Revision History for T&M 4-A10 Robert M. Hirsch and Laura A. De Cicco User Guide to Exploration and Graphics for RivEr Trends (EGRET) and dataRetrieval: R Packages for Hydrologic Data ----------------------------------------------------- Posted online October 8, 2014 ----------------------------------------------------- Revised and reposted February 5, 2015, version 2.0 Minor changes involving punctuation and style are not itemized. The following pages summarize the major updates, starting from the beginning of the report. Page 1: “A pair of tightly linked R packages, called dataRetrieval” was shortened for clarity to “An R package called. . .” Page 1: The fifth sentence in the abstract was changed, in order to express the capabilities of the dataRetrieval package’s capabilities, from “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.” to the following: “A related R package called dataRetrieval is required in order for EGRET to accomplish these data retrievals for use by the EGRET package, but dataRetrieval also provides the capability to download a broader suite of data types and organize those data in ways that facilitate many kinds of hydrologic applications. The dataRetrieval package is documented in Appendix 1 of this report.” Page 1: Immediately after the first sentence of the introduction’s third paragraph, the following sentence was added to indicate the EGRET-specific qualities contained in the dataRetrieval package: “It contains its own data-retrieval functions, based on functions in the dataRetrieval package, but which are designed to meet the very specific requirements of the EGRET package.” Page 2: In the first paragraph of the “Organization of This Report” section, in the seventh sentence of the first paragraph, the acronym “EGRET” replaces the erroneously referenced “dataRetrieval” as the package discussed in the sentence. Page 2: Following the seventh sentence in the first paragraph of the “Organization of This Report” section, the sentence “Users who want to work with a wider range of data sets (for example, multiple chemical constituents, sub-daily time steps, time series from water quality sensors) can find relevant functions for these data types in dataRetrieval (documented in appendix 1)” was added to clarify the data versatility of the dataRetrieval package. The subsequent sentence was changed so that the first word (“This”) was expanded to “The section on data entry” in order to improve clarity. Page 3: In the “Getting Help with Functions” section, the commands “getNWISSample” and “?getNWISSample” were replaced with “readNWISSample” and “?readNWISSample” in the second paragraph. Page 3: In the “Getting Help with Functions” section, the command “getNWISSample” was replaced with “readNWISSample” twice in the same sentence in the fifth paragraph. Page 3: In the “Getting Help with Functions” section’s third paragraph, the latter half of the last sentence was replaced with “with only a single argument” to provide a more technically specific explanation. Page 3: The second sentence in the fourth paragraph of the “Getting Help with Functions” section was replaced with the following two sentences and a clause: “For most of the functions, the first argument is the name of a list which specifies the four objects that contain all of the data and statistical model outputs. In general, this list is called eList. In many cases the additional arguments are for setting details of the graphical output or model estimation parameters. Generally the functions can be called with all of those arguments set to their default values;” to characterize general operation with a more technically precise language. Page 3: The language of the entire “Package Installation” section was replaced entirely to eliminate the previous command language and express a more pragmatic approach to installations and updates. Page 4: The last sentence in the “Data Entry” section was deleted, eliminating references to a specific table in an appendix. Page 4: The latter half of the final sentence in the “Daily Mean Discharge Data for Use in EGRET” section was removed so that it ends as follows: “the section ‘WRTDS Analysis of Water-Quality Data.’” Page 5: In the “Discharge Data from the U.S. Geological Survey Data Service” section, the command “getNWISDaily” was replaced with “readNWISDaily” in the first sentence of the second paragraph, in the fifth and sixth command lines of the second paragraph, in the third sentence of the third paragraph, and in the first word of the fourth sentence in paragraph three . Page 5: The fifth sentence of paragraph three in the “Discharge Data from the U.S. Geological Survey Data Service” section was changed from “However, the getNWISDaily function is designed so that it could be used” phrasing to “The dataRetrieval package contains a very similar function called readNWISdv, but it is designed so that it can be used. . .” Page 6: In the “Discharge Data from the U.S. Geological Survey Data Service” section, the command “getNWISDaily” was replaced with “readNWISDaily”in the command line of the fourth paragraph, in the third to last sentence in the fifth paragraph, and in the first sentence in the seventh paragraph. Page 7: In the “Discharge Data from a Text File” section, the third command line Daily <- getUserDaily (filePath, fileName) is changed to Daily <- readUserDaily (filePath, fileName) Page 7: In the “Discharge Data from a Text File” section, the fourth command line Daily <- getUserDaily (filePath, filename, qUnit = 2) is changed to Daily <- readUserDaily (filePath, filename, qUnit = 2) Page 7: In the final paragraph of the “Discharge Data from a Text File” section, in the final sentence, “getUserDaily” was changed to “readUserDaily.” Page 7: In the section “Water-Quality Data for Use in EGRET,” the final sentence of the first paragraph was modified. The part of the sentence that reads as “…sections ‘WRTDS analysis of water quality data,’ ‘Working with Multiple Data Frames’)” was changed so that the entire sentence is as follows: “However, once the WRTDS computations have been run using the modelEstimation function, the data frame is automatically augmented with an additional three columns computed by that function (as described below in the section ‘WRTDS analysis of water quality data.’)” Page 8: In the last sentence of the third paragraph of the “Water-Quality Data for Use in EGRET” section, the reference to “appendix 1, section 3.4” was changed to “appendix 2, section 3.2.4. . .” Page 9: In the second to last sentence in the fourth paragraph of the “Water-Quality Data for Use in EGRET” section, the first set of values was changed from (0.01, 0.015) to (0.005, 0.015). Page 9: In the second sentence in the first paragraph of the “Water-Quality Data from U.S. Geological Survey Web Services” section, the command “getNWISsample” was replaced with “readNWISSample.” Page 9: The fifth command line in the “Water-Quality Data from U.S. Geological Survey Web Services” section Sample <- getNWISSample (siteNumber ParameterCd, StartDate, EndDate) is changed to Sample <- readNWISSample (siteNumber, ParameterCd, StartDate, EndDate) Page 9: The sixth command line in the “Water-Quality Data from U.S. Geological Survey Web Services” section Sample <- getNWISSample (“01491000”,”00631”,”1979-10-01”,”2010-09-30”) is changed to Sample <- readNWISSample (“01491000”,”00631”,”1979-10-01”,”2010-09-30”) Page 9: The seventh command line in the “Water-Quality Data from U.S. Geological Survey Web Services” section Sample <- getNWISSample (siteNumber ParameterCd, StartDate=””, EndDate=””) is changed to Sample <- readNWISSample (siteNumber, ParameterCd, startDate=””, endDate=””) Page 10: In the final paragraph of the “Water-Quality Data from U.S. Geological Survey Web Services” section, the command “getNWISDaily” was replaced with “readNWISDaily.” Page 10: In the fifth sentence of the “Water-Quality Data from the Water Quality Portal” section, the command “getWQPqwData” was replaced with “readWQPSample.” Page 10: In the “Water-Quality Data from the Water Quality Portal” section, the command line Sample <- getWQPqwData(“WIDNR_WQX-10032762”,"Specific conductance", “2011-05-01”, “2011-09-30”) is changed to Sample <- readWQPSample (“WIDNR_WQX-10032762”,"Specific conductance", “2011-05-01”, “2011-09-30”) Page 10: In the section “Water-Quality Data from a User-supplied File,” the second sentence of the second paragraph was changed to reflect the corrected location of the information referenced. The updated sentence, now the third sentence, reads as follows: “Alternatives to this default structure are described in appendix 2, section 3.2 and in the help for readUserSample.” Page 10: In the section “Water-Quality Data from a User-supplied File,” the final sentence of the second paragraph was replaced with the following sentence to reflect the corrected location of the information referenced: “For details, refer to section 3.2.4 of appendix 2." Pages 11 and 12: In the section “Entering and Storing Metadata,” the sixteen lines directly following table 3 are deleted and replaced with the following block of information: “For all situations, except those where the water-quality data come from the Water Quality Portal, the metadata are entered into the system by using the function readNWISInfo. If all of the data come from a USGS data service call, the command for USGS site number 01491000 and parameter number 00631 would look like this: INFO <- readNWISInfo(siteNumber = “01491000”, parameterCd = “00631”) Or equivalently INFO <- readNWISInfo(“01491000”, “00631”) If the application deals only with discharge data and not water-quality data, the command would be: INFO <- readNWISInfo(siteNumber = “01491000”, parameterCd = “00060”) If the water-quality data came from the Water Quality Portal, then siteNumber would be either in the form “USGS-10491000” (if it is a USGS site) or of the form “WIDNR_WQX-10032762” (if it is from a non-USGS source, the initial characters before the “_” are an agency identifier, in this case the Wisconsin Department of Natural Resources). The parameterCd would be either a USGS parameter code or a “characteristic name.” So for an example of specific conductance data, the command might be: INFO <- readWQPInfo(“WIDNR_WQX-10032762”,”Specific conductance”) In a case where the discharge data came from the USGS data service but the water-quality data came from a user-supplied file, the command would be of the form: INFO <- readNWISInfo(siteNumber=”01491000”,parameterCd = “”) In this case, the program will prompt the user for parameter information. If all of the data came from user supplied files, then the command would be: INFO <- readNWISInfo(““, ““) In this case, the program will prompt the user to supply all of the metadata. When the user supplies metadata, the only elements that they must supply are those listed in table 3 and the last one could be entered as NA. Users can always supply additional information to be stored in the INFO data frame. To do this, the user defines a new variable to be a part of the INFO data frame and assigns it a value. For example, if we wanted to store the fact that there was a switch from plastic to glass sample bottles on 2005-10-01, then after INFO has been created we can give the command: INFO$bottleNote <- “switched from plastic to glass bottles 2005-10-01” Page 12: In the paragraph that begins immediately prior to the bulleted items in the “Entering and Storing Metadata” section, the command “getNWISInfo” was replaced with “readNWISInfo” in two instances. Page 12: In the second and third bulleted items (Parameter names and Station and parameter abbreviations, respectively) in the section “Entering and Storing Metadata,” the command “getNWISInfo” was replaced with “readNWISInfo.” Page 12: The entire section titled “Removing Duplicate Observations” was moved so that it immediately precedes the section titled “Moving Discharge Data from the Daily Data Frame to the Sample Data Frame.” Page 12: The command line in the section “Removing Duplicate Observations” Sample <- removeDuplicates () was changed to reflect the addition of “Sample” in the parentheses: Sample <- removeDuplicates (Sample) Page 13: In the “Moving Discharge Data from the Daily Data Frame to the Sample Data Frame” section, the final two sentences prior to figure 1 are removed, including the command “Sample <- mergeReport ()” and replaced with the following: “After running mergeReport the Sample data frame is augmented by the addition of two columns: Q and LogQ. This function does two additional things: (1) It produces a compact table of information about the content of the Sample and Daily data frames that can be helpful in spotting potential data problems and (2) it organizes the three data frames (INFO, Daily, and Sample) into a named list called eList, which is an object that the code understands to be an EGRET object. The call to the function is: eList <- mergeReport(INFO,Daily,Sample) Figure 1 is an image of the report provided in the Choptank nitrate example.” Page 13: The two sentences that appear immediately after figure 1 in the “Moving Discharge from the Daily Data Frame to the Sample Data Frame” section are replaced with the following: “From this point forward in the use of EGRET, the user typically supplies eList as an argument to each of the functions and the function then uses information from one or more of these data frames to do its computations. Users can always “unpack” the eList to see the content of the individual data frames within it. For example, to see a summary of Sample after mergeReport has been run, the user would give these two commands: Sample <- eList$Sample summary(Sample) or, alternatively, this can be done with a single command: summary(eList$Sample)” Page 13: The first sentence in the section “Saving the Workspace for Future Use,” was modified so the phrase before the comma reads as follows: “After the Daily, Sample, and INFO data frames and the object eList have been created. . .” Page 13: The second command line in the section “Saving the Workspace for Future Use” saveResults (savePath) is modified to include “eList,” as follows: saveResults (savePath, eList) Page 14: At the end of the third paragraph in the “Saving the Workspace for Future Use” section, the following sentence was added: “The use of alternative data frames and lists is discussed in the section titled ‘Working with multiple versions of data frames.’” Page 14: All the information following the third paragraph in the “Saving the Workplace for Future Use” section was deleted, so that after the third paragraph, the heading for the “Setting the Period of Analysis for Graphs, Tables, and Analyses in EGRET” section occurs. Page 19: In the “EGRET Functions for Flow History Analysis” section, the third command line Daily <- getNWISDaily(siteNumber, param, StartDate = “”, EndDate = “2014-06-30”) is modified as follows: Daily <- readNWISDaily(siteNumber, param, StartDate = “”, endDate = “2014-06-30”) Page 19: In the “EGRET Functions for Flow History Analysis” section, the fourth command line INFO <- getNWISInfo(siteNumber, param) is modified as follows: INFO <- readNWISInfo(siteNumber, param) Page 19: At the end of the final paragraph in the section “EGRET Functions for Flow History Analysis,” the following information was added: “After the INFO and Daily data frames have been created, they need to be organized into the list called eList, using command: eList <- as.egret(INFO,Daily)” Page 19: The third sentence in the first paragraph of the section “The Function setPA” is modified as follows: “The function performs no computations, but simply augments the metadata stored in the INFO data frame (stored in eList) with the paStart, paLong, and window values (where H = window).” Page 19: In the section “The Function setPA,” the first command line INFO <- setPA()is changed to eList <- setPA(eList) Page 19: In the section “The Function setPA,” the last command line is changed to eList <- setPA(eList, paStart = 12, paLong = 3, window = 15) Page 19: The following sentence was added to the beginning of the first paragraph in the “The Function makeAnnualSeries” section: “This is a function that the user doesn’t call directly, but it is central to the computations of virtually every one of the Flow History functions and, as such it is worthwhile to document it here to provide background information to the user.” Page 19: The fragment at the end of the first paragraph, the subsequent command line, and the subsequent spacing were removed from “The Function makeAnnualSeries” section. Page 20: In the “Plotting the Results for a Single Discharge Statistic by Using plotFlowSingle” section, the following command line plotFlowSingle(istat = 2, qUnit = 2) is modified by adding “eList” so that it reads as follows: plotFlowSingle(eList, istat = 2, qUnit = 2) Page 20: In the “Plotting the Results for a Single Discharge Statistic by Using plotFlowSingle” section, the following command line SpokaneSeries <- printSeries(istat = 2, runoff = TRUE) is modified by adding “eList” so that it reads as follows: SpokaneSeries <- printSeries(eList, istat = 2, runoff = TRUE) Page 20: In the second sentence of the paragraph following figure 5 in the “Printing Results for a Single Discharge Statistic by Using printSeries and tableFlowChange” section, the reference to the appendix was changed to “appendix 2, section 12.” Page 21: In the fourth paragraph of the “Printing Results for a Single Discharge Statistic by Using printSeries and tableFlowChange” section, which begins with “Four arguments are needed…,” the first sentence was modified to indicate “Five arguments are needed…,” and the following sentence was added after the first sentence: “The first is eList, which is the list containing the INFO and Daily data frames.” The remainder of the paragraph was modified to accommodate the change in the number of arguments, such that “first” becomes “second”; “second” becomes “third”; “third” becomes “fourth”; and the “the final argument” phrase was not changed. Page 21: The second command line following the fifth paragraph in the “Printing Results for a Single Discharge Statistic by Using printSeries and tableFlowChange” section, which is tableFlowChange(istat = 2, qUnit = 2, yearPoints=yearPoints) is modified to add “eList” as follows: tableFlowChange(elist, istat = 2, qUnit = 2, yearPoints=yearPoints) Page 22: The third command line following the fifth paragraph in the “Printing Results for a Single Discharge Statistic by Using printSeries and tableFlowChange” section, which is tableFlowChange(istat = 2, qUnit = 2, yearPoints = c(1892,1932,1972,2012)) is modified to add “eList” as follows: tableFlowChange(eList, istat = 2, qUnit = 2, yearPoints = c(1892,1932,1972,2012)) Page 23: The first command line after the first paragraph in the section “Plotting Changes in Variability by Using plotSDLogQ,” which is plotSDLogQ()is modified to add “eList” as follows: plotSDLogQ(eList) Page 23: The command line after the second paragraph in the section “Plotting Changes in Variability by Using plotSDLogQ,” which is plotSDLogQ(window = 20) is modified to incorporate “eList” as follows: plotSDLogQ(eList, window = 20) Page 23: The two command lines in the final paragraph of the “Plotting Changes in Variability by Using plotSDLogQ” section, which are INFO <- setPA(paStart = 6, paLong = 3) plotSDLogQ() were modified to incorporate “eList” as follows: eList <- setPA(eList, paStart = 6, paLong = 3) plotSDLogQ(eList) Page 24: The first command line of the section “Creating Graphics for Plotting the Discharge Record by Using plotQTimeDaily,” which is plotQTimeDaily (lwd = 1, qUnit = 2) was modified to incorporate “eList” as follows: plotQTimeDaily (eList, lwd = 1, qUnit = 2) Page 25: In the third paragraph of the section “Creating Graphics for Plotting the Discharge Record by Using plotQTimeDaily,” the command line plotQTimeDaily(qLower = 600, lwd = 3) was modified to incorporate “eList” as follows: plotQTimeDaily(eList, qLower = 600, lwd = 3) Page 26: In the second paragraph of the section “Creating Multipanel Graphics for Flow History,” the phrase preceding the three command lines was modified to incorporate “and eList” as follows: “The commands to produce figure 11 are this combination (after the Daily and INFO data frames and eList are created)” Page 26: The first command line following the second paragraph of the section “Creating Multipanel Graphics for Flow History,” was replaced by the following: eList <- setPA(eList, paStart = 1, paLong = 2) Page 26: The second command line following the second paragraph of the section “Creating Multipanel Graphics for Flow History,” which is annualSeries <- makeAnnualSeries() was removed. Page 26: The third command line following the second paragraph of the section “Creating Multipanel Graphics for Flow History,” which is plotFour(qUnit = 2, window = 21) was modified to incorporate “eList” as follows: plotFour(eList, qUnit = 2, window = 21) Page 27: In the section “Creating Multipanel Graphics for Flow History,” following the paragraph that begins “Finally, there is the much more elaborate graphic…,” the second command line plot15(yearStart=1900,yearEnd=2012) was modified to incorporate “eList” as follows: plot15(eList, yearStart=1900,yearEnd=2012) Page 29: In the fifth paragraph of the section “Summarizing Water-Quality Data (without Using WRTDS),” the command line in the fifth sentence, which is INFO <- setPA(paStart=12, paLong=3) was modified to incorporate “eList” as follows: eList <- setPA(eList, paStart=12, paLong=3) Page 29: In the fifth paragraph of the section “Summarizing Water-Quality Data (without Using WRTDS),” the command line in the seventh sentence, which is INFO <- setPA() was modified to incorporate “eList” as follows: eList <- setPA(eList) Page 29: In the “plotConcTime” section, the first command line, which is plotConcTime() was modified to incorporate “eList” as follows: plotConcTime(eList) Page 30: In table 6 in the “plotConcTime” section, a new first row was added below the heading row. In this row, in the “Arguments” column, “eList” was added; in the “Purpose and options” column, “Specifies the named list that contains the INFO and Sample data frames that will be used by this function” was added; in the “Default” column, “No default, name of list must be stated” was added. Page 30: In the “plotConcTime” section, the command at the end of the paragraph that begins with “To understand the way that the various features…” plotConcTime() was modified to incorporate “eList” as follows: plotConcTime(eList) Page 30: In the “plotConcTime” section, the first of the two commands at the end of the paragraph that begins with “The general idea that concentrations have trended upwards …” INFO <- setPA(paStart = 4, paLong = 3) was modified to incorporate “eList” as follows: eList <- setPA(eList, paStart = 4, paLong = 3) Page 30: In the “plotConcTime” section, the second of the two commands at the end of the paragraph that begins with “The general idea that concentrations have trended upwards …” plotConcTime() was modified to incorporate “eList” as follows: plotConcTime(eList) Page 30: In the “plotConcTime” section, near the end of the paragraph that begins with “The upward trend continues to be evident…,” the command “INFO” was replaced with the command “eList$INFO.” Page 30: In the “plotConcTime” section, the command line following the paragraph that begins with “The upward trend continues to be evident…,” plotConcTime(qUnit=1,qUpper=165,qLower=34) was modified to incorporate “eList” as follows: plotConcTime(eList, qUnit=1,qUpper=165,qLower=34) Page 32: In the “plotConcTime” section, the command line following the paragraph that begins with “Note that the graphic is entirely…,” plotConcTime(qUnit=1,qLower=165, concMax=2) was modified to incorporate “eList” as follows: plotConcTime(eList, qUnit=1,qLower=165, concMax=2) Page 33: In the “flowDuration” section, the command line at the end of the first paragraph flowDuration(qUnit = 1) was modified to incorporate “eList” as follows: flowDuration(eList, qUnit = 1) Page 33: In the “flowDuration” section, the command line at the end of the second paragraph flowDuration(centerDate = “05-16” , qUnit = 1 , span = 45) was modified to incorporate “eList” as follows: flowDuration(eList, centerDate = “05-16” , qUnit = 1 , span = 45) Page 34: In the “plotConcQ” section, the command line at the end of the first paragraph plotConcQ() was modified to incorporate “eList” as follows: plotConcQ(eList) Page 34: In the “plotConcQ” section, the command at the end of the third full paragraph, which begins “Use of the logScale option can be very helpful…,” plotConcQ(logScale=TRUE) was modified to incorporate “eList” as follows: plotConcQ(eList, logScale=TRUE) Page 35: In the caption for figure 20, the command plotConcQ(logScale=TRUE) was modified to incorporate “eList” as follows: plotConcQ(eList, logScale=TRUE) Page 36: In the “plotFluxQ” section, the command in the third sentence plotFluxQ(fluxUnit=4) was modified to incorporate “eList” as follows: plotFluxQ(eList, fluxUnit=4) Page 39: In the “WRTDS Analysis of Water-Quality Data” section, prior to the last sentence in the paragraph, which begins, “The method requires the availability of measured…,” the following sentence was inserted: “The data used in the model estimation process are all stored in eList, which contains three data frames: Sample, Daily and INFO.” Page 41: In the fourth full paragraph in the section “Estimates of Concentration and Flux,” the last sentence was updated to indicate “see appendix 2, section 3.2.4. . .” Page 41: In the fifth full paragraph of the section “Estimates of Concentration and Flux,” the parenthetical information in the third sentence was updated to read as follows: “(described above in the section titled ‘The Smoothing Method Used in Flow History Analysis.’” Page 45: In the section “Fitting the WRTDS Model,” the second sentence was replaced with the following sentence: “This function takes information from the INFO, Daily, and Sample data frames, which are all stored in the list eList, then augments each of them with additional information, creates an additional object call surfaces, and returns a new version of eList that contains the new versions of INFO, Daily, and Sample plus the newly created surfaces.” Page 45: In the section “Fitting the WRTDS Model,” the remainder of the third sentence that follows the second comma was deleted, as was the remainder of the paragraph, and the second comma was replaced by a period. The next sentence is the one that begins with “The command for conducting…” Page 45: The first full command line in the “Fitting the WRTDS Model” section modelEstimation(windowY = 7, windowQ = 2, windowS = 0.5, minNumObs = 100, minNumUncen =50, edgeAdjust = TRUE). was modified to read as follows: eList <- modelEstimation(eList, window = 7, windowQ = 2, windowS = 0.5, minNumObs = 100, minNumUncen =50, edgeAdjust = TRUE) Page 45: In the first sentence of the paragraph in the “Fitting the WRTDS Model” section that begins with “To invoke the function…,” the command modelEstimation() is modified to incorporate eList as follows: eList <- modelEstimation(eList) Page 45: A new “Argument” was added to table 7, “Information about the seven arguments used in modelEstimation,” along with accompanying “Definition and discussion” and “Default value” data. The following was added to the first row “Argument” cell: “eList” The following was added to the first row “Definition and discussion” cell: “Specifies the named list that contains the INFO, Daily, and Sample data frames that will be used by this function.” The following was added to the first row “Default value” cell: “No default, name of list must be stated.” Page 46: The final paragraph in the “Fitting the WRTDS Model” section, which begins with the sentence “The edgeAdjust option was added…,” was moved to the area immediately following table 7, and immediately preceding the sentence that begins with “The modelEstimation function carries out….” Page 47: The series of bulleted items that follow table 7 was changed so that the final bulleted item begins with “estDailyFromSurfaces,” which is now immediately followed by the section heading “Displaying and Managing WRTDS Model Results,” a heading repositioned from its previous location preceding the subheading “Computing Monthly Results.” Page 48: The previously bulleted “setupYears” item became regular body text under a subheading titled “Computing Annual Headings.” Page 48: The first two sentences of the paragraph following table 8 were deleted and replaced with the following: “The setupYears function allows to user to establish the PA that will be used for computing these annual values. It can be used to compute calendar year or water year results, but it can also be used to compute results for any PA the user chooses.” Page 48: The first command line following table 8 was replaced with the following: ApMayJuneResults <- setupYears(eList$Daily, paLong = 3, paStart = 4) Page 48: The second command line following table 8 was replaced with the following: MayResults <- setupYears(eList$Daily, paLong = 1, paStart = 5) Page 48: In the first sentence in the “Computing Monthly Results” section, the command line was changed to incorporate “eList” as follows: MonthlyResults <- calculateMonthlyResults(eList) Page 49: In the section “Issues of Large Data Gaps—Using the blankTime Function,” the command line immediately following the first paragraph was changed to incorporate “eList” as follows: eList <- blankTime(eList, startBlank, endBlank) Page 49: In the section “Issues of Large Data Gaps—Using the blankTime Function,” the third command line following the second paragraph was changed to incorporate “eList” as follows: eList <- blankTime(eList, startBlank, endBlank) Page 49: In the section “Issues of Large Data Gaps—Using the blankTime Function,” the fourth command line following the second paragraph was changed to incorporate “eList” as follows: eList <- blankTime(eList, “1979-10-01”, “1989-09-30”) Page 49: In the section “Plotting Annual Results,” the first command line following the second paragraph was changed to incorporate “eList” as follows: eList <- setPA(eList, paStart, paLong) Page 49: In the section “Plotting Annual Results,” the second command line following the second paragraph was changed to incorporate “eList” as follows: eList <- setPA(eList, paStart = 4, paLong = 3) Page 49: In the section “Plotting Annual Results,” at the end of the first sentence in the fourth paragraph, the command plotConcHist() was changed to incorporate “eList” as follows: plotConcHist(eList) Page 49: In the section “Plotting Annual Results,” the command line following the fourth paragraph was changed to incorporate “eList” as follows: plotConcHist(eList, yearStart, yearEnd, concMax, printTitle, plotFlowNorm) Page 50: In the section “Plotting Annual Results,” in the second sentence of the paragraph following table 9, the command plotFluxHist () was changed to incorporate “eList” as follows: plotFluxHist (eList) Page 50: In the section “Plotting Annual Results,” the command line at the beginning of the second paragraph following table 9 was changed to incorporate “eList” as follows: plotFluxHist(eList, yearStart, yearEnd, fluxUnit, fluxMax, printTitle, plotFlowNorm) Page 50: In the section “Plotting Annual Results,” in the final sentence of the third paragraph following table 9, there are two commands. The first command plotConcHist() was changed to incorporate “eList” as follows: plotConcHist(eList) Page 50: In the section “Plotting Annual Results,” in the final sentence of the third paragraph following table 9, there are two commands. The second command plotFluxHist(fluxUnit=8) was changed to incorporate “eList” as follows: plotFluxHist(eList, fluxUnit=8) Page 51: In the section “Producing Tables of Results,” following the first paragraph, the command line tableResults(qUnit = 3,fluxUnit = 6) was changed to incorporate “eList” as follows: tableResults(eList, qUnit = 3,fluxUnit = 6) Page 52: In the section “Producing Tables of Results,” following the second paragraph, the command line resultsTable <- tableResults(returnDataFrame = TRUE) was changed to incorporate “eList” as follows: resultsTable <- tableResults(eList, returnDataFrame = TRUE) Page 52: In the section “Producing Tables of Results,” following the third paragraph, the command line tableResults(qUnit = 3, fluxUnit = 6) was changed to incorporate “eList” as follows: tableResults(eList, qUnit = 3, fluxUnit = 6) Page 52: In the section “Computing and Displaying Tables of Change Over Time,” at the end of the first paragraph, the command line tableChange (fluxUnit, yearPoints) was changed to incorporate “eList” as follows: tableChange (eList, fluxUnit, yearPoints) Page 53: In the section “Computing and Displaying Tables of Change Over Time,” at the end of the third paragraph, the command line tableChange(fluxUnit=6, yearPoints) was changed to incorporate “eList” as follows: tableChange(eList, fluxUnit=6, yearPoints) Page 53: In the section “Computing and Displaying Tables of Change Over Time,” the first full command line following figure 31 tableChange(fluxUnit=6, yearPoints=c(1996,2003,2010)) was changed to incorporate “eList” as follows: tableChange(eList, fluxUnit=6, yearPoints=c(1996,2003,2010)) Page 53: In the section “Computing and Displaying Tables of Change Over Time,” two command lines follow the paragraph that begins “There is an alternative version….” The first of these two command lines changeTableConc <- tableChangeSingle(yearPoints, returnDataFrame=TRUE) was changed to incorporate “eList” as follows: changeTableConc <- tableChangeSingle(eList, yearPoints, returnDataFrame=TRUE) Page 53: In the section “Computing and Displaying Tables of Change Over Time,” two command lines follow the paragraph that begins “There is an alternative version….” The second of these two command lines changeTableFlux <- tableChangeSingle(fluxUnit=6, yearPoints, returnDataFrame=TRUE, flux=TRUE) was changed to incorporate “eList” as follows: changeTableFlux <- tableChangeSingle(eList, fluxUnit=6, yearPoints, returnDataFrame=TRUE, flux=TRUE) Page 55: In the section “Flux Bias Statistics,” three equations are present. In two instances, the term “i-1” in equation labeled “(14)” was replaced by the term “i=1.” Page 55: In the section “Flux Bias Statistic,” three equations are present. The equation labeled “(15),” was compressed and illegible and was replaced by the following: Page 56: In the section “Graphics for Examining the Quality of the Model,” following the third paragraph, the second command line fluxBiasMulti(fluxUnit=4) was changed to incorporate “eList” as follows: fluxBiasMulti(eList, fluxUnit=4) Page 61: In the section “Graphics for Examining the Quality of the Model,” in the first sentence of the paragraph that begins “The default command for this function. . .,” the command plotConcTimeDaily () was changed to incorporate “eList” as follows: plotConcTimeDaily (eList) Page 62: In the section “Graphics for Examining the Quality of the Model,” there is a series of alphabetically ordered paragraphs after the commands at the end of the third paragraph. After the alphabetized series ends, there are two paragraphs, the second of which begins with “The default command for this function….” In the first sentence the command line plotConcTimeDaily () was changed to incorporate “eList” as follows: plotConcTimeDaily (eList). At the end of this paragraph is a sentence containing two command lines. The first of these command lines plotConcTimeDaily(startYear = 1992, endYear = 1995) was changed to incorporate “eList” as follows: plotConcTimeDaily(eList, startYear = 1992, endYear = 1995) Page 62: In the section “Graphics for Examining the Quality of the Model,” there is a series of alphabetically ordered paragraphs after the commands at the end of the third paragraph. After the alphabetized series ends, there are two paragraphs, the second of which begins with “The default command for this function….” At the end of this paragraph is a sentence containing two command lines. The second of these command lines plotConcTimeDaily(1992, 1995) was changed to incorporate “eList” as follows: plotConcTimeDaily(eList, 1992, 1995) Page 64: A new “Argument” was added at the top of table 10, “Arguments to the plotContours function,” along with accompanying “Definition” and “Default” data. The following was added to the first row “Argument” cell: “eList” The following was added to the first row “Definition” cell: “Specifies the named list that contains the INFO and surfaces objects that will be used by this function.” The following was added to the first row “Default” cell: “No default, name of list must be stated.” Page 65: In the section “Exploring Model Behavior and Adjusting Model Parameters,” (subheaded “plotContours”) immediately following table 10, is a paragraph that begins “Setting the contourLevels variable….” At the end of this paragraph are two command lines linked by the phrase “or equivalently.” The first of these two command lines plotContours(yearStart=1989,yearEnd=1998,qBottom=0.2,qTop=100,contourLevels= seq(0,18,2)) was changed to incorporate “eList” as follows: plotContours(eList, yearStart=1989,yearEnd=1998,qBottom=0.2,qTop=100,contourLevels=seq(0,18,2)) The second of these two command lines plotContours(1989,1998,0.2,100,contourLevels=seq(0,18,2)) was changed to incorporate “eList” as follows: plotContours(eList, 1989,1998,0.2,100,contourLevels=seq(0,18,2)) Page 66: In the section “Exploring Model Behavior and Adjusting Model Parameters,” (subheaded “plotContours”), the second paragraph following table 10, which begins “Contour plots of the standard error,” and ends with the command line plotContours(yearStart=1994,yearEnd=1996,qBottom=0.2,qTop=100,whatSurface= 2,contourLevels=seq(0.2,0.8,0.1)) was changed to incorporate “eList” as follows: plotContours(eList, yearStart=1994,yearEnd=1996,qBottom=0.2,qTop=100,whatSurface= 2,contourLevels=seq(0.2,0.8,0.1)) Page 67: In the section “Introducing an Example Case: Maumee River, Ohio, Dissolved Reactive Phosphorous,” at the end of the second paragraph, the command line plotContours(yearStart=1975, yearEnd=1977, qBottom = 20,qTop = 500, contourLevels= seq(0,0.28,0.04)) was changed to incorporate “eList” as follows: plotContours(eList, yearStart=1975, yearEnd=1977, qBottom = 20,qTop = 500, contourLevels= seq(0,0.28,0.04)) Page 67: In the section “Introducing an Example Case: Maumee River, Ohio, Dissolved Reactive Phosphorous,” at the end of the fifth paragraph, the command line plotDiffContours(year0 = 1988, year1 = 2011, qBottom = 20, qTop = 500, maxDiff=0.12) was changed to incorporate “eList” as follows: plotDiffContours(eList, year0 = 1988, year1 = 2011, qBottom = 20, qTop = 500, maxDiff=0.12) Page 69: A new “Argument” was added at the top of table 11, “Arguments for the function plotConcQSmooth,” along with accompanying “Definition” and “Default” data. The following was added to the first row “Argument” cell: “eList” The following was added to the first row “Definition” cell: “Specifies the named list that contains the INFO and sample data frames that will be used by this function.” The following was added to the first row “Default” cell: “No default, name of list must be stated.” Page 70: In the paragraph following table 11 in the “plotConcQSmooth” section, in the third sentence, the command line flowDuration(centerDate="08-01",span=60) was changed to incorporate “eList” as follows: flowDuration(eList, centerDate="08-01",span=60) Page 70: In the paragraph immediately following table 11 in the “plotConcQSmooth” section, in the sixth sentence, the command flowDuration() was changed to incorporate “eList” as follows: flowDuration(eList) Page 71: In the second paragraph after table 11, which begins “One example of the use…,” the command line in the second sentence plotConcQSmooth(date1=”1975-08-01”,date2=”1988-08-01”,date3=”2010-08- 01”,qLow=10,qHigh=300, logScale=TRUE,legendLeft=100,legendTop=0.06,printTitle=FALSE) was changed to incorporate “eList” as follows: plotConcQSmooth(eList, date1=”1975-08-01”,date2=”1988-08-01”,date3=”2010-08- 01”,qLow=10,qHigh=300, logScale=TRUE,legendLeft=100,legendTop=0.06,printTitle=FALSE) Page 71: The third paragraph after table 11, which begins “This graphic depicts a very…” and ends with the command line augResults<-plotConcQSmooth(“1975-08-01”,”1988-08-01”,”2010-08-01”,10,300,printVal ues=TRUE,logScale=TRUE,legendLeft=100,legendTop=0.06,printTitle=FALSE) was changed to incorporate “eList” as follows: augResults<-plotConcQSmooth(eList, “1975-08-01”,”1988-08-01”,”2010-08-01”,10,300,printVal ues=TRUE,logScale=TRUE,legendLeft=100,legendTop=0.06,printTitle=FALSE) Page 72: The sixth paragraph after table 11, which begins “Based on these observations…” and ends with the command line mayResults<-plotConcQSmooth(“1975-05-01”,”1988-05-01”,”2010-05-01”, 40, 700, leg endLeft=200,legendTop=0.04,printValues=TRUE,logScale=TRUE,printTitle=FALSE) was changed to incorporate “eList” as follows: mayResults<-plotConcQSmooth(eList, “1975-05-01”,”1988-05-01”,”2010-05-01”, 40, 700, leg endLeft=200,legendTop=0.04,printValues=TRUE,logScale=TRUE,printTitle=FALSE) Page 73: In the “plotConcQSmooth” section, in the ninth paragraph, which begins “Yet another type of comparison…,” the command line plotConcQSmooth(“2010-01-01”,”2010-05-01”,”2010-09-01”,30,300,logScale=TRUE,legend Left=150,legendTop=0.04,printTitle=FALSE) was changed to incorporate “eList” as follows: plotConcQSmooth(eList, “2010-01-01”,”2010-05-01”,”2010-09-01”,30,300,logScale=TRUE,legendLeft=150,legendTop=0.04,printTitle=FALSE) Page 74: In the “plotConcQSmooth” section, in the eleventh paragraph, which begins “One additional type of use…,” the command line plotConcQSmooth(date1=”2010-01-01”,date2=”2010-05-01”,date3=”2010-09-01”,qBottom=3 0,qTop=300,logScale=TRUE,legendLeft=150,legendTop=0.04,printTitle=FALSE, windowQ=1) was changed to incorporate “eList” as follows: plotConcQSmooth(eList, date1=”2010-01-01”,date2=”2010-05-01”,date3=”2010-09-01”,qBottom=3 0,qTop=300,logScale=TRUE,legendLeft=150,legendTop=0.04,printTitle=FALSE, windowQ=1) Page 74: In the “plotConcQSmooth” section, in the thirteenth paragraph, which begins “There are situations, particularly when…,” the command line plotConcQSmooth(“2010-04-01”,”2010-08-01”,”2010-12-01”, 1, 300, legendLeft=10,legendTop=0.19, logScale = TRUE) was changed to incorporate “eList” as follows: plotConcQSmooth(eList, “2010-04-01”,”2010-08-01”,”2010-12-01”, 1, 300, legendLeft=10,legendTop=0.19, logScale = TRUE) Page 76: In the first paragraph of the “plotConcTimeSmooth” section, the clause subsequent to the colon was changed to the following: “If one plotted a horizontal line on the contour plot for estimated concentration at a selected discharge and then plotted a set of vertical lines on the same day of each year in the record, the plotConcTimeSmooth graph would capture the value of estimated concentration at every intersection of the horizontal and vertical lines.” Page 76: A new “Argument” was added at the top of table 12, “Arguments for the function plotConcTimeSmooth,” along with accompanying “Definition” and “Default” data. The following was added to the first row “Argument” cell: “elist” The following was added to the first row “Definition” cell: “Specifies the named list that contains the INFO and Sample data frames that will be used by this function” The following was added to the first row “Default” cell: “No default, name of list must be stated.” Page 78: In the second paragraph of the section “plotConcTimeSmooth,” which begins with “Use of the following command,” the command line plotConcTimeSmooth(q1=25, q2=125, q3=800, centerDate=”05-01”, yearStart=1975, yearEnd=2010, logScale=TRUE, legendLeft=1981, legendTop=0.18, printTitle=FALSE) was changed to incorporate “eList” as follows: plotConcTimeSmooth(eList, q1=25, q2=125, q3=800, centerDate=”05-01”, yearStart=1975, yearEnd=2010, logScale=TRUE, legendLeft=1981, legendTop=0.18, printTitle=FALSE) Page 79: Near the end of the “Editing Data Sets” section, the sentence that begins “If we want to replace values less than 10 with 10 and those same rows, then changing the Qualifier to “<” and using the following commands would work. . .” was replaced with the following: “If we want to replace values that are reported as less than or equal to 10 to have the Qualifier “<” and a Value of 10, then the following commands would work. . .” Page 79: Immediately prior to the “Deleting Values” section, a section with the heading “Working with eList” was added. Page 80: The following sentence and command line were added at the end of the “Deleting Values” section: “Once the Sample data frame has been modified, the eList object needs to be updated: eList$Sample <- Sample Page 80: The following command line was added at the end of the “Shortening the Period of Record” section: eList$Sample <- smallSample Page 81: In the section “Creating Interval Concentrations,” the third paragraph, which begins with “Now that changes have been…,” the second sentence was modified so that the phrase “will accomplish this” ends with a period, and the sentence’s subsequent phrase and command line were deleted. The deleted material was replaced with the following: “After completing our editing of the Sample data frame, we need to put the new version back into eList. We can do it with the command: eList$Sample <- Sample. Then the following command will make the needed adjustments of Sample$ConcAve and Sample$Uncen: eList <- fixSampleFrame(eList)” Page 81: In the section “Creating Interval Concentrations, a second command line has been added after the fifth paragraph, which begins “Then we would proceed. . .” eList$Sample <- keepSample Pages 81-83: In the section “Working with Multiple Versions of Data Frames,” the first six paragraphs were deleted and replaced with the following: “Throughout this User Guide up to this point, the named list has always been eList. However, it can actually take on any name the user selects. If the user wants to consider a variety of alternatives to their analysis, this can easily be done by using a different name for each alternative. The alternatives might be: different ways of handling “less than” values (we may be uncertain about what the true reporting limit was), eliminating or revising one or more suspect data values, eliminating a portion of the record, thinning out the record in some period when sampling was much more intensive than normal, using interval censoring to represent some values, or modifying some of the WRTDS parameters such as window widths or minimum numbers of samples to be used in each regression.” The seventh paragraph, which begins “Let’s look at a real…,” was retained, except for the final sentence, which was modified to read as follows: “Let us assume here that we have already run the retrievals, fit the model, and created the Sample, Daily, and INFO data frames and have the results in the form of surfaces, all of which are contained in eList.” Immediately after the modified sentence, a new paragraph begins, and the following information is added: “In this situation we would pull out INFO, Daily, and Sample from eList, as follows. INFO <- eList$INFO Daily <- eList$Daily Sample <- eList$Sample We may want to change INFO by simply adding some text to explain the nature of the change: INFO$note <- “data edited to exclude data prior to WY 1985” We want to modify Daily and Sample to eliminate the earlier data. We can do that with these two commands. Daily <- subset(Daily, Date > ”1984-09-30”) Sample <- subset(Sample, Date > “1984-09-30”) We may want to check to see if things look correct by doing summary(Daily) and summary(Sample). Then we can put these three data frames into a new list called, for example, eListLater. The command would be: eListLater <- as.egret(INFO, Daily, Sample, NA) At this point, we can proceed with all of the usual steps for exploring the data and looking at results. For example we might do: multiPlotDataOverview(eListLater) eListLater <- modelEstimation(eListLater) plotConcHist(eListLater) tableResults(eListLater) And we might want to construct graphs comparing, for example, the annual flow-normalized concentrations from the original analysis and from this alternative analysis. We can do this by creating data frames of each set of results: annualResults <- setupYears(eList) annualResultsLater <- setupYears(eListLater) We can then produce graphs, the first one being annualResults$DecYear versus annualResults$FNConc and the second one being annualResultsLater$DecYear versus annualResultsLater$FNConc. By saving INFO, Daily, Sample, and surfaces together in a single list we avoid any possible confusion of what version of the results go with what version of the data and we can return to these two lists, eList and eListLater, to make whatever comparisons we wish to make. If we wanted to make a comparison using different WRTDS parameters (as opposed to comparisons with differences in the data), we can use this approach. Say in our original analysis (stored in eList) we used all the default parameters in modelEstimation, but now we want to consider windowY = 10, windowQ = 1.5, and minNumObs = 60. We could use this command: eListAlt <- modelEstimation(eList, windowY = 10, windowQ = 1.5, minNumObs = 60) When returned, all four of the objects in eListAlt will be different from the versions in eList. eListAlt$INFO will contain information about these WRTDS parameters, eListAlt$Daily will have the daily estimates from the alternative model, eListAlt$Sample will have the cross-validation estimates from the alternative model, and eListAlt$surfaces will be the new surfaces estimated. We can explore the results with all of the usual functions (such as plotConcHist or plotContours) simply by putting in eListAlt as the first argument in the function. All of these results can be saved for future examination by using the saveResults function.” The remainder of the section was deleted. Page 83: In the “Batch Processing in EGRET” section’s second paragraph, the second sentence was modified to read as follows: These workspaces each contain the Daily, Sample, and INFO data frames, and they have been placed into eList using the command eList <- mergeReport(INFO, Daily, Sample) and everything. . . (SEE PAGE 83) Page 83: In the section “Batch Processing in EGRET,” in the first series of command lines after the clause “Here is what the file of commands might look like,” the command line modelEstimation() was modified to incorporate “eList” as follows: eList <- modelEstimation(eList) The command line tableChange(fluxUnit=5,yearPoints=c(1980,1990,2000,2010)) was modified to incorporate “eList” as follows: tableChange(eList, fluxUnit=5,yearPoints=c(1980,1990,2000,2010)) The command line tableResults(qUnit=1,fluxUnit=5) was modified to incorporate “eList” as follows: tableResults(eList, qUnit=1,fluxUnit=5) The command line saveResults(savePath) was modified to incorporate “eList” as follows: saveResults(savePath, eList) Page 83: In the section “Batch Processing in EGRET,” in the second series of command lines after the clause “Here is what the file of commands might look like,” the command line modelEstimation() was modified to incorporate “eList” as follows: eList <- modelEstimation(eList) The command line tableChange(fluxUnit=6,yearPoints=c(1980,1990,2000,2010)) was modified to incorporate “eList” as follows: tableChange(eList, fluxUnit=6,yearPoints=c(1980,1990,2000,2010)) The command line tableResults(qUnit=3,fluxUnit=6) was modified to incorporate “eList” as follows: tableResults(eList, qUnit=3,fluxUnit=6) The command line saveResults(savePath) was modified to incorporate “eList” as follows: saveResults(savePath, eList) Page 84: In the “References Cited” section, the Hirsch (2004) reference was modified by deleting “no. 13-0194-P” and adding “v. 50, no. 6, p. 1401-1424.” Page 87: In “Appendix 3. Batch Workflows,” under the comment “# Gather discharge data,” the command line Daily <- getNWISDaily(sites[i],”00060”,startDate,endDate) was modified as follows: Daily <- readNWISDaily(sites[i],”00060”,startDate,endDate) Page 87: In “Appendix 3. Batch Workflows,” under the comment “# Gather sample data,” the command line Sample <- getNWISSample(sites[i],parameter_cd,startDate,endDate) was modified as follows: Sample <- readNWISSample(sites[i],parameter_cd,startDate,endDate) Page 87: In “Appendix 3. Batch Workflows,” under the comment “# Gather site and parameter information,” the command line INFO<- getNWISInfo(sites[i],parameter_cd,interactive=FALSE) was modified as follows: INFO<- readNWISInfo(sites[i],parameter_cd,interactive=FALSE) Page 87: In “Appendix 3. Batch Workflows,” under the comment “# Gather site and parameter information,” the command line INFO <- setPA() was removed. Page 87: In “Appendix 3. Batch Workflows,” the comment # Merge discharge with sample data: was modified to include “and create eList” as follows: # Merge discharge with sample data and create eList: Page 87: In “Appendix 3. Batch Workflows,” under the comment “# Merge discharge with sample data,” the command line Sample <- mergeReport() was replaced with the following: eList <- mergeReport(INFO, Daily, Sample, NA, interactive=FALSE) Page 87: In “Appendix 3. Batch Workflows,” under the comment # Merge discharge with sample data,” the command line saveResults (savePath) was replaced with the following: saveResults (savePath, eList) Page 87: In “Appendix 3. Batch Workflows,” under the comment “# Check flow history data,” the command line annualSeries <- makeAnnualSeries() was removed. Page 87: I In “Appendix 3. Batch Workflows,” under the comment “# Check flow history data,” the the five command lines plotFlowSingle(istat=7,qUnit=”thousandCfs”) plotSDLogQ() plotQTimeDaily(qLower=1,qUnit=3) plotFour(qUnit=3) plotFourStats(qUnit=3) were each modified to incorporate “eList” as follows: plotFlowSingle(eList,istat=7,qUnit=”thousandCfs”) plotSDLogQ(eList) plotQTimeDaily(eList,qLower=1,qUnit=3) plotFour(eList,qUnit=3) plotFourStats(eList,qUnit=3) Page 88: In “Appendix 3. Batch Workflows,” under the comment “# Check sample data,” the five command lines boxConcMonth() boxQTwice() plotConcTime() plotConcQ() multiPlotDataOverview() were each modified to incorporate “eList” as follows: boxConcMonth(eList) boxQTwice(eList) plotConcTime(eList) plotConcQ(eList) multiPlotDataOverview(eList) Page 88: In “Appendix 3. Batch Workflows,” under the comment “# Run WRTDS model,” the command line modelEstimation() was modified to incorporate “eList” as follows: eList <- modelEstimation(eList) Page 88: In “Appendix 3. Batch Workflows,” under the comments “# Model results,” and “# Explore trend results,” respectively, the command lines plotConcTimeDaily() plotFluxTimeDaily() plotConcPred() plotFluxPred() plotResidPred() plotResidQ() plotResidTime() boxResidMonth() boxConcThree() #Explore trend results: plotConcHist() plotFluxHist() were modified to incorporate “eList” as follows: plotConcTimeDaily(eList) plotFluxTimeDaily(eList) plotConcPred(eList) plotFluxPred(eList) plotResidPred(eList) plotResidQ(eList) plotResidTime(eList) boxResidMonth(eList) boxConcThree(eList) #Explore trend results: plotConcHist(eList) plotFluxHist(eList) Page 88: In “Appendix 3. Batch Workflows,” under the comment “# Multi-plots,” the command line fluxBiasMulti() was modified to incorporate “eList” as follows: fluxBiasMulti(eList) Page 89: In “Appendix 3. Batch Workflows,” under the comment “#Contour plots,” the command line plotContours(yearStart,yearEnd,qBottom,qTop,contourLevels = clevel,qUnit=1) was modified to incorporate “eList” as follows: plotContours(eList,yearStart,yearEnd,qBottom,qTop, contourLevels = clevel,qUnit=1) Page 89: In “Appendix 3. Batch Workflows,” under the comment “#Contour plots,” the command line plotDiffContours(yearStart,yearEnd,qBottom,qTop,maxDiff,qUnit=1) was modified to incorporate “eList” as follows: plotDiffContours(eList,yearStart,yearEnd,qBottom,qTop,maxDiff,qUnit=1) Page 89: In “Appendix 3. Batch Workflows,” under the comment “#Contour plots,” the command lines concChange <- tableChangeSingle(returnDataFrame=TRUE,flux=FALSE) and tableFlowChange(istat=1) were modified to incorporate “eList” as follows: concChange <- tableChangeSingle(eList, returnDataFrame=TRUE,flux=FALSE) and tableFlowChange(eList, istat=1) Page 91: The last command line in “Appendix 3. Batch Workflows” was modified from saveResults (savePath) to incorporated “eList” as follows: saveResults (savePath, eList) Page 90: The entire contents of “Appendix 4. Sample Workflow,” were replaced. Page 92: An “Index of Function Names” section was added. The entire contents of Appendixes 1 and 2 were replaced.