Merge pull request #86 from ldecicco-USGS/master

Bug fix

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: EGRET
 Type: Package
 Title: Exploration and Graphics for RivEr Trends (EGRET)
-Version: 2.5.1
+Version: 2.5.2
 Authors@R: c( person("Robert", "Hirsch", role = c("aut"),
     email = "rhirsch@usgs.gov"),
     person("Laura", "DeCicco", role = c("aut","cre"),

R/makeRandomResiduals.R

@@ -4,11 +4,11 @@
 #'  rResid is the randomized residual value computed in log concentration units, and rObserved
 #'  is the randomized 'observed' value of concentration in concentration units.
 #'
-#' @param eList named list with at least the Daily dataframe
+#' @param eList named list with at least the Sample dataframe
 #' @keywords water-quality statistics
 #' @importFrom truncnorm rtruncnorm
 #' @export
-#' @return eList named list with modified Daily data frame.
+#' @return eList named list with modified Sample data frame.
 makeAugmentedSample <- function(eList){
 
   if(all(c("SE","yHat") %in% names(eList$Sample))){

R/plotConcTime.R

@@ -42,6 +42,7 @@
 #' eList <- setPA(eList, paStart=6,paLong=3)
 #' plotConcTime(eList, qUnit = 1, qLower = 100, qUpper = 10000)
 #' plotConcTime(eList, logScale=TRUE)
+#' plotConcTime(eList, qUnit = 1, qLower = 100, qUpper = 10000, rResid = TRUE)
 plotConcTime<-function(eList, qUnit = 2, 
                        qLower = NA, qUpper = NA, rResid=FALSE,
                        tinyPlot = FALSE, concMax = NA, concMin = NA, printTitle = TRUE,logScale=FALSE, 
@@ -90,16 +91,10 @@ plotConcTime<-function(eList, qUnit = 2,
   qText[3]<-paste("For Discharge <",qUpper,qUnit@qUnitName)
   qText[4]<-paste("For Discharge between",qLower,"and",qUpper,qUnit@qUnitName)
   title3<-qText[codeSum]
-  subSample<-subSample[subSample$Q>qLowerBound & subSample$Q<qUpperBound,]
-
-  subSample <- if(paLong == 12) subSample else selectDays(subSample, paLong,paStart)
-
+
   # the next section of code sets up the seasonal part of the plot title
   title2<-if(paLong==12) "" else setSeasonLabelByUser(paStartInput=paStart,paLongInput=paLong)
 
-  Uncen<-subSample$Uncen
-  x<-subSample$DecYear
-
   #########################################################
   if (logScale){
     minYLow <- concMin
@@ -112,9 +107,15 @@ plotConcTime<-function(eList, qUnit = 2,
 
   plotTitle<-if(printTitle) paste(localINFO$shortName,"\n",localINFO$paramShortName,"\n",title3,sep="") else ""
 
-  xInfo <- generalAxis(x=x, minVal=min(x), maxVal=max(x), tinyPlot=tinyPlot)  
 
   if(!rResid){
+    subSample<-subSample[subSample$Q>qLowerBound & subSample$Q<qUpperBound,]
+    subSample <- if(paLong == 12) subSample else selectDays(subSample, paLong,paStart)
+    Uncen<-subSample$Uncen
+    x<-subSample$DecYear
+
+    xInfo <- generalAxis(x=x, minVal=min(x), maxVal=max(x), tinyPlot=tinyPlot)  
+
     yLow<-subSample$ConcLow
     yHigh<-subSample$ConcHigh
 
@@ -134,10 +135,21 @@ plotConcTime<-function(eList, qUnit = 2,
       eList <- makeAugmentedSample(eList)
       localSample <- eList$Sample
     }
-    yHigh <- localSample$rObserved
 
+    subSample<-localSample
+    subSample$Q<-subSample$Q*qFactor
+
+    subSample<-subSample[subSample$Q>qLowerBound & subSample$Q<qUpperBound,]
+    subSample <- if(paLong == 12) subSample else selectDays(subSample, paLong,paStart)
+
+    Uncen<-subSample$Uncen
+    x<-subSample$DecYear
+
+    xInfo <- generalAxis(x=x, minVal=min(x), maxVal=max(x), tinyPlot=tinyPlot)
+    yHigh <- subSample$rObserved
     yInfo <- generalAxis(x=yHigh, minVal=minYLow, maxVal=concMax, logScale=logScale, 
                          tinyPlot=tinyPlot,units=attr(eList, "param.units"))
+
     genericEGRETDotPlot(x=x[Uncen == 1], y=yHigh[Uncen == 1], 
                         xlim=c(xInfo$bottom,xInfo$top), ylim=c(yInfo$bottom,yInfo$top),
                         xlab="", ylab=yInfo$label,