# Exploration and Graphics for RivEr Trends

## Documentation for package ‘EGRET’ version 3.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

A B C D E F G I L M N P Q R S T 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, Flux, FNConc, and FNFlux for the entire record.
censoredSegments | Generic plotting function to create censored line segments
checkStartEndDate | checkStartEndDate
checkSurfaceSpan | checkSurfaceSpan
Choptank_eList | Example eList
compressData | Compress sample data frame
Constants | Constants included with EGRET

## -- D --

dataOverview | Data Overview for WRTDS
dateFormatCheck | Check date format
decimalDate | Populate Date Columns
decimalHighLow | decimalHighLow

## -- E --

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 observed flux
fluxConst | Constants included with EGRET
fluxUnit-class | fluxUnit class
formatCheckDate | formatCheckDate
formatCheckParameterCd | formatCheckParameterCd

## -- 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

## -- 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
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 lowess 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
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
populateConcentrations | Populate Concentration Columns
populateDaily | Populate Daily data frame
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).
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 --

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-normalzed 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. 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

## -- Y --

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