Learn R Programming

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).

Look for new and improved documentation here: https://rconnect.usgs.gov/EGRET/

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

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

A companion package EGRETci implements a set of approaches to the analysis of uncertainty associated with WRTDS trend analysis.

If you are familiar with the traditional EGRET workflow, check out the Overview and Updates to see how all the latest updates relate.

Recent introduction to WRTDS and the EGRET package at the 12th National Monitoring Conference April 19, 2021:

New capabilities

Package Installation

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

install.packages("EGRET")

Background:

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:

https://doi.org/10.3133/tm4A10

For a thorough discussion of the generalized flow normalization method implemented in the EGRET enhancements, see the paper: “Tracking changes in nutrient delivery to western Lake Erie: Approaches to compensate for variability and trends in streamflow”:

(https://www.sciencedirect.com/science/article/pii/S0380133018302235).

Sample Workflow

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)
library(EGRET)
# Sample data included in package:
eList <- Choptank_eList

boxConcMonth(eList)

boxQTwice(eList)

plotConcTime(eList)

plotConcQ(eList)

multiPlotDataOverview(eList)

# Run WRTDS model:
eList <- modelEstimation(eList)
#> 
#>  first step running estCrossVal may take about 1 minute
#>  estCrossVal % complete:
#> 0    1   2   3   4   5   6   7   8   9   10  
#> 11   12  13  14  15  16  17  18  19  20  
#> 21   22  23  24  25  26  27  28  29  30  
#> 31   32  33  34  35  36  37  38  39  40  
#> 41   42  43  44  45  46  47  48  49  50  
#> 51   52  53  54  55  56  57  58  59  60  
#> 61   62  63  64  65  66  67  68  69  70  
#> 71   72  73  74  75  76  77  78  79  80  
#> 81   82  83  84  85  86  87  88  89  90  
#> 91   92  93  94  95  96  97  98  99  
#> Next step running  estSurfaces with survival regression:
#> Survival regression (% complete):
#> 0    1   2   3   4   5   6   7   8   9   10  
#> 11   12  13  14  15  16  17  18  19  20  
#> 21   22  23  24  25  26  27  28  29  30  
#> 31   32  33  34  35  36  37  38  39  40  
#> 41   42  43  44  45  46  47  48  49  50  
#> 51   52  53  54  55  56  57  58  59  60  
#> 61   62  63  64  65  66  67  68  69  70  
#> 71   72  73  74  75  76  77  78  79  80  
#> 81   82  83  84  85  86  87  88  89  90  
#> 91   92  93  94  95  96  97  98  99  
#> Survival regression: Done

#eList:
plotConcTimeDaily(eList)
#> plotGenConc = TRUE requires running WRTDSKalman
#>               on eList. Switching to WRTDS concentration.

plotFluxTimeDaily(eList)
#> plotGenFlux = TRUE requires running WRTDSKalman
#>               on eList. Switching to WRTDS concentration.

plotConcPred(eList)

plotFluxPred(eList)

plotResidPred(eList)

plotResidQ(eList)

plotResidTime(eList)

boxResidMonth(eList)

boxConcThree(eList)

plotConcHist(eList)

plotFluxHist(eList)

# Multi-line plots:
date1 <- "1985-09-01"
date2 <- "1997-09-01"
date3 <- "2010-09-01"
qBottom<-0.2
qTop<-10
plotConcQSmooth(eList, date1, date2, date3, qBottom, qTop, 
                   concMax=2,legendTop = 0.85)

q1 <- 2
q2 <- 10
q3 <- 20
centerDate <- "07-01"
yearEnd <- 1980
yearStart <- 2010
plotConcTimeSmooth(eList, q1, q2, q3, centerDate, yearStart, yearEnd, legendTop = 0.55, legendLeft = 1990)

# Multi-plots:
fluxBiasMulti(eList)

#Contour plots:
clevel<-seq(0,2,0.5)
yearStart <- 1980
yearEnd <- 2010

plotContours(eList, yearStart,yearEnd,qBottom=0.5,
             qTop = 20, contourLevels = clevel)


plotDiffContours(eList, year0 = 1990,
                 year1 = 2010,
                 qBottom = 0.5,
                 qTop = 20,
                 maxDiff = 0.6)

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)
#> There are 27501 data points, and 27501 days.
# Gather site and parameter information:
# Here user must input some values for
# the default (interactive=TRUE)
INFO <- readNWISInfo(siteID, "00060")
#> Your site for streamflow data is:
#>  01491000 .
#> Your site name is CHOPTANK RIVER NEAR GREENSBORO, MD 
#> but you can modify this to a short name in a style you prefer. 
#> This name will be used to label graphs and tables. 
#> If you want the program to use the name given above, just do a carriage return,
#> otherwise enter the preferred short name(no quotes):
#> 
#> The latitude and longitude of the site are:  38.99719 ,  -75.78581 (degrees north and west).
#> 
#> The drainage area at this site is  113 square miles
#>  which is being stored as 292.6687 square kilometers.
#> 
#> It is helpful to set up a station abbreviation when doing multi-site studies,
#> enter a unique id (three or four characters should work). It is case sensitive.  
#> Even if you don't feel you need an abbreviation for your site you need to enter something(no quotes):
#> 
#> Your water quality data are for parameter number:
#> 00060 
#> which has the name:' Discharge, cubic feet per second '.
#> Typically you will want a shorter name to be used in graphs and tables.
#> The suggested short name is:' Stream flow, mean. daily '.
#> If you would like to change the short name, enter it here, 
#> otherwise just hit enter (no quotes):
#> The units for the water quality data are:  ft3/s .
#> It is helpful to set up a constiuent abbreviation, enter a unique id 
#> three or four characters should work something like tn or tp or NO3).
#> Even if you don't feel you need an abbreviation you need to enter something (no quotes):
#> 
#> Required concentration units are mg/l. 
#> The INFO dataframe indicates: ft3/s 
#> Flux calculations will be wrong if units are not consistent.
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)

Model Archive

When using the WRTDS model, it is important to be able to reproduce the results in the future. The following version of R and package dependencies were used most recently to pass the embedded tests within this package. There is no guarantee of reproducible results using future versions of R or updated versions of package dependencies; however, we will make diligent efforts to test and update future modeling environments.

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.2.3 (2023-03-15 ucrt)
#>  os       Windows 10 x64 (build 19045)
#>  system   x86_64, mingw32
#>  ui       RTerm
#>  language (EN)
#>  collate  English_United States.utf8
#>  ctype    English_United States.utf8
#>  tz       America/Chicago
#>  date     2023-04-18
#>  pandoc   2.19.2 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package       * version date (UTC) lib source
#>  bit             4.0.5   2022-11-15 [1] CRAN (R 4.2.2)
#>  bit64           4.0.5   2020-08-30 [1] CRAN (R 4.2.2)
#>  class           7.3-21  2023-01-23 [2] CRAN (R 4.2.3)
#>  classInt        0.4-9   2023-02-28 [1] CRAN (R 4.2.2)
#>  cli             3.6.1   2023-03-23 [1] CRAN (R 4.2.3)
#>  colorspace      2.1-0   2023-01-23 [1] CRAN (R 4.2.2)
#>  crayon          1.5.2   2022-09-29 [1] CRAN (R 4.2.1)
#>  curl            5.0.0   2023-01-12 [1] CRAN (R 4.2.2)
#>  dataRetrieval   2.7.12  2023-04-11 [1] Github (DOI-USGS/dataRetrieval@60483d2)
#>  DBI             1.1.3   2022-06-18 [1] CRAN (R 4.2.1)
#>  digest          0.6.31  2022-12-11 [1] CRAN (R 4.2.2)
#>  dotCall64       1.0-2   2022-10-03 [1] CRAN (R 4.2.1)
#>  dplyr           1.1.1   2023-03-22 [1] CRAN (R 4.2.3)
#>  e1071           1.7-13  2023-02-01 [1] CRAN (R 4.2.2)
#>  EGRET         * 3.0.9   2023-04-16 [1] Github (DOI-USGS/EGRET@57fd93f)
#>  evaluate        0.20    2023-01-17 [1] CRAN (R 4.2.2)
#>  fansi           1.0.4   2023-01-22 [1] CRAN (R 4.2.2)
#>  fastmap         1.1.1   2023-02-24 [1] CRAN (R 4.2.2)
#>  fields          14.1    2022-08-12 [1] CRAN (R 4.2.1)
#>  generics        0.1.3   2022-07-05 [1] CRAN (R 4.2.1)
#>  ggplot2         3.4.2   2023-04-03 [1] CRAN (R 4.2.3)
#>  glue            1.6.2   2022-02-24 [1] CRAN (R 4.1.3)
#>  gridExtra       2.3     2017-09-09 [1] CRAN (R 4.2.1)
#>  gtable          0.3.3   2023-03-21 [1] CRAN (R 4.2.3)
#>  highr           0.10    2022-12-22 [1] CRAN (R 4.2.2)
#>  hms             1.1.3   2023-03-21 [1] CRAN (R 4.2.3)
#>  htmltools       0.5.5   2023-03-23 [1] CRAN (R 4.2.3)
#>  httr            1.4.5   2023-02-24 [1] CRAN (R 4.2.2)
#>  KernSmooth      2.23-20 2021-05-03 [2] CRAN (R 4.2.3)
#>  knitr           1.42    2023-01-25 [1] CRAN (R 4.2.2)
#>  lattice         0.20-45 2021-09-22 [2] CRAN (R 4.2.3)
#>  lifecycle       1.0.3   2022-10-07 [1] CRAN (R 4.2.1)
#>  magrittr        2.0.3   2022-03-30 [1] CRAN (R 4.1.3)
#>  maps            3.4.1   2022-10-30 [1] CRAN (R 4.2.2)
#>  Matrix          1.5-4   2023-04-04 [1] CRAN (R 4.2.3)
#>  munsell         0.5.0   2018-06-12 [1] CRAN (R 4.2.1)
#>  pillar          1.9.0   2023-03-22 [1] CRAN (R 4.2.3)
#>  pkgconfig       2.0.3   2019-09-22 [1] CRAN (R 4.2.1)
#>  proxy           0.4-27  2022-06-09 [1] CRAN (R 4.2.1)
#>  R6              2.5.1   2021-08-19 [1] CRAN (R 4.2.1)
#>  Rcpp            1.0.10  2023-01-22 [1] CRAN (R 4.2.2)
#>  readr           2.1.4   2023-02-10 [1] CRAN (R 4.2.2)
#>  rlang           1.1.0   2023-03-14 [1] CRAN (R 4.2.3)
#>  rmarkdown       2.21    2023-03-26 [1] CRAN (R 4.2.3)
#>  rstudioapi      0.14    2022-08-22 [1] CRAN (R 4.2.1)
#>  scales          1.2.1   2022-08-20 [1] CRAN (R 4.2.1)
#>  sessioninfo     1.2.2   2021-12-06 [1] CRAN (R 4.2.1)
#>  sf              1.0-12  2023-03-19 [1] CRAN (R 4.2.3)
#>  spam            2.9-1   2022-08-07 [1] CRAN (R 4.2.1)
#>  survival        3.5-5   2023-03-12 [1] CRAN (R 4.2.3)
#>  tibble          3.2.1   2023-03-20 [1] CRAN (R 4.2.3)
#>  tidyselect      1.2.0   2022-10-10 [1] CRAN (R 4.2.1)
#>  tzdb            0.3.0   2022-03-28 [1] CRAN (R 4.2.1)
#>  units           0.8-1   2022-12-10 [1] CRAN (R 4.2.2)
#>  utf8            1.2.3   2023-01-31 [1] CRAN (R 4.2.2)
#>  vctrs           0.6.1   2023-03-22 [1] CRAN (R 4.2.3)
#>  viridis         0.6.2   2021-10-13 [1] CRAN (R 4.2.1)
#>  viridisLite     0.4.1   2022-08-22 [1] CRAN (R 4.2.1)
#>  vroom           1.6.1   2023-01-22 [1] CRAN (R 4.2.2)
#>  xfun            0.38    2023-03-24 [1] CRAN (R 4.2.3)
#>  yaml            2.3.7   2023-01-23 [1] CRAN (R 4.2.2)
#> 
#>  [1] C:/Users/ldecicco/Documents/R/win-library/4.2
#>  [2] C:/Program Files/R/R-4.2.3/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

Reporting bugs

Please consider reporting bugs and asking questions on the Issues page: https://github.com/DOI-USGS/EGRET/issues

Subscribe

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.

Code of Conduct

We want to encourage a warm, welcoming, and safe environment for contributing to this project. See the code of conduct for more information.

Package Support

The Water Mission Area of the USGS has supported the development and maintenance of the EGRET R-package. Further maintenance is expected to be stable through October 2024. Resources are available primarily for maintenance and responding to user questions. Priorities on the development of new features are determined by the EGRET development team.

Sunset date

Funding for EGRET currently expires fall 2024. Expectations are that maintenance and customer service will continue to be supported past that date.

How to cite EGRET:

citation(package = "EGRET")
#> 
#> To cite EGRET in publications, please use:
#> 
#>   Hirsch, R.M., De Cicco, L.A., Murphy, J., 2023, Exploration and
#>   Graphics for RivEr Trends (EGRET), version 3.0.9,
#>   doi:10.5066/P9CC9JEX
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     author = {Robert Hirsch and Laura DeCicco and Jennifer Murphy},
#>     title = {Exploration and Graphics for RivEr Trends (EGRET)},
#>     publisher = {U.S. Geological Survey},
#>     year = {2023},
#>     url = {https://pubs.usgs.gov/tm/04/a10/},
#>   }

References

See this list for WRTDS applications in print:

https://rconnect.usgs.gov/EGRET/articles/References_WRTDS.html

Disclaimer

This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The software has not received final approval by the U.S. Geological Survey (USGS). No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. The software is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the software.

Copy Link

Version

Install

install.packages('EGRET')

Monthly Downloads

729

Version

3.0.9

License

CC0

Maintainer

Laura DeCicco

Last Published

April 18th, 2023

Functions in EGRET (3.0.9)

cleanUp

cleanUp eList
concUnit-class

concUnit class
checkSurfaceSpan

checkSurfaceSpan
cumQdate

Cumulative flow calculation
compressData

Compress sample data frame
censoredSegments

Generic plotting function to create censored line segments
dateFormatCheck

Check date format
checkStartEndDate

checkStartEndDate
dataOverview

Data Overview for WRTDS
decimalDate

decimalDate
errorStats

Error statistics
decimalHighLow

decimalHighLow
fixSampleFrame

Update Sample dataframe
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
flowDuration

Computes several values of the flow duration curve for streamflow centered on a specific date of the year
flexPlotAddOn

Flexible Flow Normalization Plot Add On
flexFN

Flexible Flow Normalization
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 estimated flux
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
generalAxis

Axis generation for log discharge
print.egret

EGRET helper functions
jitterSam

jitter Sample
is.egret

Check for EGRET object
makeAugmentedSample

Create randomized residuals and observations for data sets that have some censored data
getSurfaces

Get surfaces matrix from EGRET object
genericEGRETDotPlot

Generic EGRET plotting function
makeAnnualSeries

Produces annual series of 8 streamflow statistics (and a lowess smooth of them) from daily streamflow data
fluxUnit-class

fluxUnit class
getSample

Get Sample dataframe from EGRET object
logPretty1

Sets up tick marks for an axis with a log scale, where the graph is small
getInfo

Get INFO dataframe from EGRET object
modelEstimation

Estimation process for the WRTDS (Weighted Regressions on Time, Discharge, and Season)
genmissing

genmissing
getDaily

Get Daily dataframe from EGRET object
monthLabel-class

monthLabel class
multiPlotDataOverview

Produces a 4 panel plot that gives an overview of the data set prior to any processing
logPretty3

Sets up tick marks for an axis with a log scale
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.
plot15

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.
plot1of15

plots 1 of the 15 graphs of streamflow statistics on a single page
plotConcTime

Plot of Observed Concentration versus Time
makeDateInfo

makeDateInfo
plotConcHist

Graph of annual concentration and flow normalized concentration versus year
plotFlowSingle

Creates a plot of a time series of a particular flow statistic and a loess smooth of that flow statistic
plotConcTimeDaily

Plot of the time series of daily concentration estimates and the sample values for the days that were sampled
mergeReport

mergeReport
plotFluxHist

Graph of annual flux and flow normalized flux versus year
plotFluxTimeDaily

Plot of the time series of daily flux estimates and the sample values for the days that were sampled
populateDaily

Populate Daily data frame
plotConcTimeSmooth

Plot up to three curves representing the concentration versus time relationship, each curve representing a different flow.
plotFourStats

Makes four graphs of annual streamflow statistics on a single page
plotResidQ

Plot of the residuals from WRTDS (in log concentration units) versus the discharge
populateDailySamp

Merge concentration to Daily
plotFour

Makes four graphs of streamflow statistics on a single page
plotContours

Color contour plot of the estimated surfaces as a function of discharge and time (surfaces include log concentration, standard error, and concentration)
plotMonthTrend

Plot monthly trend result from runPairs
plotQTimeDaily

Plot of the discharge time series
plotFluxPred

Graph of observed versus estimated flux
populateSampleColumns

Populate Sample Columns
populateSiteINFO

Populate Site Information Columns
plotFluxQ

Sample data plot: observed log flux vs log discharge
plotSDLogQ

Graph of the standard deviation of the log of daily discharge versus year
plotTimeSlice

plotTimeSlice
plotResidPred

Plot of the residuals from WRTDS versus the estimated values (all in log concentration units)
printPairs

Print information about pairs analysis
plotResidTime

Plot of the residuals from WRTDS (in log concentration units) versus time
plotWRTDSKalman

plotWRTDSKalman
plotDiffContours

Plots the difference between two years from a contour plot created by plotContours
readNWISSample

Import NWIS Sample Data for EGRET analysis
readUserDaily

Import user daily data for EGRET analysis
printqUnitCheatSheet

Reminder to user of flow Unit properties such as cubic meters per second or thousands of cubic feet per second.
populateConcentrations

Populate Concentration Columns
printFluxUnitCheatSheet

Reminder to user of flux unit properties (such as kg/day, tons/year, etc).
populateDateColumns

Populate Date Columns
printSeries

Print annual results for a given streamflow statistic
qUnit-class

qUnit class
processQWData

Processing of Water Quality Data
randomSubset

randomSubset
readUserSample

Import user-supplied sample data for EGRET analysis
printGroups

Print information about group analysis
removeDuplicates

Remove duplicates values from Sample data frame.
runGroups

Runs a comparison of any group of years in the record.
readWQPSample

Import Sample Data from the Water Quality Portal for WRTDS
populateParameterINFO

Populate Parameter Information Columns
runSurvReg

Run the weighted survival regression for a set of estimation points (defined by DecYear and Log(Q))
Choptank_eList

Example eList
readDataFromFile

Basic Data Import for Water Flow Data
setPA

Sets up the period of analysis (the portion of the year being evaluated).
tableFlowChange

Prints table of change metrics for a given streamflow statistic
saveResults

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.
readNWISDaily

Import NWIS Daily Data for EGRET analysis
runPairs

Runs a comparison of any two years in the record.
selectDays

Creates a subset Daily data frame that only contains daily estimates for the specified period of analysis
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
tableResults

Table of annual results for discharge, concentration and flux
surfaceStartEnd

Surface date limits
runSeries

Annual series of flow-normalized concentration and flow-normalized flux
stitch

stitch surfaces
tableChange

Create a table of the changes in flow-normalized values between various points in time in the record
surfaceIndex

Compute the 6 parameters needed to lay out the grid for the surfaces computed in estSurfaces
setupYears

Creates the AnnualResults data frame from the Daily data frame
yPretty

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

startEnd
triCube

Tricube weight function
WRTDSKalman

WRTDS-Kalman
Constants

Constants included with EGRET
boxResidMonth

A box plot of WRTDS residuals by month
INFOdataframe

Import metadata to create INFO data frame
boxConcThree

Three box plots side-by-side
boxQTwice

Two box plots side-by-side, discharge on sample days, and discharge on all days
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
calculateMonthlyResults

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.
as.egret

Create named list for EGRET analysis
EGRET-package

EGRET package includes WRTDS and flowHistory