Merge pull request #91 from ldecicco-USGS/master

start/end arguments

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: EGRET
 Type: Package
 Title: Exploration and Graphics for RivEr Trends (EGRET)
-Version: 2.5.3
+Version: 2.6.0
 Authors@R: c( person("Robert", "Hirsch", role = c("aut"),
     email = "[email protected]"),
     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: 2016-06-21
+Date: 2016-07-15
 Depends:
     R (>= 3.0)
 Imports:

NEWS

@@ -1,3 +1,7 @@
+EGRET 2.6.0
+===========
+* start/end year argument names unified to yearStart and yearEnd (previously included startYear and endYear)
+
 EGRET 2.5.3
 ===========
 * Argument for randomized censored values names randomCensored

R/generalAxis.R

@@ -10,7 +10,7 @@
 #' @param padPercent number used to pad the max and min if not specified
 #' @param concentration logical if concentration=TRUE, labels returned as concentration units, otherwise flux units.
 #' @param units character concentration units. Typically found in INFO$param.units.
-#' @param prettyDate logical use 'pretty' limits for date axis if TRUE, or force the startYear/endYear as limits if FALSE
+#' @param prettyDate logical use 'pretty' limits for date axis if TRUE, or force the yearStart/yearEnd as limits if FALSE
 #' @keywords graphics water-quality statistics
 #' @export
 #' @examples

R/plotConcTime.R

@@ -16,6 +16,8 @@
 #' @param qUnit object of qUnit class \code{\link{printqUnitCheatSheet}}, or numeric represented the short code, or character representing the descriptive name. 
 #' @param qLower numeric the lower bound on values of discharge used to select the data points to be plotted, units are those specified by qUnit, default = NA which is equivalent to a lower bound of zero but if the desired lower bound is zero use qLower = NA
 #' @param 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
+#' @param yearStart numeric is the calendar year containing the first estimated annual value to be plotted, default is NA (which allows it to be set automatically by the data)
+#' @param yearEnd numeric is the calendar year just after the last estimated annual value to be plotted, default is NA (which allows it to be set automatically by the data)
 #' @param tinyPlot logical variable, if TRUE plot is designed to be plotted small as part of a multipart figure, default is FALSE.
 #' @param 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)
 #' @param concMin numeric value for lower limit on concentration shown on the vertical log graph, default is NA 
@@ -43,7 +45,7 @@
 #' plotConcTime(eList, qUnit = 1, qLower = 100, qUpper = 10000)
 #' plotConcTime(eList, logScale=TRUE)
 #' plotConcTime(eList, qUnit = 1, qLower = 100, qUpper = 10000, randomCensored = TRUE)
-plotConcTime<-function(eList, qUnit = 2, 
+plotConcTime<-function(eList, qUnit = 2, yearStart = NA, yearEnd = NA,
                        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,...){
@@ -107,14 +109,16 @@ plotConcTime<-function(eList, qUnit = 2,
 
   plotTitle<-if(printTitle) paste(localINFO$shortName,"\n",localINFO$paramShortName,"\n",title3,sep="") else ""
 
-
   if(!randomCensored){
     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)  
+    xInfo <- generalAxis(x=x, 
+                         minVal = ifelse(is.na(yearStart),min(x),yearStart),
+                         maxVal=ifelse(is.na(yearEnd),max(x),yearEnd), 
+                         tinyPlot=tinyPlot)  
 
     yLow<-subSample$ConcLow
     yHigh<-subSample$ConcHigh
@@ -144,8 +148,12 @@ plotConcTime<-function(eList, qUnit = 2,
 
     Uncen<-subSample$Uncen
     x<-subSample$DecYear
+
+    xInfo <- generalAxis(x=x, 
+                         minVal = ifelse(is.na(yearStart),min(x),yearStart),
+                         maxVal=ifelse(is.na(yearEnd),max(x),yearEnd), 
+                         tinyPlot=tinyPlot)
 
-    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"))

R/plotConcTimeDaily.R

@@ -12,8 +12,8 @@
 #' a Daily dataframe with the daily flow data,
 #' and an INFO dataframe with metadata. 
 #'
-#' @param startYear numeric specifying the starting date (expressed as decimal years, for example 1989.0) for the plot
-#' @param endYear numeric specifiying the ending date for the plot 
+#' @param yearStart numeric specifying the starting date (expressed as decimal years, for example 1989.0) for the plot
+#' @param yearEnd numeric specifiying the ending date for the plot 
 #' @param eList named list with at least the Daily, Sample, and INFO dataframes
 #' @param tinyPlot logical variable, if TRUE plot is designed to be short and wide, default is FALSE.
 #' @param concMax number specifying the maximum value to be used on the vertical axis, default is NA (which allows it to be set automatically by the data)
@@ -26,7 +26,7 @@
 #' @param col color of points on plot, see ?par 'Color Specification'
 #' @param lwd number line width
 #' @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 prettyDate logical use 'pretty' limits for date axis if TRUE, or force the yearStart/yearEnd 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
 #' @export
@@ -35,20 +35,20 @@
 #' eList <- Choptank_eList
 #' # Water year:
 #' plotConcTimeDaily(eList)
-#' plotConcTimeDaily(eList, startYear=1998,endYear=2001)
+#' plotConcTimeDaily(eList, yearStart=1998,yearEnd=2001)
 #' # Graphs consisting of Jun-Aug
 #' eList <- setPA(eList, paStart=6,paLong=3)
 #' plotConcTimeDaily(eList)
-plotConcTimeDaily<-function(eList, startYear=NA, endYear=NA, tinyPlot = FALSE, 
+plotConcTimeDaily<-function(eList, yearStart=NA, yearEnd=NA, tinyPlot = 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)
   localSample <- getSample(eList)
   localDaily <- getDaily(eList)
 
-  startYear <- if (is.na(startYear)) as.integer(min(localSample$DecYear,na.rm=TRUE)) else startYear
-  endYear <- if (is.na(endYear)) as.integer(max(localSample$DecYear,na.rm=TRUE)) else endYear
+  yearStart <- if (is.na(yearStart)) as.integer(min(localSample$DecYear,na.rm=TRUE)) else yearStart
+  yearEnd <- if (is.na(yearEnd)) as.integer(max(localSample$DecYear,na.rm=TRUE)) else yearEnd
 
   if(sum(c("paStart","paLong") %in% names(localINFO)) == 2){
     paLong <- localINFO$paLong
@@ -63,8 +63,8 @@ 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,]
+  subSample<-localSample[localSample$DecYear>=yearStart & localSample$DecYear<= yearEnd,]
+  subDaily<-localDaily[localDaily$DecYear>=yearStart & localDaily$DecYear <= yearEnd,]
 
   xSample<-subSample$DecYear
   xDaily<-subDaily$DecYear
@@ -77,7 +77,7 @@ plotConcTimeDaily<-function(eList, startYear=NA, endYear=NA, tinyPlot = FALSE,
 
   yBottom <- 0 #Not specified within script, added under assumption that it's always zero based on ylim definition in this function
 
-  xInfo <- generalAxis(x=xSample, minVal=startYear, maxVal=endYear, tinyPlot=tinyPlot,padPercent=0,prettyDate=prettyDate)  
+  xInfo <- generalAxis(x=xSample, minVal=yearStart, maxVal=yearEnd, tinyPlot=tinyPlot,padPercent=0,prettyDate=prettyDate)  
 
   if(!randomCensored){
 
@@ -99,7 +99,7 @@ plotConcTimeDaily<-function(eList, startYear=NA, endYear=NA, tinyPlot = FALSE,
     if(!("rObserved" %in% names(localSample))){
       eList <- makeAugmentedSample(eList)
       localSample <- eList$Sample
-      subSample<-localSample[localSample$DecYear>=startYear & localSample$DecYear<= endYear,]
+      subSample<-localSample[localSample$DecYear>=yearStart & localSample$DecYear<= yearEnd,]
     }
 
     yHigh <- subSample$rObserved

R/plotFluxTimeDaily.R

@@ -11,8 +11,8 @@
 #' and an INFO dataframe with metadata. 
 #'
 #' @param eList named list with at least the Daily, Sample, and INFO dataframes
-#' @param startYear numeric specifying the starting date (expressed as decimal years, for example 1989.0) for the plot
-#' @param endYear numeric specifiying the ending date for the plot 
+#' @param yearStart numeric specifying the starting date (expressed as decimal years, for example 1989.0) for the plot
+#' @param yearEnd numeric specifiying the ending date for the plot 
 #' @param tinyPlot logical variable, if TRUE plot is designed to be short and wide, default is FALSE.
 #' @param fluxUnit number representing in pre-defined fluxUnit class array. \code{\link{printFluxUnitCheatSheet}}
 #' @param fluxMax number specifying the maximum value to be used on the vertical axis, default is NA (which allows it to be set automatically by the data)
@@ -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 prettyDate logical use 'pretty' limits for date axis if TRUE, or force the startYear/endYear as limits if FALSE
+#' @param prettyDate logical use 'pretty' limits for date axis if TRUE, or force the yearStart/yearEnd as limits if FALSE
 #' @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)
 #' plotFluxTimeDaily(eList)
-plotFluxTimeDaily<-function (eList, startYear=NA, endYear=NA, 
+plotFluxTimeDaily<-function (eList, yearStart=NA, yearEnd=NA, 
                              tinyPlot = FALSE, fluxUnit = 3, fluxMax = NA, 
                              printTitle = TRUE, cex=0.8, cex.axis=1.1,cex.main=1.1, 
                              customPar=FALSE,col="black",lwd=1,prettyDate=TRUE,...) {
@@ -82,12 +82,12 @@ plotFluxTimeDaily<-function (eList, startYear=NA, endYear=NA,
 
   fluxFactor <- fluxUnit@unitFactor*86.40
 
-  startYear <- if (is.na(startYear)) as.integer(min(localSample$DecYear,na.rm=TRUE)) else startYear
-  endYear <- if (is.na(endYear)) as.integer(max(localSample$DecYear,na.rm=TRUE)) else endYear
+  yearStart <- if (is.na(yearStart)) as.integer(min(localSample$DecYear,na.rm=TRUE)) else yearStart
+  yearEnd <- if (is.na(yearEnd)) as.integer(max(localSample$DecYear,na.rm=TRUE)) else yearEnd
 
-  subSample <- localSample[localSample$DecYear >= startYear & localSample$DecYear <= endYear,]
+  subSample <- localSample[localSample$DecYear >= yearStart & localSample$DecYear <= yearEnd,]
 
-  subDaily <- localDaily[localDaily$DecYear >= startYear & localDaily$DecYear <= endYear,]
+  subDaily <- localDaily[localDaily$DecYear >= yearStart & localDaily$DecYear <= yearEnd,]
 
   xSample <- subSample$DecYear
   xDaily <- subDaily$DecYear
@@ -107,7 +107,7 @@ plotFluxTimeDaily<-function (eList, startYear=NA, endYear=NA,
 
   yBottom <- 0
 
-  xInfo <- generalAxis(x=xSample, minVal=startYear, maxVal=endYear, 
+  xInfo <- generalAxis(x=xSample, minVal=yearStart, maxVal=yearEnd, 
                        tinyPlot=tinyPlot,padPercent=0,prettyDate=prettyDate)
 
   yCombined <- c(yHigh,subDaily$ConcDay*subDaily$Q*fluxFactor)

R/plotQTimeDaily.R

@@ -10,8 +10,8 @@
 #' and an INFO dataframe with metadata.
 #'
 #' @param eList named list with at least the Daily and INFO dataframes
-#' @param startYear numeric indicating the starting year for the graph
-#' @param endYear numeric indicating the ending year for the graph (should be a time in decimal years that is after the last observations to be plotted)
+#' @param yearStart numeric indicating the starting year for the graph
+#' @param yearEnd numeric indicating the ending year for the graph (should be a time in decimal years that is after the last observations to be plotted)
 #' @param qLower numeric specifying the lower bound on discharges that are to be plotted, must be in the units specified by qUnit, default is NA (lower bound is zero)
 #' @param qUnit object of qUnit class. \code{\link{printqUnitCheatSheet}}, or numeric represented the short code, or character representing the descriptive name.  Default is qUnit=1 (cubic feet per second)
 #' @param tinyPlot logical variable, if TRUE plot is designed to be short and wide, default is FALSE.
@@ -23,7 +23,7 @@
 #' @param customPar logical defaults to FALSE. If TRUE, par() should be set by user before calling this function 
 #' (for example, adjusting margins with par(mar=c(5,5,5,5))). If customPar FALSE, EGRET chooses the best margins depending on tinyPlot.
 #' @param logScale logical whether or not to use a log scale in the y axis. Default is FALSE.
-#' @param prettyDate logical use 'pretty' limits for date axis if TRUE, or force the startYear/endYear as limits if FALSE
+#' @param prettyDate logical use 'pretty' limits for date axis if TRUE, or force the yearStart/yearEnd as limits if FALSE
 #' @param \dots arbitrary graphical parameters that will be passed to genericEGRETDotPlot function (see ?par for options)
 #' @keywords graphics streamflow
 #' @export
@@ -32,12 +32,12 @@
 #' eList <- Choptank_eList
 #' # Water year:
 #' plotQTimeDaily(eList)
-#' plotQTimeDaily(eList, startYear=1990, endYear=2000,qLower=1500)
+#' plotQTimeDaily(eList, yearStart=1990, yearEnd=2000,qLower=1500)
 #' plotQTimeDaily(eList, prettyDate=FALSE)
 #' # Graphs consisting of Jun-Aug
 #' eList <- setPA(eList, paStart=6,paLong=3)
 #' plotQTimeDaily(eList)
-plotQTimeDaily<-function (eList, startYear=NA, endYear=NA, qLower = NA, qUnit = 1, logScale=FALSE,
+plotQTimeDaily<-function (eList, yearStart=NA, yearEnd=NA, qLower = NA, qUnit = 1, logScale=FALSE,
                           tinyPlot = FALSE, printTitle = TRUE, lwd = 3, col="red", 
                           cex.main = 1.2, cex.lab = 1.2, customPar=FALSE,prettyDate=TRUE,...){
 
@@ -76,10 +76,10 @@ plotQTimeDaily<-function (eList, startYear=NA, endYear=NA, qLower = NA, qUnit =
     yLab <- qUnit@qUnitExpress
   }
 
-  startYear <- if (is.na(startYear)) as.integer(min(localDaily$DecYear,na.rm=TRUE)) else startYear
-  endYear <- if (is.na(endYear)) as.integer(max(localDaily$DecYear,na.rm=TRUE)) else endYear
+  yearStart <- if (is.na(yearStart)) as.integer(min(localDaily$DecYear,na.rm=TRUE)) else yearStart
+  yearEnd <- if (is.na(yearEnd)) as.integer(max(localDaily$DecYear,na.rm=TRUE)) else yearEnd
 
-  subDaily <- localDaily[localDaily$DecYear >= startYear & localDaily$DecYear <= endYear,]
+  subDaily <- localDaily[localDaily$DecYear >= yearStart & localDaily$DecYear <= yearEnd,]
 
   xDaily <- subDaily$DecYear
 
@@ -101,7 +101,7 @@ plotQTimeDaily<-function (eList, startYear=NA, endYear=NA, qLower = NA, qUnit =
     logText <- ""
   }
 
-  xInfo <- generalAxis(x=xDaily, minVal=startYear, maxVal=endYear, 
+  xInfo <- generalAxis(x=xDaily, minVal=yearStart, maxVal=yearEnd, 
                        tinyPlot=tinyPlot, units=localINFO$param.units, prettyDate=prettyDate)
   yInfo <- generalAxis(x=yDaily, minVal=qLower, maxVal=1.05*max(yDaily), 
                        tinyPlot=tinyPlot,padPercent=0,logScale=logScale, units=localINFO$param.units)

inst/doc/rResid.Rmd

@@ -1,7 +1,7 @@
 ---
 title: "Using Random Residuals for Censored Data in EGRET"
 author: "Robert M. Hirsch and Laura A. De Cicco"
-date: "`r format(Sys.time(), '%d %B, %Y')`"
+date: "2016-07-15"
 output: 
   rmarkdown::html_vignette:
     toc: true