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NEWS
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NEWS-ContDataQC
================
<!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
#> Last Update: 2024-03-01 13:34:32.498829
# Version History
## v2.0.7.9031
2024-03-01
- refactor: Update Shiny app
- typos
- indents
- replace some tables with figures
## v2.0.7.9031
2024-02-27
- refactor: Update Shiny app text and tables, Issue \#156
- refactor: Update Shiny app exit links, Issue \#159
## v2.0.7.9030
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
## v2.0.7.9029
2024-01-31
- refactor: Shiny app add “exit” tags to html links, Issue \#159
## v2.0.7.9028
2024-01-31
- refactor: Replace images in Shiny, Issue \#157
## v2.0.7.9027
2024-01-31
- refactor: Apply revised USEPA template (2023-12-15), Issue \#155
## v2.0.7.9026
2024-01-31
- refactor: Move version number from title to about, Issue \#161
- refactor: Add file identifiers to download links, Issue \#160
## v2.0.7.9025
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
## v2.0.7.9024
2023-09-28
- refactor: Use USEPA template
## v2.0.7.9023
2023-09-18
- refactor: Update stats plots with legend
- fun.Stats.R
- fun.Stats.File.R
## v2.0.7.9022
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
## v2.0.7.9021
2023-09-15
- refactor: Add text for tab references instead of links
## v2.0.7.9020
2023-09-14
- refactor: Added config file display name
- Main Functions - Run Functions
- Main Functions - QC Thresholds - Upload Custom Thresholds
## v2.0.7.9019
2023-09-14
- refactor: Edits to Shiny tabs
## v2.0.7.9018
2023-09-13
- refactor: Update period stats plots with legend
- inst\_PeriodStats.rmd
- fix: Update example code in PeriodStats
## v2.0.7.9017
2023-09-12
- refactor: Change widths on Edit Thresholds tab
- Some boxes too small
## v2.0.7.9016
2023-09-11
- refactor: Shiny tab text updates
- miniDOT concatenate
- miniDOT reformat
- Advanced (new tab)
- Formatting Files
## v2.0.7.9015
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
## v2.0.7.9014
2023-09-08
- refactor: Update Thresholds tab order
- refactor: Add text to Main - Import tab
## v2.0.7.9013
2023-09-08
- refactor: Update formatminiDOT function to remove columns with all NA
values
- Fixes issue with ContDataQC QC function
## v2.0.7.9012
2023-08-31
- refactor: Update config (lakes) in library and Shiny, Issue \#153
- refactor: Shiny app updates
- Update some images
- Update text
## v2.0.7.9011
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
## v2.0.7.9010
2023-08-31
- refactor: Update base config file, Issue \#153
- refactor: Update ThresholdsCheckWorksheet links in Shiny, Issue \#153
## v2.0.7.9009
2023-08-14
- style: Update formating in global.R
- refactor: Change order, locations, and names of tabs in Shiny app,
Issue \#152
## v2.0.7.9008
2023-08-11
- style: Update Report_SiteSummary spacing
## v2.0.7.9007
2022-12-22
- fix: Shiny custom edit thresholds
- Change default config to version without env statement
## v2.0.7.9006
2022-12-22
- update: Update Shiny app
- QC Thresholds, Edit Thresholds, Issue \#148
## v2.0.7.9005
2022-09-22
- update: update Shiny app
- Fix numbered tabs 7 and 8
## v2.0.7.9004
2022-09-22
- update: update Shiny app
- Update links
- Remove (comment out) EPA template
- Rearrange Console and Test Data tabs
## v2.0.7.9003
2022-09-19
- update: update Shiny app
- Update text
## v2.0.7.9002
2022-09-15
- update: update Shiny app
- Change names of navbar tabs and order
## v2.0.7.9001
2022-09-15
- style: Use EPA Template for shiny app
## v2.0.7
2022-06-15
- refactor: Bump to whole version number
## v2.0.6.9028
2022-06-15
- refactor: Add dummy files to blank Shiny app folders to avoid being
deleted
## v2.0.6.9027
2022-06-15
- refactor: Update readme examples to use remotes instead of devtools
package
## v2.0.6.9026
2022-06-15
- feature: Add miniDOT functions to Shiny, Issue \#141
## v2.0.6.9025
2022-06-07
- fix: Modify config.R for salinity, Issue \#138
- Update other copies in package
## v2.0.6.9024
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
## v2.0.6.9023
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
## v2.0.6.9022
2022-05-25
- refactor: Updates to minidot_cat function, Issue \#141
- refactor: Add missing return value for help script line 937
## v2.0.6.9021
2022-05-25
- feature: Add miniDOT concatenate function, Issue \#141
- Modified compile_do_folder.R from mnsentinellakes
## v2.0.6.9020
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
## v2.0.6.9019
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
## v2.0.6.9018
2022-05-11
- feature: Add salinity to config file, Issue \#138
- feature: Add salinity to config.out RMD, Issue \#138
## v2.0.6.9017
2022-05-11
- fix: Modify config file for DO percent saturation
## v2.0.6.9016
2022-04-14
- refactor: Add keywords internal to two new functions
- fix: Rebuild package so new functions included
- docs: Add Yadong Xu as contributor
## v2.0.6.9015
2022-04-14
- feature: Add new functions from Yadong for EMVL project
- Pull request \#137
## v2.0.6.9014
2022-01-18
- refactor: Update Tim’s Threshold Analysis zip file
## v2.0.6.9013
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
## v2.0.6.9012
2022-01-17
- refactor: Update QC Thresholds tab text in Shiny, Issue \#131
## v2.0.6.9011
2022-01-17
- refactor: Update QC Thresholds tab in Shiny, Issue \#131
- Change order and names of tabs
- Add Evaluate code as a download
## v2.0.6.9010
2021-12-22
- fix: Updated custom config thresholds to handle quotes, Issue \#130
- docs: Added Ben Block as contributor for work on custom thresholds
## v2.0.6.9009
2021-12-22
- fix: Duplicate entry in config file, Issue \#130
- Updated all versions in package and shiny folders
- Chlorophylla spike thresholds duplicated
## v2.0.6.9008
2021-12-21
- feature: Shiny, add custom thresholds for config file, Issue \#130
- merge pull request
## v2.0.6.9007
2021-10-25
- refactor: Rename “master” branch to “main”.
## v2.0.6.9006
2021-10-25
- fix: Update fun.Stats.R and fun.Stats.File.R to use WaterLevel instead
of GageHeight, Issue \#124
## v2.0.6.9005
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
## v2.0.6.9004
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
## v2.0.6.9003
2021-06-23
- refactor: Updated version number in ui.R
## v2.0.6.9002
2021-06-23 \* refactor: Shiny, pdated link locations to new repository
(ShinyAppDocuments). \* style: Updated location of .rmd files to www/
folder.
## v2.0.6.9001
2021-06-23
- refactor: Shiny updates to app description text
## v2.0.6.9000
2021-06-23
- style: Removed Documents folder
- Move to new repository
## v2.0.6
2021-06-21
- refactor: Create new version release
## v2.0.5.9109
2021-06-21
- refactor: Consolidate Shiny app updates from pull request, Issue \#126
## v2.0.5.9108
2021-06-18
- refactor: Update Shiny
- Final updates to section 7
## v2.0.5.9107
2021-06-18
- refactor: Update Shiny
- Beginning updates to section 7
## v2.0.5.9106
2021-06-18
- refactor: Update Shiny
- Updated section 8 text
## v2.0.5.9105
2021-06-18
- refactor: Update Shiny
- Updated text in section 9
## v2.0.5.9104
2021-06-18
- refactor: Update Shiny
- Updates to section 2 and section 3 - added sidebarpanels within
tabsets rather than at bottom of pages
## v2.0.5.9103
2021-06-18
- refactor: Update Shiny
- Updates sections 8 & 9.
## v2.0.5.9102
2021-06-18
- refactor: Update Shiny
- Updated section 4a, 4b, and 5.
## v2.0.5.9101
2021-06-18
- refactor: Update Shiny
- Updated 4a documents link
## v2.0.5.9100
2021-06-18
- refactor: Update Shiny
- Made final updates to section 3a code and began section 4 code
updates
## v2.0.5.9099
2021-06-18
- refactor: Update Shiny
- Updated 3b files
## v2.0.5.9098
2021-06-18
- refactor: Update Shiny
- Updated 3a section
## v2.0.5.9097
2021-06-18
- refactor: Update Shiny
- Updated tab 6 information
## v2.0.5.9096
2021-06-18
- refactor: Update Shiny
- Updated 2d HOBOware reformat
## v2.0.5.9095
2021-06-18
- refactor: Update Shiny
- Added 2c info to rmd and documents
## v2.0.5.9094
2021-06-18
- refactor: Update Shiny
- Updates to 2a and 2b text and data sources. Added files to documents
folder.
## v2.0.5.9093
2021-06-18
- refactor: Update Shiny
- Updated 2a text and created Documents folder
## v2.0.5.9092
2021-06-18
- refactor: Update Shiny
- moved tab_Reformat.R under tab_2DataPrep subtab “Formatting files”
## v2.0.5.9091
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.
## v2.0.5.9090
2021-06-18
- refactor: Update Shiny
- Beginning updates in ui.R and subsequent code to accommodate
application changes.
## v2.0.5.9089
2021-04-19
- refactor: Remove extra columns from QC routine, Issue \#123
- fun.QC.R
- fun.QC.File.R
## v2.0.5.9088
2021-04-19
- refactor: Shiny, changes to tabs
## v2.0.5.9087
2021-04-19
- refactor: Shiny
- Rearrange tabs
- Split out Advanced tab into Console, Config, and Hobo
## v2.0.5.9086
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
## v2.0.5.9085
2021-03-31
- feature: Add custom config with metric units for Lakes, Issue \#119
- extdata.Lakes.metric.R
## v2.0.5.9084
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
## v2.0.5.9083
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
## v2.0.5.9082
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
## v2.0.5.9081
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
## v2.0.5.9080
2021-02-05
- style: Trim lines and fix spelling, fun.DateTimeFormat
## v2.0.5.9079
2021-02-04
- refactor: Update config spike flags for water level, Issue \#116
- Update other versions of config
## v2.0.5.9078
2021-02-04
- refactor: Update Config_Template.zip in Shiny, Issue \#116
- docs: Retain NEWS.md for pkgdown to build changelog
## v2.0.5.9077
2021-02-04
- refactor: Update thresholds in config.R for sensor depth, Issue \#116
## v2.0.5.9076
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
## v2.0.5.9075
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
## v2.0.5.9074
2021-01-25
- docs: Update example in ContDataQC for aggregating lake/depth files,
Issue \#85
## v2.0.5.9073
2021-01-22
- refactor: Change ContDataQC() parameter fun.AddDeployCol from default
FALSE to TRUE
- Shiny app will now auto add the deployment field
## v2.0.5.9072
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
## v2.0.5.9071
2021-01-21
- refactor: Revise Vignette_Config so it doesn’t fail.
## v2.0.5.9070
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
## v2.0.5.9069
2021-01-20
- tests: Add test for export_rLakeAnalyzer
## v2.0.5.9068
2021-01-18
- refactor: Add “RAW” columns for flags in QC step Issue \#106
## v2.0.5.9067
2021-01-18
- refactor: Shiny server, turn off renameAggOutput, Issue \#104
## v2.0.5.9066
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
## v2.0.5.9065
2021-01-14
- refactor: Update name of Config.zip to Config_Template.zip in shiny
ui.R
## v2.0.5.9064
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()
## v2.0.5.9063
2021-01-13
- fix: Shiny app custom config not loading
## v2.0.5.9063
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
## v2.0.5.9062
2021-01-08
- refactor: Update version number display in Shiny app.
## v2.0.5.9061
2021-01-08
- feature: Update formatHobo to output water level, Issue \#100
## v2.0.5.9060
2021-01-08
- refactor: Update CompSite.CDF 2nd example
## v2.0.5.9059
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
## v2.0.5.9058
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
## v2.0.5.9057
2021-01-07
- feature: Modify formatHobo to use water level, issue \#100
## v2.0.5.9056
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
- Package
- data.R
- inst.COOL
- inst.ExcludeFailsFalse
- inst.ORIG
- inst.RMDdir
- inst.WARM
- Shiny
- www.R
- www.zip
- 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