Minor fixes. Missing data problem is fixed. Version moved to 1.3.1

mROC.R

@@ -7,41 +7,43 @@ mROC <- function(data, statusName = NULL, markerName = NULL, eventValue=NULL, di
 
   require(dplyr)
 
-  if (!is.null(markerName)){warnings("Marker variable is not specified.")}
+  if (!is.null(markerName)){
+    warnings("Marker variable is not specified.")
+  }
 
   if (!is.null(markerName)){
-    mrknames = markerName
-    marker = data.frame(data[,markerName])
-    colnames(marker) = mrknames
+    mrknames <- markerName
+    marker <- data.frame(data[ ,markerName])
+    colnames(marker) <- mrknames
   }
 
-  ROCstats = list()
-  ROCplotdata = list()
+  ROCstats <- list()
+  ROCplotdata <- list()
 
   #if (is.null(markerName)) marker = data.frame(data[,colnames(data)[!(colnames(data) %in% statusName)]])
   #if (!is.null(markerName)) {marker = data.frame(data[,markerName]); colnames(marker) = mrknames}
 
-  status = data[,statusName]
+  status <- data[ ,statusName]
+  nms <- colnames(marker)
 
-  nms = colnames(marker)
   for (i in 1:dim(marker)[2]){
-    roc.results = rocdata(status=status,marker=marker[,i],event=eventValue,higherValuesDiseased=diseaseHigher,
+    roc.results <- rocdata(status = status, marker = marker[ ,i],event = eventValue, higherValuesDiseased = diseaseHigher,
                           ci.method = ci.method, se.method = se.method, advanced = advanced, alpha = alpha)
-    ROCstats[[i]] = roc.results$stats
-    ROCplotdata[[i]] = roc.results$roc
+    ROCstats[[i]] <- roc.results$stats
+    ROCplotdata[[i]] <- roc.results$roc
   }
 
-  names(ROCstats) = names(ROCplotdata) = nms
-  ROCstats = ldply(ROCstats, rbind)
-  ROCplotdataframe = ldply(ROCplotdata, rbind)
+  names(ROCstats) <- names(ROCplotdata) <- nms
+  ROCstats <- ldply(ROCstats, rbind)
+  ROCplotdataframe <- ldply(ROCplotdata, rbind)
 
-  rownames(ROCstats) = NULL
-  colnames(ROCstats) = c("Marker", "AUC", "SE.AUC", "LowerLimit", paste("UpperLimit (*)", sep=""), "z", "p-value")
-  colnames(ROCplotdataframe)[1] = "Marker"
+  rownames(ROCstats) <- NULL
+  colnames(ROCstats) <- c("Marker", "AUC", "SE.AUC", "LowerLimit", paste("UpperLimit (*)", sep=""), "z", "p-value")
+  colnames(ROCplotdataframe)[1] <- "Marker"
 
-  ROCplotdataframe[,c("FPR","TPR")] = round(ROCplotdataframe[,c("FPR","TPR")], 4)
+  ROCplotdataframe[ ,c("FPR","TPR")] <- round(ROCplotdataframe[ ,c("FPR","TPR")], 4)
 
   ROCplotdataframe <- dplyr:::arrange(ROCplotdataframe, Marker, Cutpoint)
-  results = list(plotdata = ROCplotdataframe, stats = ROCstats)
+  results <- list(plotdata = ROCplotdataframe, stats = ROCstats)
   return(results)
 }

rocdata.R

@@ -10,6 +10,11 @@ rocdata <- function(status, marker, event, higherValuesDiseased, alpha=0.05,
   #         roc = data.frame with x and y co-ordinates of plot
   #         stats = data.frame containing: area under ROC curve, p value, upper and lower 95% confidence interval
 
+  ## Complete cases.
+  completeIdx <- complete.cases(status, marker)
+  status <- status[completeIdx]
+  marker <- marker[completeIdx]
+
   se.method = match.arg(se.method)
   ci.method = match.arg(ci.method)
 

ui.R

@@ -1,6 +1,6 @@
 shinyUI(pageWithSidebar(
 
-  titlePanel("easyROC: a web-tool for ROC curve analysis (ver. 1.3)"),
+  titlePanel("easyROC: a web-tool for ROC curve analysis (ver. 1.3.1)"),
 
 	sidebarPanel(width = 3,
 		conditionalPanel(condition="input.tabs1=='Introduction'",
@@ -1094,6 +1094,10 @@ shinyUI(pageWithSidebar(
         HTML('<br>'),
 
         h4("News"),
+        HTML('<br>'),
+        HTML('<p><b> Version 1.3.1 (July 25, 2016)</b><p>'),
+		HTML('<p> (1) Minor fixes: Added feature to keep only pairwise complete data. Missing cases are now removed before ROC curve analysis which causes to null return in ROC statistics.<p>'),
+
         HTML('<br>'),
         HTML('<p><b> Version 1.3 (July 25, 2016)</b><p>'),
         HTML('<p> (1) Support for prametric ROC curve approximation.<p>'),