vignettes/Vignette_Config.Rmd
Vignette_Config.RmdContDataQC uses a configuration file (config.R) that allows for customization.
Through the use of a configuration file the user can change many of the variables in the library used in the processing of data (e.g., the names of fields, thresholds, and date formats).
The ContDataQC() function allows the user to input their own configuration file. Only variables that are different from the default need to be added. That is, the default configuration is loaded in the library and then the user supplied configuration. This allows the user configuration to overwrite the defaults for that session.
The Config.out will output the contents of the configuration file as used by the package and stored in the environment ContData.env.
The contents of the default configuration file (extdata/config.ORIG.R) can be output with the Config.Out function. An HTML (default) or DOCX report is generated along with a text file (.r) of the configuration file.
library(ContDataQC)
dn_export <- tempdir()
Config.Out(fun.myDir.export = dn_export)The config file that is generated by the Config.Out function can be modified to contain the custom values. Only modified values need to be included in the custom configuration file. That is, if you only want to modify a single variable you only need to include this single variable in your custom configuration file.
However, there are some variables that reference the numeric and name/labels that also need to be modified. That is, if the user modifies a named variable then every time that named variable is referenced later in the config file it also has to be uncommented.
This process works because the default configuration is always loaded with the package at start up. Then any parameters specified in a custom configuration are loaded and overwrite the defaults.
The file can be edited in a text editor or in R-Studio. It is not recommended to use Word or other word processing programs.
If the user wanted to change the change the following three parameters and related thresholds then the lines referenced in the table below would also need to be modified.
“Air.BP.kpa”
“Water.BP.kpa”
“Water.Level.m”
| Item | AirBP | WaterP | SensorDepth | Other |
|---|---|---|---|---|
| Units | 61 | 62 | 63 | |
| Column Name | 84 | 86 | 88 | |
| Labels | 113 | 116 | 119 | |
| Discrete Name | 161 | 164 | 167 | |
| Discrete Label | 198 | 201 | 204 | |
| Data Field, Names | 244:249 | |||
| Data Field, Labels | 271:274 | |||
| Output Name Order | 307:310 | |||
| Flags | 538 | 541 | 544 | |
| Thresholds, Gross, Fail | 358:363 | |||
| Thresholds, Gross, Suspect | 385:390 | |||
| Thresholds, Spike | 413:418 | |||
| Thresholds, Rate of Change | 442:447 | |||
| Thresholds, Flat | 475:482 | |||
| Thresholds, Flat, combo | 508:417 | |||
| Flag Labels | 539:545 | |||
| Test Names | 575 |
R code has a few conventions that the user should be aware of when making edits to the configuration file.
Any text after a “#” is treated as comments and not evaluated.
The arrow, “<-”, is treated as a equal sign when assigning values to a parameter.
All parameters in the configuration file will be a part of the environment “ContData.env”.
The contents of the default configuration file (extdata/config.ORIG.R) are listed below. Sections are created with similar variables. Please note that the window below is narrow and some lines wrap to the next line.
# User Defined Values
#
# User defined values for variables used across multiple functions in this
# library. The user has the ability to modify the values for names, units, QC
# thresholds, etc.
#
# Saved in a separate environment.
#
# https://www.r-bloggers.com/package-wide-variablescache-in-r-packages/
#
# Continuous data helper script
# Default Values
# Erik.Leppo@tetratech.com (EWL)
# 20150928
# 20170323, add 3 parameters (Cond, DO, pH)
# 20210106, replace gageheight with waterlevel
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# User defined variable names for input data
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# It is assumed that this R script is stored in a directory with the data files
# as subdirectories. This script is intended to be "source"d from the main
# script.
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# @keywords continuous data
# @examples
# #Not intended to be accessed indepedant of function ContDataQC().
# #Data values only. No functions. Add to environment so only visible inside
# #library.
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# USER may make modifications in this section but not mandatory
# this section could be sourced so can use between scripts
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#UserDefinedValues <- NA # default value so shows up in help files
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Environment Name ####
# Environment for use only by ContDataQC library
ContData.env <- new.env(parent = emptyenv())
# The above line is not used in custom configurations.
# assign variables to new environment requires editing of all lines.
# For example, myDelim <- "_" BECOMES ContData.env$myDelim, "_"
###
# list all elements in environment
# ls(ContData.env) # all elements in environment
# as.list(ContData.env) # all elements in environment with assigned values
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Delimiter in File Names (e.g., test2_AW_201301_20131231.csv)
ContData.env$myDelim <- "_"
ContData.env$myDelim_LakeID <- "--"
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Acceptable column names for the data ####
## Basic
ContData.env$myName.SiteID <- "SiteID"
ContData.env$myName.Date <- "Date"
ContData.env$myName.Time <- "Time"
ContData.env$myName.DateTime <- "Date.Time"
#(special characters (e.g., %, space, or /) are converted to "." by R
# , "deg" converted to "A")
### IF CHANGE UNITS WILL NEED TO MODIFY THRESHOLDS ###
ContData.env$myUnits.AirTemp <- "C" # C or F
ContData.env$myUnits.WaterTemp <- ContData.env$myUnits.AirTemp
ContData.env$myUnits.AirBP <- "psi"
ContData.env$myUnits.WaterP <- ContData.env$myUnits.AirBP
ContData.env$myUnits.SensorDepth <- "ft"
ContData.env$myUnits.Discharge <- "ft3.s"
ContData.env$myUnits.Cond <- "uS.cm"
ContData.env$myUnits.DO <- "mg.L"
ContData.env$myUnits.DO.adj <- "mg.L"
ContData.env$myUnits.DO.pctsat <- "percent"
ContData.env$myUnits.pH <- "SU"
ContData.env$myUnits.Turbidity <- "NTU"
ContData.env$myUnits.Chlorophylla <- "g.cm3"
ContData.env$myUnits.WaterLevel <- "ft"
ContData.env$myUnits.Salinity <- "ppt"
## Logger Fields ----
ContData.env$myName.RowID.Water <- "Water.RowID"
ContData.env$myName.LoggerID.Water<- "Water.LoggerID"
ContData.env$myName.RowID.Air <- "Air.RowID"
ContData.env$myName.LoggerID.Air <- "Air.LoggerID"
ContData.env$myName.LoggerDeployment <- "Logger.Deployment"
ContData.env$myName.LoggerDeployment.start <- "start"
ContData.env$myName.LoggerDeployment.end <- "end"
## Parameters as appear in logger files
ContData.env$myName.WaterTemp <- paste0("Water.Temp."
,ContData.env$myUnits.WaterTemp)
# "deg" from HoboWare files sometimes adds "A " in front. Replace with "." in R
ContData.env$myName.AirTemp <- paste0("Air.Temp."
,ContData.env$myUnits.AirTemp)
# "deg" from HoboWare files sometimes adds "A " in front. Replace with "." in R
ContData.env$myName.AirBP <- paste0("Air.BP."
, ContData.env$myUnits.AirBP)
ContData.env$myName.WaterP <- paste0("Water.P."
, ContData.env$myUnits.WaterP)
ContData.env$myName.SensorDepth <- paste0("Sensor.Depth."
, ContData.env$myUnits.SensorDepth)
ContData.env$myName.Discharge <- paste0("Discharge."
, ContData.env$myUnits.Discharge)
ContData.env$myName.Cond <- paste0("Conductivity."
, ContData.env$myUnits.Cond)
ContData.env$myName.DO <- paste0("DO.", ContData.env$myUnits.DO)
ContData.env$myName.DO.adj <- paste0("DO.adj.", ContData.env$myUnits.DO.adj)
ContData.env$myName.DO.pctsat <- paste0("DO.pctsat.", ContData.env$myUnits.DO.pctsat)
ContData.env$myName.pH <- paste0("pH."
, ContData.env$myUnits.pH)
ContData.env$myName.Turbidity <- paste0("Turbidity."
, ContData.env$myUnits.Turbidity)
ContData.env$myName.Chlorophylla <- paste0("Chlorophylla."
, ContData.env$myUnits.Chlorophylla)
ContData.env$myName.WaterLevel <- paste0("Water.Level."
, ContData.env$myUnits.WaterLevel)
ContData.env$myName.Salinity <- paste0("Salinity."
, ContData.env$myUnits.Salinity)
## Plot Labels
ContData.env$myLab.Date <- "Date"
ContData.env$myLab.DateTime <- "Date"
ContData.env$myLab.WaterTemp <- paste0("Temperature, Water (deg "
,ContData.env$myUnits.WaterTemp
,")")
ContData.env$myLab.AirTemp <- paste0("Temperature, Air (deg "
,ContData.env$myUnits.AirTemp
,")")
ContData.env$myLab.AirBP <- paste0("Barometric Pressure, Air ("
,ContData.env$myUnits.WaterP
,")")
ContData.env$myLab.WaterP <- paste0("Pressure, Water ("
,ContData.env$myUnits.AirBP
,")")
ContData.env$myLab.SensorDepth <- paste0("Sensor Depth ("
,ContData.env$myUnits.SensorDepth
,")"
,sep="")
ContData.env$myLab.Temp.BOTH <- paste0("Temperature (deg "
,ContData.env$myUnits.WaterTemp
,")")
ContData.env$myLab.Discharge <- paste0("Discharge ("
,sub("\\.","/"
,ContData.env$myUnits.Discharge)
,")") #replace "." with "/"
ContData.env$myLab.Cond <- paste0("Conductivity ("
,sub("\\.","/"
,ContData.env$myUnits.Cond)
,")") #replace "." with "/"
ContData.env$myLab.DO <- paste0("Dissolved Oxygen ("
,sub("\\.","/"
,ContData.env$myUnits.DO)
,")") #replace "." with "/"
ContData.env$myLab.DO.adj <- paste0("Dissolved Oxygen, adjusted ("
,sub("\\.","/"
,ContData.env$myUnits.DO.adj)
,")") #replace "." with "/"
ContData.env$myLab.DO.pctsat <- paste0("Dissolved Oxygen, percent saturation ("
,sub("\\.","/"
,ContData.env$myUnits.DO.pctsat)
,")") #replace "." with "/"
ContData.env$myLab.pH <- paste0("pH ("
,ContData.env$myUnits.pH
,")")
ContData.env$myLab.Turbidity <- paste0("Turbidity ("
,ContData.env$myUnits.Turbidity
,")")
ContData.env$myLab.Chlorophylla <- paste0("Chlorophyll a ("
,sub("\\.","/"
,ContData.env$myUnits.Chlorophylla)
,")") #replace "." with "/"
ContData.env$myLab.WaterLevel <- paste0("Water Level ("
,ContData.env$myUnits.WaterLevel
,")")
ContData.env$myLab.Salinity <- paste0("Salinity ("
,ContData.env$myUnits.Salinity
,")")
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Discrete Measurements ####
ContData.env$myPrefix.Discrete <- "Discrete"
# Discrete, Names
ContData.env$myName.Discrete.WaterTemp <- paste(ContData.env$myPrefix.Discrete
,ContData.env$myName.WaterTemp
,sep=".")
ContData.env$myName.Discrete.AirTemp <- paste(ContData.env$myPrefix.Discrete
,ContData.env$myName.AirTemp
,sep=".")
ContData.env$myName.Discrete.AirBP <- paste(ContData.env$myPrefix.Discrete
,ContData.env$myName.AirBP
,sep=".")
ContData.env$myName.Discrete.WaterP <- paste(ContData.env$myPrefix.Discrete
,ContData.env$myName.WaterP
,sep=".")
ContData.env$myName.Discrete.SensorDepth <- paste(ContData.env$myPrefix.Discrete
,ContData.env$myName.SensorDepth
,sep=".")
ContData.env$myName.Discrete.Discharge <- paste(ContData.env$myPrefix.Discrete
,ContData.env$myName.Discharge
,sep=".")
ContData.env$myName.Discrete.Cond <- paste(ContData.env$myPrefix.Discrete
,ContData.env$myName.Cond
,sep=".")
ContData.env$myName.Discrete.DO <- paste(ContData.env$myPrefix.Discrete
,ContData.env$myName.DO
,sep=".")
ContData.env$myName.Discrete.DO.adj <- paste(ContData.env$myPrefix.Discrete
,ContData.env$myName.DO.adj
,sep=".")
ContData.env$myName.Discrete.DO.pctsat <- paste(ContData.env$myPrefix.Discrete
, ContData.env$myName.DO.pctsat
, sep=".")
ContData.env$myName.Discrete.pH <- paste(ContData.env$myPrefix.Discrete
,ContData.env$myName.pH
,sep=".")
ContData.env$myName.Discrete.Turbidity <- paste(ContData.env$myPrefix.Discrete
,ContData.env$myName.Turbidity
,sep=".")
ContData.env$myName.Discrete.Chlorophylla <-paste(ContData.env$myPrefix.Discrete
,ContData.env$myName.Chlorophylla
,sep=".")
ContData.env$myName.Discrete.WaterLevel <- paste(ContData.env$myPrefix.Discrete
,ContData.env$myName.WaterLevel
,sep=".")
ContData.env$myName.Discrete.Salinity <- paste(ContData.env$myPrefix.Discrete
,ContData.env$myName.Salinity
,sep=".")
# Discrete, Labels
ContData.env$myLab.Discrete.WaterTemp <- paste(ContData.env$myLab.WaterTemp
,"(Discrete)"
,sep=" ")
ContData.env$myLab.Discrete.AirTemp <- paste(ContData.env$myLab.AirTemp
,"(Discrete)"
,sep=" ")
ContData.env$myLab.Discrete.AirBP <- paste(ContData.env$myLab.AirBP
,"(Discrete)"
,sep=" ")
ContData.env$myLab.Discrete.WaterP <- paste(ContData.env$myLab.WaterP
,"(Discrete)"
,sep=" ")
ContData.env$myLab.Discrete.SensorDepth <- paste(ContData.env$myLab.SensorDepth
,"(Discrete)"
,sep=" ")
ContData.env$myLab.Discrete.Discharge <- paste(ContData.env$myLab.Discharge
,"(Discrete)"
,sep=" ")
ContData.env$myLab.Discrete.Cond <- paste(ContData.env$myLab.Cond
,"(Discrete)"
,sep=" ")
ContData.env$myLab.Discrete.DO <- paste(ContData.env$myLab.DO
,"(Discrete)"
,sep=" ")
ContData.env$myLab.Discrete.DO.adj <- paste(ContData.env$myLab.DO.adj
,"(Discrete)"
,sep=" ")
ContData.env$myLab.Discrete.DO.pctsat <- paste(ContData.env$myLab.DO.pctsat
,"(Discrete)"
,sep=" ")
ContData.env$myLab.Discrete.pH <- paste(ContData.env$myLab.pH
,"(Discrete)"
,sep=" ")
ContData.env$myLab.Discrete.Turbidity <- paste(ContData.env$myLab.Turbidity
,"(Discrete)"
,sep=" ")
ContData.env$myLab.Discrete.Chlorophylla<- paste(ContData.env$myLab.Chlorophylla
,"(Discrete)"
,sep=" ")
ContData.env$myLab.Discrete.WaterLevel <- paste(ContData.env$myLab.WaterLevel
,"(Discrete)"
,sep=" ")
ContData.env$myLab.Discrete.Salinity <- paste(ContData.env$myLab.Salinity
,"(Discrete)"
,sep=" ")
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Automated QC stuff ####
## data type/stages
ContData.env$myDataQuality.Raw <- "RAW"
ContData.env$myDataQuality.QCauto <- "QCauto"
ContData.env$myDataQuality.QCmanual <- "QCmanual"
ContData.env$myDataQuality.Final <- "Final"
ContData.env$myDataQuality.Aggregated <- "Aggregated"
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Directory Names ####
ContData.env$myName.Dir.0Original <- "Data0_Original"
ContData.env$myName.Dir.1Raw <- "Data1_Raw"
ContData.env$myName.Dir.2QC <- "Data2_QC"
ContData.env$myName.Dir.3Agg <- "Data3_Aggregated"
ContData.env$myName.Dir.4Stats <- "Data4_Stats"
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Data Fields ####
ContData.env$myNames.DataFields <- c(ContData.env$myName.WaterTemp
, ContData.env$myName.AirTemp
, ContData.env$myName.AirBP
, ContData.env$myName.WaterP
, ContData.env$myName.SensorDepth
, ContData.env$myName.Discharge
, ContData.env$myName.Cond
, ContData.env$myName.DO
, ContData.env$myName.DO.adj
, ContData.env$myName.DO.pctsat
, ContData.env$myName.pH
, ContData.env$myName.Turbidity
, ContData.env$myName.Chlorophylla
, ContData.env$myName.WaterLevel
, ContData.env$myName.Salinity
, ContData.env$myName.Discrete.WaterTemp
, ContData.env$myName.Discrete.AirTemp
, ContData.env$myName.Discrete.WaterP
, ContData.env$myName.Discrete.AirBP
, ContData.env$myName.Discrete.SensorDepth
, ContData.env$myName.Discrete.Discharge
, ContData.env$myName.Discrete.Cond
, ContData.env$myName.Discrete.DO
, ContData.env$myName.Discrete.DO.adj
, ContData.env$myName.Discrete.DO.pctsat
, ContData.env$myName.Discrete.pH
, ContData.env$myName.Discrete.Turbidity
, ContData.env$myName.Discrete.Chlorophylla
, ContData.env$myName.Discrete.WaterLevel
, ContData.env$myName.Discrete.Salinity
)
ContData.env$myNames.DataFields.Lab <- c(ContData.env$myLab.WaterTemp
, ContData.env$myLab.AirTemp
, ContData.env$myLab.AirBP
, ContData.env$myLab.WaterP
, ContData.env$myLab.SensorDepth
, ContData.env$myLab.Discharge
, ContData.env$myLab.Cond
, ContData.env$myLab.DO
, ContData.env$myLab.DO.adj
, ContData.env$myLab.DO.pctsat
, ContData.env$myLab.pH
, ContData.env$myLab.Turbidity
, ContData.env$myLab.Chlorophylla
, ContData.env$myLab.WaterLevel
, ContData.env$myLab.Salinity
, ContData.env$myLab.Discrete.WaterTemp
, ContData.env$myLab.Discrete.AirTemp
, ContData.env$myLab.Discrete.WaterP
, ContData.env$myLab.Discrete.AirBP
, ContData.env$myLab.Discrete.SensorDepth
, ContData.env$myLab.Discrete.Discharge
, ContData.env$myLab.Discrete.Cond
, ContData.env$myLab.Discrete.DO
, ContData.env$myLab.Discrete.DO.adj
, ContData.env$myLab.Discrete.DO.pctsat
, ContData.env$myLab.Discrete.pH
, ContData.env$myLab.Discrete.Turbidity
, ContData.env$myLab.Discrete.Chlorophylla
, ContData.env$myLab.Discrete.WaterLevel
, ContData.env$myLab.Discrete.Salinity
)
ContData.env$myNames.DataFields.Col <- c("blue","green","gray","gray","black"
,"brown","purple","orange","salmon"
,"rosybrown","aquamarine1")
#
## Name Order (change order below to change order in output file)
ContData.env$myNames.Order <- c(ContData.env$myName.SiteID
, ContData.env$myName.Date
, ContData.env$myName.Time
, ContData.env$myName.DateTime
, ContData.env$myName.LoggerDeployment
, ContData.env$myName.WaterTemp
, ContData.env$myName.LoggerID.Air
, ContData.env$myName.RowID.Air
, ContData.env$myName.AirTemp
, ContData.env$myName.WaterP
, ContData.env$myName.AirBP
, ContData.env$myName.SensorDepth
, ContData.env$myName.Discharge
, ContData.env$myName.Cond
, ContData.env$myName.DO
, ContData.env$myName.DO.adj
, ContData.env$myName.DO.pctsat
, ContData.env$myName.pH
, ContData.env$myName.Turbidity
, ContData.env$myName.Chlorophylla
, ContData.env$myName.WaterLevel
, ContData.env$myName.Salinity
, ContData.env$myName.LoggerID.Water
, ContData.env$myName.RowID.Water
, ContData.env$myName.Discrete.WaterTemp
, ContData.env$myName.Discrete.AirTemp
, ContData.env$myName.Discrete.WaterP
, ContData.env$myName.Discrete.AirBP
, ContData.env$myName.Discrete.SensorDepth
, ContData.env$myName.Discrete.Discharge
, ContData.env$myName.Discrete.Cond
, ContData.env$myName.Discrete.DO
, ContData.env$myName.Discrete.DO.adj
, ContData.env$myName.Discrete.DO.pctsat
, ContData.env$myName.Discrete.pH
, ContData.env$myName.Discrete.Turbidity
, ContData.env$myName.Discrete.Chlorophylla
, ContData.env$myName.Discrete.WaterLevel
, ContData.env$myName.Discrete.Salinity
)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
## Data Quality Flag Values ####
ContData.env$myFlagVal.Pass <- "P"
ContData.env$myFlagVal.NotEval <- "NA"
ContData.env$myFlagVal.Suspect <- "S"
ContData.env$myFlagVal.Fail <- "F"
ContData.env$myFlagVal.NoData <- "X"
ContData.env$myFlagVal.Order <- c(ContData.env$myFlagVal.Pass
, ContData.env$myFlagVal.Suspect
, ContData.env$myFlagVal.Fail
, ContData.env$myFlagVal.NoData)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# QC Tests and Calculations ####
#http://stackoverflow.com/questions/16143700/pasting-two-vectors-with-combinations-of-all-vectors-elements
#myNames.QCTests.Calcs.combo <- as.vector(t(outer(myNames.QCTests,myNames.QCTests.Calcs,paste,sep=".")))
# combine so can check for and remove later.
#myNames.DataFields.QCTests.Calcs.combo <- as.vector(t(outer(myNames.DataFields,myNames.QCTests.Calcs.combo,paste,sep=".")))
# Data Quality Flag Thresholds
# _QC, Gross----
## Gross Min/Max, Fail (equipment)
### Examines values as outliers versus threholds
### if value >= Hi or <= Lo then flagged as "Fail"
ContData.env$myThresh.Gross.Fail.Hi.WaterTemp <- 30
ContData.env$myThresh.Gross.Fail.Lo.WaterTemp <- -2
ContData.env$myThresh.Gross.Fail.Hi.AirTemp <- 38
ContData.env$myThresh.Gross.Fail.Lo.AirTemp <- -25
ContData.env$myThresh.Gross.Fail.Hi.AirBP <- 15
ContData.env$myThresh.Gross.Fail.Lo.AirBP <- 13
ContData.env$myThresh.Gross.Fail.Hi.WaterP <- 17
ContData.env$myThresh.Gross.Fail.Lo.WaterP <- 13
ContData.env$myThresh.Gross.Fail.Hi.SensorDepth <- 10^5 # dependent upon stream size
ContData.env$myThresh.Gross.Fail.Lo.SensorDepth <- -1 # dependent upon stream size
ContData.env$myThresh.Gross.Fail.Hi.Discharge <- 10^5 # dependent upon stream size
ContData.env$myThresh.Gross.Fail.Lo.Discharge <- -1 # dependent upon stream size
ContData.env$myThresh.Gross.Fail.Hi.Cond <- 1500 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Lo.Cond <- 10 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Hi.DO <- 20 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Lo.DO <- 1 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Hi.DO.adj <- 20 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Lo.DO.adj <- 1 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Hi.DO.pctsat <- 120 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Lo.DO.pctsat <- -1 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Hi.pH <- 12 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Lo.pH <- 3 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Hi.Turbidity <- 10^5 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Lo.Turbidity <- -1 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Hi.Chlorophylla <- 10^5 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Lo.Chlorophylla <- -1 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Hi.WaterLevel <- ContData.env$myThresh.Gross.Fail.Hi.SensorDepth
ContData.env$myThresh.Gross.Fail.Lo.WaterLevel <- ContData.env$myThresh.Gross.Fail.Lo.SensorDepth
ContData.env$myThresh.Gross.Fail.Hi.Salinity <- 41
ContData.env$myThresh.Gross.Fail.Lo.Salinity <- 2
## Gross Min/Max, Suspect (extreme)
### Examines values as outliers versus threholds
### if value >= Hi or <= Lo then flagged as "Suspect"
ContData.env$myThresh.Gross.Suspect.Hi.WaterTemp <- 25
ContData.env$myThresh.Gross.Suspect.Lo.WaterTemp <- -0.1
ContData.env$myThresh.Gross.Suspect.Hi.AirTemp <- 35
ContData.env$myThresh.Gross.Suspect.Lo.AirTemp <- -23
ContData.env$myThresh.Gross.Suspect.Hi.AirBP <- 14.8
ContData.env$myThresh.Gross.Suspect.Lo.AirBP <- 13.0
ContData.env$myThresh.Gross.Suspect.Hi.WaterP <- 16.8
ContData.env$myThresh.Gross.Suspect.Lo.WaterP <- 13.5
ContData.env$myThresh.Gross.Suspect.Hi.SensorDepth <- 10^3 # dependent upon stream size
ContData.env$myThresh.Gross.Suspect.Lo.SensorDepth <- 0 # dependent upon stream size
ContData.env$myThresh.Gross.Suspect.Hi.Discharge <- 10^3 # dependent upon stream size
ContData.env$myThresh.Gross.Suspect.Lo.Discharge <- -1 # dependent upon stream size
ContData.env$myThresh.Gross.Suspect.Hi.Cond <- 1200 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Lo.Cond <- 20 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Hi.DO <- 18 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Lo.DO <- 2 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Hi.DO.adj <- 18 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Lo.DO.adj <- 2 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Hi.DO.pctsat <- 100 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Lo.DO.pctsat <- 0 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Hi.pH <- 11 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Lo.pH <- 4 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Hi.Turbidity <- 10^3 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Lo.Turbidity <- -1 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Hi.Chlorophylla <- 10^3 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Lo.Chlorophylla <- 1 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Hi.WaterLevel <- ContData.env$myThresh.Gross.Suspect.Hi.SensorDepth
ContData.env$myThresh.Gross.Suspect.Lo.WaterLevel <- ContData.env$myThresh.Gross.Suspect.Lo.SensorDept
ContData.env$myThresh.Gross.Suspect.Hi.Salinity <- 37
ContData.env$myThresh.Gross.Suspect.Lo.Salinity <- 3
# _QC, Spike ----
## Spike thresholds (absolute change)
### Examines difference between consecutive measurements
### if delta >= Hi then flagged as "Fail"
### if delta >= Lo then flagged as "Suspect"
ContData.env$myThresh.Spike.Hi.WaterTemp <- 1.5
ContData.env$myThresh.Spike.Lo.WaterTemp <- 1
ContData.env$myThresh.Spike.Hi.AirTemp <- 10
ContData.env$myThresh.Spike.Lo.AirTemp <- 8
ContData.env$myThresh.Spike.Hi.AirBP <- 0.25
ContData.env$myThresh.Spike.Lo.AirBP <- 0.15
ContData.env$myThresh.Spike.Hi.WaterP <- 0.7
ContData.env$myThresh.Spike.Lo.WaterP <- 0.5
ContData.env$myThresh.Spike.Hi.SensorDepth <- 10^4 # dependent upon stream size
ContData.env$myThresh.Spike.Lo.SensorDepth <- 10^3 # dependent upon stream size
ContData.env$myThresh.Spike.Hi.Discharge <- 10^4 # dependent upon stream size
ContData.env$myThresh.Spike.Lo.Discharge <- 10^3 # dependent upon stream size
ContData.env$myThresh.Spike.Hi.Cond <- 10 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Lo.Cond <- 5 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Hi.DO <- 10 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Lo.DO <- 5 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Hi.DO.adj <- 10 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Lo.DO.adj <- 5 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Hi.DO.pctsat <- 25 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Lo.DO.pctsat <- 10 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Hi.pH <- 10 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Lo.pH <- 5 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Hi.Turbidity <- 10^4 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Lo.Turbidity <- 10^3 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Hi.Chlorophylla <- 10^4 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Lo.Chlorophylla <- 10^3 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Hi.WaterLevel <- ContData.env$myThresh.Spike.Hi.SensorDepth
ContData.env$myThresh.Spike.Lo.WaterLevel <- ContData.env$myThresh.Spike.Lo.SensorDepth
ContData.env$myThresh.Spike.Hi.Salinity <- 5
ContData.env$myThresh.Spike.Lo.Salinity <- 3
# _QC, ROC----
## Rate of Change (relative change)
### Examines SD over "period" and difference in consecutive values
### If delta >= SD.number * SD then flagged as "Suspect"
ContData.env$myDefault.RoC.SD.number <- 3
ContData.env$myDefault.RoC.SD.period <- 25 #hours
ContData.env$myThresh.RoC.SD.number.WaterTemp <- ContData.env$myDefault.RoC.SD.number
ContData.env$myThresh.RoC.SD.period.WaterTemp <- ContData.env$myDefault.RoC.SD.period
ContData.env$myThresh.RoC.SD.number.AirTemp <- ContData.env$myDefault.RoC.SD.number
ContData.env$myThresh.RoC.SD.period.AirTemp <- ContData.env$myDefault.RoC.SD.period
ContData.env$myThresh.RoC.SD.number.AirBP <- ContData.env$myDefault.RoC.SD.number
ContData.env$myThresh.RoC.SD.period.AirBP <- ContData.env$myDefault.RoC.SD.period
ContData.env$myThresh.RoC.SD.number.WaterP <- ContData.env$myDefault.RoC.SD.number
ContData.env$myThresh.RoC.SD.period.WaterP <- ContData.env$myDefault.RoC.SD.period
ContData.env$myThresh.RoC.SD.number.SensorDepth <- ContData.env$myDefault.RoC.SD.number
ContData.env$myThresh.RoC.SD.period.SensorDepth <- ContData.env$myDefault.RoC.SD.period
ContData.env$myThresh.RoC.SD.number.Discharge <- ContData.env$myDefault.RoC.SD.number
ContData.env$myThresh.RoC.SD.period.Discharge <- ContData.env$myDefault.RoC.SD.period
ContData.env$myThresh.RoC.SD.number.Cond <- ContData.env$myDefault.RoC.SD.number
ContData.env$myThresh.RoC.SD.period.Cond <- ContData.env$myDefault.RoC.SD.period
ContData.env$myThresh.RoC.SD.number.DO <- ContData.env$myDefault.RoC.SD.number
ContData.env$myThresh.RoC.SD.period.DO <- ContData.env$myDefault.RoC.SD.period
ContData.env$myThresh.RoC.SD.number.DO.adj <- ContData.env$myDefault.RoC.SD.number
ContData.env$myThresh.RoC.SD.period.DO.adj <- ContData.env$myDefault.RoC.SD.period
ContData.env$myThresh.RoC.SD.number.DO.pctsat <- ContData.env$myDefault.RoC.SD.number
ContData.env$myThresh.RoC.SD.period.DO.pctsat <- ContData.env$myDefault.RoC.SD.period
ContData.env$myThresh.RoC.SD.number.pH <- ContData.env$myDefault.RoC.SD.number
ContData.env$myThresh.RoC.SD.period.pH <- ContData.env$myDefault.RoC.SD.period
ContData.env$myThresh.RoC.SD.number.Turbidity <- ContData.env$myDefault.RoC.SD.number
ContData.env$myThresh.RoC.SD.period.Turbidity <- ContData.env$myDefault.RoC.SD.period
ContData.env$myThresh.RoC.SD.number.Chlorophylla <- ContData.env$myDefault.RoC.SD.number
ContData.env$myThresh.RoC.SD.period.Chlorophylla <- ContData.env$myDefault.RoC.SD.period
ContData.env$myThresh.RoC.SD.number.WaterLevel <- ContData.env$myDefault.RoC.SD.number
ContData.env$myThresh.RoC.SD.period.WaterLevel <- ContData.env$myDefault.RoC.SD.period
ContData.env$myThresh.RoC.SD.number.Salinity <- ContData.env$myDefault.RoC.SD.number
ContData.env$myThresh.RoC.SD.period.Salinity <- ContData.env$myDefault.RoC.SD.period
# QC, Flat Line----
## No Change (flat-line)
### Examines consecutive values within "Tolerance" of each other
### If number of consecutive values >= Hi then flagged as "Fail"
### If number of consecutive values >= Lo (and < Hi) then flagged as "Suspect"
ContData.env$myDefault.Flat.Hi <- 30 # maximum is myThresh.Flat.MaxComp
ContData.env$myDefault.Flat.Lo <- 15
ContData.env$myDefault.Flat.Tolerance <- 0.01 # set to one sigdig less than measurements. Check with fivenum(x)
ContData.env$myThresh.Flat.Hi.WaterTemp <- 30
ContData.env$myThresh.Flat.Lo.WaterTemp <- 20
ContData.env$myThresh.Flat.Tolerance.WaterTemp <- 0.01
ContData.env$myThresh.Flat.Hi.AirTemp <- 20
ContData.env$myThresh.Flat.Lo.AirTemp <- 15
ContData.env$myThresh.Flat.Tolerance.AirTemp <- 0.01
ContData.env$myThresh.Flat.Hi.AirBP <- 15
ContData.env$myThresh.Flat.Lo.AirBP <- 10
ContData.env$myThresh.Flat.Tolerance.AirBP <- 0.001
ContData.env$myThresh.Flat.Hi.WaterP <- 15
ContData.env$myThresh.Flat.Lo.WaterP <- 10
ContData.env$myThresh.Flat.Tolerance.WaterP <- 0.001
ContData.env$myThresh.Flat.Hi.SensorDepth <- 60
ContData.env$myThresh.Flat.Lo.SensorDepth <- 20
ContData.env$myThresh.Flat.Tolerance.SensorDepth <- 0.0
ContData.env$myThresh.Flat.Hi.Discharge <- ContData.env$myDefault.Flat.Hi * 2
ContData.env$myThresh.Flat.Lo.Discharge <- ContData.env$myDefault.Flat.Lo * 2
ContData.env$myThresh.Flat.Tolerance.Discharge <- 0.01
ContData.env$myThresh.Flat.Hi.Cond <- ContData.env$myDefault.Flat.Hi * 2
ContData.env$myThresh.Flat.Lo.Cond <- ContData.env$myDefault.Flat.Lo * 2
ContData.env$myThresh.Flat.Tolerance.Cond <- 0.01
ContData.env$myThresh.Flat.Hi.DO <- ContData.env$myDefault.Flat.Hi * 2
ContData.env$myThresh.Flat.Lo.DO <- ContData.env$myDefault.Flat.Lo * 2
ContData.env$myThresh.Flat.Tolerance.DO <- 0.01
ContData.env$myThresh.Flat.Hi.DO.adj <- ContData.env$myDefault.Flat.Hi * 2
ContData.env$myThresh.Flat.Lo.DO.adj <- ContData.env$myDefault.Flat.Lo * 2
ContData.env$myThresh.Flat.Tolerance.DO.adj <- 0.01
ContData.env$myThresh.Flat.Hi.DO.pctsat <- ContData.env$myDefault.Flat.Hi * 2
ContData.env$myThresh.Flat.Lo.DO.pctsat <- ContData.env$myDefault.Flat.Lo * 2
ContData.env$myThresh.Flat.Tolerance.DO.pctsat <- 0.01
ContData.env$myThresh.Flat.Hi.pH <- ContData.env$myDefault.Flat.Hi * 2
ContData.env$myThresh.Flat.Lo.pH <- ContData.env$myDefault.Flat.Lo * 2
ContData.env$myThresh.Flat.Tolerance.pH <- 0.01
ContData.env$myThresh.Flat.Hi.Turbidity <- ContData.env$myDefault.Flat.Hi * 2
ContData.env$myThresh.Flat.Lo.Turbidity <- ContData.env$myDefault.Flat.Lo * 2
ContData.env$myThresh.Flat.Tolerance.Turbidity <- 0.01
ContData.env$myThresh.Flat.Hi.Chlorophylla <- ContData.env$myDefault.Flat.Hi * 2
ContData.env$myThresh.Flat.Lo.Chlorophylla <- ContData.env$myDefault.Flat.Lo * 2
ContData.env$myThresh.Flat.Tolerance.Chlorophylla <- 0.01
ContData.env$myThresh.Flat.Hi.WaterLevel <- ContData.env$myThresh.Flat.Hi.SensorDepth
ContData.env$myThresh.Flat.Lo.WaterLevel <- ContData.env$myThresh.Flat.Lo.SensorDepth
ContData.env$myThresh.Flat.Tolerance.WaterLevel <- ContData.env$myThresh.Flat.Tolerance.SensorDepth
ContData.env$myThresh.Flat.Hi.Salinity <- ContData.env$myThresh.Flat.Hi.SensorDepth * 2
ContData.env$myThresh.Flat.Lo.Salinity <- ContData.env$myThresh.Flat.Lo.SensorDepth * 2
ContData.env$myThresh.Flat.Tolerance.Salinity <- 0.01
#
ContData.env$myThresh.Flat.MaxComp <- max(ContData.env$myThresh.Flat.Hi.WaterTemp
, ContData.env$myThresh.Flat.Hi.AirTemp
, ContData.env$myThresh.Flat.Hi.AirBP
, ContData.env$myThresh.Flat.Hi.WaterP
, ContData.env$myThresh.Flat.Hi.SensorDepth
, ContData.env$myThresh.Flat.Hi.Discharge
, ContData.env$myThresh.Flat.Hi.Cond
, ContData.env$myThresh.Flat.Hi.DO
, ContData.env$myThresh.Flat.Hi.DO.adj
, ContData.env$myThresh.Flat.Hi.DO.pctsat
, ContData.env$myThresh.Flat.Hi.pH
, ContData.env$myThresh.Flat.Hi.Turbidity
, ContData.env$myThresh.Flat.Hi.Chlorophylla
, ContData.env$myThresh.Flat.Hi.WaterLevel
, ContData.env$myThresh.Flat.Hi.Salinity
)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Data Fields with Flags ####
ContData.env$myName.Flag <- "Flag" # flag prefix
ContData.env$myNames.Cols4Flags <- c(ContData.env$myName.DateTime
, ContData.env$myNames.DataFields)
ContData.env$myNames.Flags <- paste(ContData.env$myName.Flag
, ContData.env$myNames.Cols4Flags
, sep=".")
# define ones using in the calling script
## flag labels
ContData.env$myName.Flag.DateTime <- paste(ContData.env$myName.Flag
, ContData.env$myName.DateTime
, sep=".")
ContData.env$myName.Flag.WaterTemp <- paste(ContData.env$myName.Flag
, ContData.env$myName.WaterTemp
, sep=".")
ContData.env$myName.Flag.AirTemp <- paste(ContData.env$myName.Flag
, ContData.env$myName.AirTemp
, sep=".")
ContData.env$myName.Flag.AirBP <- paste(ContData.env$myName.Flag
, ContData.env$myName.AirBP
, sep=".")
ContData.env$myName.Flag.WaterP <- paste(ContData.env$myName.Flag
, ContData.env$myName.WaterP
, sep=".")
ContData.env$myName.Flag.SensorDepth <- paste(ContData.env$myName.Flag
, ContData.env$myName.SensorDepth
, sep=".")
ContData.env$myName.Flag.Discharge <- paste(ContData.env$myName.Flag
, ContData.env$myName.Discharge
, sep=".")
ContData.env$myName.Flag.Cond <- paste(ContData.env$myName.Flag
, ContData.env$myName.Cond
, sep=".")
ContData.env$myName.Flag.DO <- paste(ContData.env$myName.Flag
, ContData.env$myName.DO
, sep=".")
ContData.env$myName.Flag.DO.adj <- paste(ContData.env$myName.Flag
, ContData.env$myName.DO.adj
, sep=".")
ContData.env$myName.Flag.DO.pctsat <- paste(ContData.env$myName.Flag
, ContData.env$myName.DO.pctsat
, sep=".")
ContData.env$myName.Flag.pH <- paste(ContData.env$myName.Flag
, ContData.env$myName.pH
, sep=".")
ContData.env$myName.Flag.Turbidity <- paste(ContData.env$myName.Flag
, ContData.env$myName.Turbidity
, sep=".")
ContData.env$myName.Flag.Chlorophylla <- paste(ContData.env$myName.Flag
, ContData.env$myName.Chlorophylla
, sep=".")
ContData.env$myName.Flag.WaterLevel <- paste(ContData.env$myName.Flag
, ContData.env$myName.WaterLevel
, sep=".")
ContData.env$myName.Flag.Salinity <- paste(ContData.env$myName.Flag
, ContData.env$myName.Salinity
, sep=".")
# Data Quality Test Names
ContData.env$myNames.QCTests <- c("Gross","Spike","RoC","Flat")
ContData.env$myNames.QCCalcs <- c("SD.Time"
, "SD"
, "SDxN"
, paste("n"
, seq_len(
ContData.env$myThresh.Flat.MaxComp)
, sep=".")
, "flat.Lo"
, "flat.Hi")
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Exceedance values for stats (default to Gross-Suspect-Hi value) ####
ContData.env$myExceed.WaterTemp <-
ContData.env$myThresh.Gross.Suspect.Hi.WaterTemp
ContData.env$myExceed.AirTemp <-
ContData.env$myThresh.Gross.Suspect.Hi.AirTemp
ContData.env$myExceed.SensorDepth <-
ContData.env$myThresh.Gross.Suspect.Hi.SensorDepth
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Date and Time Formats ####
ContData.env$myFormat.Date <- "%Y-%m-%d"
ContData.env$myFormat.Time <- "%H:%M:%S"
ContData.env$myFormat.DateTime <- "%Y-%m-%d %H:%M:%S"
ContData.env$DateRange.Start.Default <- format(as.Date("1900-01-01")
, ContData.env$myFormat.Date)
#YYYY-MM-DD
ContData.env$DateRange.End.Default <- format(Sys.Date()
, ContData.env$myFormat.Date)
# Time Zone, used in Gage script in dataRetrieval, OlsonNames()
ContData.env$myTZ <- Sys.timezone() #"America/New_York" (local time zone)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Time Frames (MM-DD) ####
ContData.env$myTimeFrame.Annual.Start <- "0101"
ContData.env$myTimeFrame.Annual.End <- "1231"
ContData.env$myTimeFrame.WaterYear.Start <- "1001"
#ContData.env$myTimeFrame.WaterYear.End <- "0930"
ContData.env$myTimeFrame.Season.Spring.Start <- "0301"
#ContData.env$myTimeFrame.Season.Spring.End <- "0531"
ContData.env$myTimeFrame.Season.Summer.Start <- "0601"
#ContData.env$myTimeFrame.Season.Summer.End <- "0831"
ContData.env$myTimeFrame.Season.Fall.Start <- "0901"
#ContData.env$myTimeFrame.Season.Fall.End <- "1130"
ContData.env$myTimeFrame.Season.Winter.Start <- "1201"
#ContData.env$myTimeFrame.Season.Winter.End <- "0228" #but 0229 in leap year, use start dates only
# Time Frame Names
ContData.env$myName.Yr <- "Year"
ContData.env$myName.YrMo <- "YearMonth"
ContData.env$myName.Mo <- "Month"
ContData.env$myName.MoDa <- "MonthDay"
ContData.env$myName.JuDa <- "JulianDay"
ContData.env$myName.Day <- "Day"
ContData.env$myName.Season <- "Season"
ContData.env$myName.YrSeason <- "YearSeason"
# for summary stats
ContData.env$myNames.Fields.TimePeriods <- c(ContData.env$myName.Yr
,ContData.env$myName.YrMo
,ContData.env$myName.Mo
,ContData.env$myName.MoDa
,ContData.env$myName.JuDa
,ContData.env$myName.Season
,ContData.env$myName.YrSeason)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Exclude Trigger ####
# Trigger for Stats to exclude (TRUE) or include (FALSE) where flag = "fail"
ContData.env$myStats.Fails.Exclude <- TRUE #FALSE #TRUE
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Report Format ####
ContData.env$myReport.Format <- "docx" # "html" or "docx"
# DOCX requires Pandoc.
ContData.env$myReport.Dir <- file.path(system.file(package="ContDataQC"), "rmd")