EGRETExploration 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
EGRETNote: 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.
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."
