From 0e4c47df83d07f20432e6ecbb33505f006ddfc8f Mon Sep 17 00:00:00 2001
From: Michael <mthbretscher@gmail.com>
Date: Tue, 26 Nov 2024 17:23:13 +0100
Subject: [PATCH] adress R CMD check issues

---
 DESCRIPTION       |  4 ++--
 R/data.R          | 11 +++++++++++
 README.md         |  2 +-
 man/calc_rwPFS.Rd | 12 ++++++------
 man/simprog.Rd    | 21 +++++++++++++++++++++
 5 files changed, 41 insertions(+), 9 deletions(-)
 create mode 100644 R/data.R
 create mode 100644 man/simprog.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index c44d485..b0e236b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: RwPFS
-Title: Calculate and compare a range of real-world progression-free survival (rwPFS) endpoints.
+Title: Calculate and Compare a Range of Real-World Progression-Free Survival (rwPFS) Endpoints
 Version: 0.0.3
 Authors@R: c( 
     person(given = "Michael", family = "Bretscher", role = c("aut", "cre"), email = "mthbretscher@gmail.com"),
@@ -11,7 +11,7 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.2
 Imports:
     rlang,
     dplyr (>= 1.0.0),
diff --git a/R/data.R b/R/data.R
new file mode 100644
index 0000000..2567e34
--- /dev/null
+++ b/R/data.R
@@ -0,0 +1,11 @@
+#' Simulated progression data
+#'
+#' A demo dataset containing simulated data to compute progression-free
+#' survival. For demonstration purposes only.
+#'
+#' @format A data frame with simulated patient data for PFS analysis
+#'
+#' @examples
+#' data(simprog)
+#' head(simprog)
+"simprog"
diff --git a/README.md b/README.md
index 9e745f9..3af8dfb 100644
--- a/README.md
+++ b/README.md
@@ -45,7 +45,7 @@ Get started with real-world PFS [here](https://phcanalytics.github.io/RwPFS/arti
 <!-- badges: start -->
 
 [![Lifecycle:
-maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
+maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html#maturing)
 
 
 
diff --git a/man/calc_rwPFS.Rd b/man/calc_rwPFS.Rd
index 69fa7b9..ee4f75d 100644
--- a/man/calc_rwPFS.Rd
+++ b/man/calc_rwPFS.Rd
@@ -56,18 +56,18 @@ Returns a data frame with the following new data columns added:
 
 \describe{
 
-\item{rwpfs<label>_eof_date}{The end date of progression follow-up. This is the earliest non-missing date of \code{.visit_gap_start_date},
+\item{rwpfs\if{html}{\out{<label>}}_eof_date}{The end date of progression follow-up. This is the earliest non-missing date of \code{.visit_gap_start_date},
 \code{.last_progression_abstraction_date}, and \code{.last_activity_date}}
 
-\item{rwpfs<label>_event_type}{The type of rwPFS event: "Death", "Progression", "Censored", or "Missing" (if rwPFS could not be calculated)}
+\item{rwpfs\if{html}{\out{<label>}}_event_type}{The type of rwPFS event: "Death", "Progression", "Censored", or "Missing" (if rwPFS could not be calculated)}
 
-\item{rwpfs<label>_date}{The rwPFS event- or censoring date.}
+\item{rwpfs\if{html}{\out{<label>}}_date}{The rwPFS event- or censoring date.}
 
-\item{rwpfs<label>_days}{The time from \code{.start_date} to \code{rwpfs<label>_date} in days.}
+\item{rwpfs\if{html}{\out{<label>}}_days}{The time from \code{.start_date} to \code{rwpfs<label>_date} in days.}
 
-\item{rwpfs<label>_event}{Whether a rwPFS event was recorded (1) or the observation was censored (0) }
+\item{rwpfs\if{html}{\out{<label>}}_event}{Whether a rwPFS event was recorded (1) or the observation was censored (0) }
 
-\item{rwpfs<label>_months}{The time from \code{.start_date} to \code{rwpfs<label>_date} in months.}
+\item{rwpfs\if{html}{\out{<label>}}_months}{The time from \code{.start_date} to \code{rwpfs<label>_date} in months.}
 
 }
 
diff --git a/man/simprog.Rd b/man/simprog.Rd
new file mode 100644
index 0000000..224c352
--- /dev/null
+++ b/man/simprog.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{simprog}
+\alias{simprog}
+\title{Simulated progression data}
+\format{
+A data frame with simulated patient data for PFS analysis
+}
+\usage{
+simprog
+}
+\description{
+A demo dataset containing simulated data to compute progression-free
+survival. For demonstration purposes only.
+}
+\examples{
+data(simprog)
+head(simprog)
+}
+\keyword{datasets}