Adding more residual functions.

DOI-USGS · Sep 9, 2015 · bd7a88a · bd7a88a
1 parent 7562302
commit bd7a88a
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Showing 8 changed files with 132 additions and 50 deletions.
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 option to plot randomized residuals.
 #' @keywords graphics water-quality statistics
 #' @seealso \code{\link{plotConcQ}}, \code{\link{boxConcMonth}}, \code{\link{plotConcTime}}, \code{\link{boxQTwice}}
 #' @export
@@ -24,7 +25,7 @@
 #' eList <- setPA(eList, paStart=6,paLong=3)
 #' multiPlotDataOverview(eList, qUnit=1) 
 multiPlotDataOverview<-function (eList, qUnit = 2,cex.main=1.2,
-                                 logScaleConc=TRUE, logScaleQ=TRUE){
+                                 logScaleConc=TRUE, logScaleQ=TRUE,rResid=FALSE){
 
   localINFO <- getInfo(eList)
 
@@ -39,9 +40,10 @@ multiPlotDataOverview<-function (eList, qUnit = 2,cex.main=1.2,
   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)
+  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)
+  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)
 

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 option to plot randomized residuals.
 #' @param \dots arbitrary graphical parameters that will be passed to genericEGRETDotPlot function (see ?par for options)
 #' @keywords graphics water-quality statistics
 #' @export
@@ -38,7 +39,7 @@
 #' plotConcQ(eList)
 plotConcQ<-function(eList, qUnit = 2, tinyPlot = FALSE, logScale=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,...){
+                    rmSciX=FALSE,rmSciY=FALSE, customPar=FALSE,col="black",lwd=1,rResid=FALSE,...){
   # this function shows the sample data,
   # discharge on x-axis on a log scale, concentration on y-axis
 
@@ -67,8 +68,6 @@ plotConcQ<-function(eList, qUnit = 2, tinyPlot = FALSE, logScale=FALSE,
   qFactor<-qUnit@qUnitFactor
   x<-localSample$Q*qFactor
 
-  yLow<-localSample$ConcLow
-  yHigh<-localSample$ConcHigh
   Uncen<-localSample$Uncen
 
   plotTitle<-if(printTitle) paste(localINFO$shortName,"\n",localINFO$paramShortName,"\n","Concentration versus Discharge") else ""
@@ -87,19 +86,44 @@ plotConcQ<-function(eList, qUnit = 2, tinyPlot = FALSE, logScale=FALSE,
     yMin <- 0
   }
 
-  yInfo <- generalAxis(x=yHigh, maxVal=concMax, minVal=yMin, tinyPlot=tinyPlot,logScale=logScale,units=localINFO$param.units)
   xInfo <- generalAxis(x=x, maxVal=NA, minVal=NA, logScale=TRUE, tinyPlot=tinyPlot)
 
-  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 option to plot randomized residuals.
 #' @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,...){
 
@@ -95,8 +96,7 @@ plotConcTime<-function(eList, qUnit = 2,
 
   # the next section of code sets up the seasonal part of the plot title
   title2<-if(paLong==12) "" else setSeasonLabelByUser(paStartInput=paStart,paLongInput=paLong)
-  yLow<-subSample$ConcLow
-  yHigh<-subSample$ConcHigh
+
   Uncen<-subSample$Uncen
   x<-subSample$DecYear
 
@@ -113,17 +113,42 @@ 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)  
-  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
@@ -26,6 +26,7 @@
 #' @param col color of points on plot, see ?par 'Color Specification'
 #' @param lwd number line width
 #' @param prettyDate logical use 'pretty' limits for date axis if TRUE, or force the startYear/endYear as limits if FALSE
+#' @param rResid logical option to plot randomized residuals.
 #' @param \dots arbitrary functions sent to the generic plotting function.  See ?par for details on possible parameters
 #' @keywords graphics water-quality statistics
 #' @export
@@ -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)
@@ -63,14 +64,11 @@ plotConcTimeDaily<-function(eList, startYear=NA, endYear=NA, tinyPlot = FALSE,
   title2<-if(paLong==12) "" else setSeasonLabelByUser(paStartInput=paStart,paLongInput=paLong)
 
   subSample<-localSample[localSample$DecYear>=startYear & localSample$DecYear<= endYear,]
-
   subDaily<-localDaily[localDaily$DecYear>=startYear & localDaily$DecYear <= endYear,]
 
   xSample<-subSample$DecYear
   xDaily<-subDaily$DecYear
 
-  yLow<-subSample$ConcLow
-  yHigh<-subSample$ConcHigh
   Uncen<-subSample$Uncen
 
   plotTitle<-if(printTitle) paste(localINFO$shortName,"\n",localINFO$paramShortName,"\n","Observed and Estimated Concentration versus Time") else ""
@@ -81,19 +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)  
 
-  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$label,plotTitle=plotTitle,cex.axis=cex.axis,col=col,lwd=lwd,cex=cex,
-                      cex.main=cex.main, tinyPlot=tinyPlot,customPar=customPar, xDate=TRUE,...
-  )
-
   lines(x=xDaily, y=subDaily$ConcDay, type="l",col=col,lwd=lwd)
-
-  censoredSegments(yInfo$bottom,yLow=yLow,yHigh=yHigh,x=xSample,Uncen=Uncen,col=col,lwd=lwd)
   if (!tinyPlot) mtext(title2,side=3,line=-1.5)
 
 }
diff --git a/man/multiPlotDataOverview.Rd b/man/multiPlotDataOverview.Rd
@@ -5,7 +5,7 @@
 \title{Produces a 4 panel plot that gives an overview of the data set prior to any processing}
 \usage{
 multiPlotDataOverview(eList, qUnit = 2, cex.main = 1.2,
-  logScaleConc = TRUE, logScaleQ = TRUE)
+  logScaleConc = TRUE, logScaleQ = TRUE, rResid = FALSE)
 }
 \arguments{
 \item{eList}{named list with at least Daily, Sample, and INFO dataframes}
@@ -17,6 +17,8 @@ multiPlotDataOverview(eList, qUnit = 2, cex.main = 1.2,
 \item{logScaleConc}{logical if TRUE y in concentration graphs plotted in log axis. Default is TRUE.}
 
 \item{logScaleQ}{logical if TRUE y in streamflow graphs plotted in log axis. Default is TRUE.}
+
+\item{rResid}{logical option to plot randomized residuals.}
 }
 \description{
 The four plots produced are 1) log concentration versus log discharge, 2) log concentration versus time

diff --git a/man/plotConcQ.Rd b/man/plotConcQ.Rd
@@ -7,7 +7,7 @@
 plotConcQ(eList, qUnit = 2, tinyPlot = FALSE, logScale = 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, ...)
+  customPar = FALSE, col = "black", lwd = 1, rResid = FALSE, ...)
 }
 \arguments{
 \item{eList}{named list with at least the Sample and INFO dataframes}
@@ -42,6 +42,8 @@ plotConcQ(eList, qUnit = 2, tinyPlot = FALSE, logScale = FALSE,
 
 \item{lwd}{number line width}
 
+\item{rResid}{logical option to plot randomized residuals.}
+
 \item{\dots}{arbitrary graphical parameters that will be passed to genericEGRETDotPlot function (see ?par for options)}
 }
 \description{

diff --git a/man/plotConcTime.Rd b/man/plotConcTime.Rd
@@ -4,7 +4,7 @@
 \alias{plotConcTime}
 \title{Plot of Observed Concentration versus Time}
 \usage{
-plotConcTime(eList, qUnit = 2, qLower = NA, qUpper = NA,
+plotConcTime(eList, qUnit = 2, 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, ...)
@@ -18,6 +18,8 @@ plotConcTime(eList, qUnit = 2, qLower = NA, qUpper = NA,
 
 \item{qUpper}{numeric the upper bound on values of discharge for selection of data points to be plotted, units are those specified by qUnit, default = NA which is equivalent to an upper bound of infinity}
 
+\item{rResid}{logical option to plot randomized residuals.}
+
 \item{tinyPlot}{logical variable, if TRUE plot is designed to be plotted small as part of a multipart figure, default is FALSE.}
 
 \item{concMax}{numeric value for the maximum value to be used on the vertical axis, default is NA (which allows it to be set automatically by the data)}

diff --git a/man/plotConcTimeDaily.Rd b/man/plotConcTimeDaily.Rd
@@ -6,8 +6,8 @@
 \usage{
 plotConcTimeDaily(eList, startYear = NA, endYear = NA, tinyPlot = FALSE,
   concMax = NA, printTitle = TRUE, cex = 0.8, cex.axis = 1.1,
-  cex.main = 1.1, customPar = FALSE, col = "black", lwd = 1,
-  prettyDate = TRUE, ...)
+  rResid = FALSE, cex.main = 1.1, customPar = FALSE, col = "black",
+  lwd = 1, prettyDate = TRUE, ...)
 }
 \arguments{
 \item{eList}{named list with at least the Daily, Sample, and INFO dataframes}
@@ -26,6 +26,8 @@ plotConcTimeDaily(eList, startYear = NA, endYear = NA, tinyPlot = FALSE,
 
 \item{cex.axis}{magnification to be used for axis annotation relative to the current setting of cex}
 
+\item{rResid}{logical option to plot randomized residuals.}
+
 \item{cex.main}{magnification to be used for main titles relative to the current setting of cex}
 
 \item{customPar}{logical defaults to FALSE. If TRUE, par() should be set by user before calling this function