Merge pull request #80 from ldecicco-USGS/master

More rResid
DOI-USGS · Apr 20, 2016 · bf3a9c6 · bf3a9c6
2 parents 9a89470 + 4771611
commit bf3a9c6
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Showing 17 changed files with 198 additions and 152 deletions.
diff --git a/NEWS b/NEWS
@@ -1,3 +1,8 @@
+EGRET 2.5.0
+===========
+* Added an argument to the concentration and residual plotting functions to randomize the censored values for the plots.
+* Minor bug fixes
+
 EGRET 2.3.1
 ===========
 * Removed unnecessary disclaimer.

diff --git a/R/multiPlotDataOverview.R b/R/multiPlotDataOverview.R
@@ -13,6 +13,7 @@
 #' @param cex.main magnification to be used for main titles relative to the current setting of cex
 #' @param logScaleConc logical if TRUE y in concentration graphs plotted in log axis. Default is TRUE.
 #' @param logScaleQ logical if TRUE y in streamflow graphs plotted in log axis. Default is TRUE.
+#' @param rResid logical. Show censored values as randomized.
 #' @keywords graphics water-quality statistics
 #' @seealso \code{\link{plotConcQ}}, \code{\link{boxConcMonth}}, \code{\link{plotConcTime}}, \code{\link{boxQTwice}}
 #' @export
@@ -23,37 +24,39 @@
 #' # Graphs consisting of Jun-Aug
 #' eList <- setPA(eList, paStart=6,paLong=3)
 #' multiPlotDataOverview(eList, qUnit=1) 
-multiPlotDataOverview<-function (eList, qUnit = 2,cex.main=1.2,
+multiPlotDataOverview<-function (eList, qUnit = 2,cex.main=1.2,rResid=FALSE,
                                  logScaleConc=TRUE, logScaleQ=TRUE){
 
-  localINFO <- getInfo(eList)
-
-  if(sum(c("paStart","paLong") %in% names(localINFO)) == 2){
-    paLong <- localINFO$paLong
-    paStart <- localINFO$paStart  
-  } else {
-    paLong <- 12
-    paStart <- 10
-  }
-
-  title2<-if(paLong==12) "" else setSeasonLabelByUser(paStartInput=paStart,paLongInput=paLong)
-
-  par(mfcol=c(2,2),oma=c(0,2.4,4.5,2.4),tcl=0.5)
-  plotConcQ(eList, qUnit = qUnit, tinyPlot = TRUE, printTitle = FALSE,
-            rmSciX=TRUE,logScale=logScaleConc)
-  boxConcMonth(eList, printTitle = FALSE, tinyPlot=TRUE,logScale=logScaleConc)
-  plotConcTime(eList, printTitle = FALSE, tinyPlot = TRUE,logScale=logScaleConc)
-  boxQTwice(eList, printTitle = FALSE, qUnit = qUnit, tinyPlot=TRUE,logScale=logScaleQ)
-  title<-paste(localINFO$shortName,"\n",localINFO$paramShortName)
-
-  if("" == title2){
-    mtext(title,cex=cex.main,outer=TRUE,font=2)
-  } else {
-    title <- paste(title, title2, sep="\n")
-    mtext(title, cex = cex.main*.75, outer = TRUE, font = 2)    
+  multiPlotDataOverview<-function (eList, qUnit = 2,cex.main=1.2,
+                                   logScaleConc=TRUE, logScaleQ=TRUE,rResid=FALSE){
+
+    localINFO <- getInfo(eList)
+
+    if(sum(c("paStart","paLong") %in% names(localINFO)) == 2){
+      paLong <- localINFO$paLong
+      paStart <- localINFO$paStart  
+    } else {
+      paLong <- 12
+      paStart <- 10
+    }
+
+    title2<-if(paLong==12) "" else setSeasonLabelByUser(paStartInput=paStart,paLongInput=paLong)
+
+    par(mfcol=c(2,2),oma=c(0,2.4,4.5,2.4),tcl=0.5)
+    plotConcQ(eList, qUnit = qUnit, tinyPlot = TRUE, printTitle = FALSE,
+              rmSciX=TRUE,logScale=logScaleConc,rResid=rResid)
+    boxConcMonth(eList, printTitle = FALSE, tinyPlot=TRUE,logScale=logScaleConc)
+    plotConcTime(eList, printTitle = FALSE, tinyPlot = TRUE,logScale=logScaleConc,rResid=rResid)
+    boxQTwice(eList, printTitle = FALSE, qUnit = qUnit, tinyPlot=TRUE,logScale=logScaleQ)
+    title<-paste(localINFO$shortName,"\n",localINFO$paramShortName)
+
+    if("" == title2){
+      mtext(title,cex=cex.main,outer=TRUE,font=2)
+    } else {
+      title <- paste(title, title2, sep="\n")
+      mtext(title, cex = cex.main*.75, outer = TRUE, font = 2)    
+    }
+
+    par(mfcol=c(1,1),oma=c(0,0,0,0))
   }
-
-
-
-  par(mfcol=c(1,1),oma=c(0,0,0,0))
 }
diff --git a/R/plotConcQ.R b/R/plotConcQ.R
@@ -24,6 +24,7 @@
 #' (for example, adjusting margins with par(mar=c(5,5,5,5))). If customPar FALSE, EGRET chooses the best margins depending on tinyPlot.
 #' @param col color of points on plot, see ?par 'Color Specification'
 #' @param lwd number line width
+#' @param rResid logical. Show censored values as randomized.
 #' @param \dots arbitrary graphical parameters that will be passed to genericEGRETDotPlot function (see ?par for options)
 #' @keywords graphics water-quality statistics
 #' @export
@@ -36,12 +37,9 @@
 #' # Graphs consisting of Jun-Aug
 #' eList <- setPA(eList, paStart=6,paLong=3)
 #' plotConcQ(eList)
-plotConcQ<-function(eList, qUnit = 2, tinyPlot = FALSE, logScale=FALSE,
+plotConcQ<-function(eList, qUnit = 2, tinyPlot = FALSE, logScale=FALSE,rResid=FALSE,
                     concMax = NA, concMin =NA, printTitle = TRUE, cex=0.8, cex.axis=1.1,cex.main=1.1,
                     rmSciX=FALSE,rmSciY=FALSE, customPar=FALSE,col="black",lwd=1,...){
-  # this function shows the sample data,
-  # discharge on x-axis on a log scale, concentration on y-axis
-
   localINFO <- getInfo(eList)
   localSample <- getSample(eList)
 
@@ -52,7 +50,7 @@ plotConcQ<-function(eList, qUnit = 2, tinyPlot = FALSE, logScale=FALSE,
     paLong <- 12
     paStart <- 10
   }
-
+  
   localSample <- if(paLong == 12) localSample else selectDays(localSample, paLong,paStart)
   title2<-if(paLong==12) "" else setSeasonLabelByUser(paStartInput=paStart,paLongInput=paLong)
 
@@ -68,7 +66,7 @@ plotConcQ<-function(eList, qUnit = 2, tinyPlot = FALSE, logScale=FALSE,
   x<-localSample$Q*qFactor
 
   Uncen<-localSample$Uncen
-
+  
   plotTitle<-if(printTitle) paste(localINFO$shortName,"\n",localINFO$paramShortName,"\n","Concentration versus Discharge") else ""
 
   if (tinyPlot){
@@ -87,22 +85,42 @@ plotConcQ<-function(eList, qUnit = 2, tinyPlot = FALSE, logScale=FALSE,
 
   xInfo <- generalAxis(x=x, maxVal=NA, minVal=NA, logScale=TRUE, tinyPlot=tinyPlot)
 
-  yLow<-localSample$ConcLow
-  yHigh<-localSample$ConcHigh
-
-  yInfo <- generalAxis(x=yHigh, maxVal=concMax, minVal=yMin, tinyPlot=tinyPlot,logScale=logScale,units=localINFO$param.units)
-
-  genericEGRETDotPlot(x=x, y=yHigh, 
-                      xlim=c(xInfo$bottom, xInfo$top), ylim=c(yInfo$bottom,yInfo$top),
-                      xlab=xLab, ylab=yInfo$label,
-                      xTicks=xInfo$ticks, yTicks=yInfo$ticks,
-                      plotTitle=plotTitle, log=logScaleText,cex.axis=cex.axis,cex=cex,
-                      cex.main=cex.main, tinyPlot=tinyPlot,xaxt="n",
-                      rmSciX=rmSciX,rmSciY=rmSciY,customPar=customPar,col=col,lwd=lwd,...
-  )
-
-  censoredSegments(yInfo$bottom, yLow, yHigh, x, Uncen,col=col,lwd=lwd)
-
+  if(!rResid){
+    yLow<-localSample$ConcLow
+    yHigh<-localSample$ConcHigh
+
+    yInfo <- generalAxis(x=yHigh, maxVal=concMax, minVal=yMin, tinyPlot=tinyPlot,logScale=logScale,units=localINFO$param.units)
+
+    genericEGRETDotPlot(x=x, y=yHigh, 
+                        xlim=c(xInfo$bottom, xInfo$top), ylim=c(yInfo$bottom,yInfo$top),
+                        xlab=xLab, ylab=yInfo$label,
+                        xTicks=xInfo$ticks, yTicks=yInfo$ticks,
+                        plotTitle=plotTitle, log=logScaleText,cex.axis=cex.axis,cex=cex,
+                        cex.main=cex.main, tinyPlot=tinyPlot,xaxt="n",
+                        rmSciX=rmSciX,rmSciY=rmSciY,customPar=customPar,col=col,lwd=lwd,...
+    )
+
+    censoredSegments(yInfo$bottom, yLow, yHigh, x, Uncen,col=col,lwd=lwd)
+  } else {
+    if(!("rObserved" %in% names(localSample))){
+      eList <- makeAugmentedSample(eList)
+      localSample <- eList$Sample
+    }
+    yHigh <- localSample$rObserved
+
+    yInfo <- generalAxis(x=yHigh, maxVal=concMax, minVal=yMin, tinyPlot=tinyPlot,logScale=logScale,units=localINFO$param.units)
+
+    genericEGRETDotPlot(x=x[Uncen == 1], y=yHigh[Uncen == 1], 
+                        xlim=c(xInfo$bottom, xInfo$top), ylim=c(yInfo$bottom,yInfo$top),
+                        xlab=xLab, ylab=yInfo$label,
+                        xTicks=xInfo$ticks, yTicks=yInfo$ticks,
+                        plotTitle=plotTitle, log=logScaleText,cex.axis=cex.axis,cex=cex,
+                        cex.main=cex.main, tinyPlot=tinyPlot,xaxt="n",
+                        rmSciX=rmSciX,rmSciY=rmSciY,customPar=customPar,col=col,lwd=lwd,...
+    )
+    points(x=x[Uncen == 0], y=yHigh[Uncen == 0], pch=1,cex=cex,col=col)
+
+  }
   if (!tinyPlot) mtext(title2,side=3,line=-1.5)
 
 }
diff --git a/R/plotConcTime.R b/R/plotConcTime.R
@@ -29,6 +29,7 @@
 #' (for example, adjusting margins with par(mar=c(5,5,5,5))). If customPar FALSE, EGRET chooses the best margins depending on tinyPlot.
 #' @param col color of points on plot, see ?par 'Color Specification'
 #' @param lwd number line width.
+#' @param rResid logical. Show censored values as randomized.
 #' @param \dots arbitrary functions sent to the generic plotting function.  See ?par for details on possible parameters.
 #' @keywords graphics water-quality statistics
 #' @export
@@ -42,7 +43,7 @@
 #' plotConcTime(eList, qUnit = 1, qLower = 100, qUpper = 10000)
 #' plotConcTime(eList, logScale=TRUE)
 plotConcTime<-function(eList, qUnit = 2, 
-                       qLower = NA, qUpper = NA, 
+                       qLower = NA, qUpper = NA, rResid=FALSE,
                        tinyPlot = FALSE, concMax = NA, concMin = NA, printTitle = TRUE,logScale=FALSE, 
                        cex=0.8, cex.axis=1.1,cex.main=1.1, customPar=FALSE,col="black",lwd=1,...){
 
@@ -90,12 +91,12 @@ plotConcTime<-function(eList, qUnit = 2,
   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
 
@@ -108,26 +109,46 @@ plotConcTime<-function(eList, qUnit = 2,
     logVariable <- ""
   }  
   #########################################################
-
+  
   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)  
 
-  yLow<-subSample$ConcLow
-  yHigh<-subSample$ConcHigh
-
-  yInfo <- generalAxis(x=yHigh, minVal=minYLow, maxVal=concMax, logScale=logScale, 
-                       tinyPlot=tinyPlot,units=attr(eList, "param.units"))
-
-  genericEGRETDotPlot(x=x, y=yHigh, 
-                      xlim=c(xInfo$bottom,xInfo$top), ylim=c(yInfo$bottom,yInfo$top),
-                      xlab="", ylab=yInfo$label,
-                      xTicks=xInfo$ticks, yTicks=yInfo$ticks,cex=cex,
-                      plotTitle=plotTitle, log=logVariable,
-                      cex.axis=cex.axis,cex.main=cex.main,tinyPlot=tinyPlot,col=col,customPar=customPar, ...
-  )
-  censoredSegments(yBottom=yInfo$ticks[1],yLow=yLow,yHigh=yHigh,x=x,Uncen=Uncen,col=col,lwd=lwd)
-
+  if(!rResid){
+    yLow<-subSample$ConcLow
+    yHigh<-subSample$ConcHigh
+
+    yInfo <- generalAxis(x=yHigh, minVal=minYLow, maxVal=concMax, logScale=logScale, 
+                         tinyPlot=tinyPlot,units=attr(eList, "param.units"))
+
+    genericEGRETDotPlot(x=x, y=yHigh, 
+                        xlim=c(xInfo$bottom,xInfo$top), ylim=c(yInfo$bottom,yInfo$top),
+                        xlab="", ylab=yInfo$label,
+                        xTicks=xInfo$ticks, yTicks=yInfo$ticks,cex=cex,
+                        plotTitle=plotTitle, log=logVariable,
+                        cex.axis=cex.axis,cex.main=cex.main,tinyPlot=tinyPlot,col=col,customPar=customPar, ...
+    )
+    censoredSegments(yBottom=yInfo$ticks[1],yLow=yLow,yHigh=yHigh,x=x,Uncen=Uncen,col=col,lwd=lwd)
+  } else {
+    if(!("rObserved" %in% names(localSample))){
+      eList <- makeAugmentedSample(eList)
+      localSample <- eList$Sample
+    }
+    yHigh <- localSample$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$label,
+                        xTicks=xInfo$ticks, yTicks=yInfo$ticks,cex=cex,
+                        plotTitle=plotTitle, log=logVariable,
+                        cex.axis=cex.axis,cex.main=cex.main,tinyPlot=tinyPlot,col=col,customPar=customPar, ...
+    )
+    points(x=x[Uncen == 0], y=yHigh[Uncen == 0], pch=1,cex=cex,col=col)
+
+
+  }
   if (!tinyPlot) mtext(title2,side=3,line=-1.5)
 
 }
diff --git a/R/plotConcTimeDaily.R b/R/plotConcTimeDaily.R
@@ -25,6 +25,7 @@
 #' (for example, adjusting margins with par(mar=c(5,5,5,5))). If customPar FALSE, EGRET chooses the best margins depending on tinyPlot.
 #' @param col color of points on plot, see ?par 'Color Specification'
 #' @param lwd number line width
+#' @param rResid logical. Show censored values as randomized.
 #' @param prettyDate logical use 'pretty' limits for date axis if TRUE, or force the startYear/endYear as limits if FALSE
 #' @param \dots arbitrary functions sent to the generic plotting function.  See ?par for details on possible parameters
 #' @keywords graphics water-quality statistics
@@ -39,7 +40,7 @@
 #' eList <- setPA(eList, paStart=6,paLong=3)
 #' plotConcTimeDaily(eList)
 plotConcTimeDaily<-function(eList, startYear=NA, endYear=NA, tinyPlot = FALSE, 
-                            concMax = NA, printTitle = TRUE,cex=0.8, cex.axis=1.1,
+                            concMax = NA, printTitle = TRUE,cex=0.8, cex.axis=1.1,rResid=FALSE,
                             cex.main=1.1, customPar=FALSE,col="black",lwd=1,prettyDate=TRUE,...){
 
   localINFO <- getInfo(eList)
@@ -67,9 +68,9 @@ plotConcTimeDaily<-function(eList, startYear=NA, endYear=NA, tinyPlot = FALSE,
 
   xSample<-subSample$DecYear
   xDaily<-subDaily$DecYear
-
+  
   Uncen<-subSample$Uncen
-
+  
   plotTitle<-if(printTitle) paste(localINFO$shortName,"\n",localINFO$paramShortName,"\n","Observed and Estimated Concentration versus Time") else ""
 
   ###################################
@@ -78,23 +79,44 @@ plotConcTimeDaily<-function(eList, startYear=NA, endYear=NA, tinyPlot = FALSE,
 
   xInfo <- generalAxis(x=xSample, minVal=startYear, maxVal=endYear, tinyPlot=tinyPlot,padPercent=0,prettyDate=prettyDate)  
 
-  yLow<-subSample$ConcLow
-  yHigh<-subSample$ConcHigh
-
-  yCombined <- c(yHigh,subDaily$ConcDay)
-  yInfo <- generalAxis(x = yCombined, minVal = yBottom, maxVal = concMax, 
-                       tinyPlot = tinyPlot, padPercent = 5,units=localINFO$param.units)
+  if(!rResid){
+
+    yLow<-subSample$ConcLow
+    yHigh<-subSample$ConcHigh
+
+    yCombined <- c(yHigh,subDaily$ConcDay)
+    yInfo <- generalAxis(x = yCombined, minVal = yBottom, maxVal = concMax, 
+                         tinyPlot = tinyPlot, padPercent = 5,units=localINFO$param.units)
+
+    genericEGRETDotPlot(x=xSample, y=yHigh, xTicks=xInfo$ticks, yTicks=yInfo$ticks,
+                        xlim=c(xInfo$bottom,xInfo$top), ylim=c(yInfo$bottom,yInfo$top),
+                        ylab=yInfo$label,plotTitle=plotTitle,cex.axis=cex.axis,col=col,lwd=lwd,cex=cex,
+                        cex.main=cex.main, tinyPlot=tinyPlot,customPar=customPar, xDate=TRUE,...
+    )
+
+    censoredSegments(yInfo$bottom,yLow=yLow,yHigh=yHigh,x=xSample,Uncen=Uncen,col=col,lwd=lwd)
+  } else {
+    if(!("rObserved" %in% names(localSample))){
+      eList <- makeAugmentedSample(eList)
+      localSample <- eList$Sample
+      subSample<-localSample[localSample$DecYear>=startYear & localSample$DecYear<= endYear,]
+    }
+
+    yHigh <- subSample$rObserved
+
+    yCombined <- c(yHigh,subDaily$ConcDay)
+    yInfo <- generalAxis(x = yCombined, minVal = yBottom, maxVal = concMax, 
+                         tinyPlot = tinyPlot, padPercent = 5,units=localINFO$param.units)
+    genericEGRETDotPlot(x=xSample[subSample$Uncen == 1], y=yHigh[subSample$Uncen == 1], xTicks=xInfo$ticks, yTicks=yInfo$ticks,
+                        xlim=c(xInfo$bottom,xInfo$top), ylim=c(yInfo$bottom,yInfo$top),
+                        ylab=yInfo$label,plotTitle=plotTitle,cex.axis=cex.axis,col=col,lwd=lwd,cex=cex,
+                        cex.main=cex.main, tinyPlot=tinyPlot,customPar=customPar, xDate=TRUE,...
+    )
+    points(x=xSample[Uncen == 0], y=yHigh[Uncen == 0], pch=1,cex=cex,col=col)
+
+  }
 
-  genericEGRETDotPlot(x=xSample, y=yHigh, xTicks=xInfo$ticks, yTicks=yInfo$ticks,
-                      xlim=c(xInfo$bottom,xInfo$top), ylim=c(yInfo$bottom,yInfo$top),
-                      ylab=yInfo$label,plotTitle=plotTitle,cex.axis=cex.axis,col=col,lwd=lwd,cex=cex,
-                      cex.main=cex.main, tinyPlot=tinyPlot,customPar=customPar, xDate=TRUE,...
-  )
-
-  censoredSegments(yInfo$bottom,yLow=yLow,yHigh=yHigh,x=xSample,Uncen=Uncen,col=col,lwd=lwd)
-
-
   lines(x=xDaily, y=subDaily$ConcDay, type="l",col=col,lwd=lwd)
   if (!tinyPlot) mtext(title2,side=3,line=-1.5)
-
+  
 }