Merge pull request #78 from ldecicco-USGS/master

Include randomized residuals.
DOI-USGS · Apr 15, 2016 · 491c050 · 491c050
2 parents dfbf17e + 1ad237a
commit 491c050
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Showing 14 changed files with 162 additions and 121 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: EGRET
 Type: Package
 Title: Exploration and Graphics for RivEr Trends (EGRET)
-Version: 2.4.3
+Version: 2.5.0
 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: 2016-03-04
+Date: 2016-03-07
 Depends:
     R (>= 3.0)
 Imports:
@@ -22,7 +22,8 @@ Imports:
     utils,
     graphics,
     stats,
-    grDevices
+    grDevices,
+    truncnorm
 Suggests:
     xtable,
     knitr,

diff --git a/NAMESPACE b/NAMESPACE
@@ -115,3 +115,4 @@ import(survival)
 import(utils)
 importFrom(fields,interp.surface)
 importFrom(lubridate,decimal_date)
+importFrom(truncnorm,rtruncnorm)
diff --git a/R/boxResidMonth.R b/R/boxResidMonth.R
@@ -22,6 +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 \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}}
@@ -35,7 +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,...) {
+                        font.main=2, tinyPlot=FALSE, customPar=FALSE,rResid=FALSE,...) {
 
   localINFO <- getInfo(eList)
   localSample <- getSample(eList)
@@ -64,15 +65,15 @@ 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(!rResid){
     resid<-log(localSample$ConcAve) - localSample$yHat
-  # } else {
-  #   if(!("rResid" %in% names(localSample))){
-  #     eList <- makeAugmentedSample(eList)
-  #     localSample <- eList$Sample
-  #   }
-  #   resid <- localSample$rResid
-  # }
+  } else {
+    if(!("rResid" %in% names(localSample))){
+      eList <- makeAugmentedSample(eList)
+      localSample <- eList$Sample
+    }
+    resid <- localSample$rResid
+  }
 
   if(stdResid) {
     resid<- resid/localSample$SE
@@ -96,5 +97,5 @@ boxResidMonth<-function(eList, stdResid = FALSE, las=1,
           ...)
   abline(h=0)  
   if (!tinyPlot) mtext(title2,side=3,line=-1.5)
-  # invisible(eList)
+  invisible(eList)
 }
diff --git a/R/fluxBiasEight.R b/R/fluxBiasEight.R
@@ -21,6 +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 \dots arbitrary graphical parameters that will be passed to genericEGRETDotPlot function (see ?par for options)
 #' @keywords graphics water-quality statistics
 #' @export
@@ -39,7 +40,7 @@
 #' dev.off()
 #' }
 fluxBiasMulti<-function (eList, qUnit = 2, fluxUnit = 3, moreTitle = "WRTDS", 
-                         cex = 0.7, cex.axis = 1.1,cex.main=1.1,
+                         cex = 0.7, cex.axis = 1.1,cex.main=1.1,rResid=FALSE,
                          col="black", lwd=1,...){
 
   localINFO <- getInfo(eList)
@@ -71,16 +72,16 @@ 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,...)
+                cex.axis = cex.axis, col=col,lwd=lwd,rResid=rResid,...)
   plotResidQ(eList, 
              qUnit, tinyPlot = TRUE, printTitle = FALSE,cex=cex, 
-             cex.axis = cex.axis, col=col,lwd=lwd,...)
+             cex.axis = cex.axis, col=col,lwd=lwd,rResid=rResid,...)
   plotResidTime(eList, 
                 printTitle = FALSE, tinyPlot=TRUE,cex=cex, 
-                cex.axis = cex.axis, col=col,lwd=lwd,...)
+                cex.axis = cex.axis, col=col,rResid=rResid,lwd=lwd,...)
   boxResidMonth(eList, 
                 printTitle = FALSE, tinyPlot=TRUE,cex=cex, 
-                cex.axis = cex.axis,lwd=lwd,...)
+                cex.axis = cex.axis,lwd=lwd,rResid=rResid,...)
   boxConcThree(eList, 
                localINFO = localINFO, printTitle=FALSE, tinyPlot=TRUE,cex=cex, 
                cex.axis = cex.axis, lwd=lwd,...)

diff --git a/R/makeRandomResiduals.R b/R/makeRandomResiduals.R
@@ -6,22 +6,23 @@
 #'
 #' @param eList named list with at least the Daily dataframe
 #' @keywords water-quality statistics
+#' @importFrom truncnorm rtruncnorm
 #' @return eList named list with modified Daily data frame.
-# makeAugmentedSample <- function(eList){
-# 
-#   if(all(c("SE","yHat") %in% names(eList$Sample))){
-#     localSample <- eList$Sample
-#     numSamples<-length(localSample$Uncen)
-#     a <- ifelse(localSample$Uncen==0&!is.na(localSample$ConcLow),log(localSample$ConcLow)-localSample$yHat,-Inf)
-#     b <- ifelse(localSample$Uncen==1,+Inf,log(localSample$ConcHigh) - localSample$yHat)
-#     mean <- ifelse(localSample$Uncen==1,log(localSample$ConcHigh) - localSample$yHat,0)
-#     sd <- ifelse(localSample$Uncen==1,0,localSample$SE)
-#     localSample$rResid<-truncnorm::rtruncnorm(numSamples,a,b,mean,sd)
-#     localSample$rObserved <- exp(localSample$rResid + localSample$yHat)
-#     
-#     eList	<- as.egret(eList$INFO, eList$Daily, localSample, eList$surfaces)
-#   } else {
-#     message("Pseudo only supported after running modelEstimation")
-#   }
-#   return(eList)
-# }
+makeAugmentedSample <- function(eList){
+
+  if(all(c("SE","yHat") %in% names(eList$Sample))){
+    localSample <- eList$Sample
+    numSamples<-length(localSample$Uncen)
+    a <- ifelse(localSample$Uncen==0&!is.na(localSample$ConcLow),log(localSample$ConcLow)-localSample$yHat,-Inf)
+    b <- ifelse(localSample$Uncen==1,+Inf,log(localSample$ConcHigh) - localSample$yHat)
+    mean <- ifelse(localSample$Uncen==1,log(localSample$ConcHigh) - localSample$yHat,0)
+    sd <- ifelse(localSample$Uncen==1,0,localSample$SE)
+    localSample$rResid<-truncnorm::rtruncnorm(numSamples,a,b,mean,sd)
+    localSample$rObserved <- exp(localSample$rResid + localSample$yHat)
+
+    eList	<- as.egret(eList$INFO, eList$Daily, localSample, eList$surfaces)
+  } else {
+    message("Pseudo only supported after running modelEstimation")
+  }
+  return(eList)
+}
diff --git a/R/plotResidPred.R b/R/plotResidPred.R
@@ -22,6 +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 \dots arbitrary graphical parameters that will be passed to genericEGRETDotPlot function (see ?par for options)
 #' @keywords water-quality statistics graphics
 #' @export
@@ -35,7 +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,...){
+                        cex=0.8, cex.axis=1.1,cex.main=1.1, customPar=FALSE,rResid=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 
@@ -78,7 +79,7 @@ plotResidPred<-function(eList, stdResid = FALSE,
 
   ####################
 
-  # if(!rResid){
+  if(!rResid){
 
     yLow<-log(localSample$ConcLow)-localSample$yHat
     yHigh<-log(localSample$ConcHigh)-localSample$yHat
@@ -96,33 +97,33 @@ plotResidPred<-function(eList, stdResid = FALSE,
 
     censoredSegments(yInfo$bottom, yLow, yHigh, log(x), Uncen, col=col, lwd=lwd )
 
-  # } else {
-  #   if(!("rResid" %in% names(localSample))){
-  #     eList <- makeAugmentedSample(eList)
-  #     localSample <- eList$Sample
-  #   }
-  #   
-  #   yHigh <- localSample$rResid
-  #   Uncen <- localSample$Uncen
-  #   
-  #   if(stdResid){
-  #     yHigh <- yHigh/localSample$SE
-  #   }
-  #   
-  #   yInfo <- generalAxis(x=yHigh, minVal=NA, maxVal=NA, tinyPlot=tinyPlot)
-  #   
-  #   genericEGRETDotPlot(x=log(x[Uncen == 1]), y=yHigh[Uncen == 1],
-  #                       xTicks=xInfo$ticks, yTicks=yInfo$ticks,col=col,
-  #                       xlim=c(xInfo$bottom,xInfo$top), ylim=c(yInfo$bottom,yInfo$top),
-  #                       xlab=xLab, ylab=yLab, plotTitle=plotTitle, customPar=customPar,cex=cex,
-  #                       hLine=TRUE,cex.axis=cex.axis,cex.main=cex.main, tinyPlot=tinyPlot,...
-  #   )
-  #   points(x=log(x[Uncen == 0]), y=yHigh[Uncen == 0], pch=1,cex=cex,col=col)
-  #   
-  # }
+  } else {
+    if(!("rResid" %in% names(localSample))){
+      eList <- makeAugmentedSample(eList)
+      localSample <- eList$Sample
+    }
+
+    yHigh <- localSample$rResid
+    Uncen <- localSample$Uncen
+
+    if(stdResid){
+      yHigh <- yHigh/localSample$SE
+    }
+
+    yInfo <- generalAxis(x=yHigh, minVal=NA, maxVal=NA, tinyPlot=tinyPlot)
+
+    genericEGRETDotPlot(x=log(x[Uncen == 1]), y=yHigh[Uncen == 1],
+                        xTicks=xInfo$ticks, yTicks=yInfo$ticks,col=col,
+                        xlim=c(xInfo$bottom,xInfo$top), ylim=c(yInfo$bottom,yInfo$top),
+                        xlab=xLab, ylab=yLab, plotTitle=plotTitle, customPar=customPar,cex=cex,
+                        hLine=TRUE,cex.axis=cex.axis,cex.main=cex.main, tinyPlot=tinyPlot,...
+    )
+    points(x=log(x[Uncen == 0]), y=yHigh[Uncen == 0], pch=1,cex=cex,col=col)
+
+  }
 
   if (!tinyPlot) mtext(title2,side=3,line=-1.5)
 
-  # invisible(eList)
+  invisible(eList)
 
 }
diff --git a/R/plotResidQ.R b/R/plotResidQ.R
@@ -23,6 +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 \dots arbitrary graphical parameters that will be passed to genericEGRETDotPlot function (see ?par for options)
 #' @keywords graphics water-quality statistics
 #' @export
@@ -36,7 +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,...){  
+                      cex=0.8, cex.axis=1.1,cex.main=1.1,rmSciX=FALSE, customPar=FALSE,rResid=FALSE,...){  
 
   localINFO <- getInfo(eList)
   localSample <- getSample(eList)
@@ -83,7 +84,7 @@ plotResidQ<-function (eList, qUnit = 2,
 
   xInfo <- generalAxis(x=x, minVal=NA, maxVal=NA, logScale=TRUE, tinyPlot=tinyPlot,padPercent=5)
 
-  # if(!rResid){
+  if(!rResid){
 
     yLow <- log(localSample$ConcLow) - localSample$yHat
     yHigh <- log(localSample$ConcHigh) - localSample$yHat
@@ -104,32 +105,32 @@ plotResidQ<-function (eList, qUnit = 2,
     )
 
     censoredSegments(yInfo$bottom, yLow, yHigh, x, Uncen,col=col, lwd=lwd )
-  # } else {
-  #   
-  #   if(!("rResid" %in% names(localSample))){
-  #     eList <- makeAugmentedSample(eList)
-  #     localSample <- eList$Sample
-  #   }
-  #   yHigh <- localSample$rResid
-  #   
-  #   if(stdResid){
-  #     yHigh <- yHigh/localSample$SE
-  #   }
-  #   
-  #   yInfo <- generalAxis(x=yHigh, minVal=NA, maxVal=NA, tinyPlot=tinyPlot,padPercent=5)
-  #   
-  #   genericEGRETDotPlot(x=x[Uncen == 1], y=yHigh[Uncen == 1],
-  #                       xTicks=xInfo$ticks, yTicks=yInfo$ticks,hLine=TRUE,
-  #                       xlim = c(xInfo$bottom, xInfo$top), ylim = c(yInfo$bottom, yInfo$top),
-  #                       xlab = xLab, ylab = yLab, plotTitle=plotTitle,cex=cex,
-  #                       log = "x", cex.axis=cex.axis,cex.main=cex.main, col=col,
-  #                       tinyPlot=tinyPlot,rmSciX=rmSciX, customPar=customPar,...
-  #   )
-  #   points(x=x[Uncen == 0], y=yHigh[Uncen == 0],cex=cex,col=col)
-  #   
-  # }
+  } else {
+
+    if(!("rResid" %in% names(localSample))){
+      eList <- makeAugmentedSample(eList)
+      localSample <- eList$Sample
+    }
+    yHigh <- localSample$rResid
+
+    if(stdResid){
+      yHigh <- yHigh/localSample$SE
+    }
+
+    yInfo <- generalAxis(x=yHigh, minVal=NA, maxVal=NA, tinyPlot=tinyPlot,padPercent=5)
+
+    genericEGRETDotPlot(x=x[Uncen == 1], y=yHigh[Uncen == 1],
+                        xTicks=xInfo$ticks, yTicks=yInfo$ticks,hLine=TRUE,
+                        xlim = c(xInfo$bottom, xInfo$top), ylim = c(yInfo$bottom, yInfo$top),
+                        xlab = xLab, ylab = yLab, plotTitle=plotTitle,cex=cex,
+                        log = "x", cex.axis=cex.axis,cex.main=cex.main, col=col,
+                        tinyPlot=tinyPlot,rmSciX=rmSciX, customPar=customPar,...
+    )
+    points(x=x[Uncen == 0], y=yHigh[Uncen == 0],cex=cex,col=col)
+
+  }
 
   if (!tinyPlot) mtext(title2,side=3,line=-1.5)
-  # invisible(eList)
+  invisible(eList)
 
 }