NEWS

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EGRET 3.0.12

• Changed readNWISDaily to use new USGS Water Data API services.
• Changed readNWISInfo to use new USGS Water Data API services.
• Added option ("adjust") to use the flow adjustment within the readNWISDaily and readUserDaily functions. By default, "adjust" is set to TRUE and will add a constant to zero flow values to allow log transformation. In special cases, users may want to keep the zero-flow values, keeping in mind that in those cases many of the modeling functions will not work.
• Cleaned up plotConcTimeSmooth title.
• Added a "fill" option to readDaily functions, see examples in populateDaily for more information.
• Added "fill_missing_daily" function as a standalone.
• Added code to make sure the eList returned from runSeries contained the same columns that would be returned from modelEstimation.
• Revised WRTDSKalman algorithm to speed processing of records with long sample gaps. The behavior and outputs of the WRTDSKalman function have not changed.
• Added the use of genmissing() to WRTDSKalman function on the first and last gaps of the dataset instead of the existing approach where autocorrelation doesn't extend into those gaps.

EGRET 3.0.11 (2025-04-29)

• Changed readNWISSample to use new USGS samples-data service.
• Added Activity_TypeCode to list of columns that are retained.
• Added legacy argument to readWQPSample. This allows the user to choose between legacy and beta WQP services.

EGRET 3.0.10 (2024-11-20)

• Fix bug with 0 concentration values in readWQPSample.
• Style updates.
• Port readNWISSample to Water Quality Portal. NWIS services are retired.
• Move removing the rows of Sample data with 0 concentration to outside compressData
• Add columns from raw WQP data to be retained in Sample dataframe.

EGRET 3.0.9 (2023-04-18)

• Bug fix for the monthly concentration trend results in runPairs.
• Formatting and style updates in plotMonthTrend

EGRET 3.0.8 (2023-03-03)

• Added GenConc to tableResult function
• Added monthly trend to runPairs
• Added plotMonthTrend function
• Improved support for custom axes
• In WRTDSKalman, removed genmissing from first and last iteration
• Improved documentation
• Fixed printSeries if period of record was less than 6 month
• Changed BugsReport URL to https://github.com/DOI-USGS/EGRET/issues
• Assure Sample is sorted chronologically
• plotConcHist and plotFluxHist set to default to the Sample date range instead of the Daily date range.
• Add Kalman option for plotConcTimeDaily and plotFluxTimeDaily
• Improved reproducibility in WRTDSKalman using seed argument.
• Included more columns from the raw data in the Sample data frame. These columns are not used in EGRET functions, but might be useful for further analysis.

EGRET 3.0.7 (2022-01-25)

• Fixed a flux unit label issue for plotTimeSlice
• Added nDays in calculateMonthlyResults

EGRET 3.0.6 (2021-06-01)

• Fixed broken example in saveResults. Function will be deprecated in future versions.

EGRET 3.0.5 (2021-04-09)

• WRTDSKalman function added to improve flux estimations.
• Documentation updates.
• Added a "jitter" option to help with models that do not converge.
• Updated setupYear function to handle edge years better.

EGRET 3.0.0 (2018-08-16)

• Added enhancements for generalized flow normalization
• Functions include runPairs, runSeries, and runGroups

EGRET 2.6.1

• Added foreach dependency which allows parallelizing WRTDS.
• Added the function flexFN for flexible flow normalization.

EGRET 2.6.0 (2016-07-27)

• start/end year argument names unified to yearStart and yearEnd (previously included startYear and endYear)

EGRET 2.5.3

• Argument for randomized censored values names randomCensored

EGRET 2.5.0

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

EGRET 2.3.1 (2015-08-13)

• Removed unnecessary disclaimer.

EGRET 2.2.0 (2015-04-14)

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

EGRET 2.1.4

• Updated CITATION file

EGRET 2.1.1 (2015-02-17)

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

EGRET 2.1.0 (2014-12-18)

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

EGRET 2.0.1 (2014-11-24)

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

EGRET 2.0.0 (2014-11-20)

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

EGRET 1.3.0

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

EGRET 1.2.5

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

EGRET 1.2.4

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

EGRET 1.2.3

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

• Improved documentation, especially example functions.

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

• Progress indicators modified to be more informative.

• Fixed a calculation bug in function plotLogFluxPred.

EGRET 1.2.1

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

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

EGRET 1.1.3

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

EGRET 1.0.0

• Initial release.