NEWS

---

baytrends 1.0.2

to git.ignore and .Rbuildignore \* Error; sensAdjflow2.R ‘figNum’. Add

QC check to ensure is defined. \* Warning; undocumented dataset; added

param and default to mergeFlow, gamTest, gamPlotCalc, and gamDiff. Also

added to data.R (was missing). \* Note; Namespace, importFrom.

importFrom(‘stats’, ‘BIC’, ‘StructTS’, ‘aggregate’, ‘approx’, ‘cov2cor

• ‘dnorm’, ‘filter’, ‘fitted’, ‘hat’, ‘integrate’, ‘logLik’, ‘lowess’, ‘lsfit’, ‘na.omit’, ‘na.pass’, ‘naresid’, ‘pchisq’, ‘ppoints’, ‘qf’, ‘residuals’, ‘sd’, ‘tsSmooth’, ‘update’, ‘var’) + importFrom(‘utils’, ‘flush.console’, ‘getS3method’, ‘modifyList’, ‘read.table’, ‘strOptions’, ‘write.table’) \* Added QC to define figNum. + Copied from seasAdjflow2.R to detrended.flow.R and

detrended.salinity.R \* Add functions from swmr packages: + smwrBase

• %cn%, group2row, isDateLike + smwrQW; mcenKM, mcenMLE, mcenROS, mdlMLE,

mdlROS, pcodeNWISqw + smwrStats; rmse, vif \* Adding the above led to

others that needed to be added: + smwrGraphs; refLine, xyPlot

smwrBase; importRDB \* Addition of xyPlot required more functions:

smwrGraphs; setPlot, linearPretty, setPage, timePlot, colorPlot

Remove cross references in ‘seealso’ for some of the imported smwr

functions. + importRDB, isLike, linearPretty, refLinem, setPage

setplot, timePlot, cn \* importFrom needed for 3 more packages in the

newest smwr functions that were added. + importFrom(‘grDevices

• ‘Type1Font’, ‘dev.cur’, ‘extendrange’, ‘gray’, ‘pdfFonts’, ‘rainbow’) +

importFrom(‘graphics’, ‘box’, ‘segments’, ‘strwidth’)

importFrom(‘stats’, ‘cov.wt’, ‘dist’, ‘model.matrix’) \* Add more smwr

package functions: + Base; dectime, dectime2Date + Graphs; datePretty

namePretty, numericData, setColor, setGD, setMargin , setMultiPlot

timePretty \* Fix links in most recently added functions; comment out

seealso. + datePretty, dectime, namePretty, setColor, setMargin

setMultiPlot \* Add importFrom; grDevices colors \* Add function from

smwr packages; + smwrGraphs; month.USGS, renderPretty, setExplan

transData, linewt (framewt) \* Add importFrom for the newly added

functions. + importFrom(‘grDevices’, ‘col2rgb’, ‘rgb’)

importFrom(‘graphics’, ‘axis’) \* Add function from smwr packages;

smwrGraphs; addCaption \* Fix ‘assign’ to global environment in

smwrGraphs_setPage.R + Line 180, comment out. Is setting to NULL as a

precaution but function isn’t used by baytrends. \* Data with ‘no

visible bindig for global variable’ error. + Add a line at the beginning

of each affected function to reference the data; baytrends::xyz. + Peter

Dalgaard’s proposed solution, 2014-Aug

no-visible-binding-for-global-variable-for-data-sets-in-a-package

• .chkParameter; parameterList + analysisOrganizeData; parameterList,

stationMasterList, layerLukup + selectData; stationMasterList

parameterList, layerLukup \* gamDiff, bad usage of stat. Undefined. Line

• 193. + Change to iSpec\$stat \* Remaining issues: + .gamPlotCalc;

salinity.detrended + .mergeSalinity; salinity.detrended + gamDiff

salinity.detrended

• # baytrends 1.0.2.9011 - Released - 2018-05-02 - v1.0.2.9002 - add standard error to stat.gam.result and chng.gam.result output - add USGS gage ID and name to stat.gam.result and chng.gam.result output - add mgcvOK to stat.gam.result and chng.gam.result output to indicate if mgcv::gam ran ok - removed median as option for summarizing data across layers - expose impute function for simple substitution (0, 1/2dl, dl) conversion of qw data to vector - added error handling to trap mgcv::gam non-convergence errors # baytrends 1.0.3 - Released - 2018-05-03 - Release version # baytrends 1.0.2.9013 - Released - 2018-05-03 - Fix lubridate and plyr conflict. Issue \#6. - gamTest change import lubridate mgcv plyr to importFrom for lubridate mdy and plyr rbind.fill. # baytrends 1.0.2.9012 - Released - 2018-05-03 - Update versioning in NEWS and DESCRIPTION # baytrends 1.0.2.9011 - Released - 2018-05-02 - v1.0.2.9002 in DESCRIPTION - v1.0.3.0000 in NEWS - Updates: - add standard error to stat.gam.result and chng.gam.result output - add USGS gage ID and name to stat.gam.result and chng.gam.result output - add mgcvOK to stat.gam.result and chng.gam.result output to indicate if mgcv::gam ran ok - removed median as option for summarizing data across layers - expose impute function for simple substitution (0, 1/2dl, dl) conversion of qw data to vector - added error handling to trap mgcv::gam non-convergence errors # baytrends 1.0.2.9010 - Released - 2018-05-02 - v1.0.2.9002 - add intervention label to GAM Parameter Coefficient table. # baytrends 1.0.2.9009 - Released - 2018-05-02 - v1.0.2.9002 - Added error trapping to address non-convergence of mgcv::gam # baytrends 1.0.2.9007 - Released - 2018-05-01 - Merge branch ‘master’ of <https://github.com/tetratech/baytrends> # baytrends 1.0.2.9006 - Released - 2018-05-01 - corrected storage of USGS codes # baytrends 1.0.2.9005 - Released - 2018-05-01 - documentation updates # baytrends 1.0.2.9004 - Released - 2018-05-01 - documentation updates # baytrends 1.0.2.9004 - Released - 2018-05-01 - documentation updates # baytrends 1.0.2.9003 - Released - 2018-05-01 - only allow ‘mean’ for computing layer aggregation. # baytrends 1.0.2.9002 - Released - 2018-05-01 - added USGS gage id, USGS gage name, and gam diff standard error to to stat.gam.result and chng.gam.result output data sets # baytrends 1.0.2.9001 - Released - 2018-05-01 - exposed impute function; updated impute function to focus on simple substitution # baytrends 1.0.2.0000 - Released - 2018-03-26 - Release version # baytrends 1.0.1.9015 - Released - 2018-03-26 - Function Updates - detrended.flow - detrended.salinity - Update detrended vignette for changes in functions. - Updates from ‘check’. # baytrends 1.0.1.9014 - Released - 2018-03-26 - Update vignettes - /docs/baytrends_overview.pdf - /vignettes/vignette_qw.Rmd - New vignette - /vignettes/create_Seasonally_Detrended_Flow_and_Salinity_Data_Sets.Rmd - Update detrended.salinity.R for changes in names in ‘sal’ data. # baytrends 1.0.1.9013 - Released - 2018-03-26 - salinity data. - \_GenerateData_sal.R - sal.rda - data.R # baytrends 1.0.1.9012 - Released - 2018-03-21 - Add baytrends_overview.pdf to ‘doc’ as vignette. # baytrends 1.0.1.9011 - Released - 2018-03-21 - Add detrended.salinity function. - Includes revised (smaller) data set (sal) for use with function. - Updated data.R for ‘sal’ data. # baytrends 1.0.1.9010 - Released - 2018-03-21 - Add detrended.flow function. - Add helper functions as internal functions. - Remove detrended flow and salinity data files and vignettes from package. # baytrends 1.0.1.9009 - Released - 2018-03-20 - Update internal functions. - mdlKM – hide - flwAveragePred – hide - qw.export – make visible - as.qw-method – hide - qw-class – hide # baytrends 1.0.1.9008 - Released - 2018-03-19 - Update documentation. - Vignette - data.R - baytrends.R - Code edit in SelectData.R. # baytrends 1.0.1.9007 - Released - 2018-03-16 - Fixes from ‘check’ - data.R - file size - dlimit and censorLevels from smwrQW - strip.blanks from smwrGraphs # baytrends 1.0.1.9006 - Released - 2018-03-14 - Update qw vignette. # baytrends 1.0.1.9005 - Released - 2018-03-14 - Tweak qw.export and qw.import functions and vignette. # baytrends 1.0.1.9004 - Released - 2018-03-02 - Tweak qw.export Rounding export. - QW object import internal function, qw.import. - QW object vignette. # baytrends 1.0.1.9003 - Released - 2018-03-01 - QW object export internal function, qw.export. # baytrends 1.0.1.9002 - Released - 2018-02-28 - More clean up of linked ‘see also’ references in smwr functions. - Add help file for package name, baytrends.R. - Moved detrended salinity and flow vignettes to extdata. - Rename seasonally detrended data sets (salinity and flow) without special characters. # baytrends 1.0.1.9001 - Released - 2018-02-23 - Clean up after running Check. - Move /data-raw to /inst/data-raw - Document /data in /R/data.R - DESCRIPTION, remove dataRetrieval from Suggests (already under Imports). # baytrends 1.0.1 - Released - 2018-02-16 - Clean up and send out to project users. # baytrends 1.0.0.9002 - Released - 2018-02-15 - Add back censoring.R from smwrQW package as it is needed for qw objects. Was removed in v0.3.3.9016 # baytrends 1.0.0.9001 - Released - 2018-02-05 - Improve error trap for when to allow baytrends to run an intervention model. - selectData.R - gamTest.R # baytrends 1.0.0 - Released - 2018-02-01 - Set as release on GitHub. # baytrends 0.3.3.9019 - Released - 2018-02-01 - Update vignettes. Remove setwd(). # baytrends 0.3.3.9018 - Released - 2018-02-01 - Updated Vignettes to run with data in vignettes folder. - Added function fillMissing from smwrBase for detrended flow vignette. # baytrends 0.3.3.9017 - Released - 2018-01-31 - Fix errors in Namespace noted in Check. # baytrends 0.3.3.9016 - Released - 2018-01-31 - Remove unneeded functions from smwrQW package. # baytrends 0.3.3.9015 - Released - 2018-01-31 - Created vignettes: - QW object conversion - Detrended flow data - Detrended salinity data - Add and remove funtions from index with keyword internal. # baytrends 0.3.3.9014 - Released - 2018-01-12 - Add more functions, as.x, to keywords internal to remove from help file list. - Add Erik W Leppo as author in DESCRIPTION. # baytrends 0.3.3.9013 - Released - 2018-01-11 - Modified dataCensored to include timezone. Should fluctuate between EST and EDT. - Exported original data file with TZ included with smwrQW present. Then rebuilt dataCensored with smwrQW removed. # baytrends 0.3.3.9012 - Released - 2018-01-05 - Fix files names. OneDrive on development computer introduced duplicate files. Some of older versions. - Hid all smwr\*.R files from help file index with keywords internal. # baytrends 0.3.3.9011 - Released - 2017-12-20 - dataCensored - Clean up ‘data-raw’ folder and GenerateData script. - Overwrite smwrQW dependant dataCensored.rda file with baytrends version. - Remove dataCensored CSV files from . - Move - Rename temporary R scripts from ‘x\_*’ to ’smwrQW_x\_*’. - Known files that are needed already have smwrQW prefix. Keep new ones different. # baytrends 0.3.3.9010 - Released - 2017-12-19 - Rebuild with minor edits for smwrQW references in files (Find in Files). - Added smwrQW_is.na.R. - Edits to \_GenerateData_dataCensored.R. - qw object creates but still fails when adding to data.frame. - Copy in all smwrQW function not already added. Test if builds. # baytrends 0.3.3.9009 - Released - 2017-12-06 - Added function as.qw from smwrQW. - Modified include from qw-class.R to a1_smwrQW_qw-class.R. - Did not add as.lcens or as.mcens as they require other functions in smwrBase and smwrQW. - Added ‘data-raw’ folder. - Created all parts of dataCensored object and saved to ‘data-raw’. - Added script to build dataCensored. - Renamed back to baytrends on GitHub and in development code. - a1_smwrQW_qw-class.R - Comment out ‘name’ - as.qw.R - Comment out ‘See Also’ (refers to function not ported from smwrQW). # baytrends 0.3.3.9008 - Released - 2017-12-05 - Resave dataCensored.rda. Installed smwrQW so could open and resets ‘qw’ class to first reference in namespace (baytrends). Then saved and removed smwr packages. - Add lscens class as well; a2_smwrQW_lcens-class.R. - Rename mscens from a2 to a3 to preserve collate order of smwrQW. # baytrends 0.3.3.9007 - Released - 2017-12-05 - Rename new class objects to appear in R folder first. And will load first. - ‘smwrQW_qw-class.R’ (prefix ‘a1\_’). - ‘smwrQW_mcens-class.R’ (prefix ‘a2\_’). - Need to fix functions and examples that are looking for smwrQW. - analysisOrganizeData - selectData - gamDiff - gamTest # baytrends 0.3.3.9006 - Released - 2017-12-05 - Removed swmr packages from R install. - Rebuild baytrends with smwrBase functions included. - baseDay - baseDay2decimal - Removed import from smwrQW from gamTest. Had import for smwrQW. - Added class objects qw and mcens from smwrQW. - Renamed all added R files with smwrBase\_ or smwrQW\_. # baytrends 0.3.3.9005 - Released - 2017-12-05 - Remove all smwrX packages (Base, Graphs, QW, and Stats). Not just the oprhaned QW and Stats. Base and Graphs DEPEND on QW as well. # baytrends 0.3.3.9004 - Released - 2017-12-04 - Modified NEWS to NEWS.rmd. # baytrends 0.3.3.9003 - Released - 2017-12-04 - Remove ‘smwrQW’ from Depends in DESCRIPTION. - Remove ‘smwrStats’ from Suggests in DESCRIPTION. # baytrends 0.3.3.9002 - Released - 2017-12-04 - Add Notebooks for Library Creation and Testing to . # baytrends 0.3.3.9001 - Released - 2017-12-04 - Renamed to baytrends033 - Test version to GitHub # baytrends 0.3.3 - Released - 11/24/2017 - Updated gamDiff: flow/salinity model to calculate baseline/current mean differences based on average conditions - Updated gamPlotDisp: corrected full model display option # baytrends 0.3.2 - Released - 8/09/2017 - Updated seasonal model to include averaging over season and flow\[salinity\] # baytrends 0.3.1 - Released - 8/6/2017 - Added function loadExcel to facilitate reading user Excel files. Similar functionality to the existing function loadData. - Changed nomenclature from tidalStations to stationMasterList - Enhanced knot specification to allow 2 levels of knots (gamK1 and gamK2). Previously only could specify gamK_CritSel. Specification of gamK1 and gamK2 now included as part of specifying gamModels - Enhanced to allow for including flow or salinity as an independent variable in gam models, including adding gam4 to default list of gam models evaluated. (**Does** not include updated for computing seasonally averaged/flow\[salinity\] averaged model in this version.) # baytrends 0.2.7 - Released - 7/20/2017 - Enhanced baytrends to output p-values and estimates of change related to laboratory method changes (“interventions”) in a style that compares method “A” to “B”, “B” to “C”, “C” to “D”, etc. rather than “A” to “B”, “A” to “C”, “A” to “D”, etc. # baytrends 0.2.6 - Released - 4/25/2017 - corrected usage of user specified station file # baytrends 0.2.5 - Released - 3/15/2017 - updated loadData to allow for specifying strings indicating null values, see naChar - updated multiple functions to address ‘no visible binding for global variable’ notes - added @importFrom statements for graphics and stat functions # baytrends 0.2.4 - Released - 2/9/2017 - updated seasonal average model algorithm to be independent of mn.doy - added algorithm to compute number of knots in s(cyear) term based on record length - added user ability to set ‘select’ term in mgcv::gam function to TRUE, FALSE, or algorithm selected - added user ability to set expectation maximization convergence threshold - added F-stat evaluation and ANOVA table modification # baytrends 0.2.3 - Released - 11/09/2016 - Documentation updated - Added default settings to for gam formula for intervention testing - Added functionality to trim early data where the level of censoring exceeds desired levels - Added functionality to thin prediction data set to improve speed and reduce the size of the returned results - loadData: added functionality to convert date-like fields to POSIXct format (see argument convDates) - Add error trap for when all data associated with dependent variable are NA # baytrends 0.2.2 - Released - 10/17/2016 - Updated graphics for censored data # baytrends 0.2.1 - Original release - 10/13/2016