From e18ff08d4aa0ea863b7c68269e62ae9dc3d8f1ef Mon Sep 17 00:00:00 2001
From: egillax <egillax@gmail.com>
Date: Tue, 22 Oct 2024 11:45:06 +0200
Subject: [PATCH] Add net benefit plot and tests

---
 man/PatientLevelPrediction.Rd |  4 ++--
 man/getNetBenefit.Rd          | 20 +++++++++++++++++++
 man/plotNetBenefit.Rd         | 37 +++++++++++++++++++++++++++++++++++
 3 files changed, 59 insertions(+), 2 deletions(-)
 create mode 100644 man/getNetBenefit.Rd
 create mode 100644 man/plotNetBenefit.Rd

diff --git a/man/PatientLevelPrediction.Rd b/man/PatientLevelPrediction.Rd
index 8bc15fc71..4946949d9 100644
--- a/man/PatientLevelPrediction.Rd
+++ b/man/PatientLevelPrediction.Rd
@@ -18,15 +18,15 @@ Useful links:
 
 }
 \author{
-\strong{Maintainer}: Jenna Reps \email{jreps@its.jnj.com}
+\strong{Maintainer}: Egill Fridgeirsson \email{e.fridgeirsson@erasmusmc.nl}
 
 Authors:
 \itemize{
+  \item Jenna Reps \email{jreps@its.jnj.com}
   \item Martijn Schuemie
   \item Marc Suchard
   \item Patrick Ryan
   \item Peter Rijnbeek
-  \item Egill Fridgeirsson
 }
 
 }
diff --git a/man/getNetBenefit.Rd b/man/getNetBenefit.Rd
new file mode 100644
index 000000000..af758fa79
--- /dev/null
+++ b/man/getNetBenefit.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Plotting.R
+\name{getNetBenefit}
+\alias{getNetBenefit}
+\title{Calculate net benefit in an efficient way}
+\usage{
+getNetBenefit(plpResult, evalType)
+}
+\arguments{
+\item{plpResult}{A plp result object as generated using the \code{\link{runPlp}} function.}
+
+\item{evalType}{The evaluation type column}
+}
+\value{
+A data frame with the net benefit, treat all and treat none values
+}
+\description{
+Calculate net benefit in an efficient way
+}
+\keyword{internal}
diff --git a/man/plotNetBenefit.Rd b/man/plotNetBenefit.Rd
new file mode 100644
index 000000000..35722350b
--- /dev/null
+++ b/man/plotNetBenefit.Rd
@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Plotting.R
+\name{plotNetBenefit}
+\alias{plotNetBenefit}
+\title{Plot the net benefit}
+\usage{
+plotNetBenefit(
+  plpResult,
+  typeColumn = "evaluation",
+  saveLocation = NULL,
+  fileName = "netBenefit.png",
+  evalType = NULL,
+  ylim = NULL,
+  xlim = NULL
+)
+}
+\arguments{
+\item{plpResult}{A plp result object as generated using the \code{\link{runPlp}} function.}
+
+\item{typeColumn}{The name of the column specifying the evaluation type}
+
+\item{saveLocation}{Directory to save plot (if NULL plot is not saved)}
+
+\item{fileName}{Name of the file to save to plot, for example 'plot.png'. See the function \code{ggsave} in the ggplot2 package for supported file formats.}
+
+\item{evalType}{Which evaluation type to plot for. For example `Test`, `Train`. If NULL everything is plotted}
+
+\item{ylim}{The y limits for the plot, if NULL the limits are calculated from the data}
+
+\item{xlim}{The x limits for the plot, if NULL the limits are calculated from the data}
+}
+\value{
+A list of ggplot objects
+}
+\description{
+Plot the net benefit
+}