Package index

readUserDaily()
 Import user daily data for EGRET analysis

readUserSample()
 Import usersupplied sample data for EGRET analysis

readNWISDaily()
 Import NWIS Daily Data for EGRET analysis

readNWISSample()
 Import NWIS Sample Data for EGRET analysis

readWQPSample()
 Import Sample Data from the Water Quality Portal for WRTDS

readNWISInfo()
readWQPInfo()
readUserInfo()
 Import metadata to create INFO data frame

modelEstimation()
 Estimation process for the WRTDS (Weighted Regressions on Time, Discharge, and Season)

setUpEstimation()
 setUpEstimation

WRTDSKalman()
 WRTDSKalman

runPairs()
 Runs a comparison of any two years in the record.

runGroups()
 Runs a comparison of any group of years in the record.

runSeries()
 Annual series of flownormalized concentration and flownormalized flux

runSurvReg()
run_WRTDS()
 Run the weighted survival regression for a set of estimation points (defined by DecYear and Log(Q))

estCrossVal()
 JackKnife cross validation of the WRTDS (Weighted Regressions on Time, Discharge, and Season)

estDailyFromSurfaces()
getConcFluxFromSurface()
getSurfaceEstimates()
bin_Qs()
 Estimates all daily values of Concentration, Flux, FlowNormalized Concentration, and Flow Normalized Flux

estSurfaces()
 Estimate the three surfaces (for yHat, SE and ConcHat) as a function of DecYear and logQ and store in the threedimensional object called surfaces

flexFN()
 Flexible Flow Normalization

multiPlotDataOverview()
 Produces a 4 panel plot that gives an overview of the data set prior to any processing

plotFlowSingle()
 Creates a plot of a time series of a particular flow statistic and a loess smooth of that flow statistic

plotFluxQ()
 Sample data plot: observed log flux vs log discharge

plotFour()
 Makes four graphs of streamflow statistics on a single page

plotFourStats()
 Makes four graphs of annual streamflow statistics on a single page

plotQTimeDaily()
 Plot of the discharge time series

plotSDLogQ()
 Graph of the standard deviation of the log of daily discharge versus year

boxConcMonth()
 Box plot of the water quality data by month

boxQTwice()
 Two box plots sidebyside, discharge on sample days, and discharge on all days

plotConcTime()
 Plot of Observed Concentration versus Time

plotConcQ()
 Plot of Observed Concentration versus Discharge

boxConcThree()
 Three box plots sidebyside

plot15()
 Makes 15 graphs of streamflow statistics on a single page. These encompass the 7day minimum, mean, and 1day maximum for each of the following 5 Periods of Analysis: Annual, Fall, Winter, Spring and Summer.

plot1of15()
 plots 1 of the 15 graphs of streamflow statistics on a single page

plotConcPred()
 Plot of Observed Concentration versus Estimated Concentration

plotFluxPred()
 Graph of observed versus estimated flux

plotResidPred()
 Plot of the residuals from WRTDS versus the estimated values (all in log concentration units)

plotResidQ()
 Plot of the residuals from WRTDS (in log concentration units) versus the discharge

plotResidTime()
 Plot of the residuals from WRTDS (in log concentration units) versus time

boxResidMonth()
 A box plot of WRTDS residuals by month

plotConcHist()
 Graph of annual concentration and flow normalized concentration versus year

plotFluxHist()
 Graph of annual flux and flow normalized flux versus year

plotFluxTimeDaily()
 Plot of the time series of daily flux estimates and the sample values for the days that were sampled

plotConcTimeDaily()
 Plot of the time series of daily concentration estimates and the sample values for the days that were sampled

plotConcQSmooth()
 Plot up to three curves representing the concentration versus discharge relationship. Each curve is a different point in time.

plotConcTimeSmooth()
 Plot up to three curves representing the concentration versus time relationship, each curve representing a different flow.

fluxBiasMulti()
 Produces 8panel plot that is useful for determining if there is a flux bias problem

plotContours()
 Color contour plot of the estimated surfaces as a function of discharge and time (surfaces include log concentration, standard error, and concentration)

plotDiffContours()
 Plots the difference between two years from a contour plot created by plotContours

plotWRTDSKalman()
 plotWRTDSKalman

plotTimeSlice()
 plotTimeSlice

plotMonthTrend()
 Plot monthly trend result from runPairs

flexPlotAddOn()
 Flexible Flow Normalization Plot Add On

genericEGRETDotPlot()
 Generic EGRET plotting function

generalAxis()
 Axis generation for log discharge

logPretty1()
 Sets up tick marks for an axis with a log scale, where the graph is small

logPretty3()
 Sets up tick marks for an axis with a log scale

printSeries()
 Print annual results for a given streamflow statistic

makeAnnualSeries()
 Produces annual series of 8 streamflow statistics (and a lowess smooth of them) from daily streamflow data

tableChange()
tableChangeSingle()
 Create a table of the changes in flownormalized values between various points in time in the record

tableFlowChange()
 Prints table of change metrics for a given streamflow statistic

tableResults()
 Table of annual results for discharge, concentration and flux

setupYears()
 Creates the AnnualResults data frame from the Daily data frame

calculateMonthlyResults()
 Calculates monthly mean values of Q, Conc, FNConc, Flux, and FNFlux for the entire record. If WRTDSKalman has been run it also includes the monthly mean values of GenConc and GenFlux.

blankTime()
 Deletes the computed values during periods of time when there are no sample data

cleanUp()
 cleanUp eList

compressData()
 Compress sample data frame

cumQdate()
 Cumulative flow calculation

dataOverview()
 Data Overview for WRTDS

decimalDate()
 decimalDate

errorStats()
 Error statistics

fixSampleFrame()
 Update Sample dataframe

flowDuration()
 Computes several values of the flow duration curve for streamflow centered on a specific date of the year

fluxBiasStat()
 Compute the flux bias statistic: (mean of estimated flux  mean of observed flux) / mean of estimated flux

printPairs()
 Print information about pairs analysis

printGroups()
 Print information about group analysis

getDaily()
 Get Daily dataframe from EGRET object

getInfo()
 Get INFO dataframe from EGRET object

getSample()
getSample.default()
 Get Sample dataframe from EGRET object

getSurfaces()
 Get surfaces matrix from EGRET object

jitterSam()
 jitter Sample

makeAugmentedSample()
 Create randomized residuals and observations for data sets that have some censored data

mergeReport()
 mergeReport

print(<egret>)
plot(<egret>)
nDischarge()
nObservations()
nCensoredVals()
 EGRET helper functions

printFluxUnitCheatSheet()
 Reminder to user of flux unit properties (such as kg/day, tons/year, etc).

printqUnitCheatSheet()
 Reminder to user of flow Unit properties such as cubic meters per second or thousands of cubic feet per second.

processQWData()
 Processing of Water Quality Data

randomSubset()
 randomSubset

removeDuplicates()
 Remove duplicates values from Sample data frame.

saveResults()
 A utility program for saving the contents of the workspace This function saves the workspace. Future versions of EGRET will not include this function, use saveRDS to save individual eList objects. It assigns the file a name using the abbreviations for station and constituent.

setPA()
 Sets up the period of analysis (the portion of the year being evaluated).

stitch()
 stitch surfaces

triCube()
 Tricube weight function

censoredSegments()
 Generic plotting function to create censored line segments

checkStartEndDate()
 checkStartEndDate

checkSurfaceSpan()
 checkSurfaceSpan

dateFormatCheck()
 Check date format

decimalHighLow()
 decimalHighLow

makeDateInfo()
 makeDateInfo

populateConcentrations()
 Populate Concentration Columns

populateDaily()
 Populate Daily data frame

populateDailySamp()
 Merge concentration to Daily

populateDateColumns()
 Populate Date Columns

populateParameterINFO()
 Populate Parameter Information Columns

populateSampleColumns()
 Populate Sample Columns

populateSiteINFO()
 Populate Site Information Columns

qUnitclass
 qUnit class

concUnitclass
 concUnit class

readDataFromFile()
 Basic Data Import for Water Flow Data

Choptank_eList
Arkansas_eList
 Example eList

selectDays()
 Creates a subset Daily data frame that only contains daily estimates for the specified period of analysis

setSeasonLabel()
 Create a character variable that describes the period of analysis, when period of analysis has already been set in AnnualResults

setSeasonLabelByUser()
 Creates a character variable that describes the period of analysis, when the period of analysis is being set by the user and not from AnnualResults

startEnd()
 startEnd

surfaceIndex()
 Compute the 6 parameters needed to lay out the grid for the surfaces computed in estSurfaces

surfaceStartEnd()
 Surface date limits

yPretty()
 Sets up tick marks for an axis for a graph with an arithmetic scale which starts at zero

monthLabelclass
 monthLabel class

is.egret()
 Check for EGRET object

as.egret()
 Create named list for EGRET analysis

EGRET
EGRETpackage
 EGRET package includes WRTDS and flowHistory

fluxUnitclass
 fluxUnit class