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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)
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. A pair of tightly linked R packages, called dataRetrieval and EGRET (Exploration and Graphics for RivEr Trends), have been developed for carrying out each of these steps in an integrated manner. They are 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 dataRetrieval package not only serves as a "front end" to the EGRET package, it can also be used to easily download many types of hydrologic data and organize it in ways that facilitate many other hydrologic applications. 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. This report serves as a user guide to these two R packages, 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.
To install the EGRET and dataRetrieval packages you need to be using R 3.0 or greater. Then use the following command:
install.packages(c("dataRetrieval","EGRET"),
repos=c("http://usgs-r.github.com","http://cran.us.r-project.org"),
dependencies=TRUE)
WRTDS is a method of analysis for long-term surface water quality data. It is intended for use with data sets of more than about 200 observations of water quality over a time span of about 20 years or more. There also needs to be a daily time series of streamflow data covering the entire period of the water quality data collection. The method can be used with somewhat smaller data sets, but it will not work with less than 100 water quality observations. The best way to learn about the WRTDS approach and to see examples of its application to multiple large data sets is to read two journal articles. Both 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 second is an application to nitrate data for 8 monitoring sites on the Mississippi River or its major tributaries:
The manual assumes that the user understands the concepts underlying WRTDS. Thus, reading at least the first of these papers is necessary to understanding the manual.
Load data from web services:
library(dataRetrieval)
Daily <- getNWISDaily("06934500","00060","1979-10-01","2010-09-30")
Sample <-getNWISSample("06934500","00631","1970-10-01","2011-09-30")
INFO <-getNWISInfo("06934500","00631", interactive=FALSE)
Sample <-mergeReport(Daily, Sample)
This is a sample workflow for using EGRET on the Choptank River at Greensboro MD, for Nitrate:
library(dataRetrieval)
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 <- getNWISSample(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$Date))
# Gather discharge data:
Daily <- getNWISDaily(siteID,"00060",startDate,endDate)
# Gather site and parameter information:
# Here user must input some values for
# the default (interactive=TRUE)
INFO<- getNWISInfo(siteID,parameter_cd)
INFO$shortName <- "Choptank River at Greensboro, MD"
# Merge discharge with sample data:
Sample <- mergeReport()
############################
############################
# Check sample data:
boxConcMonth()
boxQTwice()
plotConcTime()
plotConcQ()
multiPlotDataOverview()
############################
############################
# Run WRTDS model:
modelEstimation()
############################
############################
#Check model results:
#Require Sample + INFO:
plotConcTimeDaily()
plotFluxTimeDaily()
plotConcPred()
plotFluxPred()
plotResidPred()
plotResidQ()
plotResidTime()
boxResidMonth()
boxConcThree()
#Require Daily + INFO:
plotConcHist()
plotFluxHist()
# Multi-line plots:
date1 <- "2000-09-01"
date2 <- "2005-09-01"
date3 <- "2009-09-01"
qBottom<-100
qTop<-5000
plotConcQSmooth(date1, date2, date3, qBottom, qTop,
concMax=2,qUnit=1)
q1 <- 10
q2 <- 25
q3 <- 75
centerDate <- "07-01"
yearEnd <- 2009
yearStart <- 2000
plotConcTimeSmooth(q1, q2, q3, centerDate, yearStart, yearEnd)
# Multi-plots:
fluxBiasMulti()
#Contour plots:
clevel<-seq(0,2,0.5)
maxDiff<-0.8
yearStart <- 2000
yearEnd <- 2010
plotContours(yearStart,yearEnd,qBottom,qTop,
contourLevels = clevel,qUnit=1)
plotDiffContours(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(dataRetrieval)
library(EGRET)
# Flow history analysis
############################
# Gather discharge data:
siteID <- "01491000" #Choptank River at Greensboro, MD
startDate <- "" # Get earliest date
endDate <- "" # Get latest date
Daily <- getNWISDaily(siteID,"00060",startDate,endDate)
# Gather site and parameter information:
# Here user must input some values for
# the default (interactive=TRUE)
INFO<- getNWISInfo(siteID,"00060")
INFO$shortName <- "Choptank River at Greensboro, MD"
############################
############################
# Check flow history data:
annualSeries <- makeAnnualSeries()
plotFlowSingle(istat=7,qUnit="thousandCfs")
plotSDLogQ()
plotQTimeDaily(qLower=1,qUnit=3)
plotFour(qUnit=3)
plotFourStats(qUnit=3)
############################
# modify this for your own computer file structure:
savePath<-"/Users/rhirsch/Desktop/"
saveResults(savePath)
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.
####EGRET
-
Version 1.2.5 March 14, 2014
- Added period of record control to all graphs and tables (with execption of plotContours, plotDiffContours, plotConcQSmooth, and plotConcTimeSmooth).
- Changed default color palette for contour plots
- Updated vignette.
- Added setupYears call within functions to generally eliminate the need for AnnualResults.
- Updated calculateMonthlyResults to give month, year, and decimal year.
- Continued to improve documentation.
-
Version 1.2.4 July 10, 2013
-
Version 1.2.3 February 21, 2013
-
Version 1.2.1 June 8, 2012
-
Version 1.1.3 April 26, 2012
-
Version 1.0.0 March 16, 2012
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."