NEWS.md
In leppott/ContDataQC: Quality Control (QC) of Continous Monitoring Data

NEWS-ContDataQC

#> Last Update: 2025-01-02 14:40:32.353055

Version History

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

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
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
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

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.
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
Add package names for all non base functions.

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.
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 \<- “~”
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

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.

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

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

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

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.

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leppott/ContDataQC Quality Control (QC) of Continous Monitoring Data

NEWS.md In leppott/ContDataQC: Quality Control (QC) of Continous Monitoring Data

NEWS-ContDataQC

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leppott/ContDataQC
Quality Control (QC) of Continous Monitoring Data

NEWS.md
In leppott/ContDataQC: Quality Control (QC) of Continous Monitoring Data