Exploration and Graphics for RivEr Trends

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Documentation for package ‘EGRET’ version 3.0.9

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A B C D E F G I J L M N P Q R S T W Y

EGRET-package EGRET package includes WRTDS and flowHistory

-- A --

Arkansas_eList Example eList
as.egret Create named list for EGRET analysis

-- B --

bin_Qs Estimates all daily values of Concentration, Flux, Flow-Normalized Concentration, and Flow Normalized Flux
blankTime Deletes the computed values during periods of time when there are no sample data
boxConcMonth Box plot of the water quality data by month
boxConcThree Three box plots side-by-side
boxQTwice Two box plots side-by-side, discharge on sample days, and discharge on all days
boxResidMonth A box plot of WRTDS residuals by month

-- C --

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.
censoredSegments Generic plotting function to create censored line segments
checkStartEndDate checkStartEndDate
checkSurfaceSpan checkSurfaceSpan
Choptank_eList Example eList
cleanUp cleanUp eList
compressData Compress sample data frame
concConst Constants included with EGRET
concUnit-class concUnit class
Constants Constants included with EGRET
cumQdate Cumulative flow calculation

-- D --

dataOverview Data Overview for WRTDS
dateFormatCheck Check date format
decimalDate decimalDate
decimalHighLow decimalHighLow

-- E --

errorStats Error statistics
estCrossVal Jack-Knife cross validation of the WRTDS (Weighted Regressions on Time, Discharge, and Season)
estDailyFromSurfaces Estimates all daily values of Concentration, Flux, Flow-Normalized 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 three-dimensional object called surfaces

-- F --

fixSampleFrame Update Sample dataframe
flexFN Flexible Flow Normalization
flexPlotAddOn Flexible Flow Normalization Plot Add On
flowDuration Computes several values of the flow duration curve for streamflow centered on a specific date of the year
fluxBiasMulti Produces 8-panel plot that is useful for determining if there is a flux bias problem
fluxBiasStat Compute the flux bias statistic: (mean of estimated flux - mean of observed flux) / mean of estimated flux
fluxConst Constants included with EGRET
fluxUnit-class fluxUnit class

-- G --

generalAxis Axis generation for log discharge
genericEGRETDotPlot Generic EGRET plotting function
getConcFluxFromSurface Estimates all daily values of Concentration, Flux, Flow-Normalized Concentration, and Flow Normalized Flux
getDaily Get Daily dataframe from EGRET object
getDaily.default Get Daily dataframe from EGRET object
getDaily.egret Get Daily dataframe from EGRET object
getInfo Get INFO dataframe from EGRET object
getInfo.default Get INFO dataframe from EGRET object
getInfo.egret Get INFO dataframe from EGRET object
getSample Get Sample dataframe from EGRET object
getSample.default Get Sample dataframe from EGRET object
getSurfaceEstimates Estimates all daily values of Concentration, Flux, Flow-Normalized Concentration, and Flow Normalized Flux
getSurfaces Get surfaces matrix from EGRET object
getSurfaces.default Get surfaces matrix from EGRET object
getSurfaces.egret Get surfaces matrix from EGRET object

-- I --

INFOdataframe Import metadata to create INFO data frame
is.egret Check for EGRET object

-- J --

jitterSam jitter Sample

-- L --

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

-- M --

makeAnnualSeries Produces annual series of 8 streamflow statistics (and a lowess smooth of them) from daily streamflow data
makeAugmentedSample Create randomized residuals and observations for data sets that have some censored data
makeDateInfo makeDateInfo
mergeReport mergeReport
modelEstimation Estimation process for the WRTDS (Weighted Regressions on Time, Discharge, and Season)
monthInfo Constants included with EGRET
monthLabel-class monthLabel class
multiPlotDataOverview Produces a 4 panel plot that gives an overview of the data set prior to any processing

-- N --

nCensoredVals EGRET helper functions
nDischarge EGRET helper functions
nObservations EGRET helper functions

-- P --

plot.egret EGRET helper functions
plot15 Makes 15 graphs of streamflow statistics on a single page. These encompass the 7-day minimum, mean, and 1-day 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
plotConcHist Graph of annual concentration and flow normalized concentration versus year
plotConcPred Plot of Observed Concentration versus Estimated Concentration
plotConcQ Plot of Observed Concentration versus Discharge
plotConcQSmooth Plot up to three curves representing the concentration versus discharge relationship. Each curve is a different point in time.
plotConcTime Plot of Observed Concentration versus Time
plotConcTimeDaily Plot of the time series of daily concentration estimates and the sample values for the days that were sampled
plotConcTimeSmooth Plot up to three curves representing the concentration versus time relationship, each curve representing a different flow.
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
plotFlowSingle Creates a plot of a time series of a particular flow statistic and a loess smooth of that flow statistic
plotFluxHist Graph of annual flux and flow normalized flux versus year
plotFluxPred Graph of observed versus estimated flux
plotFluxQ Sample data plot: observed log flux vs log discharge
plotFluxTimeDaily Plot of the time series of daily flux estimates and the sample values for the days that were sampled
plotFour Makes four graphs of streamflow statistics on a single page
plotFourStats Makes four graphs of annual streamflow statistics on a single page
plotMonthTrend Plot monthly trend result from runPairs
plotQTimeDaily Plot of the discharge time series
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
plotSDLogQ Graph of the standard deviation of the log of daily discharge versus year
plotTimeSlice plotTimeSlice
plotWRTDSKalman plotWRTDSKalman
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
print.egret EGRET helper functions
printFluxUnitCheatSheet Reminder to user of flux unit properties (such as kg/day, tons/year, etc).
printGroups Print information about group analysis
printPairs Print information about pairs analysis
printqUnitCheatSheet Reminder to user of flow Unit properties such as cubic meters per second or thousands of cubic feet per second.
printSeries Print annual results for a given streamflow statistic
processQWData Processing of Water Quality Data

-- Q --

qConst Constants included with EGRET
qUnit-class qUnit class

-- R --

randomSubset randomSubset
readDataFromFile Basic Data Import for Water Flow Data
readNWISDaily Import NWIS Daily Data for EGRET analysis
readNWISInfo Import metadata to create INFO data frame
readNWISSample Import NWIS Sample Data for EGRET analysis
readUserDaily Import user daily data for EGRET analysis
readUserInfo Import metadata to create INFO data frame
readUserSample Import user-supplied sample data for EGRET analysis
readWQPInfo Import metadata to create INFO data frame
readWQPSample Import Sample Data from the Water Quality Portal for WRTDS
removeDuplicates Remove duplicates values from Sample data frame.
runGroups Runs a comparison of any group of years in the record.
runPairs Runs a comparison of any two years in the record.
runSeries Annual series of flow-normalized concentration and flow-normalized flux
runSurvReg Run the weighted survival regression for a set of estimation points (defined by DecYear and Log(Q))
run_WRTDS Run the weighted survival regression for a set of estimation points (defined by DecYear and Log(Q))

-- S --

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.
selectDays Creates a subset Daily data frame that only contains daily estimates for the specified period of analysis
setPA Sets up the period of analysis (the portion of the year being evaluated).
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
setUpEstimation setUpEstimation
setupYears Creates the AnnualResults data frame from the Daily data frame
startEnd startEnd
stitch stitch surfaces
surfaceIndex Compute the 6 parameters needed to lay out the grid for the surfaces computed in estSurfaces
surfaceStartEnd Surface date limits

-- T --

tableChange Create a table of the changes in flow-normalized values between various points in time in the record
tableChangeSingle Create a table of the changes in flow-normalized 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
triCube Tricube weight function

-- W --

WRTDSKalman WRTDS-Kalman

-- Y --

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