#> Last Update: 2025-01-02 14:40:32.353055
2025-01-02
- refactor: Update HOBO U20 example data file
2024-12-27
- refactor: Fix typo in Report_QC.rmd, Issue #167
- inst/rmd
- inst/shiny-examples/ContDataQC/rmd
2024-12-27
- fix: Update shinyalalert for HOBO reformat, Issue #164
- Shiny removes empty directories, add ‘remove.text’ file before upload
- tests: Add code to library creation script to add temp file to HOBO
folder
- Avoid having empty directory removed during upload to ShinyApps.io
2024-12-26
- fix: Update shinyalert for HOBO reformat for multiple files, Issue #164
2024-12-26
- fix: Update link to Shinay 3c3_QCThresh_Eval
2024-12-23
- refactor: Update Excel file in Shiny 3c3_QCThresh_Eval
2024-12-23
- refactor: Update workflow step 2 text (3a1_About)
2024-12-23
- refactor: Text edits of flags in Report_QC.rmd
- refactor: Update Report_QC.rmd in shiny rmd folder
2024-12-23
- refactor: Update thresholds display table
- DO Spike
- Add DO Adj, DO % Sat, and Salinity
2024-12-23
- refactor: Remove extra mainPanel on 3c (Main_QCThresh_EditThresh)
- Reclaim blank screen space
- Space reserved for mainPanel not being used
2024-12-17
- docs: Add vignettes to inst folder so can link to from GitHub
2024-12-17
- docs: Build vignettes
2024-12-02
- fix: Update Shiny file upload parameter check to use names from config, Issue #166
2024-11-14
- fix: Update USGS gage data retreival for midnight entries, Issue #165
- Same as miniDOT Issue #163
2024-11-04
- refactor: Add pop up on HOBOware reformat for date time conversion,
Issue #164
- Success and failure
2024-10-18
- refactor: Add error message for bad files in miniDOT concatenate in Shiny app
2024-06-26
- fix: Update minidoct_cat() function to display midnight values, Issue #163
- refactor: Update config file, Issue #162
- threshold for flat tolerance sensor depth from 0.0 to 0.01
- ext
- config.ORIG.R
- config.COOL.R
- config.WARM.R
- config.Lakes.metric.R
- shiny-examples
- Config_Default.R
- Config_default.zip
- Config_Lakes_meters.zip
- Config_Lakes_metric.R
- Config_Template.R
- Config_Template.zip
- Config.R
2024-03-01
- refactor: Update Shiny app
- typos
- indents
- replace some tables with figures
2024-02-27
- refactor: Update Shiny app text and tables, Issue #156
- refactor: Update Shiny app exit links, Issue #159
2024-02-20
- refactor: Text updates on most tabs of Shiny app
- refactor: Remove Troubleshooting info in Shiny app, except for Console
- refactor: Figures of tables to tables in Shiny app, Issue #157
2024-01-31
- refactor: Shiny app add “exit” tags to html links, Issue #159
2024-01-31
- refactor: Replace images in Shiny, Issue #157
2024-01-31
- refactor: Apply revised USEPA template (2023-12-15), Issue #155
2024-01-31
- refactor: Move version number from title to about, Issue #161
- refactor: Add file identifiers to download links, Issue #160
2024-01-25
- refactor: QC function to move QC columns, Issue #154
- Flag. and Comment.MOD cols next to measurement columns
- Ignore Date, Time, and Date.Time
2023-09-28
- refactor: Use USEPA template
2023-09-18
- refactor: Update stats plots with legend
- fun.Stats.R
- fun.Stats.File.R
2023-09-18
- fix: Change stats N from total records to non-NA records, Issue #140
- length(x) to sum(!is.na(x))
- SumStats.updated.R
- fun.Stats.R
- fun.Stats.File.R
- fun.PeriodStats.R
2023-09-15
- refactor: Add text for tab references instead of links
2023-09-14
- refactor: Added config file display name
- Main Functions - Run Functions
- Main Functions - QC Thresholds - Upload Custom Thresholds
2023-09-14
- refactor: Edits to Shiny tabs
2023-09-13
- refactor: Update period stats plots with legend
- inst_PeriodStats.rmd
- fix: Update example code in PeriodStats
2023-09-12
- refactor: Change widths on Edit Thresholds tab
- Some boxes too small
2023-09-11
- refactor: Shiny tab text updates
- miniDOT concatenate
- miniDOT reformat
- Advanced (new tab)
- Formatting Files
2023-09-08
- refactor: Shiny tab text updates
- Check Input
- Main
- Organize Files
- HOBOware Reformat
- refactor: Rename Sensor File Modification to Automated Reformatting
- Add About tab
2023-09-08
- refactor: Update Thresholds tab order
- refactor: Add text to Main - Import tab
2023-09-08
- refactor: Update formatminiDOT function to remove columns with all NA
values
- Fixes issue with ContDataQC QC function
2023-08-31
- refactor: Update config (lakes) in library and Shiny, Issue #153
- refactor: Shiny app updates
- Update some images
- Update text
2023-08-31
- refactor: Shiny app updates
- Main tab name Troubleshoot to Troubleshooting
- Date format box text on HOBOware reformat
- Move QC Tips from Main Functions to About
2023-08-31
- refactor: Update base config file, Issue #153
- refactor: Update ThresholdsCheckWorksheet links in Shiny, Issue #153
2023-08-14
- style: Update formating in global.R
- refactor: Change order, locations, and names of tabs in Shiny app, Issue #152
2023-08-11
- style: Update Report_SiteSummary spacing
2022-12-22
- fix: Shiny custom edit thresholds
- Change default config to version without env statement
2022-12-22
- update: Update Shiny app
- QC Thresholds, Edit Thresholds, Issue #148
2022-09-22
- update: update Shiny app
- Fix numbered tabs 7 and 8
2022-09-22
- update: update Shiny app
- Update links
- Remove (comment out) EPA template
- Rearrange Console and Test Data tabs
2022-09-19
- update: update Shiny app
- Update text
2022-09-15
- update: update Shiny app
- Change names of navbar tabs and order
2022-09-15
- style: Use EPA Template for shiny app
2022-06-15
- refactor: Bump to whole version number
2022-06-15
- refactor: Add dummy files to blank Shiny app folders to avoid being deleted
2022-06-15
- refactor: Update readme examples to use remotes instead of devtools package
2022-06-15
- feature: Add miniDOT functions to Shiny, Issue #141
2022-06-07
- fix: Modify config.R for salinity, Issue #138
- Update other copies in package
2022-05-31
- fix: Modify flags so can handle all na, Issue #143
- fun.QC.file.R
- fun.QC.R
- Report_QC.rmd
- Base package and Shiny
2022-05-25
- refactor: Update minidot_cat function, Issue #141
- Remove filename parameter and use serial number from input file
- feature: Add format minidot function, Issue #141
2022-05-25
- refactor: Updates to minidot_cat function, Issue #141
- refactor: Add missing return value for help script line 937
2022-05-25
- feature: Add miniDOT concatenate function, Issue #141
- Modified compile_do_folder.R from mnsentinellakes
2022-05-24
- refactor: Update Report_QC.rmd used in Shiny app, Issue #117
- feature: Prototype site data summary report, Issue #142
- feature: Add google analytics to Shiny app
2022-05-17
- fix: Update Report_QC.rmd table statements with useNA = ifany, Issue #117
- fix: Add new parameters to QC routine
- DO adj, Issue #117
- DO pct sat, Issue #117
- Salinity, Issue #138
2022-05-11
- feature: Add salinity to config file, Issue #138
- feature: Add salinity to config.out RMD, Issue #138
2022-05-11
- fix: Modify config file for DO percent saturation
2022-04-14
- refactor: Add keywords internal to two new functions
- fix: Rebuild package so new functions included
- docs: Add Yadong Xu as contributor
2022-04-14
- feature: Add new functions from Yadong for EMVL project
- Pull request #137
2022-01-18
- refactor: Update Tim’s Threshold Analysis zip file
2022-01-18
- fix: Update broken links in Shiny to Config_Lakes_Metric.R, Issue
#132
- Linux case sensitive and wasn’t working online
- refactor: Update text for readability in Shiny for Edit Thresholds
2022-01-17
- refactor: Update QC Thresholds tab text in Shiny, Issue #131
2022-01-17
- refactor: Update QC Thresholds tab in Shiny, Issue #131
- Change order and names of tabs
- Add Evaluate code as a download
2021-12-22
- fix: Updated custom config thresholds to handle quotes, Issue #130
- docs: Added Ben Block as contributor for work on custom thresholds
2021-12-22
- fix: Duplicate entry in config file, Issue #130
- Updated all versions in package and shiny folders
- Chlorophylla spike thresholds duplicated
2021-12-21
- feature: Shiny, add custom thresholds for config file, Issue #130
- merge pull request
2021-10-25
- refactor: Rename “master” branch to “main”.
2021-10-25
- fix: Update fun.Stats.R and fun.Stats.File.R to use WaterLevel instead of GageHeight, Issue #124
2021-06-25
- refactor: Update config file with changes to units.
- Correct some that were not correct
- refactor: Update config copy script in data-raw
- docs: Add markdown package to DESCRIPTION Suggests
- Needed to to avoid GitHub Action build failure when creating vignettes
2021-06-25
- style: Shiny, update code style in ui, server, and global
- Not all code just code relevant to current refactor item
- refactor: Shiny add all parameters to table on 4MainFunction,
CheckInput tab
- Issue #127
2021-06-23
- refactor: Updated version number in ui.R
2021-06-23 * refactor: Shiny, pdated link locations to new repository (ShinyAppDocuments). * style: Updated location of .rmd files to www/ folder.
2021-06-23
- refactor: Shiny updates to app description text
2021-06-23
- style: Removed Documents folder
- Move to new repository
2021-06-21
- refactor: Create new version release
2021-06-21
- refactor: Consolidate Shiny app updates from pull request, Issue #126
2021-06-18
- refactor: Update Shiny
- Final updates to section 7
2021-06-18
- refactor: Update Shiny
- Beginning updates to section 7
2021-06-18
- refactor: Update Shiny
- Updated section 8 text
2021-06-18
- refactor: Update Shiny
- Updated text in section 9
2021-06-18
- refactor: Update Shiny
- Updates to section 2 and section 3 - added sidebarpanels within tabsets rather than at bottom of pages
2021-06-18
- refactor: Update Shiny
- Updates sections 8 & 9.
2021-06-18
- refactor: Update Shiny
- Updated section 4a, 4b, and 5.
2021-06-18
- refactor: Update Shiny
- Updated 4a documents link
2021-06-18
- refactor: Update Shiny
- Made final updates to section 3a code and began section 4 code updates
2021-06-18
- refactor: Update Shiny
- Updated 3b files
2021-06-18
- refactor: Update Shiny
- Updated 3a section
2021-06-18
- refactor: Update Shiny
- Updated tab 6 information
2021-06-18
- refactor: Update Shiny
- Updated 2d HOBOware reformat
2021-06-18
- refactor: Update Shiny
- Added 2c info to rmd and documents
2021-06-18
- refactor: Update Shiny
- Updates to 2a and 2b text and data sources. Added files to documents folder.
2021-06-18
- refactor: Update Shiny
- Updated 2a text and created Documents folder
2021-06-18
- refactor: Update Shiny
- moved tab_Reformat.R under tab_2DataPrep subtab “Formatting files”
2021-06-18
- refactor: Update Shiny
- Update to ui.R subfiles - added all necessary new tab structures.
- Added content to tab_1Overview using .rmd file.
2021-06-18
- refactor: Update Shiny
- Beginning updates in ui.R and subsequent code to accommodate application changes.
2021-04-19
- refactor: Remove extra columns from QC routine, Issue #123
- fun.QC.R
- fun.QC.File.R
2021-04-19
- refactor: Shiny, changes to tabs
2021-04-19
- refactor: Shiny
- Rearrange tabs
- Split out Advanced tab into Console, Config, and Hobo
2021-04-02
- style: Fix spelling, devtools::spell_check()
- README
- NEWS
- fun.parseID.R
- fun.Report.File.R
- Vignette_ContDataQC.Rmd
- Vignette_Config.RMD
- fun.GageData.R
- Vignette_Lakes.Rmd
- refactor: Reknit files
- README
- Vignettes
- style: Fix items from goodpractice::gp()
- Trim lines to 80 characters
- CompSiteCDF.R
- test_export_rLakeAnalyzer.R
- RBIcalc.R
- format.Hobo.R
- fun.Helper.R
- Export.IHA.R
- Export.StreamThermal.R
- fun.CustomConfig.R
- fun.PeriodStats.R
- fun.Stats.R (partial)
- fun.DateFormat.R (partial)
- Replace ‘=’ with ‘<-’
- fun.Helper.R
- Change T or F to TRUE or FALSE
- CompSiteCDF.R
- Trim lines to 80 characters
2021-03-31
- feature: Add custom config with metric units for Lakes, Issue #119
- extdata.Lakes.metric.R
2021-02-24
- feature: Shiny formatHobo add inputselect for date format, Issue #117
- refactor: Shiny server.R remove full.names from zip routine preventing proper construction of download zip file, Issue #109
2021-02-23
- refactor: Fix date in example reformatHobo for DO file, Issue #117
- refactor: Update reformatHobo date time conversion to account for no seconds and 2 vs 4 digit years, Issue #117
2021-02-23
- refactor: Shiny server, zip files add -j to strip folder names, Issue #109
- feature: Add additional DO parameters to config, Issue #117
- refactor: Update other versions of config, Issue #117
- docs: Update README install directions
- docs: README, trim lines to 80 characters
- docs: Move planned updates from NEWS to README
- refactor: Update Report_Config.rmd for new DO parameters, Issue #117
- refactor: Update Report_Config.rmd so sensor depth and water level are next to each other
- refactor: Copy updated Report_Config.rmd to Shiny app, Issue #117
- feature: Add additional DO parameters (n=3) to reformatHobo function , Issue #117
2021-02-08
- refactor: Rework logger deployment start/end to use first non-NA date
time instead of first and last row; Issue #107
- fun.QC.R
- fun.QC.File.R
2021-02-05
- style: Trim lines and fix spelling, fun.DateTimeFormat
2021-02-04
- refactor: Update config spike flags for water level, Issue #116
- Update other versions of config
2021-02-04
- refactor: Update Config_Template.zip in Shiny, Issue #116
- docs: Retain NEWS.md for pkgdown to build changelog
2021-02-04
- refactor: Update thresholds in config.R for sensor depth, Issue #116
2021-02-04
- refactor: Modify “gross” check for water level, sensor depth, and
discharge , Issue #113
- Was only checking for negative values
- Set to evaluate like all other measured values
- fun.Helper.R, fun.CalcQCStats()
- refactor: Update config.R comments for gross check as above, Issue
#113
- Update other copies of config
- refactor: Add missing spike thresholds for water level, config.R
- refactor: Set water level tests to values for sensor depth
2021-01-27
- feature: Begin updates to add comparison of deployment periods, Issue
#108
- Add helper functions for rquery.t.test()
- feature: Add MonthDay to data during QC operation, Issue #111
- style: Trim some lines to 80 characters
- fun.Stats.R
2021-01-25
- docs: Update example in ContDataQC for aggregating lake/depth files, Issue #85
2021-01-22
- refactor: Change ContDataQC() parameter fun.AddDeployCol from default
FALSE to TRUE
- Shiny app will now auto add the deployment field
2021-01-21
- refactor: Report_QC.rmd, add Water Level vs. Water Temp plots, Issue #110
- style: Report_QC.rmd, trim lines to 80 characters
- refactor: Copy Report_QC.rmd to shiny
2021-01-21
- refactor: Revise Vignette_Config so it doesn’t fail.
2021-01-21
- refactor: Replace getwd() with tempdir() in examples
- export_rLakeAnalyzer
- PeriodStats
- Export.IHA of getwd() to save file
- feature: Create logger deployment column during QC routine, Issue
#107
- ContDataQC
- fun.QC
- fun.QC.File
- feature: Add logger deployment to config.R, Issue #107
- myName.LoggerDeployment
- myName.LoggerDeployment.start
- myName.LoggerDeployment.end
- Added to myNames.Order (add after DateTime)
- style: Trim lines to 80 characters
- Export.rLakeAnalyzer
- Vignette_Config
- ContDataQC_Vignette
- refactor: Rename ContDataQC_Vignette to Vignette_ContDataQC
- refactor: Update config.R
- style: Updates to config.R, make order of Air and Water Pressure consistent
- refactor: Create data-raw file to propagate changes in config.R to shiny
- refactor: Update Vignette_Config with changes to config.R
- refactor: Update Config.R and its dependent versions
- inst.ORIG.R
- inst-examples_Template.R
- inst-examples_Template.zip
- refactor: Replace getwd() with tempdir()
- Vignette_Lakes
- Vignette_ContDataQC
- docs: Update examples in Vignette_ContDataQC
- docs: Update example in Export.IHA with text from ContDataQC
2021-01-20
- tests: Add test for export_rLakeAnalyzer
2021-01-18
- refactor: Add “RAW” columns for flags in QC step Issue #106
2021-01-18
- refactor: Shiny server, turn off renameAggOutput, Issue #104
2021-01-15
- refactor: Add ability to Shiny to handle DOCX files to renameAggOutput in global.R
- refactor: Redefine file name output for AggregateData.File
- Use input file names to get date range
- docs: Remove docs folder for pkgdown site
- Using GitHub Actions to build pkgdown in a different branch
- style: Trim to 80 character lines
- zfun.AggregateData
- zfun.AggregateData.File
2021-01-14
- refactor: Update name of Config.zip to Config_Template.zip in shiny ui.R
2021-01-14
- refactor: Rename custom config and add instructions, Issue #104
- Won’t work if use newenv() within custom file
- docs: Update text in config.out function about newenv()
2021-01-13
- fix: Shiny app custom config not loading
2021-01-13
- fix: Correct download of www/Config.zip
- fix: Replace unneeded concatenation without arguments
- Aquarius_Data_Acquisition_PADEP
- style: Trim lines to 80 characters
- fun.Config.Out
- fix: Example output to tempdir() rather than getwd()
- fun.Config.Out
2021-01-08
- refactor: Update version number display in Shiny app.
2021-01-08
- feature: Update formatHobo to output water level, Issue #100
2021-01-08
- refactor: Update CompSite.CDF 2nd example
2021-01-08
- fix: Update CompSite.CDF so does not save to working directory
- use tempdir in example and update code to use dir.output
- style: Trim to 80 character lines
- fun.Helper.R
2021-01-08
- refactor: Modify LakeID~Depth siteID to LakeID–Depth
- File names with ~ are non-portable.
- style: Trim to 80 characters.
- Vignette_Lakes
- fun.ParseID
- refactor: Update help text in fun.ParseID for change in Lake ID delimiter
2021-01-07
- feature: Modify formatHobo to use water level, issue #100
2021-01-07
- feature: Add water level as a parameter for QC checks, Issue #100
- refactor: Remove gage height as a parameter for QC checks, Issue #100
- feature: Modify USGS download to change gage height to water level,
Issue #100
- Match HOBOware terminology (most of user base)
- style: Trim lines to 80 characters
- config.R
- fun.GageData.R
- fun.Report.R
- fun.Report.File.R
- fix: Update copies and version of config.R with edits, Issue #100
- feature: Update rmd files from GageHeight to WaterLevel
- Report_Config
- Report_QC
- refactor: Copy RMD files from package directory to shiny
- refactor: Remove unneeded concatenation of a constant
- server.R
- Export.rlakeAnalyzer.R
- feature: Change Gage Height to Water Level, fun.QC
- feature: Add Water Level, fun.QC.File
- refactor: Change getwd() to tempdir(), ContDataQC example
- refactor: Update ContDataQC example
- getwd() to tempdir()
- paste0() to file.path()
- fix: Fix typo in fun.Stats.File.R
- seq_len(row… to seq_len(nrow…
- refactor: Remove use of installr package as is windows only
- Move example text to details of ContDataQC function
2021-01-04
- refactor: Add config_R.zip to shiny app in www folder
- refactor: server.R update fun.myReport.format to “” from “html”
2021-01-04
- chore: Recreate pkgdown GitHub Action
2021-01-04
- chore: Rebuild pkgdown by removing all
2021-01-04
- chore: Pkgdown site
- chore: Config change default report format from HTML to DOCX, Issue
#102
- Update data/config.R
- Copy to inst/shiny-examples/ContDataQC/www
- Update inst/shiny-examples/ContDataQC/config.RMDdir.R
- Copy to inst/extdata/config.ORIG.R
- Update inst/extdata/config.RMDdir.R
- chore: Add to .Rbuildignore
- data-raw folder
- shiny rsconnect
- fix: Add missing global variable bindings
- ContDataQC
- fun.AggregateData
- fun.Report
- fun.Report.File
- fun.Stats
- fix: README, replace failing license badge
2020-12-29
- chore: Add docs folder for pkgdown
2020-12-29
- style: Replace ‘=’ with ‘<-’
- style: Avoid long code lines over 80 characters
- partial
- style: Remove trailing blank lines
- partial
- docs: DESCRIPTION, add reshape2 to Suggests
- Only used in Export.rLakeAnalyzer
- docs: Update license information
- fix: Export.IHA, Add missing parameter to function and update code
- fix: Add foo:: to function calls where missing
- fun.Helper
- docs: CompSiteCDF, add missing argument to documentation.
- docs: fun.ParseID, rename arguments so function and documentation match
- docs: data.R, Add “data_raw_ECO66G12_AW_20160128_20160418”
- fix: Export.IHA, fix argument name, myFile to fun.myFile
- chore: CompSiteCDF, fix agument name, myFile to file.input
2020-12-28
- fix: Add foo:: to function calls where missing
- fun.QC.File
- fun.PeriodStats
- fun.QC.File
- fun.Helper
- ProcessData_CompSiteCDF
- ProcessData_PeriodSummary
- ProcessData_test2
- ProcessData_test4
- fix: ContDataQC example, comment out installr section.
2020-12-28
- docs: Reapply GitHub Action pkgdown.
2020-12-28
- docs: DESCRIPTION, installr to Remotes
2020-12-28
- docs: Remove old pkgdown yaml from root directory.
- GitHub Action for pkgdown was not building.
2020-12-28
style: RBIcalc, remove trailing ; refactor: replace 1:foo() with seq_len(foo()) + server + global + CompSiteCDF + Export.IHA + fun.DateFormat + fun.GageData + fun.Helper + fun.QC.File + fun.QC + fun.Stats.File + fun.Stats + zfun.AggregateData.Files + zFun.AggregateData + config docs: DESCRIPTION, Add Remotes for non-CRAN (GitHub) packages + StreamThermal + IHA
2020-12-25
- ci: Add GitHub Action test-coverage
- docs: ReadMe, Add codecov badge
- docs: ReadMe, Add codefactor badge
2020-12-25
- docs: Add GitHub Action pkgdown (adds gh-pages branch)
- docs: Remove docs folder for pkgdown website
2020-12-25
- ci: Add GitHub Actions CI
- ci: Remove Travis CI yaml
- docs: ReadMe, Add GitHub Actions CI CMD check badge
- docs: ReadMe, Add lifecycle badge
2020-12-22
- Shiny, USGS gage data
- Add placeholder text for start and end dates (YYYY-MM-DD).
- Add console message output for QA testing.
- Modify zip file name for download, Issue #98
2020-12-21
- Shiny add helper function for QC routine to keep only first entry when
group by Date.Time.
- Also add ‘unique’ after QC checks to avoid extra lines being created.
2020-12-18
- Shiny, minor tweak.
- v2.0.5.9038 had an edit to server.R that broke the formatHobo function when run on ShinyApps.io.
- Undid the edit.
- Added message output for the log file to track the error’s location.
2020-12-16
- formatHobo, update help text, Issue #97
2020-12-16
- Shiny app, add ContDataQC::formatHobo(), Issue #96.
- ui.R
- server.R
2020-12-11
- global.R
- Change timeFormater function to show time without seperators.
- 20201211_16_32_00 to 20201211_163200
- Change timeFormater function to show time without seperators.
2020-12-11
- zfun.ContDataQC.R
- Update example for file version of Aggregate.
- myFile “Aw” to “AW”.
- Update example for file version of SummaryStats.
- Add comment characters for second myFile.
- Update example for file version of Aggregate.
- fun.Stats.File.R
- Remove as.numeric() from doBy::summaryBy() statements.
- server.R
- Remove “.” from file path for zip for stats procedure.
2020-12-11
- global.R and server.R
- Fix Aggregate not working (file error), Issue #92
- Fix file delete issues, Issue #93
2020-12-10
- server.R
- Add outline headers.
- Change Config file download.
- ui.R
- Update version number.
- Aggregate Report in Shiny app.
2020-12-03
- data
- Test2 files and data to ‘test2’.
- Shiny app update RMD files with current ones.
2020-10-16
- CRAN checks.
- Example lines longer than 100 characters.
- ContDataQC
- RBIcalc
- Example lines longer than 100 characters.
2020-10-07
- Update to config.load() to ensure custom config files load into the proper environment.
- zfun.ContDataQC.R
- Load config.ORIG.R from package as first step before custom config.
2020-01-27
- Rebuild pkgdown website.
2020-01-27
- Rebuild pkgdown website.
2020-01-27
- README
- Add more info about sometimes package dependencies not loading and things not working.
2019-06-11
- Add pkgdown website.
2019-06-11
- Update config vignette to be more specific on modifying variables.
2019-05-17
- Fix for R v3.6.0 staged install, Issue #88.
- DESCRIPTION
- Remove StagedInstall: no
- README
- Installation instructions, added extra line for devtools to work properly.
- DESCRIPTION
- README
- Add badges.
2019-05-02
- DESCRIPTION
- StagedInstall: no for R v3.6.0. Issue #88.
2019-05-02
- DESCRIPTION
- StagedInstall: false for R v3.6.0. Issue #88.
2019-04-17
- Add formatting directions for Hoboware files.
- extdata powerpoint
- Meta PDF
2019-04-02
- Update version number.
- Repeated 9018.
2019-03-26
- Report_PeriodStats.rmd, Issue #76
- Points to lines.
- Add min/max shaded
2019-03-07
- ReadMe
- Add link for config file modifications. Issue #86
2019-03-05
- Vignette for editing config file. Issue #86
2019-02-25
- Ensure the package can handle “LakeID~Depth” as “SiteID”
- Add Lake delimiter to Config files.
- ContData.env$myDelim_LakeID <- “~”
- Add Lake delimiter to Config files.
- Reporte_Aggregate.rmd
- Turn on ggplot for dual parameter plots.
- ContDataQC
- Add example (and data) for File Aggregate with Lake data. Issue #85.
- Add a “Lakes” vignette.
2019-02-22
- Config.Out
- Add functionality to save a copy of the config file.
2019-02-22
- Update code to allow for plots in PeriodStats Report to use ggplot.
Issues #83 and 84.
- Incomplete. Still using base graphics.
2019-02-21
- Update plots in Aggregate Report to ggplot. Issues #83 and 84.
2019-02-21
- Update plots in QC Report to ggplot. Issues #83 and 84.
- Import files fix, na.strings=
- Use c(““,”NA”) not just ““.
2019-02-19
- Export.rLakeAnalyzer, Issue #82
- Examples for rLakeAnalyzer functions:
- schmidt.plot
- ts.schmidt.stability
- Examples for rLakeAnalyzer functions:
2019-02-13
- Export.rLakeAnalyzer
- Add rLakeAnalyzer package DESCRIPTION under suggests.
- Generate output function. Issue #82.
- Include example for rLakeAnalyzer::wtr.heat.map
- Added example plot of multiple depths using ggplot2.
- Added ggplot2 to DESCRIPTION suggests.
2019-01-21
- formatHobo
- Update to account for Lake SiteIDs to include depth.
2019-01-17
- Add shiny app to package, Issue #81
- DESCRIPTION
- Add David Gibbs
- Add packages for Shiny and sort.
2019-01-17
- Make report output optional in ContDataQC, Issue #80.
- ContDataQC
2019-01-09
- Example script to get data from Aquarius.
- Vignette (at end)
- extdata/Aquarius_Data_Aquisition_PADEP.r
2019-01-09
- configuration files.
- Add Data0_Original folder to each configuration file.
2019-01-09
- formatHobo, deal with 2 digit years in Date Time field, Issue #75
2019-01-09
- Configuration thresholds not displaying correctly, Issue #74.
- Suspect gross hi value was reported incorrectly for all parameters.
- Used the gross fail low value.
- Updated RMD files.
- Report_Config.rmd
- Report_QC.rmd
- Updated Vignette to use extdata/config.ORIG.R rather than a manual copy and paste of R/config.R.
- Ensured R/config.R and extdata/config.ORIG.R are identical (used
compare in Notepad++). Differences noted below.
- Section header for Report Format
- myReport.Dir
- different number of blank lines at end of file.
2019-01-07
- folder “Data0_Original”, Issue #73.
- Function ContDataQC
- So is the same as the formatHobo function.
- Update Vignette.
- Function ContDataQC
2018-12-21
- Config.
- Add Warm.
- Rename Cold to Cool.
2018-12-13
- Revised release including vignette.
2018-12-13
- gitignore contained inst/doc. Removed so will load correctly to GitHub.
2018-12-13
- Rebuild Vignette. Not visible in v2.0.4.
2018-12-05
- New release version.
2018-12-05
- Fix error introduced in v2.0.2.9013, Issue #68.
- Moved fun.CalcQCStats from fun.QC.R to fun.Helper.R.
2018-12-04
- New release version.
2018-12-04
- Add formatHobo to Vignette. Issue #69
2018-11-27
- Fix file version of functions error. Issue #68
- zfun.ContDataQC.R
2018-11-27
- Add function for reformatting HoboWare files.
2018-11-16
- DESCRIPTION
- Remove Jon van Sickles as contributor since removed rarify function.
2018-11-16
- rarify, move to another package, Issue #67
- Moved to separate package.
_ https://github.com/leppott/BioMonTools- BioMonTools is for bioassessment and biomonitoring.
- ContDataQC should stay focused on continuous dat.
- DESCRIPTION
- Remote: leppott/BioMonTools
- Vignette
- rarify section updated.
- R/data.R
- Remove reference to data_bio2rarify
- Remove
- R/rarify.R
- data-raw/ProcessData_rarify.R
- data-raw/data_bio2rarify.txt
- dat/data_bio2rarify.rda
- Moved to separate package.
2018-11-15
- PeriodStats
- Modify for input of 1 or 2 parameters.
- If have 2 parameters get:
- 2 sets of output stat files.
- And get plots with 2 y-axes (i.e., both are plotted).
- fun.PeriodStats.R
- Report_PeriodStats.rmd
2018-11-14
- fun.Stats.R
- Fix tapply arguments must have same length error. Issue # 60.
2018-11-14
- Add links to issues in commit. Issues #57 and #59.
2018-11-14
- Reports, Issue #57 and Issue #59.
- Modify function to use a single report rather than one for each
output format (docx and html).
- fun.Report.R
- fun.Report.File.R
- fun.Config.Out.R
- fun.PeriodStats.R
- fun.QC.R
- fun.QC.File.R
- zfun.AggregateData.R
- zfun.AggregateData.File.R
- fun.Stats.R
- fun.Stats.File.R
- RMD Report files.
- Update YAML header for multiple formats (word and html).
- Update YAML header for table of contents and other items.
- Add “setup” chunk with knitr options so don’t need to specify in each chunk.
- Make render statement consistent by specifying output format.
- Removed docx and html versions of RMD files. Only 1 RMD file per report.
- Report_Aggregate.RMD
- Report_PeriodStats.RMD
- Report_QC.RMD
- Report_Stats.RMD
- Report_Config.RMD
- Modify function to use a single report rather than one for each
output format (docx and html).
2018-11-09
- Thresholds in QC Report, Issue #15
- Report_QC.rmd
- Report_QC_docx.rmd
- Report_QC_html.rmd
2018-11-08
- Configuration Report, Issue #15
- Report_Config.rmd
- New report in RMD folder
- fun.ConfigOut.R
- New function to output new report
- Report_Config.rmd
2018-09-25
- Update help file for rarify. Make the same as BCGcalc::rarify. Issue #65.
- Still need to modify vignette.
2018-02-12
- Added parameter for RMD (report template) directory.
- For Shiny (Issue #39) and custom reports. Includes error checking for no RMD file found.
- Added config.RMDdir.R to “extdata” as a test.
2018-01-31
- Set release on GitHub.
2018-01-31
- Updated ReadMe.
- Provide links to “Guides”; training videos on YouTube with powerpoint slides and R Notebooks (with video files) on GitHub.
2018-01-29
- Add an unmodified version of config.R to external data as config.ORIG.R. Need for guide videos examples.
2018-01-18
- Reports. Missed updating some headers. Searched all files thoroughly. Issue #56.
- PeriodStats. Minor update to description in help file.
2018-01-18
- PeriodStats
- Make example easier to follow. Issue #55.
- Allow for use of config file for inclusion/exclusion of parameter flag “fails”. Issue #54.
- Report to user in console number of fails removed.
- Added example with config file with exclude.fails = FALSE.
- Update some section headers in report RMD files. Add space between pound sign and header text. Issue #56.
- Added more information to the header section of the PeriodStats
report.
- Minimum date in file.
- Difference between minimum date in file and benchmark date.
2018-01-17
- No reproducible error with vignette not being present. Added code to ReadMe that forces the vignette to build on users computer when the package is installed. Issue #49.
2018-01-17
- Updated functions with keywords ‘internal’ so they won’t show up in help file index. These are functions that shouldn’t be accessed individually.
2018-01-17
- OneDrive created multiple versions of files on computer. Clean up and resubmit. Some minor work done on package.
2017-11-30
-
PeriodStats
-
Added data input requirements. 20171130.
-
Updated example for default report from DOCX to HTML. 20171130.
-
Updated Vignette. 20171130.
-
2017-11-30
-
Export.IHA
-
Updated example to use system username. 20171130.
-
Repeated SiteID line in example. 20171130.
-
Updated Vignette. 20171130.
-
2017-11-30
-
Export.StreamThermal
-
Update Excel file with category definitions from journal article. 20171130.
-
Add metric definition Excel file to extdata so can use when create data export. 20171130.
-
Update examples in vignette. 20171130.
-
2017-11-29
-
Readme, fix typo in github install function. 20171129.
-
Update example in Export.StreamThermal so is self contained. Vignette did not need to be updated. Included example code for export to Excel (same as in Export.IHA example). 20171129.
2017-11-29
-
Update “=” to “<-” in Export.IHA example in function and vignette. 20171129.
-
SummaryStats (File) example for non-ContDataQC file. Add minimum necessary fields to a USGS download. 20171129.
-
Update vignette:
-
Revised config.R thresholds. 20171129.
-
SummaryStats (File) for non-ContDataQC file. 20171129.
-
2017-11-29
- Reports, typo in “Generated by:”. 20171129.
2017-11-27
- Updated some QC thresholds in config.R. 20171127.
2017-11-16
-
Fix error in myReport.format and then examples. 20171115.
-
Renamed report RMD files and altered reference in PeriodStats(). 20171115.
-
Added myReport.Format to config.R and set the default there rather than in code. 20171115.
-
Add “username” to reports. 20171116.
-
Update vignette. 20171116.
2017-11-15
-
Add variable for report format (docx or html). Default will be “docx”. Needed for Shiny app since won’t have Pandoc. Pandoc now ships with RStudio but still don’t have when run package via Shiny.
-
Test version. Not complete. Vignette needs to be rebuilt.
2017-09-29
-
Aggregate.File. Example file mispelled (AW vs. Aw). 20170928.
-
File versions of QCRaw, Aggregate, and Stats; change input and output directory name. 20170929.
-
File QC. Turn off report. Mixed case issue in file names. 20170929.
2017-09-28
-
Add packages used in vignette to “Suggests” in DESCRIPTION.
-
Fixed function example lines wider than 100 characters.
-
Moved necessary packages from “Suggests” to “Imports” in DESCRIPTION.
-
DESCRIPTION, License, out of sync with GitHub. Fixed.
2017-09-28
-
Add knitr:: to all kable commands in RMD files. Had error after moving knitr from Depends to Suggests. 20170928.
-
Renamed RMD files with ’ - ’ to ’_’. Recommended in check(). 20170928.
2017-09-28
-
CompSiteCDF funtion complete. 20170928.
-
Vignette updated. 20170928.
2017-09-27
-
DESCRIPTION. As suggested by check(), move packages from Depends to Suggests. 20170927.
-
Update ReadMe. 20170927.
2017-09-21
- CompSiteCDF() to compare multiple sites on a site CDF. 20170921.
2017-09-20
-
Export.StreamThermal.
-
Rename from Export.ST() to Export.StreamThermal() .20170920.
-
Complete function and documentation. 20170920.
-
Update Vignette. 20170920.
-
Export.IHA. Tweak opening text. 20170920.
2017-09-20
- Vignette.
- Tweaked language. 20170919.
- Added section about requiring dataRetrieval v2.7.3 that isn’t on CRAN yet. 20170919.
2017-09-19
-
Vignette added. 20170919.
-
Added daily mean visualization Excel file to . 20170919.
2017-09-12
- Rename fun.Export.IHA() to Export.IHA(). 20170912.
2017-09-12
-
Added function, rarify(), from RIVPACS code by John van Sickles (USEPA). Modified to be a stand alone function and with a seed parameter for reproducible results. Included example dataset with 2 samples. 20170912.
-
Added “Bug Reports” to DESCRIPTION file. 20170912.
-
Modified fun.Export.IHA() argument fun.myCol.Discharge to fun.myCol.Parameter. 20170912.
2017-09-11
- Added function, fun.Export.IHA(), to export data in format ready to use in IHA package. 20170911.
2017-09-11
- Updated fun.GageData.R. USGS updated their webservices to use https instead of http. dataRetrieval package updated to v2.7.3 on GitHub. Some functions modified within dataRetrieval as had to modify some code in ContDataQC package. Version number of dataRetrieval not added to DESCRIPTION (not available on CRAN yet). 20170911.
2017-09-06
- Added PeriodStats() to calculate daily stats (mean, min, max, etc) for a period (N) before a given date. Outputs a CSV of data and DOCX report. 20170905.
2017-08-24
- Changed reports back to DOCX. Will add a user parameter to change in the future. 20170824.
2017-08-23
-
Added rmarkdown to dependencies in Description. It should install with Pandoc but some users had to install separately. 20170823
-
Added install.packages(“installr”) to example in ContDataQC() for installing Pandoc. 20170823.
2017-08-23
- Reload on GitHub. Shiny can’t download. 20170823.
2017-08-23
- Another DOCX reference fix. 20170823.
2017-08-23
- Change reference to DOCX variable to .ext to easier to change in the future. 20170823.
2017-08-23
- Convert Reports from DOCX to HTML. Needed for use with Shiny. 20170823.
2017-08-23
- Rebuild before update to GitHub. 20170823.
2017-08-23
- Ensure use file.path when read and save files. 20170823.
2017-07-31
- Thresholds. Tweaked config.R. Issue #36. 20170731.
2017-07-27
-
Thresholds. Updated config.R with more informed thresholds after working with more data. Issue #36. 20170728.
-
DESCRIPTION. Added Jen Stamp as contributor and added my middle initial. 20170728.
2017-06-22
- QC report (and aggregate report), fixed water temp vs. sensor depth legend. Colors were swapped. Issue # 35. 20170622.
2017-06-21
- QC report header for water temp and sensor depth says water level. Fixed. Issue #34. 20170621.
2017-06-21
- Dec 31 not being assigned a season in summary stats. Fixed. Issue #33. 20170621.
2017-06-09
-
QC of gage data not using all parameters present. Fixed. Issue #32. 20170609.
-
Added air and water pressure in psi to gage download. fun.GageData.R. 20170609.
-
ContData.env$myNames.Order missing new fields. Was dropping fields not included (e.g., gage height). config.R. 20170609.
-
fun.QC.R missing QC routine for gage height. 20170609.
2017-06-07
- Updated data flow for “aggregate” step so the QC report is generated “after” the compiled file is created. Issue #31. 20170607.
2017-06-07
- Updated main function to allow for a single file or a vector of files. New “file” versions of most scripts. Some updates to the Reports (rmd files). Issue #24. 20170607.
2017-06-06
- Report_QC.rmd. Correct typo in “Flags” descriptions. Issue #28. 20170606.
2017-05-31
- File delimiter for strsplit(). Also a regex issue with “.” (dot). Created special check. 20170531.
2017-05-31
- File delimiter. Configuration file allows for user defined values. However, the QC check for StationIDs containing this value uses regular expressions. Added a special condition for the dot, “.”, delimiter as regex treats this character as a match for (almost) any character. 20170531.
2017-05-26
- Time interval. Fixed calculation of time interval. Certain date time formats would stop processing or be reported as zero. fun.QC.R, Report_Aggregate.rmd, Report_QC.rmd, and Report_Stats.rmd. 20170526.
2017-05-24
- fun.Stats.R. Had previously commented out stats and plots due to errors. Single typo fixed in year season stats and reworked daily summaryBy stats section. 20170524.
2017-05-24
- fun.Gage.R. Changed variable “myTZ” to “fun.myTZ” for consistency. 20170524.
2017-05-23
- Remove unused argument “fun.myFile.Prefix” from help file for ContDataQC(). 20170523.
2017-05-22
- Modify input and export directories so can be any folder. The default directory is now the working directory. Modified input parameters for ContDataQC() by removing “fun.myDir.BASE”. Modified examples and all other necessary scripts.
2017-05-19
-
Report_Aggregate.rmd. Fix sampling interval (seconds to minutes,line 23). Left plots as dots instead of lines. 20170519.
-
ContDataQC(). Update examples to with date range. After adding in “test4” the dates don’t match for “test2”. 20170519.
-
Update “test4” dataset. Change “Water Level ft”” to “Sensor Depth ft”. 20170519.
-
Summary Stats quit with error. Fixed in summaryBy statements. 20170519.
2017-05-18
-
Add example for offset data for QC in main function (ContDataQC()). 20170518.
-
Fix plots (legend) in Report_QC.R (remove box as it is only partially displaying). 20170518.
-
Config file. Update Sensor Depth and Water Pressure display names. 20170518.
-
Label code chunks in RMD files. 20170518.
-
Fix plots (blank) in Report_QC.R for “offset” data. With point type of “line” the NAs in the data caused nothing to be plotted. Fixed with na.omit(as.numeric(x)) when subsetted data for plotting. Then had to fix date range on x-axis. 20170518.
2017-05-17
- Add additional config file. Modified config.R to include OlsonNames() in timezone section. Added /extdata/config.TZ.central.R with only time zone change. Modified examples in zfun.ContaDataQC.R to include a USGS gage in the central time zone. Modified ContDataQC() with optional parameter to use helper functions to include different config files. Will only need paramters that are different. User provides path to the new R file for new variables to include in the environment ContData.env.
2017-05-17
-
zfun.ContDataQC.R. Add in “test4” data (offset times) to examples. 20170515.
-
config.R. Fix typo in ContData.env$myName.GageHeight; missing “.” between name and unites. 20170517.
-
fun.QC.R. Line 1034 bad reference for difftime; renamed myTimeDiff.all to myT.diff.all.
-
Confirmed that knitr is silent so the user does not get code scrolling across screen. 20170517.
-
Confirmed that steps/tasks in the process are independent of each other. That is, someone can use some or all routines as each is a separate function. 20170517.
2017-05-15
-
Add data.R to desribe data inlcuded in library. 20170508.
-
fun.QC.R. Fix typo in myT.diff.all operation (line 965). 20170508.
-
Create data process script in “data-raw” for three example “test1” files. 20170509.
-
Revised fun.OffsetCollectionCheck() in fun.Helper.R. Return value is not boolean. 20170509.
-
Revised fun.CalcQCStats() in fun.QC.R. Added ability to handle offset timing for Air/Water data files. 20170509.
-
Fixed typo in finding time interval in markdown files; Report_Aggregate.RMD, Report_Stats.RMD, and Report_QC.RMD. 20170510.
-
Offset time collections (e.g., Air and Water data in same file but not starting at the same time). Fixed fun.QC.R(fun.QC() and fun.CalcQCStats()) to account for this disparity. Previous iteration flagged every other row. Rows without data are no longer flagged (unless the data at the regular time interval was missing). 20170512.
-
Applied fix from fun.QC.R for difftime to report markdown files; Report_Aggregate.RMD, Report_Stats.RMD, and Report_QC.RMD.. 20170512.
-
Modified example files in /data-raw/ to use “Sensor Depth” instead of “Water Level”. Reran ProcessData scripts to recreate data files. 20170512.
-
fun.QC(); moved “Working” message inside of IF statement to only reports to user if that data type is present in the data. Avoids printing to the console all 11 parameters being checked. 20170512.
-
config.R; ContData.env$myName.Turbidity modified value, ContData.env$myName.Chlorophylla modified typo in name (and changed value), ContData.env$myLab.Chlorophylla modified value typo, ContData.env$myThresh.RoC.SD.number.Chlorophylla name fix, ContData.env$myName.Flag.Chlorophylla name fix, ContData.env$myUnits.Chlorophylla name fix. 20170512.
-
Offset data files. Fix overall data flags for each parameters. Currently giving “NA” if any “NA”. And have “NA” due to offset data. fun.QC.R. 20170512.
2017-05-05
-
Reformat file comments for proper outlining in RStudio. 20170505.
-
Fix development version from 2.0.1.0004 to 2.0.1.9004. 20170505.
-
Update Description with version number (last edit was 2.0.1.0000). 20170505.
2017-05-05
-
Change WaterLevel to SensorDepth; config.R, config_COLD.R, Report_Aggregate.RMD, Report_QC.RMD, fun.QC.R, fun.Stats.R, zfunAggregateData.R. 20170505.
-
Changed WaterLevel to GageHeight in fun.GageData.R and added new parameter to config.R. Added to config.R with thresholds. 20170505.
-
Corrected flag names for Turbidity and Chlorophyll a; config.R. 20170505.
2017-05-04
-
Corrected error in Julian Day (0:364 instead of 1:365). Fixed in fun.Stats.R (line 131) by adding “+1”. 20170320.
-
Added 5 parameters (Conductivity, Dissolved Oxygen, pH, Turbidity, and Chlorophyl a) to those that can be evaluated. Changes made to env.UserDefinedValues.R and fun.QC.R. 20170323.
-
Renamed env.UserDefinedValues.R to config.R. 20170421.
-
Added “config” functions to load user configuration (e.g., thresholds specific to coldwater streams) [fun.CustomConfig.R] 20170421.
-
Tweak Reports (Report_Aggregate.RMD, Report_QC.RMD, and Report_Stats.RMD) and fun.QC.R for determining time frequency for sampling. Was using interval for 10th and 11th samples (or 4th and 5th in fun.QC.R). Now using median of all time differences. Will always work as long as have at least 1 sample. Previously could fail with less than 5 samples (or 11).
2017-03-08
- Bug fix for missed references to new environment for variables introduced in v2.0.1. Multiple files affected. Gage data, QC, and Aggregate working but not Stats. One table in the QC and Aggregate reports has been commented out. (To be fixed later).
2017-03-06
-
Bug fix for variable names not showing up.
-
Created environment ContData.env and assigned all variables in fun.UserDefinedValues.R file to it.
-
Renamed fun.UserDefinedValues.R to env.UserDefinedValues.R.
-
Converted all RMD and R files in package to use ContData.env$.
-
Added NEWS.md
-
Edited earlier fix to fun.QC.R for adding day, month, year to data. Did not use variable names in previous edit.
-
Create RMD files for ReadMe and NEWS. Added RMD to ignore list.
2017-02-28
-
Released on GitHub as a fully documented package.
-
Update for TN, Modified QC report (RMD) to summarize number of samples differently.
-
Included tables in Aggregate report (RMD).
-
Reworked scripts to be run as a library.
-
Uploaded to GitHub.
2017-01-16
-
Update for NJ, fixed date/time issue when resaving files in Excel.
-
Added date/time QC process to be run again at the aggregate step.
2016-05-04
- NWQMC 2016, Tampa, FL
2016-03-31
-
AMAAB 2016, Cacapon, WV
-
Minor
2015-10-26
-
SWPBA 2015, Myrtle Beach, SC
-
Initial public release.