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.
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
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
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