NEWS.rmd

---
title: "NEWS-ContDataQC"
output: github_document
  #md_document:
   # variant: markdown_github
---

<!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "NEWS-"
)
```

```{r, echo = FALSE}
cat(paste0("Last Update: ",Sys.time()))
```

# Version History

# v2.1.0.9004
2026-04-28

* fix: Update Global to account for change in config.ORIG.R
    + Add environment statement that was commented out in the last commit

# v2.1.0.9003
2025-10-03

* refactor: Change config.ORIG.R to be a custom file

# v2.1.0.9002
2025-10-02

* fix: Manual merge changes from GitHub and local.  Out of sync.
    + NEWS.rmd
    + DESCRIPTION
    + fun.QC.File.R
    + zfun.ContDataQC.R
* refactor: Add 10 extra generic variables
    + extdata\config.ORIG.R
    + R\config.R
    + fun.QC.R
    + fun.QC.File.R
    + rmd\Report_QC.rmd

# v2.1.0.9001
2025-10-01

* docs: Update config vignette to reference new parameters
* docs: Update config vignette to show line numbers in config output

# v2.1.0
2024-10-07

* update: EPA version produced for publication in SoftwareX journal.  
    + R package code did not change
    + Updates to readme, description, and other similar files. 
    + link to R shiny app now included

# v2.0.7.9049
2025-01-02

* refactor: Update HOBO U20 example data file

## v2.0.7.9048
2024-12-27

* refactor: Fix typo in Report_QC.rmd, Issue #167
    + inst/rmd
    + inst/shiny-examples/ContDataQC/rmd

## v2.0.7.9047
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

## v2.0.7.9046
2024-12-26

* fix: Update shinyalert for HOBO reformat for multiple files, Issue #164

## v2.0.7.9045
2024-12-26

* fix: Update link to Shinay 3c3_QCThresh_Eval

## v2.0.7.9044
2024-12-23

* refactor: Update Excel file in Shiny 3c3_QCThresh_Eval

## v2.0.7.9043
2024-12-23

* refactor: Update workflow step 2 text (3a1_About)

## v2.0.7.9042
2024-12-23

* refactor: Text edits of flags in Report_QC.rmd
* refactor: Update Report_QC.rmd in shiny rmd folder

## v2.0.7.9041
2024-12-23

* refactor: Update thresholds display table
    + DO Spike
    + Add DO Adj, DO % Sat, and Salinity

## v2.0.7.9040
2024-12-23

* refactor: Remove extra mainPanel on 3c (Main_QCThresh_EditThresh)
    + Reclaim blank screen space
    + Space reserved for mainPanel not being used

## v2.0.7.9039
2024-12-17

* docs: Add vignettes to inst folder so can link to from GitHub

## v2.0.7.9038
2024-12-17

* docs: Build vignettes

## v2.0.7.9037
2024-12-02

* fix: Update Shiny file upload parameter check to use names from config, Issue #166

## v2.0.7.9036
2024-11-14

* fix: Update USGS gage data retreival for midnight entries, Issue #165
   + Same as miniDOT Issue #163

## v2.0.7.9035
2024-11-04

* refactor: Add pop up on HOBOware reformat for date time conversion, Issue #164
    + Success and failure

## v2.0.7.9034
2024-10-18

* refactor: Add error message for bad files in miniDOT concatenate in Shiny app

## v2.0.7.9033
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\ContDataQC\www
        - Config_Default.R
        - Config_default.zip
        - Config_Lakes_meters.zip
        - Config_Lakes_metric.R
        - Config_Template.R
        - Config_Template.zip
        - Config.R

## v2.0.7.9032
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\RMD\Report_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\config.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\extdata\config.ORIG.R
    + inst\shiny-examples\ContDataQC\www\Config_Template.R
    + inst\shiny-examples\ContDataQC\www\Config_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\Config.R
        - inst\extdata\config.COOL
        - inst\extdata\config.ExcludeFailsFalse
        - inst\extdata\config.ORIG
        - inst\extdata\config.RMDdir
        - inst\extdata\config.WARM
    + Shiny
        - www\Config.R
        - www\Config.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

## v2.0.5.9055
2021-01-04

* refactor: Add config_R.zip to shiny app in www folder
* refactor: server.R update fun.myReport.format to "" from "html"

## v2.0.5.9054
2021-01-04

* chore: Recreate pkgdown GitHub Action

## v2.0.5.9053
2021-01-04

* chore: Rebuild pkgdown by removing all

## v2.0.5.9052
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

## v2.0.5.9051
2020-12-29

* chore: Add docs folder for pkgdown

## v2.0.5.9050
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

## v2.0.5.9049
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.

## v2.0.5.9048
2020-12-28

* docs: Reapply GitHub Action pkgdown.

## v2.0.5.9047
2020-12-28

* docs: DESCRIPTION, installr to Remotes

## v2.0.5.9046
2020-12-28

* docs: Remove old pkgdown yaml from root directory.  
    + GitHub Action for pkgdown was not building.

## v2.0.5.9045
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

## v2.0.5.9044
2020-12-25

* ci: Add GitHub Action test-coverage
* docs: ReadMe, Add codecov badge
* docs: ReadMe, Add codefactor badge

## v2.0.5.9043
2020-12-25

* docs: Add GitHub Action pkgdown (adds gh-pages branch)
* docs: Remove docs folder for pkgdown website

## v2.0.5.9042
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

## v2.0.5.9041
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

## v2.0.5.9040
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.

## v2.0.5.9039
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.

## v2.0.5.9038
2020-12-16

* formatHobo, update help text, Issue #97

## v2.0.5.9037
2020-12-16

* Shiny app, add ContDataQC::formatHobo(), Issue #96.
    - ui.R
    - server.R

## v2.0.5.9036
2020-12-11

* global.R
    + Change timeFormater function to show time without seperators.
        - 20201211_16_32_00 to 20201211_163200

## v2.0.5.9035
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.

## v2.0.5.9034
2020-12-11

* global.R and server.R
    + Fix Aggregate not working (file error), Issue #92
    + Fix file delete issues, Issue #93

## v2.0.5.9033
2020-12-10

* server.R
    + Add outline headers.
    + Change Config file download.
* ui.R
    + Update version number.
* Aggregate Report in Shiny app.

## v2.0.5.9032
2020-12-03

* data
    + Test2 files and data to 'test2'.
* Shiny app update RMD files with current ones.

## v2.0.5.9031
2020-10-16

* CRAN checks.
    + Example lines longer than 100 characters.
        - ContDataQC
        - RBIcalc
    + Add package names for all non base functions.
        - 

## v2.0.5.9030
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.

## v2.0.5.9029
2020-01-27

* Rebuild pkgdown website.

## v2.0.5.9028
2020-01-27

* Rebuild pkgdown website.

## v2.0.5.9027
2020-01-27

* README
    + Add more info about sometimes package dependencies not loading and things not working.

## v2.0.5.9026
2019-06-11

* Add pkgdown website.

## v2.0.5.9025
2019-06-11

* Update config vignette to be more specific on modifying variables.

## v2.0.5.9024
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.

## v2.0.5.9023
2019-05-02

* DESCRIPTION
    + StagedInstall: no for R v3.6.0.  Issue #88.

## v2.0.5.9022
2019-05-02

* DESCRIPTION
    + StagedInstall: false for R v3.6.0.  Issue #88.

## v2.0.5.9021
2019-04-17

* Add formatting directions for Hoboware files.
    + extdata powerpoint
    + Meta PDF

## v2.0.5.9020
2019-04-02

* Update version number.
   + Repeated 9018.

## v2.0.5.9019
2019-03-26

* Report_PeriodStats.rmd, Issue #76
    + Points to lines.
    + Add min/max shaded

## v2.0.5.9018
2019-03-07

* ReadMe
    + Add link for config file modifications.  Issue #86

## v2.0.5.9017
2019-03-05

* Vignette for editing config file.  Issue #86

## v2.0.5.9016
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.

## v2.0.5.9015
2019-02-22

* Config.Out
    + Add functionality to save a copy of the config file.

## v2.0.5.9014
2019-02-22

* Update code to allow for plots in PeriodStats Report to use ggplot.  Issues #83 and 84.
    + Incomplete.  Still using base graphics.

## v2.0.5.9013
2019-02-21

* Update plots in Aggregate Report to ggplot.  Issues #83 and 84.

## v2.0.5.9012
2019-02-21

* Update plots in QC Report to ggplot.  Issues #83 and 84.
* Import files fix, na.strings=
    + Use c("","NA") not just "".

## v2.0.5.9011
2019-02-19

* Export.rLakeAnalyzer, Issue #82
    + Examples for rLakeAnalyzer functions:
        - schmidt.plot
        - ts.schmidt.stability

## v2.0.5.9010
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.

## v2.0.5.9009
2019-01-21

* formatHobo
    + Update to account for Lake SiteIDs to include depth.

## v2.0.5.9008
2019-01-17

* Add shiny app to package, Issue #81
* DESCRIPTION
    + Add David Gibbs
    + Add packages for Shiny and sort.

## v2.0.5.9007
2019-01-17

* Make report output optional in ContDataQC, Issue #80.
    + ContDataQC

## v2.0.5.9006
2019-01-09

* Example script to get data from Aquarius.
    + Vignette (at end)
    + extdata/Aquarius_Data_Aquisition_PADEP.r

## v2.0.5.9005
2019-01-09

* configuration files.
    + Add Data0_Original folder to each configuration file.

## v2.0.5.9004
2019-01-09

* formatHobo, deal with 2 digit years in Date Time field, Issue #75

## v2.0.5.9003
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.

## v2.0.5.9002
2019-01-07

* folder "Data0_Original", Issue #73.
    + Function ContDataQC
        - So is the same as the formatHobo function.
    + Update Vignette.

## v2.0.5.9001
2018-12-21

* Config.
    + Add Warm.
    + Rename Cold to Cool.

## v2.0.5
2018-12-13

* Revised release including vignette.

## v2.0.4.9002
2018-12-13

* gitignore contained inst/doc.  Removed so will load correctly to GitHub.

## v2.0.4.9001
2018-12-13

* Rebuild Vignette.  Not visible in v2.0.4.

## v2.0.4
2018-12-05

* New release version.

## v2.0.3.9001
2018-12-05

* Fix error introduced in v2.0.2.9013, Issue #68.
* Moved fun.CalcQCStats from fun.QC.R to fun.Helper.R.

## v2.0.3
2018-12-04

* New release version.

## v2.0.2.9014
2018-12-04

* Add formatHobo to Vignette.  Issue #69

## v2.0.2.9013
2018-11-27

* Fix file version of functions error.  Issue #68
    + zfun.ContDataQC.R

## v2.0.2.9012
2018-11-27

* Add function for reformatting HoboWare files.

## v2.0.2.9010
2018-11-16

* DESCRIPTION
    + Remove Jon van Sickles as contributor since removed rarify function.

## v2.0.2.9009
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

## v2.0.2.9008
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

## v2.0.2.9007
2018-11-14

* fun.Stats.R
    + Fix tapply arguments must have same length error.  Issue # 60.

## v2.0.2.9006
2018-11-14

* Add links to issues in commit.  Issues #57 and #59.

## v2.0.2.9005
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

## v2.0.2.9004
2018-11-09

* Thresholds in QC Report, Issue #15
    + Report_QC.rmd
    + Report_QC_docx.rmd
    + Report_QC_html.rmd

## v2.0.2.9003
2018-11-08

* Configuration Report, Issue #15
    + Report_Config.rmd
        - New report in RMD folder
    + fun.ConfigOut.R
        - New function to output new report

## v2.0.2.9002
2018-09-25

* Update help file for rarify.  Make the same as BCGcalc::rarify.  Issue #65.
* Still need to modify vignette.

## v2.0.2.9001
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.

## v2.0.2
2018-01-31

* Set release on GitHub.

## v2.0.1.9063
2018-01-31

* Updated ReadMe.
    + Provide links to "Guides"; training videos on YouTube with powerpoint slides and R Notebooks (with video files) on GitHub.

## v2.0.1.9062
2018-01-29

* Add an unmodified version of config.R to external data as config.ORIG.R.  Need for guide videos examples.

## v2.0.1.9061
2018-01-18

* Reports.  Missed updating some headers.  Searched all files thoroughly.  Issue #56.
* PeriodStats.  Minor update to description in help file.

## v2.0.1.9060
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.

## v2.0.1.9059
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.

## v2.0.1.9058
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.

## v2.0.1.9057
2018-01-17

* OneDrive created multiple versions of files on computer.  Clean up and resubmit.  Some minor work done on package.

## v2.0.1.9056
2017-11-30

* PeriodStats

    + Added data input requirements.  20171130.
    
    + Updated example for default report from DOCX to HTML.  20171130.
    
    + Updated Vignette.  20171130.
    
## v2.0.1.9055
2017-11-30

* Export.IHA

    + Updated example to use system username.  20171130.
    
    + Repeated SiteID line in example.  20171130.
    
    + Updated Vignette.  20171130.

## v2.0.1.9054
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.

## v2.0.1.9053
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.

## v2.0.1.9052
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.

## v2.0.1.9051
2017-11-29

* Reports, typo in "Generated by:".  20171129.

## v2.0.1.9050
2017-11-27

* Updated some QC thresholds in config.R.  20171127.

## v2.0.1.9049
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.

## v2.0.1.9048
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.

## v2.0.1.9047
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.

## v2.0.1.9046
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.

## v2.0.1.9045
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.

## v2.0.1.9044
2017-09-28

* CompSiteCDF funtion complete.  20170928.

* Vignette updated.  20170928.

## v2.0.1.9043
2017-09-27

* DESCRIPTION.  As suggested by check(), move packages from Depends to Suggests.  20170927.

* Update ReadMe.  20170927.

## v2.0.1.9042
2017-09-21

* CompSiteCDF() to compare multiple sites on a site CDF.  20170921.

## v2.0.1.9041
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.

## v2.0.1.9040
2017-09-20

* Vignette. 
    + Tweaked language.  20170919.
    + Added section about requiring dataRetrieval v2.7.3 that isn't on CRAN yet.  20170919.

## v2.0.1.9039
2017-09-19

* Vignette added.  20170919.

* Added daily mean visualization Excel file to \extdata.  20170919.

## v2.0.1.9038
2017-09-12

* Rename fun.Export.IHA() to Export.IHA().  20170912.

## v2.0.1.9037
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.

## v2.0.1.9036
2017-09-11

* Added function, fun.Export.IHA(), to export data in format ready to use in IHA package.  20170911.

## v2.0.1.9035
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.

## v2.0.1.9034
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.

## v2.0.1.9033
2017-08-24

* Changed reports back to DOCX.  Will add a user parameter to change in the future.  20170824.

## v2.0.1.9032
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.

## v2.0.1.9031
2017-08-23

* Reload on GitHub.  Shiny can't download.  20170823.

## v2.0.1.9030
2017-08-23

* Another DOCX reference fix. 20170823.

## v2.0.1.9029
2017-08-23

* Change reference to DOCX variable to .ext to easier to change in the future.  20170823.

## v2.0.1.9028
2017-08-23

* Convert Reports from DOCX to HTML.  Needed for use with Shiny.  20170823.

## v2.0.1.9027
2017-08-23

* Rebuild before update to GitHub.  20170823.

## v2.0.1.9026
2017-08-23

* Ensure use file.path when read and save files.  20170823.

## v2.0.1.9025
2017-07-31

* Thresholds.  Tweaked config.R.  Issue #36.  20170731.

## v2.0.1.9024
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.

## v2.0.1.9023
2017-06-22

* QC report (and aggregate report), fixed water temp vs. sensor depth legend.  Colors were swapped.  Issue # 35.  20170622.

## v2.0.1.9022
2017-06-21

* QC report header for water temp and sensor depth says water level.  Fixed.  Issue #34.  20170621.

## v2.0.1.9021
2017-06-21

* Dec 31 not being assigned a season in summary stats.  Fixed.  Issue #33. 20170621.

## v2.0.1.9020
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.

## v2.0.1.9019
2017-06-07

* Updated data flow for "aggregate" step so the QC report is generated "after" the compiled file is created.  Issue #31. 20170607.

## v2.0.1.9018
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.

## v2.0.1.9017
2017-06-06

* Report_QC.rmd.  Correct typo in "Flags" descriptions.  Issue #28.  20170606.

## v2.0.1.9016
2017-05-31

* File delimiter for strsplit().  Also a regex issue with "." (dot).  Created special check.  20170531.

## v2.0.1.9015
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.

## v2.0.1.9014
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.

## v2.0.1.9013
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.

## v2.0.1.9012
2017-05-24

* fun.Gage.R.  Changed variable "myTZ" to "fun.myTZ" for consistency.  20170524.

## v2.0.1.9011
2017-05-23

* Remove unused argument "fun.myFile.Prefix" from help file for ContDataQC().  20170523.

## v2.0.1.9010
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.

## v2.0.1.9009
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.

## v2.0.1.9008
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.

## v2.0.1.9007
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.

## v2.0.1.9006
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.


## v2.0.1.9005
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.

## v2.0.1.9004
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.

## v2.0.1.0003
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.

## v2.0.1.0002
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).

## v2.0.1.0001
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).

## v2.0.1
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.

## v2.0.0
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.

## v1.2.1
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.

## v1.2.0
2016-05-04

* NWQMC 2016, Tampa, FL

## v1.1.0
2016-03-31

* AMAAB 2016, Cacapon, WV

* Minor 

## v1.0.0
2015-10-26

* SWPBA 2015, Myrtle Beach, SC

* Initial public release.