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

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

    #> Last Update: 2024-02-12 12:03:12.250764

# baytrends 2.0.11

- Release 2024-02-12
- refactor: Bump version for CRAN submittal

# baytrends 2.0.10.9001

- Release 2024-02-12
- fix: Bad URL in NEWS (1.0.4.9011) Remove, no longer valid

# baytrends 2.0.10

- Release 2024-02-09
- refactor: Bump version for CRAN submittal

# baytrends 2.0.9.9003

- Release 2024-02-07
- refactor: Update GitHub Actions to v2;
  usethis::use_github_actions(“foo”)

# baytrends 2.0.9.9002

- Release 2024-02-07
- docs: Update package documentation, Issue \#80
- refactor: Update analysisOrganizeData for time periods, 12/13 to 14/15

# baytrends 2.0.9.9001

- Release 2024-02-07
- docs: Add URL to DESCRIPTION per Pull Request, PR \#81

# baytrends 2.0.9

- Release 2023-04-04
- gamTest.R: updated \|\| to \| to remove coercion to ‘logical(1)’
  warning

# baytrends 2.0.8.9001

- Release 2022-05-05
- docs: Remove logo

# 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 owi USGS gov slash
    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
