NEWS

Erik.Leppo@tetratech.com and jon.harcum@tetratech.com

#> Last Update: 2024-07-26 09:35:21.683005

baytrends 2.0.12

• release 2024-07-27
• refactor: Bump version number for submittal to CRAN

baytrends 2.0.11.9004

• release 2024-07-27
• refactor: Update CRAN comments

baytrends 2.0.11.9003

• release 2024-07-26
• docs: Add rhubv2 for testing before posting to CRAN

baytrends 2.0.11.9002

• refactor: Function impute to pass a dataframe with two columns named left and right to fitdistrplus::fitdistcens

baytrends 2.0.11.9001

• refactor: Function gamTestSeason to address logic error with gamPenaltyCrit

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• fix: Bad URL in NEWS (1.0.4.9011) Remove, no longer valid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
• .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