Package: EGRET 3.0.9

Laura DeCicco

EGRET: Exploration and Graphics for RivEr Trends

Statistics and graphics for streamflow history, water quality trends, and the statistical modeling algorithm: Weighted Regressions on Time, Discharge, and Season (WRTDS).

Authors:Robert Hirsch [aut], Laura DeCicco [aut, cre], Tim Cohn [ctb], David Watkins [ctb], Lindsay Carr [ctb], Jennifer Murphy [aut]

EGRET_3.0.9.tar.gz
EGRET_3.0.9.zip(r-4.5)EGRET_3.0.9.zip(r-4.4)EGRET_3.0.9.zip(r-4.3)
EGRET_3.0.9.tgz(r-4.4-any)EGRET_3.0.9.tgz(r-4.3-any)
EGRET_3.0.9.tar.gz(r-4.5-noble)EGRET_3.0.9.tar.gz(r-4.4-noble)
EGRET_3.0.9.tgz(r-4.4-emscripten)EGRET_3.0.9.tgz(r-4.3-emscripten)
EGRET.pdf |EGRET.html✨
EGRET/json (API)
NEWS

# Install 'EGRET' in R:

install.packages('EGRET', repos = c('https://doi-usgs.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/doi-usgs/egret/issues

Datasets:

Arkansas_eList - Example eList
Choptank_eList - Example eList

On CRAN:

usgs water-quality water-quality-data

127 exports 85 stars 4.95 score 51 dependencies 1 dependents 20 mentions 258 scripts 653 downloads

Last updated 7 months agofrom:2a070f9660. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 05 2024
R-4.5-win	NOTE	Sep 05 2024
R-4.5-linux	NOTE	Sep 05 2024
R-4.4-win	NOTE	Sep 05 2024
R-4.4-mac	NOTE	Sep 05 2024
R-4.3-win	OK	Sep 05 2024
R-4.3-mac	OK	Sep 05 2024

Exports:as.egret bin_Qs blankTime boxConcMonth boxConcThree boxQTwice boxResidMonth calculateMonthlyResults censoredSegments checkStartEndDate checkSurfaceSpan cleanUp compressData concConst cumQdate dataOverview dateFormatCheck decimalDate decimalHighLow errorStats estCrossVal estDailyFromSurfaces estSurfaces fixSampleFrame flexFN flexPlotAddOn flowDuration fluxBiasMulti fluxBiasStat fluxConst generalAxis genericEGRETDotPlot getConcFluxFromSurface getDaily getInfo getSample getSample.default getSurfaceEstimates getSurfaces is.egret jitterSam logPretty1 logPretty3 makeAnnualSeries makeAugmentedSample makeDateInfo mergeReport modelEstimation monthInfo multiPlotDataOverview nCensoredVals nDischarge nObservations plot15 plot1of15 plotConcHist plotConcPred plotConcQ plotConcQSmooth plotConcTime plotConcTimeDaily plotConcTimeSmooth plotContours plotDiffContours plotFlowSingle plotFluxHist plotFluxPred plotFluxQ plotFluxTimeDaily plotFour plotFourStats plotMonthTrend plotQTimeDaily plotResidPred plotResidQ plotResidTime plotSDLogQ plotTimeSlice plotWRTDSKalman populateConcentrations populateDaily populateDailySamp populateDateColumns populateParameterINFO populateSampleColumns populateSiteINFO printFluxUnitCheatSheet printGroups printPairs printqUnitCheatSheet printSeries processQWData qConst randomSubset readDataFromFile readNWISDaily readNWISInfo readNWISSample readUserDaily readUserInfo readUserSample readWQPInfo readWQPSample removeDuplicates run_WRTDS runGroups runPairs runSeries runSurvReg saveResults selectDays setPA setSeasonLabel setSeasonLabelByUser setUpEstimation setupYears startEnd stitch surfaceIndex surfaceStartEnd tableChange tableChangeSingle tableFlowChange tableResults triCube WRTDSKalman yPretty

Dependencies:askpass bit bit64 cli clipr codetools cpp11 crayon curl dataRetrieval dotCall64 fansi fields foreach generics glue hms httr iterators jsonlite lattice lifecycle lubridate magrittr maps MASS Matrix mime openssl pillar pkgconfig prettyunits progress R6 Rcpp readr rlang spam survival sys tibble tidyselect timechange truncnorm tzdb utf8 vctrs viridisLite vroom withr xml2

Custom Axis Labels

Rendered fromunits.Rmdusingknitr::rmarkdownon Sep 05 2024.

Last update: 2023-03-01
Started: 2022-09-12

EGRET Overview and Update

Robert M. Hirsch

Rendered fromOverview.Rmdusingknitr::rmarkdownon Sep 05 2024.

Last update: 2022-12-12
Started: 2021-03-20

Introduction to the EGRET package

Robert M. Hirsch and Laura DeCicco

Rendered fromEGRET.Rmdusingknitr::rmarkdownon Sep 05 2024.

Last update: 2021-10-13
Started: 2019-03-14

Running WRTDS in parallel

Laura A. De Cicco and Robert M. Hirsch

Rendered fromparallel.Rmdusingknitr::rmarkdownon Sep 05 2024.

Last update: 2018-08-07
Started: 2017-07-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
EGRET package includes WRTDS and flowHistory	EGRET-package
Create named list for EGRET analysis	as.egret
Deletes the computed values during periods of time when there are no sample data	blankTime
Box plot of the water quality data by month	boxConcMonth
Three box plots side-by-side	boxConcThree
Two box plots side-by-side, discharge on sample days, and discharge on all days	boxQTwice
A box plot of WRTDS residuals by month	boxResidMonth
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.	calculateMonthlyResults
Generic plotting function to create censored line segments	censoredSegments
checkStartEndDate	checkStartEndDate
checkSurfaceSpan	checkSurfaceSpan
Example eList	Arkansas_eList Choptank_eList
cleanUp eList	cleanUp
Compress sample data frame	compressData
concUnit class	concUnit-class
Constants included with EGRET	concConst Constants fluxConst monthInfo qConst
Cumulative flow calculation	cumQdate
Data Overview for WRTDS	dataOverview
Check date format	dateFormatCheck
decimalDate	decimalDate
decimalHighLow	decimalHighLow
Error statistics	errorStats
Jack-Knife cross validation of the WRTDS (Weighted Regressions on Time, Discharge, and Season)	estCrossVal
Estimates all daily values of Concentration, Flux, Flow-Normalized Concentration, and Flow Normalized Flux	bin_Qs estDailyFromSurfaces getConcFluxFromSurface getSurfaceEstimates
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	estSurfaces
Update Sample dataframe	fixSampleFrame
Flexible Flow Normalization	flexFN
Flexible Flow Normalization Plot Add On	flexPlotAddOn
Computes several values of the flow duration curve for streamflow centered on a specific date of the year	flowDuration
Produces 8-panel plot that is useful for determining if there is a flux bias problem	fluxBiasMulti
Compute the flux bias statistic: (mean of estimated flux - mean of observed flux) / mean of estimated flux	fluxBiasStat
fluxUnit class	fluxUnit-class
Axis generation for log discharge	generalAxis
Generic EGRET plotting function	genericEGRETDotPlot
Get Daily dataframe from EGRET object	getDaily getDaily.default getDaily.egret
Get INFO dataframe from EGRET object	getInfo getInfo.default getInfo.egret
Get Sample dataframe from EGRET object	getSample getSample.default
Get surfaces matrix from EGRET object	getSurfaces getSurfaces.default getSurfaces.egret
Import metadata to create INFO data frame	INFOdataframe readNWISInfo readUserInfo readWQPInfo
Check for EGRET object	is.egret
jitter Sample	jitterSam
Sets up tick marks for an axis with a log scale, where the graph is small	logPretty1
Sets up tick marks for an axis with a log scale	logPretty3
Produces annual series of 8 streamflow statistics (and a lowess smooth of them) from daily streamflow data	makeAnnualSeries
Create randomized residuals and observations for data sets that have some censored data	makeAugmentedSample
makeDateInfo	makeDateInfo
mergeReport	mergeReport
Estimation process for the WRTDS (Weighted Regressions on Time, Discharge, and Season)	modelEstimation
monthLabel class	monthLabel-class
Produces a 4 panel plot that gives an overview of the data set prior to any processing	multiPlotDataOverview
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.	plot15
plots 1 of the 15 graphs of streamflow statistics on a single page	plot1of15
Graph of annual concentration and flow normalized concentration versus year	plotConcHist
Plot of Observed Concentration versus Estimated Concentration	plotConcPred
Plot of Observed Concentration versus Discharge	plotConcQ
Plot up to three curves representing the concentration versus discharge relationship. Each curve is a different point in time.	plotConcQSmooth
Plot of Observed Concentration versus Time	plotConcTime
Plot of the time series of daily concentration estimates and the sample values for the days that were sampled	plotConcTimeDaily
Plot up to three curves representing the concentration versus time relationship, each curve representing a different flow.	plotConcTimeSmooth
Color contour plot of the estimated surfaces as a function of discharge and time (surfaces include log concentration, standard error, and concentration)	plotContours
Plots the difference between two years from a contour plot created by plotContours	plotDiffContours
Creates a plot of a time series of a particular flow statistic and a loess smooth of that flow statistic	plotFlowSingle
Graph of annual flux and flow normalized flux versus year	plotFluxHist
Graph of observed versus estimated flux	plotFluxPred
Sample data plot: observed log flux vs log discharge	plotFluxQ
Plot of the time series of daily flux estimates and the sample values for the days that were sampled	plotFluxTimeDaily
Makes four graphs of streamflow statistics on a single page	plotFour
Makes four graphs of annual streamflow statistics on a single page	plotFourStats
Plot monthly trend result from runPairs	plotMonthTrend
Plot of the discharge time series	plotQTimeDaily
Plot of the residuals from WRTDS versus the estimated values (all in log concentration units)	plotResidPred
Plot of the residuals from WRTDS (in log concentration units) versus the discharge	plotResidQ
Plot of the residuals from WRTDS (in log concentration units) versus time	plotResidTime
Graph of the standard deviation of the log of daily discharge versus year	plotSDLogQ
plotTimeSlice	plotTimeSlice
plotWRTDSKalman	plotWRTDSKalman
Populate Concentration Columns	populateConcentrations
Populate Daily data frame	populateDaily
Merge concentration to Daily	populateDailySamp
Populate Date Columns	populateDateColumns
Populate Parameter Information Columns	populateParameterINFO
Populate Sample Columns	populateSampleColumns
Populate Site Information Columns	populateSiteINFO
EGRET helper functions	nCensoredVals nDischarge nObservations plot.egret print.egret
Reminder to user of flux unit properties (such as kg/day, tons/year, etc).	printFluxUnitCheatSheet
Print information about group analysis	printGroups
Print information about pairs analysis	printPairs
Reminder to user of flow Unit properties such as cubic meters per second or thousands of cubic feet per second.	printqUnitCheatSheet
Print annual results for a given streamflow statistic	printSeries
Processing of Water Quality Data	processQWData
qUnit class	qUnit-class
randomSubset	randomSubset
Basic Data Import for Water Flow Data	readDataFromFile
Import NWIS Daily Data for EGRET analysis	readNWISDaily
Import NWIS Sample Data for EGRET analysis	readNWISSample
Import user daily data for EGRET analysis	readUserDaily
Import user-supplied sample data for EGRET analysis	readUserSample
Import Sample Data from the Water Quality Portal for WRTDS	readWQPSample
Remove duplicates values from Sample data frame.	removeDuplicates
Runs a comparison of any group of years in the record.	runGroups
Runs a comparison of any two years in the record.	runPairs
Annual series of flow-normalized concentration and flow-normalized flux	runSeries
Run the weighted survival regression for a set of estimation points (defined by DecYear and Log(Q))	runSurvReg run_WRTDS
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.	saveResults
Creates a subset Daily data frame that only contains daily estimates for the specified period of analysis	selectDays
Sets up the period of analysis (the portion of the year being evaluated).	setPA
Create a character variable that describes the period of analysis, when period of analysis has already been set in AnnualResults	setSeasonLabel
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	setSeasonLabelByUser
setUpEstimation	setUpEstimation
Creates the AnnualResults data frame from the Daily data frame	setupYears
startEnd	startEnd
stitch surfaces	stitch
Compute the 6 parameters needed to lay out the grid for the surfaces computed in estSurfaces	surfaceIndex
Surface date limits	surfaceStartEnd
Create a table of the changes in flow-normalized values between various points in time in the record	tableChange tableChangeSingle
Prints table of change metrics for a given streamflow statistic	tableFlowChange
Table of annual results for discharge, concentration and flux	tableResults
Tricube weight function	triCube
WRTDS-Kalman	WRTDSKalman
Sets up tick marks for an axis for a graph with an arithmetic scale which starts at zero	yPretty