Failing tests on CRAN - Githubissues

... hmmm ... looks like quite a lot of legacy material

==> devtools::check(args = c('--as-cran'))

N checking package subdirectories (855ms) Problems with news in 'NEWS': Cannot process chunk/lines: to git.ignore and .Rbuildignore * Error; sensAdjflow2.R ‘figNum’. Add Cannot process chunk/lines: QC check to ensure is defined. * Warning; undocumented dataset; added Cannot process chunk/lines: param and default to mergeFlow, gamTest, gamPlotCalc, and gamDiff. Also Cannot process chunk/lines: added to data.R (was missing). * Note; Namespace, importFrom. + Cannot process chunk/lines: 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 Cannot process chunk/lines: detrended.salinity.R * Add functions from swmr packages: + smwrBase; %cn%, group2row, isDateLike + smwrQW; mcenKM, mcenMLE, mcenROS, mdlMLE, Cannot process chunk/lines: mdlROS, pcodeNWISqw + smwrStats; rmse, vif * Adding the above led to Cannot process chunk/lines: others that needed to be added: + smwrGraphs; refLine, xyPlot + Cannot process chunk/lines: smwrBase; importRDB * Addition of xyPlot required more functions: + Cannot process chunk/lines: smwrGraphs; setPlot, linearPretty, setPage, timePlot, colorPlot * Cannot process chunk/lines: Remove cross references in ‘seealso’ for some of the imported smwr Cannot process chunk/lines: functions. + importRDB, isLike, linearPretty, refLinem, setPage, Cannot process chunk/lines: setplot, timePlot, cn * importFrom needed for 3 more packages in the Cannot process chunk/lines: newest smwr functions that were added. + importFrom(‘grDevices’, ‘Type1Font’, ‘dev.cur’, ‘extendrange’, ‘gray’, ‘pdfFonts’, ‘rainbow’) + Cannot process chunk/lines: importFrom(‘graphics’, ‘box’, ‘segments’, ‘strwidth’) + Cannot process chunk/lines: importFrom(‘stats’, ‘cov.wt’, ‘dist’, ‘model.matrix’) * Add more smwr Cannot process chunk/lines: package functions: + Base; dectime, dectime2Date + Graphs; datePretty, Cannot process chunk/lines: namePretty, numericData, setColor, setGD, setMargin , setMultiPlot, Cannot process chunk/lines: timePretty * Fix links in most recently added functions; comment out Cannot process chunk/lines: seealso. + datePretty, dectime, namePretty, setColor, setMargin, Cannot process chunk/lines: setMultiPlot * Add importFrom; grDevices colors * Add function from Cannot process chunk/lines: smwr packages; + smwrGraphs; month.USGS, renderPretty, setExplan, Cannot process chunk/lines: transData, linewt (framewt) * Add importFrom for the newly added Cannot process chunk/lines: functions. + importFrom(‘grDevices’, ‘col2rgb’, ‘rgb’) + Cannot process chunk/lines: importFrom(‘graphics’, ‘axis’) * Add function from smwr packages; + Cannot process chunk/lines: smwrGraphs; addCaption * Fix ‘assign’ to global environment in Cannot process chunk/lines: smwrGraphs_setPage.R + Line 180, comment out. Is setting to NULL as a Cannot process chunk/lines: precaution but function isn’t used by baytrends. * Data with ‘no Cannot process chunk/lines: visible bindig for global variable’ error. + Add a line at the beginning Cannot process chunk/lines: of each affected function to reference the data; baytrends::xyz. + Peter Cannot process chunk/lines: Dalgaard’s proposed solution, 2014-Aug - Cannot process chunk/lines: no-visible-binding-for-global-variable-for-data-sets-in-a-package + .chkParameter; parameterList + analysisOrganizeData; parameterList, Cannot process chunk/lines: stationMasterList, layerLukup + selectData; stationMasterList, Cannot process chunk/lines: parameterList, layerLukup * gamDiff, bad usage of stat. Undefined. Line
1. - Change to iSpec\$stat * Remaining issues: + .gamPlotCalc; Cannot process chunk/lines: salinity.detrended + .mergeSalinity; salinity.detrended + gamDiff; Cannot process chunk/lines: 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 ’smwrQWx\’.
- 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
Relea
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 ’smwrQWx\’.
- 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
Relea ✔ checking code files for non-ASCII characters ... ✔ checking R files for syntax errors ... ✔ checking whether the package can be loaded (1.4s) ✔ checking whether the package can be loaded with stated dependencies (1.4s) ✔ checking whether the package can be unloaded cleanly (1.4s) ✔ checking whether the namespace can be loaded with stated dependencies (1.4s) ✔ checking whether the namespace can be unloaded cleanly (1.5s) ✔ checking loading without being on the library search path (1.7s) ✔ checking whether startup messages can be suppressed (3.1s) ✔ checking dependencies in R code (2.4s) ✔ checking S3 generic/method consistency (1.6s) ✔ checking replacement functions (1.3s) ✔ checking foreign function calls (1.7s) ─ checking R code for possible problems ... [17s] OK (17.3s) ✔ checking Rd files (865ms) ✔ checking Rd metadata ... ✔ checking Rd line widths ... ✔ checking Rd cross-references ... ✔ checking for missing documentation entries (1.4s) ✔ checking for code/documentation mismatches (4.2s) ✔ checking Rd \usage sections (2.1s) ✔ checking Rd contents ... ✔ checking for unstated dependencies in examples (549ms) ✔ checking contents of 'data' directory (507ms) ✔ checking data for non-ASCII characters (757ms) ✔ checking LazyData ✔ checking data for ASCII and uncompressed saves ... ✔ checking R/sysdata.rda ... N checking sizes of PDF files under 'inst/doc' ... Unable to find GhostScript executable to run checks on size reduction ✔ checking installed files from 'inst/doc' ... ✔ checking files in 'vignettes' ... ─ checking examples ... [11s] OK (12s) ✔ checking for unstated dependencies in 'tests' ... ─ checking tests ... ✔ Running 'testthat.R' (1.9s) ✔ checking for unstated dependencies in vignettes (521ms) ✔ checking package vignettes ... ─ checking re-building of vignette outputs ... [15s] OK (15.4s) ✔ checking for non-standard things in the check directory ✔ checking for detritus in the temp directory

See 'C:/Users/jharc/Repositories/baytrends.Rcheck/00check.log' for details.

── R CMD check results ─────────────────────────────────────────────────────────────────── baytrends 2.0.11.9002 ──── Duration: 1m 41.6s

❯ checking package subdirectories ... NOTE Problems with news in 'NEWS': Cannot process chunk/lines: to git.ignore and .Rbuildignore * Error; sensAdjflow2.R ‘figNum’. Add Cannot process chunk/lines: QC check to ensure is defined. * Warning; undocumented dataset; added Cannot process chunk/lines: param and default to mergeFlow, gamTest, gamPlotCalc, and gamDiff. Also Cannot process chunk/lines: added to data.R (was missing). * Note; Namespace, importFrom. + Cannot process chunk/lines: 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 Cannot process chunk/lines: detrended.salinity.R * Add functions from swmr packages: + smwrBase; %cn%, group2row, isDateLike + smwrQW; mcenKM, mcenMLE, mcenROS, mdlMLE, Cannot process chunk/lines: mdlROS, pcodeNWISqw + smwrStats; rmse, vif * Adding the above led to Cannot process chunk/lines: others that needed to be added: + smwrGraphs; refLine, xyPlot + Cannot process chunk/lines: smwrBase; importRDB * Addition of xyPlot required more functions: + Cannot process chunk/lines: smwrGraphs; setPlot, linearPretty, setPage, timePlot, colorPlot * Cannot process chunk/lines: Remove cross references in ‘seealso’ for some of the imported smwr Cannot process chunk/lines: functions. + importRDB, isLike, linearPretty, refLinem, setPage, Cannot process chunk/lines: setplot, timePlot, cn * importFrom needed for 3 more packages in the Cannot process chunk/lines: newest smwr functions that were added. + importFrom(‘grDevices’, ‘Type1Font’, ‘dev.cur’, ‘extendrange’, ‘gray’, ‘pdfFonts’, ‘rainbow’) + Cannot process chunk/lines: importFrom(‘graphics’, ‘box’, ‘segments’, ‘strwidth’) + Cannot process chunk/lines: importFrom(‘stats’, ‘cov.wt’, ‘dist’, ‘model.matrix’) * Add more smwr Cannot process chunk/lines: package functions: + Base; dectime, dectime2Date + Graphs; datePretty, Cannot process chunk/lines: namePretty, numericData, setColor, setGD, setMargin , setMultiPlot, Cannot process chunk/lines: timePretty * Fix links in most recently added functions; comment out Cannot process chunk/lines: seealso. + datePretty, dectime, namePretty, setColor, setMargin, Cannot process chunk/lines: setMultiPlot * Add importFrom; grDevices colors * Add function from Cannot process chunk/lines: smwr packages; + smwrGraphs; month.USGS, renderPretty, setExplan, Cannot process chunk/lines: transData, linewt (framewt) * Add importFrom for the newly added Cannot process chunk/lines: functions. + importFrom(‘grDevices’, ‘col2rgb’, ‘rgb’) + Cannot process chunk/lines: importFrom(‘graphics’, ‘axis’) * Add function from smwr packages; + Cannot process chunk/lines: smwrGraphs; addCaption * Fix ‘assign’ to global environment in Cannot process chunk/lines: smwrGraphs_setPage.R + Line 180, comment out. Is setting to NULL as a Cannot process chunk/lines: precaution but function isn’t used by baytrends. * Data with ‘no Cannot process chunk/lines: visible bindig for global variable’ error. + Add a line at the beginning Cannot process chunk/lines: of each affected function to reference the data; baytrends::xyz. + Peter Cannot process chunk/lines: Dalgaard’s proposed solution, 2014-Aug - Cannot process chunk/lines: no-visible-binding-for-global-variable-for-data-sets-in-a-package + .chkParameter; parameterList + analysisOrganizeData; parameterList, Cannot process chunk/lines: stationMasterList, layerLukup + selectData; stationMasterList, Cannot process chunk/lines: parameterList, layerLukup * gamDiff, bad usage of stat. Undefined. Line
1. - Change to iSpec\$stat * Remaining issues: + .gamPlotCalc; Cannot process chunk/lines: salinity.detrended + .mergeSalinity; salinity.detrended + gamDiff; Cannot process chunk/lines: 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 ’smwrQWx\’.
- 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
Relea

❯ checking sizes of PDF files under 'inst/doc' ... NOTE Unable to find GhostScript executable to run checks on size reduction

0 errors ✔ | 0 warnings ✔ | 2 notes ✖

R CMD check succeeded

tetratech / baytrends

Failing tests on CRAN #84

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