Merge pull request #88 from ldecicco-USGS/master

randomCensored

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: EGRET
 Type: Package
 Title: Exploration and Graphics for RivEr Trends (EGRET)
-Version: 2.5.2
+Version: 2.5.3
 Authors@R: c( person("Robert", "Hirsch", role = c("aut"),
     email = "rhirsch@usgs.gov"),
     person("Laura", "DeCicco", role = c("aut","cre"),
@@ -10,7 +10,7 @@ Description: Statistics and graphics for streamflow history,
     water quality trends, and the statistical modeling algorithm: Weighted
     Regressions on Time, Discharge, and Season (WRTDS).
 License: CC0
-Date: 2016-03-07
+Date: 2016-06-21
 Depends:
     R (>= 3.0)
 Imports:

NEWS

@@ -1,3 +1,7 @@
+EGRET 2.5.3
+===========
+* Argument for randomized censored values names randomCensored
+
 EGRET 2.5.0
 ===========
 * Added an argument to the concentration and residual plotting functions to randomize the censored values for the plots.

R/boxConcThree.R

@@ -45,11 +45,6 @@ boxConcThree<-function (eList, tinyPlot=FALSE,
     paStart <- 10
   } 
 
-  # if(rResid & !all((c("SE","yHat") %in% names(eList$Sample)))){
-  #   message("Pseudo only supported after running modelEstimation, defaulting to rResid=FALSE")
-  #   rResid <- FALSE
-  # }
-
   localSample <- if(paLong == 12) localSample else selectDays(localSample,paLong,paStart)
   localDaily <- if(paLong == 12) localDaily else selectDays(localDaily, paLong,paStart)
 

R/boxResidMonth.R

@@ -22,7 +22,7 @@
 #' @param font.main font to be used for plot main titles
 #' @param customPar logical defaults to FALSE. If TRUE, par() should be set by user before calling this function 
 #' @param las numeric in {0,1,2,3}; the style of axis labels
-#' @param rResid logical. Show censored residuals as randomized.
+#' @param randomCensored logical. Show censored residuals as randomized.
 #' @param \dots arbitrary graphical parameters that will be passed to genericEGRETDotPlot function (see ?par for options)
 #' @keywords graphics water-quality statistics
 #' @seealso \code{\link[graphics]{boxplot}}
@@ -36,7 +36,7 @@
 #' boxResidMonth(eList)
 boxResidMonth<-function(eList, stdResid = FALSE, las=1,
                         printTitle = TRUE, cex=0.8, cex.axis=1.1, cex.main=1.1,
-                        font.main=2, tinyPlot=FALSE, customPar=FALSE,rResid=FALSE,...) {
+                        font.main=2, tinyPlot=FALSE, customPar=FALSE,randomCensored=FALSE,...) {
 
   localINFO <- getInfo(eList)
   localSample <- getSample(eList)
@@ -65,7 +65,7 @@ boxResidMonth<-function(eList, stdResid = FALSE, las=1,
 
   plotTitle<-if(printTitle) paste(localINFO$shortName,"\n",localINFO$paramShortName,"\nBoxplots of residuals by month") else ""
 
-  if(!rResid){
+  if(!randomCensored){
     resid<-log(localSample$ConcAve) - localSample$yHat
   } else {
     if(!("rResid" %in% names(localSample))){

R/fluxBiasEight.R

@@ -21,7 +21,7 @@
 #' @param cex.axis magnification to be used for axis annotation relative to the current setting of cex
 #' @param col color of points on plot, see ?par 'Color Specification'
 #' @param lwd number line width
-#' @param rResid logical. Show censored residuals as randomized.
+#' @param randomCensored logical. Show censored residuals as randomized.
 #' @param \dots arbitrary graphical parameters that will be passed to genericEGRETDotPlot function (see ?par for options)
 #' @keywords graphics water-quality statistics
 #' @export
@@ -40,7 +40,7 @@
 #' dev.off()
 #' }
 fluxBiasMulti<-function (eList, qUnit = 2, fluxUnit = 3, moreTitle = "WRTDS", 
-                         cex = 0.7, cex.axis = 1.1,cex.main=1.1,rResid=FALSE,
+                         cex = 0.7, cex.axis = 1.1,cex.main=1.1,randomCensored=FALSE,
                          col="black", lwd=1,...){
 
   localINFO <- getInfo(eList)
@@ -72,27 +72,27 @@ fluxBiasMulti<-function (eList, qUnit = 2, fluxUnit = 3, moreTitle = "WRTDS",
   par(oma = c(0, 10, 4, 10),mfrow=c(4,2))
   plotResidPred(eList, 
                 stdResid = FALSE, tinyPlot=TRUE, printTitle = FALSE,cex=cex, 
-                cex.axis = cex.axis, col=col,lwd=lwd,rResid=rResid,...)
+                cex.axis = cex.axis, col=col,lwd=lwd,randomCensored=randomCensored,...)
   plotResidQ(eList, 
              qUnit, tinyPlot = TRUE, printTitle = FALSE,cex=cex, 
-             cex.axis = cex.axis, col=col,lwd=lwd,rResid=rResid,...)
+             cex.axis = cex.axis, col=col,lwd=lwd,randomCensored=randomCensored,...)
   plotResidTime(eList, 
                 printTitle = FALSE, tinyPlot=TRUE,cex=cex, 
-                cex.axis = cex.axis, col=col,rResid=rResid,lwd=lwd,...)
+                cex.axis = cex.axis, col=col,randomCensored=randomCensored,lwd=lwd,...)
   boxResidMonth(eList, 
                 printTitle = FALSE, tinyPlot=TRUE,cex=cex, 
-                cex.axis = cex.axis,lwd=lwd,rResid=rResid,...)
+                cex.axis = cex.axis,lwd=lwd,randomCensored=randomCensored,...)
   boxConcThree(eList, 
                localINFO = localINFO, printTitle=FALSE, tinyPlot=TRUE,cex=cex, 
                cex.axis = cex.axis, lwd=lwd,...)
   plotConcPred(eList, printTitle=FALSE, 
                tinyPlot=TRUE,cex=cex, 
-               cex.axis = cex.axis, col=col,lwd=lwd,rResid = rResid,...)
+               cex.axis = cex.axis, col=col,lwd=lwd,randomCensored = randomCensored,...)
   boxQTwice(eList, printTitle = FALSE, qUnit = qUnit,tinyPlot=TRUE,cex=cex, 
             cex.axis = cex.axis, lwd=lwd,...)
   plotFluxPred(eList, 
                fluxUnit, tinyPlot = TRUE, printTitle = FALSE,cex=cex, 
-               cex.axis = cex.axis, col=col,lwd=lwd,rResid=rResid,...)
+               cex.axis = cex.axis, col=col,lwd=lwd,randomCensored=randomCensored,...)
   fluxBias <- fluxBiasStat(localSample)
   fB <- as.numeric(fluxBias[3])
   fB <- format(fB, digits = 3)

R/multiPlotDataOverview.R

@@ -13,7 +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.
+#' @param randomCensored 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
@@ -24,7 +24,7 @@
 #' # 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,rResid=FALSE,
+multiPlotDataOverview<-function (eList, qUnit = 2,cex.main=1.2,randomCensored=FALSE,
                                  logScaleConc=TRUE, logScaleQ=TRUE){
 
   localINFO <- getInfo(eList)
@@ -41,9 +41,9 @@ multiPlotDataOverview<-function (eList, qUnit = 2,cex.main=1.2,rResid=FALSE,
 
   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)
+            rmSciX=TRUE,logScale=logScaleConc,randomCensored=randomCensored)
   boxConcMonth(eList, printTitle = FALSE, tinyPlot=TRUE,logScale=logScaleConc)
-  plotConcTime(eList, printTitle = FALSE, tinyPlot = TRUE,logScale=logScaleConc,rResid=rResid)
+  plotConcTime(eList, printTitle = FALSE, tinyPlot = TRUE,logScale=logScaleConc,randomCensored=randomCensored)
   boxQTwice(eList, printTitle = FALSE, qUnit = qUnit, tinyPlot=TRUE,logScale=logScaleQ)
   title<-paste(localINFO$shortName,"\n",localINFO$paramShortName)
 

R/plotConcPred.R

@@ -18,7 +18,7 @@
 #' (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 randomCensored 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
 #' @seealso \code{\link{selectDays}}, \code{\link{genericEGRETDotPlot}}
@@ -33,7 +33,7 @@
 #' plotConcPred(eList)
 plotConcPred<-function(eList, concMax = NA, logScale=FALSE,
                        printTitle = TRUE,tinyPlot=FALSE,cex=0.8, cex.axis=1.1,
-                       cex.main=1.1, customPar=FALSE,col="black",lwd=1, rResid = FALSE,...){
+                       cex.main=1.1, customPar=FALSE,col="black",lwd=1, randomCensored = FALSE,...){
 
   localINFO <- getInfo(eList)
   localSample <- getSample(eList) 
@@ -80,7 +80,7 @@ plotConcPred<-function(eList, concMax = NA, logScale=FALSE,
 
   xInfo <- generalAxis(x=x, minVal=minXLow, maxVal=concMax, tinyPlot=tinyPlot,logScale=logScale)  
 
-  if(rResid){
+  if(randomCensored){
     if(!("rObserved" %in% names(localSample))){
       eList <- makeAugmentedSample(eList)
       localSample <- eList$Sample

R/plotConcQ.R

@@ -24,7 +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 randomCensored 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
@@ -37,7 +37,7 @@
 #' # Graphs consisting of Jun-Aug
 #' eList <- setPA(eList, paStart=6,paLong=3)
 #' plotConcQ(eList)
-plotConcQ<-function(eList, qUnit = 2, tinyPlot = FALSE, logScale=FALSE,rResid=FALSE,
+plotConcQ<-function(eList, qUnit = 2, tinyPlot = FALSE, logScale=FALSE,randomCensored=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,...){
   localINFO <- getInfo(eList)
@@ -85,7 +85,7 @@ plotConcQ<-function(eList, qUnit = 2, tinyPlot = FALSE, logScale=FALSE,rResid=FA
 
   xInfo <- generalAxis(x=x, maxVal=NA, minVal=NA, logScale=TRUE, tinyPlot=tinyPlot)
 
-  if(!rResid){
+  if(!randomCensored){
     yLow<-localSample$ConcLow
     yHigh<-localSample$ConcHigh
 

R/plotConcTime.R

@@ -29,7 +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 randomCensored 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
@@ -42,9 +42,9 @@
 #' 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(eList, qUnit = 1, qLower = 100, qUpper = 10000, randomCensored = TRUE)
 plotConcTime<-function(eList, qUnit = 2, 
-                       qLower = NA, qUpper = NA, rResid=FALSE,
+                       qLower = NA, qUpper = NA, randomCensored=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,...){
 
@@ -108,7 +108,7 @@ plotConcTime<-function(eList, qUnit = 2,
   plotTitle<-if(printTitle) paste(localINFO$shortName,"\n",localINFO$paramShortName,"\n",title3,sep="") else ""
 
 
-  if(!rResid){
+  if(!randomCensored){
     subSample<-subSample[subSample$Q>qLowerBound & subSample$Q<qUpperBound,]
     subSample <- if(paLong == 12) subSample else selectDays(subSample, paLong,paStart)
     Uncen<-subSample$Uncen

R/plotConcTimeDaily.R

@@ -25,7 +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 randomCensored 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
@@ -40,7 +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,rResid=FALSE,
+                            concMax = NA, printTitle = TRUE,cex=0.8, cex.axis=1.1,randomCensored=FALSE,
                             cex.main=1.1, customPar=FALSE,col="black",lwd=1,prettyDate=TRUE,...){
 
   localINFO <- getInfo(eList)
@@ -79,7 +79,7 @@ plotConcTimeDaily<-function(eList, startYear=NA, endYear=NA, tinyPlot = FALSE,
 
   xInfo <- generalAxis(x=xSample, minVal=startYear, maxVal=endYear, tinyPlot=tinyPlot,padPercent=0,prettyDate=prettyDate)  
 
-  if(!rResid){
+  if(!randomCensored){
 
     yLow<-subSample$ConcLow
     yHigh<-subSample$ConcHigh

R/plotFluxPred.R

@@ -20,7 +20,7 @@
 #' (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 randomCensored 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
@@ -36,7 +36,7 @@
 #' plotFluxPred(eList)
 plotFluxPred<-function(eList, fluxUnit = 3, fluxMax = NA, 
                        printTitle = TRUE, oneToOneLine=TRUE, customPar=FALSE,col="black", lwd=1,
-                       cex=0.8, cex.axis=1.1,cex.main=1.1,tinyPlot=FALSE,logScale=FALSE,rResid = FALSE,...){
+                       cex=0.8, cex.axis=1.1,cex.main=1.1,tinyPlot=FALSE,logScale=FALSE,randomCensored = FALSE,...){
   # this function shows observed versus estimated flux
   # estimated flux on the x-axis (these include the bias correction), 
   # observed flux on y-axis 
@@ -109,7 +109,7 @@ plotFluxPred<-function(eList, fluxUnit = 3, fluxMax = NA,
 
   xInfo <- generalAxis(x=x, minVal=minX, maxVal=NA, logScale=logScale, tinyPlot=tinyPlot,padPercent=5)  
 
-  if(!rResid){
+  if(!randomCensored){
     yLow<-localSample$ConcLow*localSample$Q*fluxFactor
     yHigh<-localSample$ConcHigh*localSample$Q*fluxFactor
 

R/plotResidPred.R

@@ -22,7 +22,7 @@
 #' (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 residuals as randomized.
+#' @param randomCensored logical. Show censored residuals as randomized.
 #' @param \dots arbitrary graphical parameters that will be passed to genericEGRETDotPlot function (see ?par for options)
 #' @keywords water-quality statistics graphics
 #' @export
@@ -36,7 +36,7 @@
 #' plotResidPred(eList)
 plotResidPred<-function(eList, stdResid = FALSE, 
                         tinyPlot = FALSE, printTitle = TRUE, col="black",lwd=1,
-                        cex=0.8, cex.axis=1.1,cex.main=1.1, customPar=FALSE,rResid=FALSE,...){
+                        cex=0.8, cex.axis=1.1,cex.main=1.1, customPar=FALSE,randomCensored=FALSE,...){
   # this function shows residual versus estimated in log space
   # estimated log concentration on the x-axis (these are prior to bias correction), 
   # observed log concentration on y-axis 
@@ -79,7 +79,7 @@ plotResidPred<-function(eList, stdResid = FALSE,
 
   ####################
 
-  if(!rResid){
+  if(!randomCensored){
 
     yLow<-log(localSample$ConcLow)-localSample$yHat
     yHigh<-log(localSample$ConcHigh)-localSample$yHat

R/plotResidQ.R

@@ -23,7 +23,7 @@
 #' (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 residuals as randomized.
+#' @param randomCensored logical. Show censored residuals as randomized.
 #' @param \dots arbitrary graphical parameters that will be passed to genericEGRETDotPlot function (see ?par for options)
 #' @keywords graphics water-quality statistics
 #' @export
@@ -37,7 +37,7 @@
 #' plotResidQ(eList)
 plotResidQ<-function (eList, qUnit = 2, 
                       tinyPlot = FALSE, stdResid = FALSE, printTitle = TRUE,col="black",lwd=1,
-                      cex=0.8, cex.axis=1.1,cex.main=1.1,rmSciX=FALSE, customPar=FALSE,rResid=FALSE,...){  
+                      cex=0.8, cex.axis=1.1,cex.main=1.1,rmSciX=FALSE, customPar=FALSE,randomCensored=FALSE,...){  
 
   localINFO <- getInfo(eList)
   localSample <- getSample(eList)
@@ -84,7 +84,7 @@ plotResidQ<-function (eList, qUnit = 2,
 
   xInfo <- generalAxis(x=x, minVal=NA, maxVal=NA, logScale=TRUE, tinyPlot=tinyPlot,padPercent=5)
 
-  if(!rResid){
+  if(!randomCensored){
 
     yLow <- log(localSample$ConcLow) - localSample$yHat
     yHigh <- log(localSample$ConcHigh) - localSample$yHat

R/plotResidTime.R

@@ -22,7 +22,7 @@
 #' (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 residuals as randomized.
+#' @param randomCensored logical. Show censored residuals as randomized.
 #' @param \dots arbitrary graphical parameters that will be passed to genericEGRETDotPlot function (see ?par for options)
 #' @keywords graphics water-quality statistics
 #' @export
@@ -36,7 +36,7 @@
 #' plotResidTime(eList)
 plotResidTime<-function(eList, stdResid = FALSE, 
                         printTitle = TRUE, hLine=TRUE, tinyPlot=FALSE,col="black",lwd=1,
-                        cex=0.8, cex.axis=1.1,cex.main=1.1, customPar=FALSE,rResid=FALSE,...){
+                        cex=0.8, cex.axis=1.1,cex.main=1.1, customPar=FALSE,randomCensored=FALSE,...){
 
   localINFO <- getInfo(eList)
   localSample <- getSample(eList)
@@ -73,7 +73,7 @@ plotResidTime<-function(eList, stdResid = FALSE,
 
   xInfo <- generalAxis(x=x, maxVal=xMax, minVal=xMin,padPercent=0, tinyPlot=tinyPlot)
 
-  if(!rResid){
+  if(!randomCensored){
     yLow<-log(localSample$ConcLow)-localSample$yHat
     yHigh<-log(localSample$ConcHigh)-localSample$yHat