Adding simple.plotROC

DESCRIPTION

@@ -10,3 +10,6 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
+Imports: 
+    base,
+    graphics

NAMESPACE

@@ -6,6 +6,7 @@ export(selectValid)
 export(setEventTime)
 export(simple.compute_roc_metrics)
 export(simple.getAUC)
+export(simple.plotROC)
 export(simple.roc)
 export(simple.sAUC)
 export(simple.sAUC2)

R/roc.R

@@ -195,3 +195,41 @@ simple.sAUC2<-function(rocA,rocB){
 
 }
 
+#' Plot a ROC curve with associated annotations
+#'
+#'@param df data frame
+#'@param var variable to use to stratify patients
+#'@param col color of the line drawn
+#'@param x x coordinate of legend
+#'@param y y coordinate of legend
+#'@param unit - what unit to associate to thrshold on legend (ml)
+#'@param precise number of decimal places to use when reporting opt threshold, TRUE:2, FALSE:0
+#'@param target column that holds binary outcomes
+#'
+#'@return list object with items: roc object as created by simple.roc, thr optimal threshold, legend_text text to be put on final legend
+#'@export
+
+
+simple.plotROC<-function(df,var,col="black",x=0.65,y=0.1,unit="ml",precise=FALSE,target='alive'){
+
+	roc=simple.roc(df[,target],df[,var])
+   auc=simple.getAUC(roc)
+   #calculate sAUC (sigma AUC, see DeLonghi)
+   sAUC=simple.sAUC(roc)
+   #approximate version of sAUC for historical reasons
+   sAUCapprox <- simple.sAUCapprox(roc)
+   #determine optimum point for test use (Youden index)
+   roc_metrics <- simple.compute_roc_metrics(roc)
+   #report sensitivity/specificity/CI95 at opt threshold
+   print(sprintf('[%s] Opt: sens %.2f (%.2f,%.2f), spec %.2f (%.2f,%.2f)',
+      var,roc_metrics$TPR,roc_metrics$lTPR,roc_metrics$hTPR,
+      1-roc_metrics$FPR,1-roc_metrics$hFPR,1-roc_metrics$lFPR))
+
+   legend_text <- sprintf("[%s] AUC: %.2f (+- %.2f/%.2f), OPT THR: %.2f", 
+                           var, auc, sAUC, sAUCapprox, roc_metrics$threshold)
+   #draw opt point
+   graphics::points(roc_metrics$FPR,roc_metrics$TPR,pch=1,col=col,cex=2)
+   graphics::lines(roc$FPR,roc$TPR,col=col)
+   base::list(roc=roc,thr=roc_metrics$threshold,legend_text=legend_text)
+}
+

man/simple.plotROC.Rd

@@ -0,0 +1,42 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/roc.R
+\name{simple.plotROC}
+\alias{simple.plotROC}
+\title{Plot a ROC curve with associated annotations}
+\usage{
+simple.plotROC(
+  df,
+  var,
+  col = "black",
+  x = 0.65,
+  y = 0.1,
+  unit = "ml",
+  precise = FALSE,
+  target = "alive"
+)
+}
+\arguments{
+\item{df}{data frame}
+
+\item{var}{variable to use to stratify patients}
+
+\item{col}{color of the line drawn}
+
+\item{x}{x coordinate of legend}
+
+\item{y}{y coordinate of legend}
+
+\item{unit}{\itemize{
+\item what unit to associate to thrshold on legend (ml)
+}}
+
+\item{precise}{number of decimal places to use when reporting opt threshold, TRUE:2, FALSE:0}
+
+\item{target}{column that holds binary outcomes}
+}
+\value{
+list object with items: roc object as created by simple.roc, thr optimal threshold, legend_text text to be put on final legend
+}
+\description{
+Plot a ROC curve with associated annotations
+}