Exploration and Graphics for RivEr Trends (EGRET)

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


EGRET

Exploration and Graphics for RivEr Trends (EGRET): An R-package for the analysis of long-term changes in water quality and streamflow, including the water-quality method Weighted Regressions on Time, Discharge, and Season (WRTDS).

Please visit the wiki for more information: EGRET Wiki

The link for the official USGS publication user guide is here:

http://pubs.usgs.gov/tm/04/a10/

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To install the EGRET package, you must be using R 3.0 or greater and run the following command:

install.packages("EGRET")

To get inter-CRAN release updates, use the command:

install.packages("EGRET",repos="http://owi.usgs.gov/R")

To get cutting-edge changes, install from GitHub using the devtools packages:

library(devtools)
install_github("USGS-R/EGRET")

Please consider reporting any bugs or asking general questions to the Issues page:

https://github.com/USGS-R/EGRET/issues

Follow @USGS-R on Twitter for updates on all USGS R packages: https://twitter.com/USGS_R

Please email questions, comments, and feedback to: egret_comments@usgs.gov

Additionally, to subscribe to an email list concerning updates to these R packages, please send a request to egret_comments@usgs.gov.

Evaluating long-term changes in river conditions (water quality and discharge) is an important use of hydrologic data. To carry out such evaluations, the hydrologist needs tools to facilitate several key steps in the process: acquiring the data records from a variety of sources, structuring it in ways that facilitate the analysis, routines that will process the data to extract information about changes that may be happening, and graphical techniques that can display findings about change. The R package EGRET (Exploration and Graphics for RivEr Trends) was developed for carrying out each of these steps in an integrated manner. It is designed to accept easily data from three sources: U.S. Geological Survey hydrologic data, Water Quality Portal Data (currently including U.S. Environmental Protection Agency (EPA) STORET data, and USDA STEWARDS data), and user-supplied flat files. The EGRET package has components oriented towards the description of long-term changes in streamflow statistics (high flow, average flow, and low flow) as well as changes in water quality. For the water-quality analysis, it uses Weighted Regressions on Time, Discharge and Season (WRTDS) to describe long-term trends in both concentration and flux. EGRET also creates a wide range of graphical presentations of the water-quality data and of the WRTDS results. The following report serves as a user guide, providing detailed guidance on installation and use of the software, documentation of the analysis methods used, as well as guidance on some of the kinds of questions and approaches that the software can facilitate.

EGRET includes statistics and graphics for streamflow history, water quality trends, and the statistical modeling algorithm Weighted Regressions on Time, Discharge, and Season (WRTDS). Please see the official EGRET User Guide for more information on the EGRET package:

http://dx.doi.org/10.3133/tm4A10

The best ways to learn about the WRTDS approach is to read the User Guide and two journal articles. These articles are available, for free, from the journals in which they were published. The first relates to nitrate and total phosphorus data for 9 rivers draining to Chesapeake Bay. The URL is:

http://onlinelibrary.wiley.com/doi/10.1111/j.1752-1688.2010.00482.x/full.

The second is an application to nitrate data for 8 monitoring sites on the Mississippi River or its major tributaries. The URL is:

http://pubs.acs.org/doi/abs/10.1021/es201221s

Note: As of February 5, 2015 a new version of the user guide has been posted at the URL given above. If you were using previous versions of EGRET you should take a look here to see a list of the major changes in the workflow and some function names.

link

Load data from web services:

    library(EGRET)
    Daily <- readNWISDaily("06934500","00060","1979-10-01","2010-09-30")
    Sample <-readNWISSample("06934500","00631","1970-10-01","2011-09-30")
    INFO <-readNWISInfo("06934500","00631", interactive=FALSE)
 
    eList <-mergeReport(INFO, Daily, Sample)
 

This is a sample workflow for using WRTDS on the Choptank River at Greensboro MD, for Nitrate:

    library(EGRET)
    
    ############################
    # Gather discharge data:
    siteID <- "01491000" #Choptank River at Greensboro, MD
    startDate <- "" #Gets earliest date
    endDate <- "2011-09-30"
    # Gather sample data:
    parameter_cd<-"00631" #5 digit USGS code
    Sample <- readNWISSample(siteID,parameter_cd,startDate,endDate)
    #Gets earliest date from Sample record:
    #This is just one of many ways to assure the Daily record
    #spans the Sample record
    startDate <- min(as.character(Sample$Date)) 
    # Gather discharge data:
    Daily <- readNWISDaily(siteID,"00060",startDate,endDate)
    # Gather site and parameter information:
    
    # Here user must input some values for
    # the default (interactive=TRUE)
    INFO<- readNWISInfo(siteID,parameter_cd)
    INFO$shortName <- "Choptank River at Greensboro, MD"
    
    # Merge discharge with sample data:
    eList <- mergeReport(INFO, Daily, Sample)
    ############################
    
    ############################
    # Check sample data:
    boxConcMonth(eList)
    boxQTwice(eList)
    plotConcTime(eList)
    plotConcQ(eList)
    multiPlotDataOverview(eList)
    ############################
    
    ############################
    # Run WRTDS model:
    eList <- modelEstimation(eList)
    ############################
    
    ############################
    #Check model results:
    
    #eList:
    plotConcTimeDaily(eList)
    plotFluxTimeDaily(eList)
    plotConcPred(eList)
    plotFluxPred(eList)
    plotResidPred(eList)
    plotResidQ(eList)
    plotResidTime(eList)
    boxResidMonth(eList)
    boxConcThree(eList)
    
    #Require Daily + INFO:
    plotConcHist(eList)
    plotFluxHist(eList)
    
    # Multi-line plots:
    date1 <- "2000-09-01"
    date2 <- "2005-09-01"
    date3 <- "2009-09-01"
    qBottom<-100
    qTop<-5000
    plotConcQSmooth(eList, date1, date2, date3, qBottom, qTop, 
                       concMax=2,qUnit=1)
    q1 <- 10
    q2 <- 25
    q3 <- 75
    centerDate <- "07-01"
    yearEnd <- 2009
    yearStart <- 2000
    plotConcTimeSmooth(eList, q1, q2, q3, centerDate, yearStart, yearEnd)
    
    # Multi-plots:
    fluxBiasMulti(eList)
    
    #Contour plots:
    clevel<-seq(0,2,0.5)
    maxDiff<-0.8
    yearStart <- 2000
    yearEnd <- 2010
    
    plotContours(eList, yearStart,yearEnd,qBottom,qTop, 
                 contourLevels = clevel,qUnit=1)
    plotDiffContours(eList, yearStart,yearEnd,
                     qBottom,qTop,maxDiff,qUnit=1)
    # modify this for your own computer file structure
    savePath<-"/Users/rhirsch/Desktop/" 
    saveResults(savePath)

This is a sample workflow for a flowHistory application for the entire record.

    library(EGRET)
    
    # Flow history analysis
    ############################
    # Gather discharge data:
    siteID <- "01491000" #Choptank River at Greensboro, MD
    startDate <- "" # Get earliest date
    endDate <- "" # Get latest date
    Daily <- readNWISDaily(siteID,"00060",startDate,endDate)
    # Gather site and parameter information:
    # Here user must input some values for
    # the default (interactive=TRUE)
    INFO<- readNWISInfo(siteID,"00060")
    INFO$shortName <- "Choptank River at Greensboro, MD"
    eList <- as.egret(INFO, Daily, NA, NA)
    ############################
    
    ############################
    # Check flow history data:
    plotFlowSingle(eList, istat=7,qUnit="thousandCfs")
    plotSDLogQ(eList)
    plotQTimeDaily(eList, qLower=1,qUnit=3)
    plotFour(eList, qUnit=3)
    plotFourStats(eList, qUnit=3)
    ############################
 
    # modify this for your own computer file structure:
    savePath<-"/Users/rhirsch/Desktop/" 
 
    saveResults(savePath, eList)
 

This software is in the public domain because it contains materials that originally came from the U.S. Geological Survey (USGS), an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at http://www.usgs.gov/visual-id/credit_usgs.html#copyright

Although this software program has been used by the USGS, no warranty, expressed or implied, is made by the USGS or the U.S. Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.

This software is provided "AS IS."

News

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

EGRET 2.5.0

  • Added an argument to the concentration and residual plotting functions to randomize the censored values for the plots.
  • Minor bug fixes

EGRET 2.3.1

  • Removed unnecessary disclaimer.

EGRET 2.2.0

  • Minor bug fixes
  • Added kg/year option for flux

EGRET 2.1.4

  • Updated CITATION file

EGRET 2.1.1

  • Exposed sysdata.rda constants
  • Fixed some inconsistancies in readUserInfo function
  • Added prettyDate argument to plotFluxTimeDaily, plotConcTimeDaily, and plotQTimeDaily. This overrides the 'pretty' axis so that the plot starts and ends exactly at the startYear/endYear arguments
  • Added testthat unit tests
  • Added kg/year flux constant

EGRET 2.1.0

  • Updated processQWData to be more inclusive of Water Quality Portal data
  • Moved some lookup files (month labels, flux labels) to sysdata.rda

EGRET 2.0.1

  • Dec. 2, 2014
  • Minor update to account for changes to dataRetrieval
  • Help file updates.

EGRET 2.0.0

  • November 13, 2014
  • Changed workflow so that most functions accept a single argument: eList, which is a named list with the Daily, Sample, and INFO dataframes (and surface matrix if available)

EGRET 1.3.0

  • July 31, 2014
  • Added alternative runSurvReg option, which deals with edge effects of the model.The modified method tends to reduce curvature near the start and end of record.

EGRET 1.2.5

  • March 10, 2014
  • Added period of analysis control to all graphs and tables so they can present outputs by season as well as the full year. The only graph or table functions without this capability are now: plotContours, plotDiffContours, plotConcQSmooth, and plotConcTimeSmooth.
  • Changed the way that period of analysis is now specified: by using the function setPA. It sets paLong and paStart and applies to all subsequent functions until setPA is used again.
  • For plots where time is on the x-axis and the length is 4-years or less, the axis labels now give more date information.
  • Added more flexibility in character sizes, colors, line weights and other features and graphics.
  • Changed default color palette for plotContours and plotDiffContours.
  • Updated vignette.
  • Added setupYears call within most graphic and table functions to generally eliminate the need to create an AnnualResults data frame.
  • Continued to improve documentation.

EGRET 1.2.4

  • September 25, 2013
  • Plotting functions updated to allow users better control.
  • Fixed small leap year bug.
  • Added dataframe returns to table functions.
  • plotLogXXX functions were removed, logScale argument was added to linear plots

EGRET 1.2.3

  • New estDailyFromSurfaces function utilizing "fields" package, written by Jeffrey Chanat. Greatly increases the speed of computations of the daily results. Two additional R packages are needed: fields and spam

  • Improved documentation, especially example functions.

  • runSurvReg modified to include the option of a very wide seasonal window (windowS), which has the effect of eliminating the influence of the seasonal weights.

  • Progress indicators modified to be more informative.

  • Fixed a calculation bug in function plotLogFluxPred.

EGRET 1.2.1

  • Adds four new functions to the flowHistory capability. The four new flow History functions are: plot15 (makes an array of 15 plots for a given site - a matrix of 3 flow statistics (7-day min, mean, and 1-day max) versus 5 periods of analysis (annual, fall, winter, spring, and summer), plotSDLogQ (makes a plot of the running standard deviation of the Log Discharge versus time), plotFour (makes a set of four graphs: 1-day max, mean, 7-day min, and running standard deviation of the logs), and plotQTimeDaily (a way to plot discharge versus time, setup particularly to show flows above some threshold discharge).

  • Bug fix in WRTDS made no changes to calculations, it just prevents a crash in a situation where the user has shortened the length of the daily record.

EGRET 1.1.3

  • A few small bug fixes and cosmetic changes in some graphics, improved saveResults function, and better formatting of help pages for the functions.

EGRET 1.0.0

  • Initial release.

Reference manual

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install.packages("EGRET")

2.6.0 by Laura DeCicco, a year ago


http://pubs.usgs.gov/tm/04/a10/, https://github.com/USGS-R/EGRET/wiki


Browse source code at https://github.com/cran/EGRET


Authors: Robert Hirsch [aut], Laura DeCicco [aut, cre]


Documentation:   PDF Manual  


CC0 license


Imports dataRetrieval, survival, fields, lubridate, methods, utils, graphics, stats, grDevices, truncnorm

Suggests xtable, knitr, rmarkdown, extrafont, testthat, rkt


Imported by EGRETci.


See at CRAN