From 17822a2fc679578af8f82a1aaafef93bc926699f Mon Sep 17 00:00:00 2001 From: Laura DeCicco Date: Thu, 14 Jul 2016 14:01:30 -0500 Subject: [PATCH 1/3] Starting to think about start/end dates --- R/plotConcTime.R | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/R/plotConcTime.R b/R/plotConcTime.R index 18435363..a3fa2c38 100644 --- a/R/plotConcTime.R +++ b/R/plotConcTime.R @@ -43,7 +43,7 @@ #' 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, startYear = NA, endYear = 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,...){ @@ -108,13 +108,17 @@ plotConcTime<-function(eList, qUnit = 2, plotTitle<-if(printTitle) paste(localINFO$shortName,"\n",localINFO$paramShortName,"\n",title3,sep="") else "" + if(is.na(startYear)){ + + } + if(!randomCensored){ subSample<-subSample[subSample$Q>qLowerBound & subSample$Q Date: Fri, 15 Jul 2016 10:08:29 -0500 Subject: [PATCH 2/3] Unified start/end arguments --- DESCRIPTION | 4 ++-- NEWS | 4 ++++ R/generalAxis.R | 2 +- R/plotConcTime.R | 20 ++++++++++++-------- R/plotConcTimeDaily.R | 22 +++++++++++----------- R/plotFluxTimeDaily.R | 18 +++++++++--------- R/plotQTimeDaily.R | 18 +++++++++--------- man/generalAxis.Rd | 2 +- man/plotConcTime.Rd | 13 +++++++++---- man/plotConcTimeDaily.Rd | 10 +++++----- man/plotFluxTimeDaily.Rd | 8 ++++---- man/plotQTimeDaily.Rd | 10 +++++----- 12 files changed, 72 insertions(+), 59 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index bd451123..176a9f29 100644 --- a/DESCRIPTION +++ b/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 = "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: 2016-06-21 +Date: 2016-07-15 Depends: R (>= 3.0) Imports: diff --git a/NEWS b/NEWS index 0a90ee4d..c2ab2527 100644 --- a/NEWS +++ b/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 diff --git a/R/generalAxis.R b/R/generalAxis.R index 3e69bcbd..bbb413ea 100644 --- a/R/generalAxis.R +++ b/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 diff --git a/R/plotConcTime.R b/R/plotConcTime.R index a3fa2c38..870f4fb8 100644 --- a/R/plotConcTime.R +++ b/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, startYear = NA, endYear = NA, +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,...){ @@ -107,18 +109,16 @@ plotConcTime<-function(eList, qUnit = 2, startYear = NA, endYear = NA, plotTitle<-if(printTitle) paste(localINFO$shortName,"\n",localINFO$paramShortName,"\n",title3,sep="") else "" - - if(is.na(startYear)){ - - } - if(!randomCensored){ subSample<-subSample[subSample$Q>qLowerBound & subSample$Q=startYear & localSample$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 diff --git a/R/plotFluxTimeDaily.R b/R/plotFluxTimeDaily.R index ab6575ae..31769919 100644 --- a/R/plotFluxTimeDaily.R +++ b/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) diff --git a/R/plotQTimeDaily.R b/R/plotQTimeDaily.R index 044eb2bc..34ab07dc 100644 --- a/R/plotQTimeDaily.R +++ b/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) diff --git a/man/generalAxis.Rd b/man/generalAxis.Rd index 25c6a72e..25eca936 100644 --- a/man/generalAxis.Rd +++ b/man/generalAxis.Rd @@ -25,7 +25,7 @@ generalAxis(x, maxVal, minVal, units = NA, logScale = FALSE, \item{concentration}{logical if concentration=TRUE, labels returned as concentration units, otherwise flux units.} -\item{prettyDate}{logical use 'pretty' limits for date axis if TRUE, or force the startYear/endYear as limits if FALSE} +\item{prettyDate}{logical use 'pretty' limits for date axis if TRUE, or force the yearStart/yearEnd as limits if FALSE} } \description{ Discharge axis tick generation diff --git a/man/plotConcTime.Rd b/man/plotConcTime.Rd index 2f181944..454de110 100644 --- a/man/plotConcTime.Rd +++ b/man/plotConcTime.Rd @@ -4,16 +4,21 @@ \alias{plotConcTime} \title{Plot of Observed Concentration versus Time} \usage{ -plotConcTime(eList, qUnit = 2, 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, ...) +plotConcTime(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, ...) } \arguments{ \item{eList}{named list with at least the Sample and INFO dataframes} \item{qUnit}{object of qUnit class \code{\link{printqUnitCheatSheet}}, or numeric represented the short code, or character representing the descriptive name.} +\item{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)} + +\item{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)} + \item{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} \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} diff --git a/man/plotConcTimeDaily.Rd b/man/plotConcTimeDaily.Rd index 3c3ce0f4..e30739a4 100644 --- a/man/plotConcTimeDaily.Rd +++ b/man/plotConcTimeDaily.Rd @@ -4,7 +4,7 @@ \alias{plotConcTimeDaily} \title{Plot of the time series of daily concentration estimates and the sample values for the days that were sampled} \usage{ -plotConcTimeDaily(eList, startYear = NA, endYear = NA, tinyPlot = FALSE, +plotConcTimeDaily(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, ...) @@ -12,9 +12,9 @@ plotConcTimeDaily(eList, startYear = NA, endYear = NA, tinyPlot = FALSE, \arguments{ \item{eList}{named list with at least the Daily, Sample, and INFO dataframes} -\item{startYear}{numeric specifying the starting date (expressed as decimal years, for example 1989.0) for the plot} +\item{yearStart}{numeric specifying the starting date (expressed as decimal years, for example 1989.0) for the plot} -\item{endYear}{numeric specifiying the ending date for the plot} +\item{yearEnd}{numeric specifiying the ending date for the plot} \item{tinyPlot}{logical variable, if TRUE plot is designed to be short and wide, default is FALSE.} @@ -37,7 +37,7 @@ plotConcTimeDaily(eList, startYear = NA, endYear = NA, tinyPlot = FALSE, \item{lwd}{number line width} -\item{prettyDate}{logical use 'pretty' limits for date axis if TRUE, or force the startYear/endYear as limits if FALSE} +\item{prettyDate}{logical use 'pretty' limits for date axis if TRUE, or force the yearStart/yearEnd as limits if FALSE} \item{\dots}{arbitrary functions sent to the generic plotting function. See ?par for details on possible parameters} } @@ -57,7 +57,7 @@ and an INFO dataframe with metadata. 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) diff --git a/man/plotFluxTimeDaily.Rd b/man/plotFluxTimeDaily.Rd index 79db28b3..72ba173d 100644 --- a/man/plotFluxTimeDaily.Rd +++ b/man/plotFluxTimeDaily.Rd @@ -4,7 +4,7 @@ \alias{plotFluxTimeDaily} \title{Plot of the time series of daily flux estimates and the sample values for the days that were sampled} \usage{ -plotFluxTimeDaily(eList, startYear = NA, endYear = NA, tinyPlot = FALSE, +plotFluxTimeDaily(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, ...) @@ -12,9 +12,9 @@ plotFluxTimeDaily(eList, startYear = NA, endYear = NA, tinyPlot = FALSE, \arguments{ \item{eList}{named list with at least the Daily, Sample, and INFO dataframes} -\item{startYear}{numeric specifying the starting date (expressed as decimal years, for example 1989.0) for the plot} +\item{yearStart}{numeric specifying the starting date (expressed as decimal years, for example 1989.0) for the plot} -\item{endYear}{numeric specifiying the ending date for the plot} +\item{yearEnd}{numeric specifiying the ending date for the plot} \item{tinyPlot}{logical variable, if TRUE plot is designed to be short and wide, default is FALSE.} @@ -37,7 +37,7 @@ plotFluxTimeDaily(eList, startYear = NA, endYear = NA, tinyPlot = FALSE, \item{lwd}{number line width} -\item{prettyDate}{logical use 'pretty' limits for date axis if TRUE, or force the startYear/endYear as limits if FALSE} +\item{prettyDate}{logical use 'pretty' limits for date axis if TRUE, or force the yearStart/yearEnd as limits if FALSE} \item{\dots}{arbitrary graphical parameters that will be passed to genericEGRETDotPlot function (see ?par for options)} } diff --git a/man/plotQTimeDaily.Rd b/man/plotQTimeDaily.Rd index 03199d30..a722b0b4 100644 --- a/man/plotQTimeDaily.Rd +++ b/man/plotQTimeDaily.Rd @@ -4,7 +4,7 @@ \alias{plotQTimeDaily} \title{Plot of the discharge time series} \usage{ -plotQTimeDaily(eList, startYear = NA, endYear = NA, qLower = NA, +plotQTimeDaily(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, ...) @@ -12,9 +12,9 @@ plotQTimeDaily(eList, startYear = NA, endYear = NA, qLower = NA, \arguments{ \item{eList}{named list with at least the Daily and INFO dataframes} -\item{startYear}{numeric indicating the starting year for the graph} +\item{yearStart}{numeric indicating the starting year for the graph} -\item{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)} +\item{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)} \item{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)} @@ -37,7 +37,7 @@ plotQTimeDaily(eList, startYear = NA, endYear = NA, qLower = NA, \item{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.} -\item{prettyDate}{logical use 'pretty' limits for date axis if TRUE, or force the startYear/endYear as limits if FALSE} +\item{prettyDate}{logical use 'pretty' limits for date axis if TRUE, or force the yearStart/yearEnd as limits if FALSE} \item{\dots}{arbitrary graphical parameters that will be passed to genericEGRETDotPlot function (see ?par for options)} } @@ -54,7 +54,7 @@ and an INFO dataframe with metadata. 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) From 1ae3475d7c924b51312400fe1d9101941ba7bad4 Mon Sep 17 00:00:00 2001 From: Laura DeCicco Date: Fri, 15 Jul 2016 10:14:55 -0500 Subject: [PATCH 3/3] Vignette updates --- inst/doc/EGRET.pdf | Bin 777435 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@@ -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 diff --git a/inst/doc/rResid.html b/inst/doc/rResid.html index bf7dfba2..107b0aca 100644 --- a/inst/doc/rResid.html +++ b/inst/doc/rResid.html @@ -12,6 +12,7 @@ + Using Random Residuals for Censored Data in EGRET @@ -69,7 +70,7 @@

Using Random Residuals for Censored Data in EGRET

Robert M. Hirsch and Laura A. De Cicco

-

21 June, 2016

+

2016-07-15

@@ -101,11 +102,11 @@

2 The concept of randomized estim

The solid circles are the uncensored observations and the open circles are these rObserved values. One thing to note is that if these values were to be generated a second time the graph would look slightly different. There is no unique set of values that will be plotted. The random numbers used will be different if we go back to the same data set and generate them again. Below we show such a figure and then redo the graphic with a second set of random numbers. The code is shown with the graphics.

eList <- makeAugmentedSample(eList)
 plotConcQ(eList, qUnit = 4, randomCensored = TRUE)
-

+

# now do it all over again
 eList <- makeAugmentedSample(eList)
 plotConcQ(eList, qUnit = 4, randomCensored = TRUE)
-

+

Careful examination of these two figures reveals that the black dots are exactly the same in both, but the open circles are different between the two. In looking at these kinds of plots we are not necessarily looking to see what actually happened on a particular day, but rather to understand the pattern of the relationship between the two variables being plotted.

@@ -114,9 +115,9 @@

3 Randomized residuals

rResid = rObserved - predicted value. All three variables in this equation are in log concentration units.

We can look at our residuals plots in the following manner (using the second set of rObserved values computed above).

plotResidTime(eList, randomCensored = TRUE)
-

+

plotResidQ(eList, qUnit = 4, randomCensored = TRUE)
-

+

4 Details for how to include random residuals in your computations

@@ -130,9 +131,9 @@

4 Details for how to include rand

For example.

multiPlotDataOverview(eList, qUnit = 4, randomCensored = TRUE)
-

+

fluxBiasMulti(eList, qUnit = 4, fluxUnit = 9, randomCensored = TRUE)
-

+

5 Two final thoughts

diff --git a/vignettes/rResid.Rmd b/vignettes/rResid.Rmd index b158d9e2..7a64350c 100644 --- a/vignettes/rResid.Rmd +++ b/vignettes/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