strata)) {
-  annot_tbl <- with(annot_tbl, data.frame(n.risk = n.risk, time = time, strata = "All"))
-} else {
-  strata_lst <- strsplit(sub("=", "equals", levels(annot_tbl$strata)), "equals")
-  levels(annot_tbl$strata) <- matrix(unlist(strata_lst), ncol = 2, byrow = TRUE)[, 2]
-  annot_tbl <- data.frame(
-    n.risk = annot_tbl$n.risk,
-    time = annot_tbl$time,
-    strata = annot_tbl$strata
-  )
-}
-
-# The annotation table is transformed into a grob.
-tbl <- h_grob_tbl_at_risk(data = data_plot, annot_tbl = annot_tbl, xlim = max(xticks))
-
-# For the representation, the layout is estimated for which the decomposition
-# of the graphic element is necessary.
-g_el <- h_decompose_gg(gg)
-lyt <- h_km_layout(data = data_plot, g_el = g_el, title = "t", footnotes = "f")
-
-grid::grid.newpage()
-pushViewport(viewport(layout = lyt, height = .95, width = .95))
-grid.rect(gp = grid::gpar(lty = 1, col = "purple", fill = "gray85", lwd = 1))
-pushViewport(viewport(layout.pos.row = 4, layout.pos.col = 2))
-grid.rect(gp = grid::gpar(lty = 1, col = "orange", fill = "gray85", lwd = 1))
-grid::grid.draw(tbl$at_risk)
-popViewport()
-pushViewport(viewport(layout.pos.row = 4, layout.pos.col = 1))
-grid.rect(gp = grid::gpar(lty = 1, col = "green3", fill = "gray85", lwd = 1))
-grid::grid.draw(tbl$label)
-}
-
 }
diff --git a/man/h_grob_y_annot.Rd b/man/h_grob_y_annot.Rd
index 8d2e0a224c..b12c15ba5b 100644
--- a/man/h_grob_y_annot.Rd
+++ b/man/h_grob_y_annot.Rd
@@ -1,11 +1,9 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/h_km.R, R/kaplan_meier_plot.R
+% Please edit documentation in R/h_km.R
 \name{h_grob_y_annot}
 \alias{h_grob_y_annot}
 \title{Helper function to create grid object with y-axis annotation}
 \usage{
-h_grob_y_annot(ylab, yaxis)
-
 h_grob_y_annot(ylab, yaxis)
 }
 \arguments{
@@ -15,16 +13,10 @@ h_grob_y_annot(ylab, yaxis)
 }
 \value{
 A \code{gTree} object containing the y-axis annotation from a \code{ggplot}.
-
-a \code{gTree} object containing the y-axis annotation from a \code{ggplot}.
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}
 
-Build the y-axis annotation from a decomposed \code{ggplot}.
-
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-
 Build the y-axis annotation from a decomposed \code{ggplot}.
 }
 \examples{
@@ -54,30 +46,4 @@ grid::grid.draw(h_grob_y_annot(ylab = g_el$ylab, yaxis = g_el$yaxis))
 grid.rect(gp = grid::gpar(lty = 1, col = "gray35", fill = NA))
 }
 
-\dontrun{
-library(dplyr)
-library(survival)
-library(grid)
-
-fit_km <- tern_ex_adtte \%>\%
-  filter(PARAMCD == "OS") \%>\%
-  survfit(form = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .)
-data_plot <- h_data_plot(fit_km = fit_km)
-xticks <- h_xticks(data = data_plot)
-gg <- h_ggkm(
-  data = data_plot,
-  censor_show = TRUE,
-  xticks = xticks, xlab = "Days", ylab = "Survival Probability",
-  title = "title", footnotes = "footnotes", yval = "Survival"
-)
-
-g_el <- h_decompose_gg(gg)
-
-grid::grid.newpage()
-pvp <- grid::plotViewport(margins = c(5, 4, 2, 20))
-pushViewport(pvp)
-grid::grid.draw(h_grob_y_annot(ylab = g_el$ylab, yaxis = g_el$yaxis))
-grid.rect(gp = grid::gpar(lty = 1, col = "gray35", fill = NA))
-}
-
 }
diff --git a/man/h_km_layout.Rd b/man/h_km_layout.Rd
index 8744b64e02..a84b8ca617 100644
--- a/man/h_km_layout.Rd
+++ b/man/h_km_layout.Rd
@@ -1,49 +1,42 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/h_km.R, R/kaplan_meier_plot.R
+% Please edit documentation in R/h_km.R
 \name{h_km_layout}
 \alias{h_km_layout}
 \title{Helper function to prepare a KM layout}
 \usage{
-h_km_layout(data, g_el, title, footnotes, annot_at_risk = TRUE)
-
-h_km_layout(data, g_el, title, footnotes, annot_at_risk = TRUE)
+h_km_layout(
+  data,
+  g_el,
+  title,
+  footnotes,
+  annot_at_risk = TRUE,
+  annot_at_risk_title = TRUE
+)
 }
 \arguments{
 \item{data}{(\code{data.frame})\cr survival data as pre-processed by \code{h_data_plot}.}
 
 \item{g_el}{(\code{list} of \code{gtable})\cr list as obtained by \code{h_decompose_gg()}.}
 
-\item{title}{(\code{string})\cr title for plot.}
+\item{title}{(\code{string})\cr plot title.}
 
-\item{footnotes}{(\code{string})\cr footnotes for plot.}
+\item{footnotes}{(\code{string})\cr plot footnotes.}
 
 \item{annot_at_risk}{(\code{flag})\cr compute and add the annotation table reporting the number of
 patient at risk matching the main grid of the Kaplan-Meier curve.}
+
+\item{annot_at_risk_title}{(\code{flag})\cr whether the "Patients at Risk" title should be added above the \code{annot_at_risk}
+table. Has no effect if \code{annot_at_risk} is \code{FALSE}. Defaults to \code{TRUE}.}
 }
 \value{
-A grid layout.
-
 A grid layout.
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}
 
-Prepares a (5 rows) x (2 cols) layout for the Kaplan-Meier curve.
-
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-
 Prepares a (5 rows) x (2 cols) layout for the Kaplan-Meier curve.
 }
 \details{
-The layout corresponds to a grid of two columns and five rows of unequal dimensions. Most of the
-dimension are fixed, only the curve is flexible and will accommodate with the remaining free space.
-\itemize{
-\item The left column gets the annotation of the \code{ggplot} (y-axis) and the names of the strata for the patient
-at risk tabulation. The main constraint is about the width of the columns which must allow the writing of
-the strata name.
-\item The right column receive the \code{ggplot}, the legend, the x-axis and the patient at risk table.
-}
-
 The layout corresponds to a grid of two columns and five rows of unequal dimensions. Most of the
 dimension are fixed, only the curve is flexible and will accommodate with the remaining free space.
 \itemize{
@@ -75,24 +68,4 @@ lyt <- h_km_layout(data = data_plot, g_el = g_el, title = "t", footnotes = "f")
 grid.show.layout(lyt)
 }
 
-\dontrun{
-library(dplyr)
-library(survival)
-
-fit_km <- tern_ex_adtte \%>\%
-  filter(PARAMCD == "OS") \%>\%
-  survfit(form = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .)
-data_plot <- h_data_plot(fit_km = fit_km)
-xticks <- h_xticks(data = data_plot)
-gg <- h_ggkm(
-  data = data_plot,
-  censor_show = TRUE,
-  xticks = xticks, xlab = "Days", ylab = "Survival Probability",
-  title = "tt", footnotes = "ff", yval = "Survival"
-)
-g_el <- h_decompose_gg(gg)
-lyt <- h_km_layout(data = data_plot, g_el = g_el, title = "t", footnotes = "f")
-grid.show.layout(lyt)
-}
-
 }
diff --git a/man/h_tbl_coxph_pairwise.Rd b/man/h_tbl_coxph_pairwise.Rd
index f3e1c5cc30..2dbe3ad95c 100644
--- a/man/h_tbl_coxph_pairwise.Rd
+++ b/man/h_tbl_coxph_pairwise.Rd
@@ -1,12 +1,16 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/h_km.R, R/kaplan_meier_plot.R
+% Please edit documentation in R/h_km.R
 \name{h_tbl_coxph_pairwise}
 \alias{h_tbl_coxph_pairwise}
 \title{Helper function for generating a pairwise Cox-PH table}
 \usage{
-h_tbl_coxph_pairwise(df, variables, control_coxph_pw = control_coxph())
-
-h_tbl_coxph_pairwise(df, variables, control_coxph_pw = control_coxph())
+h_tbl_coxph_pairwise(
+  df,
+  variables,
+  ref_group_coxph = NULL,
+  control_coxph_pw = control_coxph(),
+  annot_coxph_ref_lbls = FALSE
+)
 }
 \arguments{
 \item{df}{(\code{data.frame})\cr data set containing all analysis variables.}
@@ -16,16 +20,19 @@ h_tbl_coxph_pairwise(df, variables, control_coxph_pw = control_coxph())
 \item \code{tte} (\code{numeric})\cr variable indicating time-to-event duration values.
 \item \code{is_event} (\code{logical})\cr event variable. \code{TRUE} if event, \code{FALSE} if time to event is censored.
 \item \code{arm} (\code{factor})\cr the treatment group variable.
-\item \code{strat} (\code{character} or \code{NULL})\cr variable names indicating stratification factors.
+\item \code{strata} (\code{character} or \code{NULL})\cr variable names indicating stratification factors.
 }}
 
-\item{control_coxph_pw}{(\code{list})\cr parameters for comparison details, specified by using
-the helper function \code{\link[=control_coxph]{control_coxph()}}. Some possible parameter options are:
+\item{ref_group_coxph}{(\code{string} or \code{NULL})\cr level of arm variable to use as reference group in calculations for
+\code{annot_coxph} table. If \code{NULL} (default), uses the first level of the arm variable.}
+
+\item{control_coxph_pw}{(\code{list})\cr parameters for comparison details, specified using the helper function
+\code{\link[=control_coxph]{control_coxph()}}. Some possible parameter options are:
 \itemize{
 \item \code{pval_method} (\code{string})\cr p-value method for testing hazard ratio = 1.
-Default method is "log-rank", can also be set to "wald" or "likelihood".
-\item \code{ties} (\code{string})\cr method for tie handling. Default is "efron",
-can also be set to "breslow" or "exact". See more in \code{\link[survival:coxph]{survival::coxph()}}
+Default method is \code{"log-rank"}, can also be set to \code{"wald"} or \code{"likelihood"}.
+\item \code{ties} (\code{string})\cr method for tie handling. Default is \code{"efron"},
+can also be set to \code{"breslow"} or \code{"exact"}. See more in \code{\link[survival:coxph]{survival::coxph()}}
 \item \code{conf_level} (\code{proportion})\cr confidence level of the interval for HR.
 }}
 
@@ -33,9 +40,6 @@ can also be set to "breslow" or "exact". See more in \code{\link[survival:coxph]
 \code{annot_coxph} table. If \code{FALSE} (default), only comparison groups will be printed in \code{annot_coxph} table labels.}
 }
 \value{
-A \code{data.frame} containing statistics \code{HR}, \verb{XX\% CI} (\code{XX} taken from \code{control_coxph_pw}),
-and \code{p-value (log-rank)}.
-
 A \code{data.frame} containing statistics \code{HR}, \verb{XX\% CI} (\code{XX} taken from \code{control_coxph_pw}),
 and \code{p-value (log-rank)}.
 }
@@ -43,10 +47,6 @@ and \code{p-value (log-rank)}.
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
 
 Create a \code{data.frame} of pairwise stratified or unstratified Cox-PH analysis results.
-
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-
-Create a \code{data.frame} of pairwise stratified or unstratified CoxPH analysis results.
 }
 \examples{
 library(dplyr)
@@ -61,18 +61,4 @@ h_tbl_coxph_pairwise(
   control_coxph_pw = control_coxph(conf_level = 0.9)
 )
 
-\dontrun{
-library(dplyr)
-
-adtte <- tern_ex_adtte \%>\%
-  filter(PARAMCD == "OS") \%>\%
-  mutate(is_event = CNSR == 0)
-
-h_tbl_coxph_pairwise(
-  df = adtte,
-  variables = list(tte = "AVAL", is_event = "is_event", arm = "ARM"),
-  control_coxph_pw = control_coxph(conf_level = 0.9)
-)
-}
-
 }
diff --git a/man/h_tbl_median_surv.Rd b/man/h_tbl_median_surv.Rd
index 13bcc8c0a0..06ab4c1817 100644
--- a/man/h_tbl_median_surv.Rd
+++ b/man/h_tbl_median_surv.Rd
@@ -1,30 +1,22 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/h_km.R, R/kaplan_meier_plot.R
+% Please edit documentation in R/h_km.R
 \name{h_tbl_median_surv}
 \alias{h_tbl_median_surv}
 \title{Helper function for survival estimations}
 \usage{
-h_tbl_median_surv(fit_km, armval = "All")
-
 h_tbl_median_surv(fit_km, armval = "All")
 }
 \arguments{
 \item{fit_km}{(\code{survfit})\cr result of \code{\link[survival:survfit]{survival::survfit()}}.}
 
-\item{armval}{(\code{string})\cr used as strata name when treatment arm variable only has one level. Default is "All".}
+\item{armval}{(\code{string})\cr used as strata name when treatment arm variable only has one level. Default is \code{"All"}.}
 }
 \value{
-A summary table with statistics \code{N}, \code{Median}, and \verb{XX\% CI} (\code{XX} taken from \code{fit_km}).
-
 A summary table with statistics \code{N}, \code{Median}, and \verb{XX\% CI} (\code{XX} taken from \code{fit_km}).
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
 
-Transform a survival fit to a table with groups in rows characterized by N, median and confidence interval.
-
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-
 Transform a survival fit to a table with groups in rows characterized by N, median and confidence interval.
 }
 \examples{
@@ -38,16 +30,4 @@ fit <- survfit(
 )
 h_tbl_median_surv(fit_km = fit)
 
-\dontrun{
-library(dplyr)
-library(survival)
-
-adtte <- tern_ex_adtte \%>\% filter(PARAMCD == "OS")
-fit <- survfit(
-  form = Surv(AVAL, 1 - CNSR) ~ ARMCD,
-  data = adtte
-)
-h_tbl_median_surv(fit_km = fit)
-}
-
 }
diff --git a/man/h_xticks.Rd b/man/h_xticks.Rd
index 4c799d80e8..a304f50ca9 100644
--- a/man/h_xticks.Rd
+++ b/man/h_xticks.Rd
@@ -1,37 +1,27 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/h_km.R, R/kaplan_meier_plot.R
+% Please edit documentation in R/h_km.R
 \name{h_xticks}
 \alias{h_xticks}
 \title{Helper function to calculate x-tick positions}
 \usage{
-h_xticks(data, xticks = NULL, max_time = NULL)
-
 h_xticks(data, xticks = NULL, max_time = NULL)
 }
 \arguments{
 \item{data}{(\code{data.frame})\cr survival data as pre-processed by \code{h_data_plot}.}
 
-\item{xticks}{(\code{numeric}, \code{number}, or \code{NULL})\cr numeric vector of ticks or single number with spacing
-between ticks on the x axis. If \code{NULL} (default), \code{\link[labeling:extended]{labeling::extended()}} is used to determine
-an optimal tick position on the x axis.}
+\item{xticks}{(\code{numeric} or \code{NULL})\cr numeric vector of tick positions or a single number with spacing
+between ticks on the x-axis. If \code{NULL} (default), \code{\link[labeling:extended]{labeling::extended()}} is used to determine
+optimal tick positions on the x-axis.}
 
-\item{max_time}{(\code{numeric})\cr maximum value to show on X axis. Only data values less than or up to
+\item{max_time}{(\code{numeric(1)})\cr maximum value to show on x-axis. Only data values less than or up to
 this threshold value will be plotted (defaults to \code{NULL}).}
 }
 \value{
-A vector of positions to use for x-axis ticks on a \code{ggplot} object.
-
 A vector of positions to use for x-axis ticks on a \code{ggplot} object.
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
 
-Calculate the positions of ticks on the x-axis. However, if \code{xticks} already
-exists it is kept as is. It is based on the same function \code{ggplot2} relies on,
-and is required in the graphic and the patient-at-risk annotation table.
-
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-
 Calculate the positions of ticks on the x-axis. However, if \code{xticks} already
 exists it is kept as is. It is based on the same function \code{ggplot2} relies on,
 and is required in the graphic and the patient-at-risk annotation table.
@@ -52,21 +42,4 @@ h_xticks(data, xticks = 500, max_time = 6000)
 h_xticks(data, xticks = c(0, 500), max_time = 300)
 h_xticks(data, xticks = 500, max_time = 300)
 
-\dontrun{
-library(dplyr)
-library(survival)
-
-data <- tern_ex_adtte \%>\%
-  filter(PARAMCD == "OS") \%>\%
-  survfit(form = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) \%>\%
-  h_data_plot()
-
-h_xticks(data)
-h_xticks(data, xticks = seq(0, 3000, 500))
-h_xticks(data, xticks = 500)
-h_xticks(data, xticks = 500, max_time = 6000)
-h_xticks(data, xticks = c(0, 500), max_time = 300)
-h_xticks(data, xticks = 500, max_time = 300)
-}
-
 }
diff --git a/man/try_car_anova.Rd b/man/try_car_anova.Rd
index a81cde8287..b3ba87bf83 100644
--- a/man/try_car_anova.Rd
+++ b/man/try_car_anova.Rd
@@ -9,12 +9,12 @@ try_car_anova(mod, test.statistic)
 \arguments{
 \item{mod}{\code{lm}, \code{aov}, \code{glm}, \code{multinom}, \code{polr}
     \code{mlm}, \code{coxph}, \code{coxme}, \code{lme}, \code{mer}, \code{merMod}, \code{svyglm}, \code{svycoxph},
-    \code{rlm}, or other suitable model object.}
+    \code{rlm}, \code{clm}, \code{clmm}, or other suitable model object.}
 
 \item{test.statistic}{for a generalized linear model, whether to calculate
     \code{"LR"} (likelihood-ratio), \code{"Wald"}, or \code{"F"} tests; for a Cox
     or Cox mixed-effects model, whether to calculate \code{"LR"} (partial-likelihood ratio) or
-    \code{"Wald"} tests; in the default case or for linear mixed models fit by
+    \code{"Wald"} tests (with \code{"LR"} tests unavailable for Cox models using the \code{tt} argument); in the default case or for linear mixed models fit by
     \code{lmer}, whether to calculate Wald \code{"Chisq"} or Kenward-Roger
     \code{"F"} tests with Satterthwaite degrees of freedom (\emph{warning:} the KR F-tests
     can be very time-consuming).