Update to description adding Cole & Hernan (2014) reference

Author: larry-leon

.DS_Store

@@ -1,15 +1,8 @@
 Package: weightedsurv
 Title: Survival Analysis with Subject-Specific (Case Weights) and Time-Dependent Weighting
 Version: 0.1.0
-Authors@R: 
-    person("Larry", "Leon", , "larry.leon.05@post.harvard.edu", role = c("aut", "cre"))
-Description:
-  Survival analysis functions allowing for time-dependent and subject-specific
-  (for example, propensity-scores) weighting. Weighted estimation for Cox model,
-  Kaplan-Meier treatment survival curves as well as treatment difference along
-  with point-wise and simultaneous confidence bands, and restricted mean
-  survival time comparisons where 'RMST' estimates are evaluated across all
-  potential truncation times (point-wise and simultaneous bands).
+Authors@R: person("Larry", "Leon", , "larry.leon.05@post.harvard.edu", role = c("aut", "cre"))
+Description: Survival analysis functions allowing for time-dependent and subject-specific (for example, propensity-scores) weighting. Weighted estimation for Cox model, Kaplan-Meier treatment survival curves as well as treatment difference along with point-wise and simultaneous confidence bands, and restricted mean survival time comparisons where 'RMST' estimates are evaluated across all potential truncation times (point-wise and simultaneous bands). See for example, Cole, S. R. & Hernán, M. A. (2004). Adjusted survival curves with inverse probability weights. Computer Methods and Programs in Biomedicine, 75(1), 45–49. doi:10.1016/j.cmpb.2003.10.012  
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

DESCRIPTION

@@ -6,9 +6,11 @@
 #' @param x Numeric vector of time points.
 #' @param surv Numeric vector of survival probabilities.
 #' @param se Numeric vector of standard errors of survival probabilities.
-#' @param conf_level Confidence level for interval (default 0.95).
+#' @param conf_level Numeric; confidence level for interval (default 0.95).
 #' @param col Color for the polygon.
+#'
 #' @importFrom graphics polygon
+#' @return Invisibly returns NULL. Used for plotting side effects.
 #' @export
 
 plot_km_confint_polygon <- function(x, surv, se, conf_level, col) {
@@ -51,9 +53,12 @@ plot_km_confint_polygon <- function(x, surv, se, conf_level, col) {
 #' @param conf.int Logical; show confidence intervals (default FALSE).
 #' @param conf_level Confidence level (default 0.95).
 #' @param censor.cex Numeric; censoring mark size (default 1.0).
+#' @param time.zero Numeric; time zero value for risk table alignment (default 0).
+#' @param tpoints.add Numeric vector; additional time points to include (default c(0)).
 #' @param ... Additional arguments to plot.
-#' @inheritParams KM_plot_2sample_weighted_counting
+#'
 #' @importFrom graphics plot lines legend title axis box points
+#' @return Invisibly returns NULL. Used for plotting side effects.
 #' @export
 
 plot_km_curves_counting <- function(
@@ -129,6 +134,7 @@ check_km_curve <- function(S.KM, group_name = "Group", stop_on_error = TRUE) {
 #' @param y.risk0 Numeric; y position for group 0 risk table.
 #' @param y.risk1 Numeric; y position for group 1 risk table.
 #' @importFrom graphics text axis
+#' @return Invisibly returns NULL. Used for plotting side effects.
 #' @export
 
 add_risk_table <- function(risk.points, rpoints0, rpoints1, col.0, col.1, risk.cex, ymin, risk_offset, risk_delta, y.risk0, y.risk1) {
@@ -142,13 +148,15 @@ add_risk_table <- function(risk.points, rpoints0, rpoints1, col.0, col.1, risk.c
 #'
 #' Adds median survival annotation to a Kaplan-Meier plot.
 #'
-#' @param medians_df Data frame with quantile results.
-#' @param med.digits Integer; digits for median.
-#' @param med.cex Numeric; text size for median.
-#' @param med.font Integer; font for median.
-#' @param xmed.fraction Numeric; x position fraction.
-#' @param ymed.offset Numeric; y offset.
+#' @param medians_df Data frame with quantile results. Should contain columns \code{quantile}, \code{lower}, \code{upper}, and \code{group}.
+#' @param med.digits Integer; number of digits to display for median and confidence interval.
+#' @param med.cex Numeric; text size for median annotation.
+#' @param med.font Integer; font for median annotation.
+#' @param xmed.fraction Numeric; fraction of the x-axis for annotation placement (e.g., 0.8 for 80\% to the right).
+#' @param ymed.offset Numeric; offset from the top of the plot for annotation placement.
+#'
 #' @importFrom graphics text
+#' @return Invisibly returns NULL. Used for plotting side effects.
 #' @export
 
 add_median_annotation <- function(medians_df, med.digits, med.cex, med.font, xmed.fraction, ymed.offset) {
@@ -173,22 +181,24 @@ add_median_annotation <- function(medians_df, med.digits, med.cex, med.font, xme
 #'
 #' Adds legends for Cox model, log-rank test, and arms to a Kaplan-Meier plot.
 #'
-#' @param dfcount List with results.
+#' @param dfcount List with results, typically output from a survival analysis function. Should contain elements such as \code{cox_results}, \code{z.score}, and \code{zlogrank_text}.
 #' @param show.cox Logical; show Cox legend.
 #' @param cox.cex Numeric; Cox legend size.
-#' @param put.legend.cox Character; Cox legend position.
+#' @param put.legend.cox Character; Cox legend position (e.g., "topright").
 #' @param show.logrank Logical; show logrank legend.
 #' @param logrank.cex Numeric; logrank legend size.
-#' @param put.legend.lr Character; logrank legend position.
+#' @param put.legend.lr Character; logrank legend position (e.g., "topleft").
 #' @param show_arm_legend Logical; show arm legend.
 #' @param arms Character vector of arm labels.
 #' @param col.1 Color for group 1.
 #' @param col.0 Color for group 0.
 #' @param ltys Line types.
 #' @param lwds Line widths.
 #' @param arm.cex Numeric; arm legend size.
-#' @param put.legend.arms Character; arm legend position.
+#' @param put.legend.arms Character; arm legend position (e.g., "left").
+#'
 #' @importFrom graphics legend
+#' @return Invisibly returns NULL. Used for plotting side effects.
 #' @export
 
 add_legends <- function(dfcount, show.cox, cox.cex, put.legend.cox, show.logrank, logrank.cex, put.legend.lr, show_arm_legend, arms, col.1, col.0, ltys, lwds, arm.cex, put.legend.arms) {

R/kmplotting_helpers.R

@@ -143,6 +143,7 @@ Key Features
 
 
 ```{r, message = FALSE, warning = FALSE}
+oldpar <- par(no.readonly = TRUE)
 library(survival)
 # to install weightedKMplots
 # library(devtools)
@@ -312,6 +313,7 @@ dfcount_rotterdam_unwtd <- get_dfcounting(df=df_rotterdam, tte.name=tte.name, ev
 
 dfcount_rotterdam_wtd <- get_dfcounting(df=df_rotterdam, tte.name=tte.name, event.name=event.name, treat.name=treat.name, arms=arms, by.risk=24, 
                                   weight.name="sw.weights")
+
 ```
 
 ---- Plotting Weighted vs Unweighted ----
@@ -788,6 +790,9 @@ non-stratified (should be same as above results without stratification)
 ```{r}
 with(res,lr^2/sig2_lr)
 with(res,z.score^2)
+
+# Restore when done
+par(oldpar)
 ```