From 9ca55786478f8a342f1a2beeb2c4f01981a62800 Mon Sep 17 00:00:00 2001
From: Nan Xiao <me@nanx.me>
Date: Fri, 12 Jan 2024 11:00:32 -0500
Subject: [PATCH] Move details into `@details` and improve formula

---
 R/define.R                | 34 ++++++++++++++++++++--------------
 man/define_enroll_rate.Rd | 14 ++++++++------
 man/define_fail_rate.Rd   | 20 +++++++++++---------
 3 files changed, 39 insertions(+), 29 deletions(-)

diff --git a/R/define.R b/R/define.R
index 4fdf861d..f2935f0a 100644
--- a/R/define.R
+++ b/R/define.R
@@ -18,12 +18,16 @@
 
 #' Define enrollment rate
 #'
-#' Define the enrollment rate of subjects for a study as following a piecewise exponential distribution.
-#' The `duration` are ordered piecewise for a duration equal to \eqn{t_i - t_{i-1}}.
-#' where \eqn{0=t_0<t_i\ldots,t_M=\infty}.
+#' Define the enrollment rate of subjects for a study as following a piecewise
+#' exponential distribution.
+#'
+#' @details
+#' The `duration` are ordered piecewise for a duration equal to
+#' \eqn{t_i - t_{i-1}}, where \eqn{0 = t_0 < t_i < \cdots < t_M = \infty}.
 #' The enrollment rates are defined in each duration with the same length.
 #'
-#' For a study with multiple strata, different duration and rate can be specified in each stratum.
+#' For a study with multiple strata, different duration and rate can be
+#' specified in each stratum.
 #'
 #' @param duration A numeric vector of ordered piecewise study duration interval.
 #' @param rate A numeric vector of enrollment rate in each `duration`.
@@ -46,7 +50,6 @@
 #'   rate = c((1:4) / 3, (1:4) / 2, (1:4) / 6),
 #'   stratum = c(array("High", 4), array("Moderate", 4), array("Low", 4))
 #' )
-#'
 define_enroll_rate <- function(
     duration,
     rate,
@@ -84,22 +87,25 @@ define_enroll_rate <- function(
 
 #' Define failure rate
 #'
-#' The function define subject failure rate for a study with two treatment groups.
-#' It also supports stratified design that have different failure rate in
+#' Define subject failure rate for a study with two treatment groups.
+#' Also supports stratified designs that have different failure rate in
 #' each stratum.
 #'
-#' Define the failure and dropout rate of subjects for a study as following a piecewise exponential distribution.
-#' The `duration` are ordered piecewise for a duration equal to \eqn{t_i - t_{i-1}}.
-#' where \eqn{0=t_0<t_i\ldots,t_M=\infty}.
-#' The failure rate, dropout rate, and hazard ratio in a study duration can be specified.
+#' @details
+#' Define the failure and dropout rate of subjects for a study as following
+#' a piecewise exponential distribution.
+#' The `duration` are ordered piecewise for a duration equal to
+#' \eqn{t_i - t_{i-1}}, where \eqn{0 = t_0 < t_i < \cdots < t_M = \infty}.
+#' The failure rate, dropout rate, and hazard ratio in a study duration
+#' can be specified.
 #'
-#' For a study with multiple strata,
-#' different duration, failure rate, dropout rate and hazard ratio can be specified in each stratum.
+#' For a study with multiple strata, different duration, failure rate,
+#' dropout rate, and hazard ratio can be specified in each stratum.
 #'
 #' @param duration A numeric vector of ordered piecewise study duration interval.
 #' @param fail_rate A numeric vector of failure rate in each `duration` in the control group.
 #' @param dropout_rate A numeric vector of dropout rate in each `duration`.
-#' @param hr A numeric vector of hazard ratio between case and control group.
+#' @param hr A numeric vector of hazard ratio between treatment and control group.
 #' @param stratum A character vector of stratum name.
 #'
 #' @return A `fail_rate` data frame.
diff --git a/man/define_enroll_rate.Rd b/man/define_enroll_rate.Rd
index 5c49991d..50c827db 100644
--- a/man/define_enroll_rate.Rd
+++ b/man/define_enroll_rate.Rd
@@ -17,13 +17,16 @@ define_enroll_rate(duration, rate, stratum = "All")
 An \code{enroll_rate} data frame.
 }
 \description{
-Define the enrollment rate of subjects for a study as following a piecewise exponential distribution.
-The \code{duration} are ordered piecewise for a duration equal to \eqn{t_i - t_{i-1}}.
-where \eqn{0=t_0<t_i\ldots,t_M=\infty}.
-The enrollment rates are defined in each duration with the same length.
+Define the enrollment rate of subjects for a study as following a piecewise
+exponential distribution.
 }
 \details{
-For a study with multiple strata, different duration and rate can be specified in each stratum.
+The \code{duration} are ordered piecewise for a duration equal to
+\eqn{t_i - t_{i-1}}, where \eqn{0 = t_0 < t_i < \cdots < t_M = \infty}.
+The enrollment rates are defined in each duration with the same length.
+
+For a study with multiple strata, different duration and rate can be
+specified in each stratum.
 }
 \examples{
 # Define enroll rate without stratum
@@ -38,5 +41,4 @@ define_enroll_rate(
   rate = c((1:4) / 3, (1:4) / 2, (1:4) / 6),
   stratum = c(array("High", 4), array("Moderate", 4), array("Low", 4))
 )
-
 }
diff --git a/man/define_fail_rate.Rd b/man/define_fail_rate.Rd
index ac3a094b..5740943a 100644
--- a/man/define_fail_rate.Rd
+++ b/man/define_fail_rate.Rd
@@ -13,7 +13,7 @@ define_fail_rate(duration, fail_rate, dropout_rate, hr = 1, stratum = "All")
 
 \item{dropout_rate}{A numeric vector of dropout rate in each \code{duration}.}
 
-\item{hr}{A numeric vector of hazard ratio between case and control group.}
+\item{hr}{A numeric vector of hazard ratio between treatment and control group.}
 
 \item{stratum}{A character vector of stratum name.}
 }
@@ -21,18 +21,20 @@ define_fail_rate(duration, fail_rate, dropout_rate, hr = 1, stratum = "All")
 A \code{fail_rate} data frame.
 }
 \description{
-The function define subject failure rate for a study with two treatment groups.
-It also supports stratified design that have different failure rate in
+Define subject failure rate for a study with two treatment groups.
+Also supports stratified designs that have different failure rate in
 each stratum.
 }
 \details{
-Define the failure and dropout rate of subjects for a study as following a piecewise exponential distribution.
-The \code{duration} are ordered piecewise for a duration equal to \eqn{t_i - t_{i-1}}.
-where \eqn{0=t_0<t_i\ldots,t_M=\infty}.
-The failure rate, dropout rate, and hazard ratio in a study duration can be specified.
+Define the failure and dropout rate of subjects for a study as following
+a piecewise exponential distribution.
+The \code{duration} are ordered piecewise for a duration equal to
+\eqn{t_i - t_{i-1}}, where \eqn{0 = t_0 < t_i < \cdots < t_M = \infty}.
+The failure rate, dropout rate, and hazard ratio in a study duration
+can be specified.
 
-For a study with multiple strata,
-different duration, failure rate, dropout rate and hazard ratio can be specified in each stratum.
+For a study with multiple strata, different duration, failure rate,
+dropout rate, and hazard ratio can be specified in each stratum.
 }
 \examples{
 # Define enroll rate