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Erik.Leppo@tetratech.comandjon.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 namedleft and right to fitdistrplus::fitdistcens

baytrends 2.0.11.9001

• refactor: Function gamTestSeason to address logic error withgamPenaltyCrit

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• fix: Bad URL in NEWS (1.0.4.9011) Remove, no longer valid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 to14/15

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 againststring
  • 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 forcedependencies

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 in2.0.4.9002 , 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 combinedata frames with Surv objects
• refactor: Updated default gamDiffPeriods to 1999-2001 and2011-2013
• refactor: Updated calculation of fraction of observations that arecensored
• refactor: Updated layer aggregation to allow for computing mediansin 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 previousvalue
• 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 2years to 3 years. New parameter analySpec$gamDiffNumChgYrs set to 3years, but can be set back to 2 years (or any number of years based onuser 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 builderror.

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 frommaintainer 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 andmakeSurvDF.

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 inmakeSurvDF; Issue #50

baytrends 1.2.1.8015

• Release 2020-07-20
• Allow user values for column names / suffixes in unSurv andunSurvDF; 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 Survfields

baytrends 1.2.1.8001

• Release 2020-03-31
• migrated demonstration data set, dataCensored, from qw to Survfields 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 alldocumentation 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 runwithout 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, ratherthan just a vector

baytrends 1.1.0.9004

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

baytrends 1.1.0.9003

• Release 2019-06-06
• Improved error trapping related to required station and parameterlist fields. Added detrended salinity, detrended flow and method listwarnings.

baytrends 1.1.0.9002

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

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 PDFdocs
  • ‘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 foranalySpec_gamLegend_descrip equal to ‘seasMean’, compute predictedvalues based on doy’s spread across above date range. seasMeandoy.xyzmaintained 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 calculatingresiduals (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 orgam4 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 allowfor any gam0-gam5 model

baytrends 1.0.7.9002

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

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 gamformula

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 submitto 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 estimationassuming 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 togamTest
• Added passing stationMasterList, parameterList, and layerLukup toanalyzeOrganizeData
• Corrected getUSGSflow function to accommodate missing values atbeginning/ending of record
• Moved packageplyr from Suggests to Imports inDESCRIPTION
• 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 fromtetratech/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, andlayerLukup to argument list. If not passed then default baytrend dataframes are used. added parmRecensor to depVarList, added usgsGageName tostationList
• selectData: migrated from using stationMasterList, parameterList tostationList and depVarList.
• gamTest: added salinity.detrended to argument list, updatedconditionals used to skip flw_sal models, embedded explicit passing offlow.detrended and salinity.detrended to mergeFlow andmergeSalinity.

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 fromtetratech/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 thebeginning and ending of time series.

baytrends 1.0.3.9007

• Released 2018-05-11
• GitHub commit; Merge pull request #10 fromtetratech/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 thebeginning and ending of time series.

baytrends 1.0.3.9005

• Released 2018-05-09
• GitHub commit; Merge pull request #8 fromtetratech/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 basedon v1.0.2 (release) * Clean up from check for CRAN * Note; NEWS.rmd. Addto git.ignore and .Rbuildignore * Error; sensAdjflow2.R ‘figNum’. Add QCcheck to ensure is defined. * Warning; undocumented dataset; added paramand default to mergeFlow, gamTest, gamPlotCalc, and gamDiff. Also addedto 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 anddetrended.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 toothers that needed to be added: + smwrGraphs; refLine, xyPlot +smwrBase; importRDB * Addition of xyPlot required more functions: +smwrGraphs; setPlot, linearPretty, setPage, timePlot, colorPlot * Removecross 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 functionsthat 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 recentlyadded 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 newlyadded functions. + importFrom(‘grDevices’, ‘col2rgb’, ‘rgb’) +importFrom(‘graphics’, ‘axis’) * Add function from smwr packages; +smwrGraphs; addCaption * Fix ‘assign’ to global environment insmwrGraphs_setPage.R + Line 180, comment out. Is setting to NULL as aprecaution but function isn’t used by baytrends. * Data with ‘no visiblebindig for global variable’ error. + Add a line at the beginning of eachaffected function to reference the data; baytrends::xyz. + PeterDalgaard’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. Line193. + 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.resultoutput
• add USGS gage ID and name to stat.gam.result and chng.gam.resultoutput
• add mgcvOK to stat.gam.result and chng.gam.result output to indicateif 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 forlubridate 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.resultoutput
  • add USGS gage ID and name to stat.gam.result and chng.gam.resultoutput
  • add mgcvOK to stat.gam.result and chng.gam.result output to indicateif 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’ ofhttps://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 toto 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 simplesubstitution

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 withfunction.
  • 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 frompackage.

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 smwrfunctions.
• Add help file for package name, baytrends.R.
• Moved detrended salinity and flow vignettes to extdata.
• Rename seasonally detrended data sets (salinity and flow) withoutspecial 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 underImports).

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 qwobjects. 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 anintervention 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 flowvignette.

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 helpfile 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 betweenEST 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 introducedduplicate files. Some of older versions.
• Hid all smwr*.R files from help file index with keywordsinternal.

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 baytrendsversion.
  • 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 newones different.

baytrends 0.3.3.9010

• Released - 2017-12-19
• Rebuild with minor edits for smwrQW references in files (Find inFiles).
• 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 insmwrBase 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 fromsmwrQW).

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 andremoved smwr packages.
• Add lscens class as well; a2_smwrQW_lcens-class.R.
• Rename mscens from a2 to a3 to preserve collate order ofsmwrQW.

baytrends 0.3.3.9007

• Released - 2017-12-05
• Rename new class objects to appear in R folder first. And will loadfirst.
  • ‘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 justthe 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/currentmean 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 andflow[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 andgamK2). Previously only could specify gamK_CritSel. Specification ofgamK1 and gamK2 now included as part of specifying gamModels
• Enhanced to allow for including flow or salinity as an independentvariable in gam models, including adding gam4 to default list of gammodels evaluated. (Does not include updated forcomputing seasonally averaged/flow[salinity] averaged model in thisversion.)

baytrends 0.2.7

• Released - 7/20/2017
• Enhanced baytrends to output p-values and estimates of changerelated to laboratory method changes (“interventions”) in a style thatcompares 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 nullvalues, see naChar
• updated multiple functions to address ‘no visible binding for globalvariable’ notes
• added@importFrom statements for graphics andstat functions

baytrends 0.2.4

• Released - 2/9/2017
• updated seasonal average model algorithm to be independent ofmn.doy
• added algorithm to compute number of knots in s(cyear) term based onrecord length
• added user ability to set ‘select’ term in mgcv::gam function toTRUE, FALSE, or algorithm selected
• added user ability to set expectation maximization convergencethreshold
• 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 interventiontesting
• Added functionality to trim early data where the level of censoringexceeds desired levels
• Added functionality to thin prediction data set to improve speed andreduce the size of the returned results
• loadData: added functionality to convert date-like fields to POSIXctformat (see argument convDates)
• Add error trap for when all data associated with dependent variableare NA

baytrends 0.2.2

• Released - 10/17/2016
• Updated graphics for censored data

baytrends 0.2.1

• Original release - 10/13/2016