inst/extdata/config.ORIG.R
In leppott/ContDataQC: Quality Control (QC) of Continous Monitoring Data
# 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
# 20230828, updated were QC flag test thresholds, Jen
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# 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 <- -1
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$myThresh.Gross.Fail.Hi.DO <- 18 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Lo.DO <- 1 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Hi.DO.adj <- 18 # this threshold has not been closely evaluated
ContData.env$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 <- -0.5
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$myThresh.Gross.Suspect.Hi.DO <- 16 # this threshold has not been closely evaluated
ContData.env$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$myThresh.Spike.Hi.WaterTemp <- 2
ContData.env$myThresh.Spike.Lo.WaterTemp <- 1.5
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$myThresh.Spike.Hi.DO <- 4 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Lo.DO <- 2 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Hi.DO.adj <- 4 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Lo.DO.adj <- 2 # 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$myDefault.RoC.SD.number <- 6
ContData.env$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 <- 100
ContData.env$myThresh.Flat.Lo.WaterTemp <- 60
ContData.env$myThresh.Flat.Tolerance.WaterTemp <- 0.01
ContData.env$myThresh.Flat.Hi.AirTemp <- 60
ContData.env$myThresh.Flat.Lo.AirTemp <- 30
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$myThresh.Flat.Lo.SensorDepth <- 30
ContData.env$myThresh.Flat.Tolerance.SensorDepth <- 0.01
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$myThresh.Flat.Hi.Salinity <- ContData.env$myDefault.Flat.Hi * 2
ContData.env$myThresh.Flat.Lo.Salinity <- ContData.env$myDefault.Flat.Lo * 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")
leppott/ContDataQC documentation built on Jan. 5, 2025, 10:12 a.m.
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# 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
# 20230828, updated were QC flag test thresholds, Jen
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# 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 <- -1
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$myThresh.Gross.Fail.Hi.DO <- 18 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Lo.DO <- 1 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Hi.DO.adj <- 18 # this threshold has not been closely evaluated
ContData.env$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 <- -0.5
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$myThresh.Gross.Suspect.Hi.DO <- 16 # this threshold has not been closely evaluated
ContData.env$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$myThresh.Spike.Hi.WaterTemp <- 2
ContData.env$myThresh.Spike.Lo.WaterTemp <- 1.5
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$myThresh.Spike.Hi.DO <- 4 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Lo.DO <- 2 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Hi.DO.adj <- 4 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Lo.DO.adj <- 2 # 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$myDefault.RoC.SD.number <- 6
ContData.env$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 <- 100
ContData.env$myThresh.Flat.Lo.WaterTemp <- 60
ContData.env$myThresh.Flat.Tolerance.WaterTemp <- 0.01
ContData.env$myThresh.Flat.Hi.AirTemp <- 60
ContData.env$myThresh.Flat.Lo.AirTemp <- 30
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$myThresh.Flat.Lo.SensorDepth <- 30
ContData.env$myThresh.Flat.Tolerance.SensorDepth <- 0.01
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$myThresh.Flat.Hi.Salinity <- ContData.env$myDefault.Flat.Hi * 2
ContData.env$myThresh.Flat.Lo.Salinity <- ContData.env$myDefault.Flat.Lo * 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")
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