NEWS
================
<Erik.Leppo@tetratech.com> and <jon.harcum@tetratech.com>

<!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->

    #> Last Update: 2022-05-05 15:07:56

# baytrends 2.0.8

-   Release 2022-05-05
-   refactor: Update for CRAN submittal
    -   Fixed error associated with update to R 4.2

# baytrends 2.0.7.9003

-   Release 2022-05-05
-   style: Truncate long lines to 80 characters (not all done)
    -   baytrends.R
    -   checkRange.R
    -   chkParameter.R
    -   closeOut.R
    -   data.R
    -   detrended.flow.R
    -   detrended.salinity.R
    -   expectMaxFunctions.R
    -   findFile.R
    -   flwAveragePred.R
    -   gamDiff.R
    -   gdata_nobs.R
    -   getUSGSflow.R
    -   imputeCensored.R
    -   unSurv.R
    -   zzz.R
-   style: Update files with incomplete final lines
-   refactor: Modify if(class()) to if(typeof()) when checking against
    string
    -   createResiduals.R
-   docs: Add logo

# baytrends 2.0.7.9002

-   Release 2022-05-02
-   updated is.na(…) usage: analysisOrganizeData, gamTest, gamTestSeason
    , loadData, selectData, unSurv

# baytrends 2.0.7.9001

-   Release 2022-05-01
-   analysisOrganizeData: updated gamDiffPeriods

# baytrends 2.0.7

-   Release 2022-02-25
-   refactor: Update for CRAN resubmission

# baytrends 2.0.6.9001

-   Release 2022-02-25
-   refactor: Update for CRAN resubmission
    -   Modify if(class) for text comparison in createResiduals.R
    -   Failed check for r-devel-linux-x86_64-debian-gcc,
        r-devel-windows-x86_64
    -   Trim to 80 character lines

# baytrends 2.0.6

-   Release 2022-02-24
-   refactor: Update for CRAN resubmission

# baytrends 2.0.5.8004

-   Release 2022-02-24
-   docs: Move unused packages to suggests in DESCRIPTION
    -   imputeTS and nlme
-   docs: Remove bad URL in NEWS
    -   1.0.2.9012, URL no longer exists

# baytrends 2.0.5.8003

-   Release 2022-02-23
-   refactor: Update analysisOrganizeData time periods, Issue #72

# baytrends 2.0.5.8002

-   Release 2022-02-23
-   refactor: Set default gam years back to 2 from 3, Issue #70
    -   analysisOrganizeData.R
    -   This undoes the edit in Issue #59

# baytrends 2.0.5.8001

-   Release 2022-02-23
-   docs: Move packages from suggests to imports, Issue #71
    -   Force required packages to install by default
-   docs: Update README with example for install package to force
    dependencies

# baytrends 2.0.5

-   Release 2021-05-14
-   refactor: Update for CRAN resubmission, Issue #64

# baytrends 2.0.4.9003

-   Release 2021-05-14
-   refactor: Merge pull request to main branch with updates in
    2.0.4.9002 , Issue #64
-   refactor: Update README install example

# baytrends 2.0.4.9002

-   Release 2021-05-12
-   fix: Updated layer aggregration to use dplyr::bind_rows to combine
    data frames with Surv objects
-   refactor: Updated default gamDiffPeriods to 1999-2001 and 2011-2013
-   refactor: Updated calculation of fraction of observations that are
    censored
-   refactor: Updated layer aggregation to allow for computing medians
    in addition to mean

# baytrends 2.0.4

-   Release 2021-04-19
-   refactor: Update for CRAN resubmission, Issue #61
    -   Fix lifecycle badge URL

# baytrends 2.0.3

-   Release 2021-04-16
-   refactor: Update for CRAN resubmission, Issue #61

# baytrends 2.0.2.9003

-   Release 2021-04-16
-   refactor: DESCRIPTION
    -   Add markdown to Suggests

# baytrends 2.0.2.9002

-   Release 2021-04-16
-   docs: README
    -   Install text update
    -   Removed date field
    -   Trim to 80 characters
-   refactor: DESCRIPTION
    -   Move lubridate from depends to imports
    -   Remove XML (not used), 2.0.0.8005
    -   Add BugReports
-   refactor: Fix misspellings detected with devtools::spell_check()
    -   DESCRIPTION
    -   analysisOrganizeData
-   refactor: Remove unneeded vignette “test”
-   refactor: Use ‘\<-’ instead of ‘=’ for assignment
    -   detrended.flow
    -   detrended.salinity
    -   findFile
    -   gamPlotDisp
    -   gamPlotDispSeason
    -   gamTest
    -   gamTestSeason
    -   imputeCensored
    -   layerAggregation
    -   loadData
    -   makeSurvDF
    -   seasAdjFlow2
    -   selectData
    -   smwrBase_baseDay
    -   smwrBase_eventProcessing
    -   unSurv
    -   zzz
-   refactor: Omit trailing semicolons
    -   analysisOrganizeData
    -   detrendedFlow
    -   detrendedSalinity
-   refactor: findFile
    -   Use on.exit() after setwd() to ensure it returns the previous
        value
-   refactor: Set up GitHub Actions
    -   check
    -   pkgdown
        -   Remove ‘docs’ folder

# baytrends 2.0.2.9001

-   Release 2021-04-15
-   Change default number of years used in computing differences from 2
    years to 3 years. New parameter analySpec$gamDiffNumChgYrs set to 3
    years, but can be set back to 2 years (or any number of years based
    on user input).

# baytrends 2.0.2

-   Release 2020-11-23
-   Submit to CRAN

# baytrends 2.0.1.9001

-   Release 2020-11-23
-   Add .git to .Rbuildignore
-   Remove one RDA from vignette folder (too large).

# baytrends 2.0.1

-   Release 2020-11-20
-   Submit to CRAN

# baytrends 2.0.0.9002

-   Release 2020-11-20
-   Edit DESCRIPTION for CRAN.
-   Tweak Detrending_Flow_and_Salinity_Data vignette for build error.

# baytrends 2.0.0.9001

-   Release 2020-11-19
-   DESCRIPTION
    -   Remove Disclaimer.
    -   Add journal reference.
-   baytrends package help.
    -   Added Disclaimer text.

# baytrends 2.0.0

-   Release 2020-11-18
-   Ready for CRAN submittal

# baytrends 2.0.0.8005

-   Release 2020-11-13
-   Run rhub::check_for_linux
    -   DESCRIPTION, Remove packages not being used.
        -   methods
        -   XML
        -   zCompositions
    -   DESCRIPTION, Move package from Import to Suggests (vignette
        only)
        -   dplyr
    -   Processing_Censored_Data.R
        -   remove library(dplyr)
        -   Add dplyr:: to bind_rows

# baytrends 2.0.0.8004

-   Release 2020-11-12
-   Run rhub::check_for_linux
    -   Update png to PNG in vignette for compatibility with Linux.
-   detrended.flow.R
    -   baytrends::nobs to nobs
-   Rebuild pkgdown site.
-   DESCRIPTION
    -   Remove gdata from Imports.

# baytrends 2.0.0.8003

-   Release 2020-11-09
-   Run rhub::check_for_cran
    -   Update date in DESCRIPTION
-   Add tests for impute function.

# baytrends 2.0.0.8002

-   Release 2020-11-09
-   Import nobs from gdata as a new function.
    -   gdata in danger of being archived. No meaningful response from
        maintainer after 6 weeks.
    -   Imported ‘as is’ with a note in the help section.
-   detrended.flow
    -   Modified to use baytrends::nobs instead of gdata::nobs.
-   Add tests for nobs function.

# baytrends 2.0.0.8001

-   Release 2020-08-25
-   Test and check for CRAN.
    -   NEWS
        -   Two URLs from http to https
    -   DESCRIPTION
        -   Maintainer, add middle initial to match Authors

# baytrends 2.0.0

-   Beta Release 2020-08-05

# baytrends 1.2.1.8020

-   Release 2020-08-04
-   vignette & documentation cleanup

# baytrends 1.2.1.8019

-   Release 2020-07-29
-   added vignette for processing censored data

# baytrends 1.2.1.8018

-   Release 2020-07-22
-   updated documentation for versions >v1.2.1.8015 code

# baytrends 1.2.1.8017

-   Release 2020-07-22
-   Add tests
    -   unSurv
    -   unSurvDF
    -   makeSurvDF
-   unSurv.R
    -   Tweak example text to match examples in unSurvDF and makeSurvDF.

# baytrends 1.2.1.8016

-   Release 2020-07-22
-   Allow user values for column names / suffixes in makeSurvDF; Issue
    #49
-   Update example in unSurv and unSurvDF to match example in
    makeSurvDF; Issue #50

# baytrends 1.2.1.8015

-   Release 2020-07-20
-   Allow user values for column names / suffixes in unSurv and
    unSurvDF; Issue #50

# baytrends 1.2.1.8014

-   Release 2020-07-20
-   Expose layeraggregation as a function available to the user; Issue
    #47
    -   Update reference in analysisOrganizeData

# baytrends 1.2.1.8013

-   Release 2020-07-14
-   added dplyr to DESCRIPTION > Imports
-   move survival & mgcv to DESCRIPTION > Imports

# baytrends 1.2.1.8012

-   Release 2020-07-07
-   added makeSurvDF functions

# baytrends 1.2.1.8011

-   Release 2020-07-06
-   added unSurvDF and imputeDF functions

# baytrends 1.2.1.8010

-   Release 2020-07-02
-   updated .layerAggregation for Survival objects

# baytrends 1.2.1.8009

-   Release 2020-07-02
-   Updates after “check”; Issue #46
    -   Add survival::foo for new functions from survival package.
        -   selectData.R
        -   imputeCensored.R
    -   Add importFrom survival Suv to selectData.R

# baytrends 1.2.1.8008

-   Release 2020-07-01
-   remove deprecated html files and data sets

# baytrends 1.2.1.8007

-   Release 2020-06-30
-   createResiduals: corrected error for non-Surv objects

# baytrends 1.2.1.8006

-   Release 2020-06-30
-   remove depracated qw functions

# baytrends 1.2.1.8005

-   Release 2020-06-29
-   remove qw vignette

# baytrends 1.2.1.8004

-   Release 2020-06-23
-   updated to gamTestSeason to process Surv and non-Surv objects

# baytrends 1.2.1.8003

-   Release 2020-06-23
-   updated to gamTest to process non-Surv objects

# baytrends 1.2.1.8002

-   Release 2020-05-22
-   updated gamTest (and related support functions) to run using Surv
    fields

# baytrends 1.2.1.8001

-   Release 2020-03-31
-   migrated demonstration data set, dataCensored, from qw to Surv
    fields for censored data

# baytrends 1.2.1

-   Release 2020-03-31
-   Wrap up new version number for CRAN submittal.

# baytrends 1.2.0.9001

-   Release 2020-03-31
-   Additional changes for CRAN.
    -   Bad URL, comment out.
        -   smwrQW_x\_dlimit.R
    -   Example run time > 10 seconds, add ‘dontrun’.
        -   gamPlotDispSeason
        -   gamTestSeason
        -   gamTest
-   Changes for Linux build.
    -   data_censored_text.csv and data_censored_test.rda
    -   Remove from examples with ‘dontrun’.
        -   qw.export.R
        -   qw.import.R
    -   Leave in vignette_qw.R

# baytrends 1.2

-   Release 2020-03-30
-   Final version for resubmittal to CRAN.

# baytrends 1.1.0.9020

-   Release 2020-03-30
-   Recheck master branch.
-   Update pdfs in “doc” folder.
    -   Replace ‘baytrends_overview.pdf’..
    -   Add ‘statgam_and_statchng_output_fields.pdf’
-   NEWS
    -   Not showing. Ensure NEWS.md available.
    -   Replace double-quotes with single-quotes.

# baytrends 1.1.0.9019

-   Release 2020-03-29
-   Merge Dev_04 branch with master branch.

# baytrends 1.1.0.9018

-   Release 2020-03-29
-   Updates for CRAN in Dev_04 branch.

# baytrends 1.1.0.9017

-   Release 2020-03-23
-   Updates for CRAN prior to re-submittal to CRAN.

# baytrends 1.1.0.9016

-   Release 2020-03-20
-   Rebuild package after merging with dev02 branch to ensure all
    documentation is copacetic.

# baytrends 1.1.0.9015

-   Release 2020-03-09
-   Check with R version 3.6.2 (released 2020-02-29).
-   Add links to gamTest documentation. Issue #40.
-   Add ReadMe.RMD and update it.
    -   Updated badges from overall CRAN to individual flavors.
        -   Windows, OSX, and Linux.
-   Update saveDF documentation.
-   IsLike updates to structure. Issue #39.
-   Checked with rhub for Linux dev versions of R.
-   Update pkgdown website.

# baytrends 1.1.0.9014

-   Release 2020-01-28
-   Add missing functions from smwrGraphs so all examples will run
    without any errors.
    -   Keyword internal so won’t show in help.
        -   smwrGraphs_colors.R
        -   smwrGraphs_logPretty.R
        -   smwrGraphs_setAxis.R
-   Remove references to smwrGraphs package vignette in help files.
    -   Several function had in the ‘dont run’ section of their
        examples.
        -   smwrGraphs_addCaption.R
        -   smwrGraphs_colorPlot.R
        -   smwrGraphs_month.USGS.R
        -   smwrGraphs_refLine.R
        -   smwrGraphs_setColor.R
        -   smwrGraphs_setPage.R
        -   smwrGraphs_timePlot.R
        -   smwrGraphs_xyPlot.R
-   rdname block error.
    -   smwrBase_isLike.R
-   Update examples for errors
    -   findFile.R
-   Add data to data folder and data.R from smwr\* packages.
    -   pcodeColData
    -   Q05078470
    -   QW05078470
    -   QWstacked
-   Comment out examples.
    -   smwrBase_importRDB.R
    -   swmrQW_x\_readNWQLdl.R
-   DESCRIPTION
    -   R >= 3.5.0 based on Check warning.

# baytrends 1.1.0.9013

-   Release 2020-01-20
-   Updates to pass testing with development version of R for Linux.
    -   \_saveDF to \_save_df
        -   saveDF.R
    -   dataCensored.test.rd to data_censored_test.rd
        -   vignette_qw.Rmd
        -   vignette_qw.r
        -   qw.import.Rd
        -   qw.imoprt.R
    -   dataCensored_TEST.csv to data_censored_test.csv
        -   vignette_qw.Rmd
        -   vignette_qw.r
        -   qw.export.R
        -   qw.import.R
-   pkgdown
    -   Update files.
    -   Add URL to GitHub repo header.

# baytrends 1.1.0.9012

-   Release 2019-11-06
-   Added pkgdown website.

# baytrends 1.1.0.9011

-   Release 2019-12-21
-   Function createResiduals modified to return data frame, df, rather
    than just a vector

# baytrends 1.1.0.9004

-   Release 2019-06-25
-   Minor punch list issues from v\*.9003 and .9002. Add option
    analySpec$showGamNumOnPlot to add gam # onto plot

# baytrends 1.1.0.9003

-   Release 2019-06-06
-   Improved error trapping related to required station and parameter
    list fields. Added detrended salinity, detrended flow and method
    list warnings.

# baytrends 1.1.0.9002

-   Release 2019-05-31
-   Added functions gamTestSeasonal and gamPlotDispSeasonal to compute
    and only display a seasonal mean for a single date or for a date
    range.

# baytrends 1.1.0

-   Release 2019-03-14
-   Release update for CRAN
    -   As minor upgrade.

# baytrends 1.0.8

-   Release 2019-03-14
-   Release update for CRAN
    -   As bug fix.

# baytrends 1.0.7.9011

-   Release 2019-03-14
-   Fix date in DESCRIPTION.
-   Add library creation notebook to .Rbuildignore

# baytrends 1.0.7.9010

-   Release 2019-03-13
-   Updates based on ‘check’ to prepare for submittal to CRAN.
    -   Added some oxygen tags
    -   Added .install_extras to vignettes folder for additional PDF
        docs
    -   ‘dot’ prefix functions with keyword internal
    -   Removed example for hidden function .createResiduals
    -   .findFile examples marked as do not run.

# baytrends 1.0.7.9009

-   Release 2019-03-11
-   Update from devtools::session_info to sessioninfo::session_info.
    Issue #31.
    -   closeOut function.
-   Rebuild vignettes.
    -   Names not showing in help file.

# baytrends 1.0.7.9008

-   Release 2019-03-05
-   seasMeandoy.xyz removed from prediction data set

# baytrends 1.0.7.9007

-   Release 2018-12-28
-   Based on date range entered into analySpec_gamLegend_legend for
    analySpec_gamLegend_descrip equal to ‘seasMean’, compute predicted
    values based on doy’s spread across above date range.
    seasMeandoy.xyz maintained in prediction data set along with
    seasMeanMin, seasMeanMean, and seasMeanMax.

# baytrends 1.0.7.9006

-   Release 2018-08-08
-   created loadModelsResid function to include models for calculating
    residuals (i.e., primarily gam4 and gam5 without cyear)
-   updated createResidual to save plots to file

# baytrends 1.0.7.9005

-   Release 2018-08-03
-   updated createResidual to skip over cases (i.e., specific stations)
    where there were insufficient data to run specified gam formula

# baytrends 1.0.7.9004

-   Release 2018-08-01
-   added loadModels function to facilitate gam formula specification;
    updated createResidual to include a ‘fall back’ option to use gam2
    or gam4 if user had selected gam3 or gam5 and the model did not run
    (expected due to intervention)

# baytrends 1.0.7.9003

-   Release 2018-07-30
-   function deSeasonalize renamed to createResiduals; extended to allow
    for any gam0-gam5 model

# baytrends 1.0.7.9002

-   Release 2018-07-18
-   update function deSeasonalize to allow for s(doy) and perform basic
    testing

# baytrends 1.0.7.9001

-   Release 2018-07-13
-   added function deSeasonalize

# baytrends 1.0.7

-   Release 2018-07-12
-   Resubmit to CRAN

# baytrends 1.0.6.9001

-   Release 2018-07-12
-   DESCRIPTION
    -   Additional_repositories to URL
    -   Update and lengthen Description.

# baytrends 1.0.6

-   Release 2018-07-09

-   # Resubmit to CRAN

    # baytrends 1.0.5.9002

-   Release 2018-07-11

-   Update ANOVA table to allow for no parametric terms in gam formula

# baytrends 1.0.5.9001

-   Release 2018-07-09
-   Fix CRAN submission NOTES
    -   Restructure my names with middle initial as maintainer.
    -   donotrun on examples for detrended.flow and detrended.salinity

# baytrends 1.0.5

-   Released 2018-07-06
-   Create ‘release’ on GitHub.
-   Submit to CRAN

# baytrends 1.0.4.9012

-   Released 2018-07-06
-   selectData
    -   Remove example.
-   CHECK
    -   0 errors \| 0 warnings \| 0 notes

# baytrends 1.0.4.9011

-   Released 2018-07-06
-   DESCRIPTION
    -   Change ‘maintainer’ from Jon Harcum to Erik Leppo so Erik can
        submit to CRAN.
    -   Change ‘additional repositories’ to GitHub. Was
        <https://owi.usgs.gov/R>.
-   .Rbuildignore
    -   Add cran-comments.md
-   qw.import; example qw.names
    -   Rename variables without ‘f’; po4, no23, and nh4
    -   Remove variables pp and pn.
-   detrended.flow
    -   Fix CHECK NOTE for figNum.
    -   Added ‘figNum’ to globalVariables in zzz.R
    -   Assigned figNum as NULL before assign as zero.
-   dataCensored
    -   Fix CHECK WARNING
-   selectData
    -   Example not working. Mark as ‘donotrun’ while troubleshoot.

# baytrends 1.0.4.9010

-   Released 2018-07-05
-   Add .github to .Rbuildignore to avoid CHECK note.
-   Added dates to NEWS releases.
-   Update data.R for dataCensored.

# baytrends 1.0.4.9009

-   Released 2018-07-03
-   dataCensored: aligned data set with companion journal article

# baytrends 1.0.4.9008

-   Released 2018-07-03
-   dataCensored: aligned data set with companion journal article

# baytrends 1.0.4.9007

-   Released 2018-07-02
-   selectData: improved error trap for lack of data

# baytrends 1.0.4.9006

-   Released 2018-6-12
-   updated documentation

# baytrends 1.0.4.9005

-   Released 2018-6-12
-   Added baytrends version to to iSpec and improved readme file

# baytrends 1.0.4.9004

-   Released 2018-6-12
-   Added list of seasonal models to iSpec

# baytrends 1.0.4.9003

-   Released 2018-6-12
-   Updated impute function to include maximum likelihood estimation
    assuming normal and lognormal distribution

# baytrends 1.0.4.9002

-   Released 2018-6-12
-   Updated NEWS and DESCRIPTION.
-   Updated online documentation for analysisOrganizeData function
-   pass parameterList from gamTest to .chkParameter

# baytrends 1.0.4.9001

-   Released 2018-6-12
-   Updated NEWS and DESCRIPTION.
-   Updated online documentation for analysisOrganizeData function
-   pass parameterList from gamTest to .chkParameter

# baytrends 1.0.4

-   Released 2018-05-14
-   Created release 1.0.4 on GitHub

# baytrends 1.0.3.9021

-   Released 2018-05-14
-   Updated NEWS and DESCRIPTION.
-   Check results: no errors, warnings, or notes.

# baytrends 1.0.3.9020

-   Released 2018-05-13
-   GitHub commit; Merge pull request #16 from tetratech/12Mar2018

# baytrends 1.0.3.9019

-   Released 2018-05-13
-   GitHub commit; v1.0.3.9011
-   missed layerLukup -> layerList naming convention

# baytrends 1.0.3.9019

-   Released 2018-05-12
-   GitHub commit; Merge pull request #15 from tetratech/12Mar2018

# baytrends 1.0.3.9018

-   Released 2018-05-12
-   GitHub commit; v1.0.4

# baytrends 1.0.3.9017

-   Released 2018-05-12
-   GitHub commit; v1.0.4

# baytrends 1.0.3.9016

-   Released 2018-05-12
-   GitHub commit; v1.0.4
-   Added passing of salinity.detrended and flow.detrended to gamTest
-   Added passing stationMasterList, parameterList, and layerLukup to
    analyzeOrganizeData
-   Corrected getUSGSflow function to accommodate missing values at
    beginning/ending of record
-   Moved package `plyr` from Suggests to Imports in DESCRIPTION
-   Remaining Check issue with no visible binding for global variable;
    salinity.detrended
    -   .gamPlotCalc
    -   .mergeSalinity
    -   gamDiff

# baytrends 1.0.3.9015

-   Released 2018-05-12
-   GitHub commit; Merge pull request #14 from tetratech/detrended_files
-   Detrended files

# baytrends 1.0.3.9014

-   Released 2018-05-12
-   GitHub commit; v1.0.3.9009
-   Set data frames for station and layer list to not use factors

# baytrends 1.0.3.9013

-   Released 2018-05-12
-   GitHub commit; v1.0.3.9009
-   Further clean up for handling detrended files.

# baytrends 1.0.3.9012

-   Released 2018-05-12
-   GitHub commit; v1.0.3.9009
-   Migrate gamDiff for detrended flow and salinity.

# baytrends 1.0.3.9011

-   Released 2018-05-12
-   GitHub commit; v1.0.3.9008
-   analysisOrganizeData: add parameterList, stationMasterList, and
    layerLukup to argument list. If not passed then default baytrend
    data frames are used. added parmRecensor to depVarList, added
    usgsGageName to stationList
-   selectData: migrated from using stationMasterList, parameterList to
    stationList and depVarList.
-   gamTest: added salinity.detrended to argument list, updated
    conditionals used to skip flw_sal models, embedded explicit passing
    of flow.detrended and salinity.detrended to mergeFlow and
    mergeSalinity.

# baytrends 1.0.3.9010

-   Released 2018-05-12
-   GitHub commit; documentation typographical error correction

# baytrends 1.0.3.9009

-   Released 2018-05-11
-   GitHub commit; Merge pull request #11 from
    tetratech/fix_flow_retrieval

# baytrends 1.0.3.9008

-   Released 2018-05-11
-   GitHub commit; v1.0.3.9005
-   updated getUSGSflow function to fill in missing flow values at the
    beginning and ending of time series.

# baytrends 1.0.3.9007

-   Released 2018-05-11
-   GitHub commit; Merge pull request #10 from
    tetratech/fix_flow_retrieval

# baytrends 1.0.3.9006

-   Released 2018-05-011
-   GitHub commit; v1.0.3.9005
-   updated getUSGSflow function to fill in missing flow values at the
    beginning and ending of time series.

# baytrends 1.0.3.9005

-   Released 2018-05-09
-   GitHub commit; Merge pull request #8 from
    tetratech/harcum_development

# baytrends 1.0.3.9004

-   Released 2018-05-09
-   GitHub commit; v1.0.3.9004

# baytrends 1.0.3.9003

-   Released 2018-05-07
-   GitHub commit; v1.0.3.9003
-   Last fix for Check. Ready for submittal to CRAN. Issue #1

# baytrends 1.0.3.9002

-   Released 2018-05-07
-   GitHub commit; v1.0.3.9002
-   Verified merge of DEV branch into Master.  
-   Fixed an issue with plyr and
-   Re-ran Check to get ready for CRAN submittal (Issue #1 ).

# baytrends 1.0.3.9001

-   Released 2018-05-07
-   Merge Development Branch (v.0.2.9012 DEV) with master branch.
-   Resolve conflicts:
    -   DESCRIPTION
    -   NAMESPACE
    -   NEWS (left alone as will rebuild)
    -   NEWS.rmd
    -   mergeFlow.R
    -   baytrends_LibraryCration.nb.html (left alone as will rebuild)

# baytrends 1.0.2.9012

development branch \* Released - 2018-05-03 \* branch of master based on
v1.0.2 (release) \* Clean up from check for CRAN \* Note; NEWS.rmd. Add
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
