In leppott/ContDataQC: Quality Control (QC) of Continous Monitoring Data
knitr::opts_chunk$set(results='asis', echo=FALSE, warning=FALSE)
# needed for trouble shooting
myConfig <- file.path(system.file(package="ContDataQC"), "extdata", "config.ORIG.R")
#source(myConfig)
FILE INFORMATION
# Report Info
myReportDate <- format(Sys.Date(), ContData.env$myFormat.Date)
cat(paste("**Report Date:** ",myReportDate,"\n\n",sep=""))
myUser <- Sys.getenv("USERNAME")
cat(paste("**Generated By:** ",myUser,"\n\n",sep=""))
#file name
cat("**File Name:** ",basename(myConfig),"\n\n",sep="")
#dir name
cat("**File Location:** ",dirname(myConfig),"\n\n",sep="")
# Last Modified Date
cat("**Last Modified:** ",format(file.info(myConfig)$mtime, ContData.env$myFormat.DateTime),"\n\n",sep="")
CONFIGURATION SETTINGS
Output of configuration file used in the ContDataQC package.
Thresholds
Table of most relevant thresholds in report ready format. This is the same table that appears in the QC Report. The four test types are column headers.
kbl_caption <- "Thresholds, Quick Reference"
txt_header <- c("Analyte", "Flag", "Gross", "Spike", "Rate of Change", "Flat Line")
# WaterTemp
nam_WaterTemp <- c("myLab.WaterTemp" #1
, "myUnits.WaterTemp" #2
, "myThresh.Gross.Fail.Hi.WaterTemp" #3
, "myThresh.Gross.Fail.Lo.WaterTemp" #4
, "myThresh.Gross.Suspect.Hi.WaterTemp" #5
, "myThresh.Gross.Suspect.Lo.WaterTemp" #6
, "myThresh.Spike.Hi.WaterTemp" #7
, "myThresh.Spike.Lo.WaterTemp" #8
, "myThresh.RoC.SD.number.WaterTemp" #9
, "myThresh.RoC.SD.period.WaterTemp" #10
, "myThresh.Flat.Hi.WaterTemp" #11
, "myThresh.Flat.Lo.WaterTemp" #12
, "myThresh.Flat.Tolerance.WaterTemp" #13
)
val_WaterTemp <- mget(nam_WaterTemp, envir=ContData.env)
txt_WaterTemp_F <- c(val_WaterTemp[1]
, "Fail"
, paste0("> ",val_WaterTemp[3]," deg ",val_WaterTemp[2]
," or < ",val_WaterTemp[4]," deg ",val_WaterTemp[2])
, paste0(">= ", val_WaterTemp[7]," deg ",val_WaterTemp[2]," (+/-)")
, "NA"
, paste0("> ",val_WaterTemp[11]
," consecutive measurements within ",val_WaterTemp[13]
," units of one another"))
txt_WaterTemp_S <- c(val_WaterTemp[1]
, "Suspect"
, paste0("> ",val_WaterTemp[5]," deg ",val_WaterTemp[2]
," or < ",val_WaterTemp[6]," deg ",val_WaterTemp[2])
, paste0(">= ", val_WaterTemp[8]," deg ",val_WaterTemp[2]," (+/-)")
, paste0(">= ",val_WaterTemp[9]," standard deviations within "
,val_WaterTemp[10]," hours")
, paste0("> ",val_WaterTemp[12]
," consecutive measurements within ",val_WaterTemp[13]
," units of one another"))
# AirTemp
nam_AirTemp <- c("myLab.AirTemp" #1
, "myUnits.AirTemp" #2
, "myThresh.Gross.Fail.Hi.AirTemp" #3
, "myThresh.Gross.Fail.Lo.AirTemp" #4
, "myThresh.Gross.Suspect.Hi.AirTemp" #5
, "myThresh.Gross.Suspect.Lo.AirTemp" #6
, "myThresh.Spike.Hi.AirTemp" #7
, "myThresh.Spike.Lo.AirTemp" #8
, "myThresh.RoC.SD.number.AirTemp" #9
, "myThresh.RoC.SD.period.AirTemp" #10
, "myThresh.Flat.Hi.AirTemp" #11
, "myThresh.Flat.Lo.AirTemp" #12
, "myThresh.Flat.Tolerance.AirTemp" #13
)
val_AirTemp <- mget(nam_AirTemp, envir=ContData.env)
txt_AirTemp_F <- c(val_AirTemp[1]
, "Fail"
, paste0("> ",val_AirTemp[3]," deg ",val_AirTemp[2]
," or < ",val_AirTemp[4]," deg ",val_AirTemp[2])
, paste0(">= ", val_AirTemp[7]," deg ",val_AirTemp[2]," (+/-)")
, "NA"
, paste0("> ",val_AirTemp[11]
," consecutive measurements within ",val_AirTemp[13]
," units of one another"))
txt_AirTemp_S <- c(val_AirTemp[1]
, "Suspect"
, paste0("> ",val_AirTemp[5]," deg ",val_AirTemp[2]
," or < ",val_AirTemp[6]," deg ",val_AirTemp[2])
, paste0(">= ", val_AirTemp[8]," deg ",val_AirTemp[2]," (+/-)")
, paste0(">= ",val_AirTemp[9]," standard deviations within "
,val_AirTemp[10]," hours")
, paste0("> ",val_AirTemp[12]
," consecutive measurements within ",val_AirTemp[13]
," units of one another"))
# WaterP
nam_WaterP <- c("myLab.WaterP" #1
, "myUnits.WaterP" #2
, "myThresh.Gross.Fail.Hi.WaterP" #3
, "myThresh.Gross.Fail.Lo.WaterP" #4
, "myThresh.Gross.Suspect.Hi.WaterP" #5
, "myThresh.Gross.Suspect.Lo.WaterP" #6
, "myThresh.Spike.Hi.WaterP" #7
, "myThresh.Spike.Lo.WaterP" #8
, "myThresh.RoC.SD.number.WaterP" #9
, "myThresh.RoC.SD.period.WaterP" #10
, "myThresh.Flat.Hi.WaterP" #11
, "myThresh.Flat.Lo.WaterP" #12
, "myThresh.Flat.Tolerance.WaterP" #13
)
val_WaterP <- mget(nam_WaterP, envir=ContData.env)
txt_WaterP_F <- c(val_WaterP[1]
, "Fail"
, paste0("> ",val_WaterP[3]," ",val_WaterP[2]
," or < ",val_WaterP[4]," ",val_WaterP[2])
, paste0(">= ", val_WaterP[7]," ",val_WaterP[2]," (+/-)")
, "NA"
, paste0("> ",val_WaterP[11]
," consecutive measurements within ",val_WaterP[13]
," units of one another"))
txt_WaterP_S <- c(val_WaterP[1]
, "Suspect"
, paste0("> ",val_WaterP[5]," ",val_WaterP[2]
," or < ",val_WaterP[6]," ",val_WaterP[2])
, paste0(">= ", val_WaterP[8]," ",val_WaterP[2]," (+/-)")
, paste0(">= ",val_WaterP[9]," standard deviations within "
,val_WaterP[10]," hours")
, paste0("> ",val_WaterP[12]
," consecutive measurements within ",val_WaterP[13]
," units of one another"))
# AirBP
nam_AirBP <- c("myLab.AirBP" #1
, "myUnits.AirBP" #2
, "myThresh.Gross.Fail.Hi.AirBP" #3
, "myThresh.Gross.Fail.Lo.AirBP" #4
, "myThresh.Gross.Suspect.Hi.AirBP" #5
, "myThresh.Gross.Suspect.Lo.AirBP" #6
, "myThresh.Spike.Hi.AirBP" #7
, "myThresh.Spike.Lo.AirBP" #8
, "myThresh.RoC.SD.number.AirBP" #9
, "myThresh.RoC.SD.period.AirBP" #10
, "myThresh.Flat.Hi.AirBP" #11
, "myThresh.Flat.Lo.AirBP" #12
, "myThresh.Flat.Tolerance.AirBP" #13
)
val_AirBP <- mget(nam_AirBP, envir=ContData.env)
txt_AirBP_F <- c(val_AirBP[1]
, "Fail"
, paste0("> ",val_AirBP[3]," ",val_AirBP[2]
," or < ",val_AirBP[4]," ",val_AirBP[2])
, paste0(">= ", val_AirBP[7]," ",val_AirBP[2]," (+/-)")
, "NA"
, paste0("> ",val_AirBP[11]
," consecutive measurements within ",val_AirBP[13]
," units of one another"))
txt_AirBP_S <- c(val_AirBP[1]
, "Suspect"
, paste0("> ",val_AirBP[5]," ",val_AirBP[2]
," or < ",val_AirBP[6]," ",val_AirBP[2])
, paste0(">= ", val_AirBP[8]," ",val_AirBP[2]," (+/-)")
, paste0(">= ",val_AirBP[9]," standard deviations within "
,val_AirBP[10]," hours")
, paste0("> ",val_AirBP[12]
," consecutive measurements within ",val_AirBP[13]
," units of one another"))
# SensorDepth
nam_SensorDepth <- c("myLab.SensorDepth" #1
, "myUnits.SensorDepth" #2
, "myThresh.Gross.Fail.Hi.SensorDepth" #3
, "myThresh.Gross.Fail.Lo.SensorDepth" #4
, "myThresh.Gross.Suspect.Hi.SensorDepth" #5
, "myThresh.Gross.Suspect.Lo.SensorDepth" #6
, "myThresh.Spike.Hi.SensorDepth" #7
, "myThresh.Spike.Lo.SensorDepth" #8
, "myThresh.RoC.SD.number.SensorDepth" #9
, "myThresh.RoC.SD.period.SensorDepth" #10
, "myThresh.Flat.Hi.SensorDepth" #11
, "myThresh.Flat.Lo.SensorDepth" #12
, "myThresh.Flat.Tolerance.SensorDepth" #13
)
val_SensorDepth <- mget(nam_SensorDepth, envir=ContData.env)
txt_SensorDepth_F <- c(val_SensorDepth[1]
, "Fail"
, paste0("> ",val_SensorDepth[3]," ",val_SensorDepth[2]
," or < ",val_SensorDepth[4]," ",val_SensorDepth[2])
, paste0(">= ", val_SensorDepth[7]," ",val_SensorDepth[2]," (+/-)")
, "NA"
, paste0("> ",val_SensorDepth[11]
," consecutive measurements within ",val_SensorDepth[13]
," units of one another"))
txt_SensorDepth_S <- c(val_SensorDepth[1]
, "Suspect"
, paste0("> ",val_SensorDepth[5]," ",val_SensorDepth[2]
," or < ",val_SensorDepth[6]," ",val_SensorDepth[2])
, paste0(">= ", val_SensorDepth[8]," ",val_SensorDepth[2]," (+/-)")
, paste0(">= ",val_SensorDepth[9]," standard deviations within "
,val_SensorDepth[10]," hours")
, paste0("> ",val_SensorDepth[12]
," consecutive measurements within ",val_SensorDepth[13]
," units of one another"))
# Discharge
nam_Discharge <- c("myLab.Discharge" #1
, "myUnits.Discharge" #2
, "myThresh.Gross.Fail.Hi.Discharge" #3
, "myThresh.Gross.Fail.Lo.Discharge" #4
, "myThresh.Gross.Suspect.Hi.Discharge" #5
, "myThresh.Gross.Suspect.Lo.Discharge" #6
, "myThresh.Spike.Hi.Discharge" #7
, "myThresh.Spike.Lo.Discharge" #8
, "myThresh.RoC.SD.number.Discharge" #9
, "myThresh.RoC.SD.period.Discharge" #10
, "myThresh.Flat.Hi.Discharge" #11
, "myThresh.Flat.Lo.Discharge" #12
, "myThresh.Flat.Tolerance.Discharge" #13
)
val_Discharge <- mget(nam_Discharge, envir=ContData.env)
txt_Discharge_F <- c(val_Discharge[1]
, "Fail"
, paste0("> ",val_Discharge[3]," ",val_Discharge[2]
," or < ",val_Discharge[4]," ",val_Discharge[2])
, paste0(">= ", val_Discharge[7]," ",val_Discharge[2]," (+/-)")
, "NA"
, paste0("> ",val_Discharge[11]
," consecutive measurements within ",val_Discharge[13]
," units of one another"))
txt_Discharge_S <- c(val_Discharge[1]
, "Suspect"
, paste0("> ",val_Discharge[5]," ",val_Discharge[2]
," or < ",val_Discharge[6]," ",val_Discharge[2])
, paste0(">= ", val_Discharge[8]," ",val_Discharge[2]," (+/-)")
, paste0(">= ",val_Discharge[9]," standard deviations within "
,val_Discharge[10]," hours")
, paste0("> ",val_Discharge[12]
," consecutive measurements within ",val_Discharge[13]
," units of one another"))
# WaterLevel
nam_WaterLevel <- c("myLab.WaterLevel" #1
, "myUnits.WaterLevel" #2
, "myThresh.Gross.Fail.Hi.WaterLevel" #3
, "myThresh.Gross.Fail.Lo.WaterLevel" #4
, "myThresh.Gross.Suspect.Hi.WaterLevel" #5
, "myThresh.Gross.Suspect.Lo.WaterLevel" #6
, "myThresh.Spike.Hi.WaterLevel" #7 -removed
, "myThresh.Spike.Lo.WaterLevel" #8 - removed
, "myThresh.RoC.SD.number.WaterLevel" #9 - 7
, "myThresh.RoC.SD.period.WaterLevel" #10 - 8
, "myThresh.Flat.Hi.WaterLevel" #11 - 9
, "myThresh.Flat.Lo.WaterLevel" #12 - 10
, "myThresh.Flat.Tolerance.WaterLevel" #13 - 11
)
val_WaterLevel <- mget(nam_WaterLevel, envir=ContData.env)
txt_WaterLevel_F <- c(val_WaterLevel[1]
, "Fail"
, paste0("> ",val_WaterLevel[3]," ",val_WaterLevel[2]
," or < ",val_WaterLevel[4]," ",val_WaterLevel[2])
, "NA"
, "NA"
, paste0("> ",val_WaterLevel[9]
," consecutive measurements within ",val_WaterLevel[11]
," units of one another"))
txt_WaterLevel_S <- c(val_WaterLevel[1]
, "Suspect"
, paste0("> ",val_WaterLevel[5]," ",val_WaterLevel[2]
," or < ",val_WaterLevel[6]," ",val_WaterLevel[2])
, "NA"
, paste0(">= ",val_WaterLevel[7]," standard deviations within "
,val_WaterLevel[8]," hours")
, paste0("> ",val_WaterLevel[10]
," consecutive measurements within ",val_WaterLevel[11]
," units of one another"))
# Cond
nam_Cond <- c("myLab.Cond" #1
, "myUnits.Cond" #2
, "myThresh.Gross.Fail.Hi.Cond" #3
, "myThresh.Gross.Fail.Lo.Cond" #4
, "myThresh.Gross.Suspect.Hi.Cond" #5
, "myThresh.Gross.Suspect.Lo.Cond" #6
, "myThresh.Spike.Hi.Cond" #7
, "myThresh.Spike.Lo.Cond" #8
, "myThresh.RoC.SD.number.Cond" #9
, "myThresh.RoC.SD.period.Cond" #10
, "myThresh.Flat.Hi.Cond" #11
, "myThresh.Flat.Lo.Cond" #12
, "myThresh.Flat.Tolerance.Cond" #13
)
val_Cond <- mget(nam_Cond, envir=ContData.env)
txt_Cond_F <- c(val_Cond[1]
, "Fail"
, paste0("> ",val_Cond[3]," ",val_Cond[2]
," or < ",val_Cond[4]," ",val_Cond[2])
, paste0(">= ", val_Cond[7]," ",val_Cond[2]," (+/-)")
, "NA"
, paste0("> ",val_Cond[11]
," consecutive measurements within ",val_Cond[13]
," units of one another"))
txt_Cond_S <- c(val_Cond[1]
, "Suspect"
, paste0("> ",val_Cond[5]," ",val_Cond[2]
," or < ",val_Cond[6]," ",val_Cond[2])
, paste0(">= ", val_Cond[8]," ",val_Cond[2]," (+/-)")
, paste0(">= ",val_Cond[9]," standard deviations within "
,val_Cond[10]," hours")
, paste0("> ",val_Cond[12]
," consecutive measurements within ",val_Cond[13]
," units of one another"))
# DO
nam_DO <- c("myLab.DO" #1
, "myUnits.DO" #2
, "myThresh.Gross.Fail.Hi.DO" #3
, "myThresh.Gross.Fail.Lo.DO" #4
, "myThresh.Gross.Suspect.Hi.DO" #5
, "myThresh.Gross.Suspect.Lo.DO" #6
, "myThresh.Spike.Hi.DO" #7
, "myThresh.Spike.Lo.DO" #8
, "myThresh.RoC.SD.number.DO" #9
, "myThresh.RoC.SD.period.DO" #10
, "myThresh.Flat.Hi.DO" #11
, "myThresh.Flat.Lo.DO" #12
, "myThresh.Flat.Tolerance.DO" #13
)
val_DO <- mget(nam_DO, envir=ContData.env)
txt_DO_F <- c(val_DO[1]
, "Fail"
, paste0("> ",val_DO[3]," ",val_DO[2]
," or < ",val_DO[4]," ",val_DO[2])
, paste0(">= ", val_DO[7]," ",val_DO[2]," (+/-)")
, "NA"
, paste0("> ",val_DO[11]
," consecutive measurements within ",val_DO[13]
," units of one another"))
txt_DO_S <- c(val_DO[1]
, "Suspect"
, paste0("> ",val_DO[5]," ",val_DO[2]
," or < ",val_DO[6]," ",val_DO[2])
, paste0(">= ", val_DO[8]," ",val_DO[2]," (+/-)")
, paste0(">= ",val_DO[9]," standard deviations within "
,val_DO[10]," hours")
, paste0("> ",val_DO[12]
," consecutive measurements within ",val_DO[13]
," units of one another"))
# DO.adj
nam_DO.adj <- c("myLab.DO.adj" #1
, "myUnits.DO.adj" #2
, "myThresh.Gross.Fail.Hi.DO.adj" #3
, "myThresh.Gross.Fail.Lo.DO.adj" #4
, "myThresh.Gross.Suspect.Hi.DO.adj" #5
, "myThresh.Gross.Suspect.Lo.DO.adj" #6
, "myThresh.Spike.Hi.DO.adj" #7
, "myThresh.Spike.Lo.DO.adj" #8
, "myThresh.RoC.SD.number.DO.adj" #9
, "myThresh.RoC.SD.period.DO.adj" #10
, "myThresh.Flat.Hi.DO.adj" #11
, "myThresh.Flat.Lo.DO.adj" #12
, "myThresh.Flat.Tolerance.DO.adj" #13
)
val_DO.adj <- mget(nam_DO.adj, envir=ContData.env)
txt_DO.adj_F <- c(val_DO.adj[1]
, "Fail"
, paste0("> ",val_DO.adj[3]," ",val_DO.adj[2]
," or < ",val_DO.adj[4]," ",val_DO.adj[2])
, paste0(">= ", val_DO.adj[7]," ",val_DO.adj[2]," (+/-)")
, "NA"
, paste0("> ",val_DO.adj[11]
," consecutive measurements within ",val_DO.adj[13]
," units of one another"))
txt_DO.adj_S <- c(val_DO.adj[1]
, "Suspect"
, paste0("> ",val_DO.adj[5]," ",val_DO.adj[2]
," or < ",val_DO.adj[6]," ",val_DO.adj[2])
, paste0(">= ", val_DO.adj[8]," ",val_DO.adj[2]," (+/-)")
, paste0(">= ",val_DO[9]," standard deviations within "
,val_DO[10]," hours")
, paste0("> ",val_DO[12]
," consecutive measurements within ",val_DO.adj[13]
," units of one another"))
# DO.pctsat
nam_DO.pctsat <- c("myLab.DO.pctsat" #1
, "myUnits.DO.pctsat" #2
, "myThresh.Gross.Fail.Hi.DO.pctsat" #3
, "myThresh.Gross.Fail.Lo.DO.pctsat" #4
, "myThresh.Gross.Suspect.Hi.DO.pctsat" #5
, "myThresh.Gross.Suspect.Lo.DO.pctsat" #6
, "myThresh.Spike.Hi.DO.pctsat" #7
, "myThresh.Spike.Lo.DO.pctsat" #8
, "myThresh.RoC.SD.number.DO.pctsat" #9
, "myThresh.RoC.SD.period.DO.pctsat" #10
, "myThresh.Flat.Hi.DO.pctsat" #11
, "myThresh.Flat.Lo.DO.pctsat" #12
, "myThresh.Flat.Tolerance.DO.pctsat" #13
)
val_DO.pctsat <- mget(nam_DO.pctsat, envir=ContData.env)
txt_DO.pctsat_F <- c(val_DO.pctsat[1]
, "Fail"
, paste0("> ",val_DO.pctsat[3]," ",val_DO.pctsat[2]
," or < ",val_DO.pctsat[4]," ",val_DO.pctsat[2])
, paste0(">= ", val_DO.pctsat[7]," ",val_DO.pctsat[2]," (+/-)")
, "NA"
, paste0("> ",val_DO.pctsat[11]
," consecutive measurements within ",val_DO.pctsat[13]
," units of one another"))
txt_DO.pctsat_S <- c(val_DO.pctsat[1]
, "Suspect"
, paste0("> ",val_DO.pctsat[5]," ",val_DO.pctsat[2]
," or < ",val_DO.pctsat[6]," ",val_DO.pctsat[2])
, paste0(">= ", val_DO.pctsat[8]," ",val_DO.pctsat[2]," (+/-)")
, paste0(">= ",val_DO.pctsat[9]," standard deviations within "
,val_DO.pctsat[10]," hours")
, paste0("> ",val_DO.pctsat[12]
," consecutive measurements within ",val_DO.pctsat[13]
," units of one another"))
# pH
nam_pH <- c("myLab.pH" #1
, "myUnits.pH" #2
, "myThresh.Gross.Fail.Hi.pH" #3
, "myThresh.Gross.Fail.Lo.pH" #4
, "myThresh.Gross.Suspect.Hi.pH" #5
, "myThresh.Gross.Suspect.Lo.pH" #6
, "myThresh.Spike.Hi.pH" #7
, "myThresh.Spike.Lo.pH" #8
, "myThresh.RoC.SD.number.pH" #9
, "myThresh.RoC.SD.period.pH" #10
, "myThresh.Flat.Hi.pH" #11
, "myThresh.Flat.Lo.pH" #12
, "myThresh.Flat.Tolerance.pH" #13
)
val_pH <- mget(nam_pH, envir=ContData.env)
txt_pH_F <- c(val_pH[1]
, "Fail"
, paste0("> ",val_pH[3]," ",val_pH[2]
," or < ",val_pH[4]," ",val_pH[2])
, paste0(">= ", val_pH[7]," ",val_pH[2]," (+/-)")
, "NA"
, paste0("> ",val_pH[11]
," consecutive measurements within ",val_pH[13]
," units of one another"))
txt_pH_S <- c(val_pH[1]
, "Suspect"
, paste0("> ",val_pH[5]," ",val_pH[2]
," or < ",val_pH[6]," ",val_pH[2])
, paste0(">= ", val_pH[8]," ",val_pH[2]," (+/-)")
, paste0(">= ",val_pH[9]," standard deviations within "
,val_pH[10]," hours")
, paste0("> ",val_pH[12]
," consecutive measurements within ",val_pH[13]
," units of one another"))
# Turbidity
nam_Turbidity <- c("myLab.Turbidity" #1
, "myUnits.Turbidity" #2
, "myThresh.Gross.Fail.Hi.Turbidity" #3
, "myThresh.Gross.Fail.Lo.Turbidity" #4
, "myThresh.Gross.Suspect.Hi.Turbidity" #5
, "myThresh.Gross.Suspect.Lo.Turbidity" #6
, "myThresh.Spike.Hi.Turbidity" #7
, "myThresh.Spike.Lo.Turbidity" #8
, "myThresh.RoC.SD.number.Turbidity" #9
, "myThresh.RoC.SD.period.Turbidity" #10
, "myThresh.Flat.Hi.Turbidity" #11
, "myThresh.Flat.Lo.Turbidity" #12
, "myThresh.Flat.Tolerance.Turbidity" #13
)
val_Turbidity <- mget(nam_Turbidity, envir=ContData.env)
txt_Turbidity_F <- c(val_Turbidity[1]
, "Fail"
, paste0("> ",val_Turbidity[3]," ",val_Turbidity[2]
," or < ",val_Turbidity[4]," ",val_Turbidity[2])
, paste0(">= ", val_Turbidity[7]," ",val_Turbidity[2]," (+/-)")
, "NA"
, paste0("> ",val_Turbidity[11]
," consecutive measurements within ",val_Turbidity[13]
," units of one another"))
txt_Turbidity_S <- c(val_Turbidity[1]
, "Suspect"
, paste0("> ",val_Turbidity[5]," ",val_Turbidity[2]
," or < ",val_Turbidity[6]," ",val_Turbidity[2])
, paste0(">= ", val_Turbidity[8]," ",val_Turbidity[2]," (+/-)")
, paste0(">= ",val_Turbidity[9]," standard deviations within "
,val_Turbidity[10]," hours")
, paste0("> ",val_Turbidity[12]
," consecutive measurements within ",val_Turbidity[13]
," units of one another"))
# Chlorophylla
nam_Chlorophylla <- c("myLab.Chlorophylla" #1
, "myUnits.Chlorophylla" #2
, "myThresh.Gross.Fail.Hi.Chlorophylla" #3
, "myThresh.Gross.Fail.Lo.Chlorophylla" #4
, "myThresh.Gross.Suspect.Hi.Chlorophylla" #5
, "myThresh.Gross.Suspect.Lo.Chlorophylla" #6
, "myThresh.Spike.Hi.Chlorophylla" #7
, "myThresh.Spike.Lo.Chlorophylla" #8
, "myThresh.RoC.SD.number.Chlorophylla" #9
, "myThresh.RoC.SD.period.Chlorophylla" #10
, "myThresh.Flat.Hi.Chlorophylla" #11
, "myThresh.Flat.Lo.Chlorophylla" #12
, "myThresh.Flat.Tolerance.Chlorophylla" #13
)
val_Chlorophylla <- mget(nam_Chlorophylla, envir=ContData.env)
txt_Chlorophylla_F <- c(val_Chlorophylla[1]
, "Fail"
, paste0("> ",val_Chlorophylla[3]," ",val_Chlorophylla[2]
," or < ",val_Chlorophylla[4]," ",val_Chlorophylla[2])
, paste0(">= ", val_Chlorophylla[7]," ",val_Chlorophylla[2]," (+/-)")
, "NA"
, paste0("> ",val_Chlorophylla[11]
," consecutive measurements within ",val_Chlorophylla[13]
," units of one another"))
txt_Chlorophylla_S <- c(val_Chlorophylla[1]
, "Suspect"
, paste0("> ",val_Chlorophylla[5]," ",val_Chlorophylla[2]
," or < ",val_Chlorophylla[6]," ",val_Chlorophylla[2])
, paste0(">= ", val_Chlorophylla[8]," ",val_Chlorophylla[2]," (+/-)")
, paste0(">= ",val_Chlorophylla[9]," standard deviations within "
,val_Chlorophylla[10]," hours")
, paste0("> ",val_Chlorophylla[12]
," consecutive measurements within ",val_Chlorophylla[13]
," units of one another"))
## Salinity
nam_Salinity <- c("myLab.Salinity" #1
, "myUnits.Salinity" #2
, "myThresh.Gross.Fail.Hi.Salinity" #3
, "myThresh.Gross.Fail.Lo.Salinity" #4
, "myThresh.Gross.Suspect.Hi.Salinity" #5
, "myThresh.Gross.Suspect.Lo.Salinity" #6
, "myThresh.Spike.Hi.Salinity" #7
, "myThresh.Spike.Lo.Salinity" #8
, "myThresh.RoC.SD.number.Salinity" #9
, "myThresh.RoC.SD.period.Salinity" #10
, "myThresh.Flat.Hi.Salinity" #11
, "myThresh.Flat.Lo.Salinity" #12
, "myThresh.Flat.Tolerance.Salinity" #13
)
val_Salinity <- mget(nam_Salinity, envir=ContData.env)
txt_Salinity_F <- c(val_Salinity[1]
, "Fail"
, paste0("> ",val_Salinity[3]," ",val_Salinity[2]
," or < ",val_Salinity[4]," ",val_Salinity[2])
, paste0(">= ", val_Salinity[7]," ",val_Salinity[2]," (+/-)")
, "NA"
, paste0("> ",val_Salinity[11]
," consecutive measurements within ",val_Salinity[13]
," units of one another"))
txt_Salinity_S <- c(val_Salinity[1]
, "Suspect"
, paste0("> ",val_Salinity[5]," ",val_Salinity[2]
," or < ",val_Salinity[6]," ",val_Salinity[2])
, paste0(">= ", val_Salinity[8]," ",val_Salinity[2]," (+/-)")
, paste0(">= ",val_Salinity[9]," standard deviations within "
,val_Salinity[10]," hours")
, paste0("> ",val_Salinity[12]
," consecutive measurements within ",val_Salinity[13]
," units of one another"))
# Create Table
df_Env <- data.frame(rbind(txt_WaterTemp_F, txt_WaterTemp_S
, txt_AirTemp_F, txt_AirTemp_S
, txt_WaterP_F, txt_WaterP_S
, txt_AirBP_F, txt_AirBP_S
, txt_SensorDepth_F, txt_SensorDepth_S
, txt_WaterLevel_F, txt_WaterLevel_S
, txt_Discharge_F, txt_Discharge_S
, txt_Cond_F, txt_Cond_S
, txt_DO_F, txt_DO_S
, txt_DO.adj_F, txt_DO.adj_S
, txt_DO.pctsat_F, txt_DO.pctsat_S
, txt_pH_F, txt_pH_S
, txt_Turbidity_F, txt_Turbidity_S
, txt_Chlorophylla_F, txt_Chlorophylla_S
, txt_Salinity_F, txt_Salinity_S
)
, row.names = NULL)
names(df_Env) <- txt_header
knitr::kable(df_Env, caption = kbl_caption)
All Settings, Alphabetical
All settings listed by name in alphabetical order with values.
# sapply(ls(ContData.env), function(x) get(x, envir=ContData.env))
kbl_caption <- "Thresholds, ALL, Alphabetical"
env_Nam <- ls(ContData.env)
env_Val <- mget(env_Nam, envir=ContData.env)
df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL)
names(df_Env) <- c("Names", "Values")
knitr::kable(df_Env, caption = kbl_caption)
All Settings, Categories
All settings by category listed by name with values.
The order presented here is the order in the config file.
Column Names
- Acceptable column names for the data
- Units
- Logger Fields
- Parameters as appear in logger files
- Plot Labels
kbl_caption <- "Thresholds, Column Names"
env_Nam <- c("myDelim"
, "myName.SiteID"
, "myName.Date"
, "myName.Time"
, "myName.DateTime"
, "myUnits.AirTemp"
, "myUnits.WaterTemp"
, "myUnits.AirBP"
, "myUnits.WaterP"
, "myUnits.SensorDepth"
, "myUnits.WaterLevel"
, "myUnits.Discharge"
, "myUnits.Cond"
, "myUnits.DO"
, "myUnits.DO.adj"
, "myUnits.DO.pctsat"
, "myUnits.pH"
, "myUnits.Turbidity"
, "myUnits.Chlorophylla"
, "myUnits.Salinity"
, "myName.RowID.Water"
, "myName.LoggerID.Water"
, "myName.RowID.Air"
, "myName.LoggerID.Air"
, "myName.WaterTemp"
, "myName.AirTemp"
, "myName.WaterP"
, "myName.AirBP"
, "myName.SensorDepth"
, "myName.WaterLevel"
, "myName.Discharge"
, "myName.Cond"
, "myName.DO"
, "myName.DO.adj"
, "myName.DO.pctsat"
, "myName.pH"
, "myName.Turbidity"
, "myName.Chlorophylla"
, "myName.Salinity"
, "myLab.WaterTemp"
, "myLab.AirTemp"
, "myLab.Date"
, "myLab.DateTime"
, "myLab.WaterP"
, "myLab.AirBP"
, "myLab.SensorDepth"
, "myLab.WaterLevel"
, "myLab.Temp.BOTH"
, "myLab.Discharge"
, "myLab.Cond"
, "myLab.DO"
, "myLab.DO.adj"
, "myLab.DO.pctsat"
, "myLab.pH"
, "myLab.Turbidity"
, "myLab.Chlorophylla"
, "myLab.Salinity"
)
env_Val <- mget(env_Nam, envir=ContData.env)
df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL)
names(df_Env) <- c("Names", "Values")
knitr::kable(df_Env, caption = kbl_caption)
Discrete Measurements
- Discrete, Names
- Discrete, Labels
kbl_caption <- "Thresholds, Discrete Measurements"
env_Nam <- c("myPrefix.Discrete"
, "myName.Discrete.WaterTemp"
, "myName.Discrete.AirTemp"
, "myName.Discrete.WaterP"
, "myName.Discrete.AirBP"
, "myName.Discrete.SensorDepth"
, "myName.Discrete.WaterLevel"
, "myName.Discrete.Discharge"
, "myName.Discrete.Cond"
, "myName.Discrete.DO"
, "myName.Discrete.DO.adj"
, "myName.Discrete.DO.pctsat"
, "myName.Discrete.pH"
, "myName.Discrete.Turbidity"
, "myName.Discrete.Chlorophylla"
, "myName.Discrete.Salinity"
, "myLab.Discrete.WaterTemp"
, "myLab.Discrete.AirTemp"
, "myLab.Discrete.WaterP"
, "myLab.Discrete.AirBP"
, "myLab.Discrete.SensorDepth"
, "myLab.Discrete.Discharge"
, "myLab.Discrete.WaterLevel"
, "myLab.Discrete.Cond"
, "myLab.Discrete.DO"
, "myLab.Discrete.DO.adj"
, "myLab.Discrete.DO.pctsat"
, "myLab.Discrete.pH"
, "myLab.Discrete.Turbidity"
, "myLab.Discrete.Chlorophylla"
, "myLab.Discrete.Salinity"
)
env_Val <- mget(env_Nam, envir=ContData.env)
df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL)
names(df_Env) <- c("Names", "Values")
knitr::kable(df_Env, caption = kbl_caption)
Automated QC Stuff
- data type/stages
kbl_caption <- "Thresholds, Automated QC Stuff"
env_Nam <- c("myDataQuality.Raw"
, "myDataQuality.QCauto"
, "myDataQuality.QCmanual"
, "myDataQuality.Final"
, "myDataQuality.Aggregated"
)
env_Val <- mget(env_Nam, envir=ContData.env)
df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL)
names(df_Env) <- c("Names", "Values")
knitr::kable(df_Env, caption = kbl_caption)
Directory Names
kbl_caption <- "Thresholds, Directory Names"
env_Nam <- c("myName.Dir.1Raw"
, "myName.Dir.2QC"
, "myName.Dir.3Agg"
, "myName.Dir.4Stats"
)
env_Val <- mget(env_Nam, envir=ContData.env)
df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL)
names(df_Env) <- c("Names", "Values")
knitr::kable(df_Env, caption = kbl_caption)
Data Fields
- Field Names
- Field Labels for plots
kbl_caption <- "Thresholds, Data Fields"
env_Nam <- c("myNames.DataFields"
, "myNames.DataFields.Lab"
, "myNames.DataFields.Col"
)
env_Val <- mget(env_Nam, envir=ContData.env)
df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL)
names(df_Env) <- c("Names", "Values")
knitr::kable(df_Env, caption = kbl_caption)
Data Quality Flag Values
kbl_caption <- "Thresholds, Data Quality Flag Values"
env_Nam <- c("myFlagVal.Pass"
, "myFlagVal.NotEval"
, "myFlagVal.Suspect"
, "myFlagVal.Fail"
, "myFlagVal.NoData"
, "myFlagVal.Order"
)
env_Val <- mget(env_Nam, envir=ContData.env)
df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL)
names(df_Env) <- c("Names", "Values")
knitr::kable(df_Env, caption = kbl_caption)
QC Tests and Calculations
Parameters grouped by type of QC check.
Gross Min/Max, Fail (equipment)
Examines values as outliers versus threholds.
- if value >= Hi or <= Lo then flagged as "Fail"
kbl_caption <- "Thresholds, QC Tests and Calculations, Gross Min/Max, Fail (equipment)"
env_Nam <- c("myThresh.Gross.Fail.Hi.WaterTemp"
, "myThresh.Gross.Fail.Lo.WaterTemp"
, "myThresh.Gross.Fail.Hi.AirTemp"
, "myThresh.Gross.Fail.Lo.AirTemp"
, "myThresh.Gross.Fail.Hi.WaterP"
, "myThresh.Gross.Fail.Lo.WaterP"
, "myThresh.Gross.Fail.Hi.AirBP"
, "myThresh.Gross.Fail.Lo.AirBP"
, "myThresh.Gross.Fail.Hi.SensorDepth"
, "myThresh.Gross.Fail.Lo.SensorDepth"
, "myThresh.Gross.Fail.Hi.WaterLevel"
, "myThresh.Gross.Fail.Lo.WaterLevel"
, "myThresh.Gross.Fail.Hi.Discharge"
, "myThresh.Gross.Fail.Lo.Discharge"
, "myThresh.Gross.Fail.Hi.Cond"
, "myThresh.Gross.Fail.Lo.Cond"
, "myThresh.Gross.Fail.Hi.DO"
, "myThresh.Gross.Fail.Lo.DO"
, "myThresh.Gross.Fail.Hi.DO.adj"
, "myThresh.Gross.Fail.Lo.DO.adj"
, "myThresh.Gross.Fail.Hi.DO.pctsat"
, "myThresh.Gross.Fail.Lo.DO.pctsat"
, "myThresh.Gross.Fail.Hi.pH"
, "myThresh.Gross.Fail.Lo.pH"
, "myThresh.Gross.Fail.Hi.Turbidity"
, "myThresh.Gross.Fail.Lo.Turbidity"
, "myThresh.Gross.Fail.Hi.Chlorophylla"
, "myThresh.Gross.Fail.Lo.Chlorophylla"
, "myThresh.Gross.Fail.Hi.Salinity"
, "myThresh.Gross.Fail.Lo.Salinity"
)
env_Val <- mget(env_Nam, envir=ContData.env)
df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL)
names(df_Env) <- c("Names", "Values")
knitr::kable(df_Env, caption = kbl_caption)
Gross Min/Max, Suspect (extreme)
Examines values as outliers versus threholds.
- if value >= Hi or <= Lo then flagged as "Suspect"
kbl_caption <- "Thresholds, QC Tests and Calculations, Gross Min/Max, Fail (equipment)"
env_Nam <- c("myThresh.Gross.Suspect.Hi.WaterTemp"
, "myThresh.Gross.Suspect.Lo.WaterTemp"
, "myThresh.Gross.Suspect.Hi.AirTemp"
, "myThresh.Gross.Suspect.Lo.AirTemp"
, "myThresh.Gross.Suspect.Hi.WaterP"
, "myThresh.Gross.Suspect.Lo.WaterP"
, "myThresh.Gross.Suspect.Hi.AirBP"
, "myThresh.Gross.Suspect.Lo.AirBP"
, "myThresh.Gross.Suspect.Hi.SensorDepth"
, "myThresh.Gross.Suspect.Lo.SensorDepth"
, "myThresh.Gross.Suspect.Hi.WaterLevel"
, "myThresh.Gross.Suspect.Lo.WaterLevel"
, "myThresh.Gross.Suspect.Hi.Discharge"
, "myThresh.Gross.Suspect.Lo.Discharge"
, "myThresh.Gross.Suspect.Hi.Cond"
, "myThresh.Gross.Suspect.Lo.Cond"
, "myThresh.Gross.Suspect.Hi.DO"
, "myThresh.Gross.Suspect.Lo.DO"
, "myThresh.Gross.Suspect.Hi.DO.adj"
, "myThresh.Gross.Suspect.Lo.DO.adj"
, "myThresh.Gross.Suspect.Hi.DO.pctsat"
, "myThresh.Gross.Suspect.Lo.DO.pctsat"
, "myThresh.Gross.Suspect.Hi.pH"
, "myThresh.Gross.Suspect.Lo.pH"
, "myThresh.Gross.Suspect.Hi.Turbidity"
, "myThresh.Gross.Suspect.Lo.Turbidity"
, "myThresh.Gross.Suspect.Hi.Chlorophylla"
, "myThresh.Gross.Suspect.Lo.Chlorophylla"
, "myThresh.Gross.Suspect.Hi.Salinity"
, "myThresh.Gross.Suspect.Lo.Salinity"
)
env_Val <- mget(env_Nam, envir=ContData.env)
df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL)
names(df_Env) <- c("Names", "Values")
knitr::kable(df_Env, caption = kbl_caption)
Spike thresholds (absolute change)
Examines difference between consecutive measurements.
- if delta >= Hi then flagged as "Fail"
- if delta >= Lo then flagged as "Suspect"
kbl_caption <- "Thresholds, QC Tests and Calculations, Spike thresholds (absolute change)"
env_Nam <- c("myThresh.Spike.Hi.WaterTemp"
, "myThresh.Spike.Lo.WaterTemp"
, "myThresh.Spike.Hi.AirTemp"
, "myThresh.Spike.Lo.AirTemp"
, "myThresh.Spike.Hi.WaterP"
, "myThresh.Spike.Lo.WaterP"
, "myThresh.Spike.Hi.AirBP"
, "myThresh.Spike.Lo.AirBP"
, "myThresh.Spike.Hi.SensorDepth"
, "myThresh.Spike.Lo.SensorDepth"
, "myThresh.Spike.Hi.WaterLevel"
, "myThresh.Spike.Lo.WaterLevel"
, "myThresh.Spike.Hi.Discharge"
, "myThresh.Spike.Lo.Discharge"
, "myThresh.Spike.Hi.Cond"
, "myThresh.Spike.Lo.Cond"
, "myThresh.Spike.Hi.DO"
, "myThresh.Spike.Lo.DO"
, "myThresh.Spike.Hi.DO.adj"
, "myThresh.Spike.Lo.DO.adj"
, "myThresh.Spike.Hi.DO.pctsat"
, "myThresh.Spike.Lo.DO.pctsat"
, "myThresh.Spike.Hi.pH"
, "myThresh.Spike.Lo.pH"
, "myThresh.Spike.Hi.Turbidity"
, "myThresh.Spike.Lo.Turbidity"
, "myThresh.Spike.Hi.Chlorophylla"
, "myThresh.Spike.Lo.Chlorophylla"
, "myThresh.Spike.Hi.Salinity"
, "myThresh.Spike.Lo.Salinity"
)
env_Val <- mget(env_Nam, envir=ContData.env)
df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL)
names(df_Env) <- c("Names", "Values")
knitr::kable(df_Env, caption = kbl_caption)
Rate of Change (relative change)
Examines Standard Deviation (SD) over "period" and difference in consecutive values.
- If delta >= SD.number * SD then flagged as "Suspect"
kbl_caption <- "Thresholds, QC Tests and Calculations, Rate of Change (relative change)"
env_Nam <- c("myDefault.RoC.SD.number"
, "myDefault.RoC.SD.period"
, "myThresh.RoC.SD.number.WaterTemp"
, "myThresh.RoC.SD.period.WaterTemp"
, "myThresh.RoC.SD.number.AirTemp"
, "myThresh.RoC.SD.period.AirTemp"
, "myThresh.RoC.SD.number.WaterP"
, "myThresh.RoC.SD.period.WaterP"
, "myThresh.RoC.SD.number.AirBP"
, "myThresh.RoC.SD.period.AirBP"
, "myThresh.RoC.SD.number.SensorDepth"
, "myThresh.RoC.SD.period.SensorDepth"
, "myThresh.RoC.SD.number.WaterLevel"
, "myThresh.RoC.SD.period.WaterLevel"
, "myThresh.RoC.SD.number.Discharge"
, "myThresh.RoC.SD.period.Discharge"
, "myThresh.RoC.SD.number.Cond"
, "myThresh.RoC.SD.period.Cond"
, "myThresh.RoC.SD.number.DO"
, "myThresh.RoC.SD.period.DO"
, "myThresh.RoC.SD.number.DO.adj"
, "myThresh.RoC.SD.period.DO.adj"
, "myThresh.RoC.SD.number.DO.pctsat"
, "myThresh.RoC.SD.period.DO.pctsat"
, "myThresh.RoC.SD.number.pH"
, "myThresh.RoC.SD.period.pH"
, "myThresh.RoC.SD.number.Turbidity"
, "myThresh.RoC.SD.period.Turbidity"
, "myThresh.RoC.SD.number.Chlorophylla"
, "myThresh.RoC.SD.period.Chlorophylla"
, "myThresh.RoC.SD.number.Salinity"
, "myThresh.RoC.SD.period.Salinity"
)
env_Val <- mget(env_Nam, envir=ContData.env)
df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL)
names(df_Env) <- c("Names", "Values")
knitr::kable(df_Env, caption = kbl_caption)
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"
kbl_caption <- "Thresholds, QC Tests and Calculations, No Change (flat-line)"
env_Nam <- c("myDefault.Flat.Hi"
, "myDefault.Flat.Lo"
, "myDefault.Flat.Tolerance"
, "myThresh.Flat.Hi.WaterTemp"
, "myThresh.Flat.Lo.WaterTemp"
, "myThresh.Flat.Tolerance.WaterTemp"
, "myThresh.Flat.Hi.AirTemp"
, "myThresh.Flat.Lo.AirTemp"
, "myThresh.Flat.Tolerance.AirTemp"
, "myThresh.Flat.Hi.WaterP"
, "myThresh.Flat.Lo.WaterP"
, "myThresh.Flat.Tolerance.WaterP"
, "myThresh.Flat.Hi.AirBP"
, "myThresh.Flat.Lo.AirBP"
, "myThresh.Flat.Tolerance.AirBP"
, "myThresh.Flat.Hi.SensorDepth"
, "myThresh.Flat.Lo.SensorDepth"
, "myThresh.Flat.Tolerance.SensorDepth"
, "myThresh.Flat.Hi.WaterLevel"
, "myThresh.Flat.Lo.WaterLevel"
, "myThresh.Flat.Tolerance.WaterLevel"
, "myThresh.Flat.Hi.Discharge"
, "myThresh.Flat.Lo.Discharge"
, "myThresh.Flat.Tolerance.Discharge"
, "myThresh.Flat.Hi.Cond"
, "myThresh.Flat.Lo.Cond"
, "myThresh.Flat.Tolerance.Cond"
, "myThresh.Flat.Hi.DO"
, "myThresh.Flat.Lo.DO"
, "myThresh.Flat.Tolerance.DO"
, "myThresh.Flat.Hi.DO.adj"
, "myThresh.Flat.Lo.DO.adj"
, "myThresh.Flat.Tolerance.DO.adj"
, "myThresh.Flat.Hi.DO.pctsat"
, "myThresh.Flat.Lo.DO.pctsat"
, "myThresh.Flat.Tolerance.DO.pctsat"
, "myThresh.Flat.Hi.pH"
, "myThresh.Flat.Lo.pH"
, "myThresh.Flat.Tolerance.pH"
, "myThresh.Flat.Hi.Turbidity"
, "myThresh.Flat.Lo.Turbidity"
, "myThresh.Flat.Tolerance.Turbidity"
, "myThresh.Flat.Hi.Chlorophylla"
, "myThresh.Flat.Lo.Chlorophylla"
, "myThresh.Flat.Tolerance.Chlorophylla"
, "myThresh.Flat.Hi.Salinity"
, "myThresh.Flat.Lo.Salinity"
, "myThresh.Flat.Tolerance.Salinity"
, "myThresh.Flat.MaxComp"
)
env_Val <- mget(env_Nam, envir=ContData.env)
df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL)
names(df_Env) <- c("Names", "Values")
knitr::kable(df_Env, caption = kbl_caption)
Data Fields with Flags
- flag labels
- Data Quality Test Names
kbl_caption <- "Thresholds, Data Fields with Flags"
env_Nam <- c("myName.Flag"
, "myNames.Cols4Flags"
, "myNames.Flags"
, "myName.Flag.DateTime"
, "myName.Flag.WaterTemp"
, "myName.Flag.AirTemp"
, "myName.Flag.WaterP"
, "myName.Flag.AirBP"
, "myName.Flag.SensorDepth"
, "myName.Flag.WaterLevel"
, "myName.Flag.Discharge"
, "myName.Flag.Cond"
, "myName.Flag.DO"
, "myName.Flag.DO.adj"
, "myName.Flag.DO.pctsat"
, "myName.Flag.pH"
, "myName.Flag.Turbidity"
, "myName.Flag.Chlorophylla"
, "myName.Flag.Salinity"
, "myNames.QCTests"
, "myNames.QCCalcs"
)
env_Val <- mget(env_Nam, envir=ContData.env)
df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL)
names(df_Env) <- c("Names", "Values")
knitr::kable(df_Env, caption = kbl_caption)
Exceedance Values for Statistics
Exceedance values for stats (default to Gross-Suspect-Hi value)
kbl_caption <- "Thresholds, Exceedance Values for Statistics"
env_Nam <- c("myExceed.WaterTemp"
, "myExceed.AirTemp"
, "myExceed.SensorDepth"
)
env_Val <- mget(env_Nam, envir=ContData.env)
df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL)
names(df_Env) <- c("Names", "Values")
knitr::kable(df_Env, caption = kbl_caption)
Date and Time Formats
- Date and Time Formats
- Time zone
kbl_caption <- "Thresholds, Date and Time Formats"
env_Nam <- c("myFormat.Date"
, "myFormat.Time"
, "myFormat.DateTime"
, "DateRange.Start.Default"
, "DateRange.End.Default"
, "myTZ"
)
env_Val <- mget(env_Nam, envir=ContData.env)
df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL)
names(df_Env) <- c("Names", "Values")
knitr::kable(df_Env, caption = kbl_caption)
Time Frames
- Time Frames (MM-DD)
- Time Frame Names
- for summary stats
kbl_caption <- "Thresholds, Time Frames"
env_Nam <- c("myTimeFrame.Annual.Start"
, "myTimeFrame.Annual.End"
, "myTimeFrame.WaterYear.Start"
, "myTimeFrame.Season.Spring.Start"
, "myTimeFrame.Season.Summer.Start"
, "myTimeFrame.Season.Fall.Start"
, "myTimeFrame.Season.Winter.Start"
, "myName.Yr"
, "myName.YrMo"
, "myName.Mo"
, "myName.MoDa"
, "myName.JuDa"
, "myName.Day"
, "myName.Season"
, "myName.YrSeason"
, "myNames.Fields.TimePeriods"
)
env_Val <- mget(env_Nam, envir=ContData.env)
df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL)
names(df_Env) <- c("Names", "Values")
knitr::kable(df_Env, caption = kbl_caption)
Exclude Trigger
Trigger for Stats to exclude (TRUE) or include (FALSE) where flag = "fail"
kbl_caption <- "Thresholds, Exclude Trigger"
env_Nam <- c("myStats.Fails.Exclude"
)
env_Val <- mget(env_Nam, envir=ContData.env)
df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL)
names(df_Env) <- c("Names", "Values")
knitr::kable(df_Env, caption = kbl_caption)
Report Format
Default report format output.
kbl_caption <- "Thresholds, Report Format"
env_Nam <- c("myReport.Format"
#, "myReport.Dir"
)
env_Val <- mget(env_Nam, envir=ContData.env)
df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL)
names(df_Env) <- c("Names", "Values")
knitr::kable(df_Env, caption = kbl_caption)
leppott/ContDataQC documentation built on Jan. 5, 2025, 10:12 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
knitr::opts_chunk$set(results='asis', echo=FALSE, warning=FALSE) # needed for trouble shooting myConfig <- file.path(system.file(package="ContDataQC"), "extdata", "config.ORIG.R") #source(myConfig)
FILE INFORMATION
# Report Info myReportDate <- format(Sys.Date(), ContData.env$myFormat.Date) cat(paste("**Report Date:** ",myReportDate,"\n\n",sep="")) myUser <- Sys.getenv("USERNAME") cat(paste("**Generated By:** ",myUser,"\n\n",sep="")) #file name cat("**File Name:** ",basename(myConfig),"\n\n",sep="") #dir name cat("**File Location:** ",dirname(myConfig),"\n\n",sep="") # Last Modified Date cat("**Last Modified:** ",format(file.info(myConfig)$mtime, ContData.env$myFormat.DateTime),"\n\n",sep="")
CONFIGURATION SETTINGS
Output of configuration file used in the ContDataQC package.
Thresholds
Table of most relevant thresholds in report ready format. This is the same table that appears in the QC Report. The four test types are column headers.
kbl_caption <- "Thresholds, Quick Reference" txt_header <- c("Analyte", "Flag", "Gross", "Spike", "Rate of Change", "Flat Line") # WaterTemp nam_WaterTemp <- c("myLab.WaterTemp" #1 , "myUnits.WaterTemp" #2 , "myThresh.Gross.Fail.Hi.WaterTemp" #3 , "myThresh.Gross.Fail.Lo.WaterTemp" #4 , "myThresh.Gross.Suspect.Hi.WaterTemp" #5 , "myThresh.Gross.Suspect.Lo.WaterTemp" #6 , "myThresh.Spike.Hi.WaterTemp" #7 , "myThresh.Spike.Lo.WaterTemp" #8 , "myThresh.RoC.SD.number.WaterTemp" #9 , "myThresh.RoC.SD.period.WaterTemp" #10 , "myThresh.Flat.Hi.WaterTemp" #11 , "myThresh.Flat.Lo.WaterTemp" #12 , "myThresh.Flat.Tolerance.WaterTemp" #13 ) val_WaterTemp <- mget(nam_WaterTemp, envir=ContData.env) txt_WaterTemp_F <- c(val_WaterTemp[1] , "Fail" , paste0("> ",val_WaterTemp[3]," deg ",val_WaterTemp[2] ," or < ",val_WaterTemp[4]," deg ",val_WaterTemp[2]) , paste0(">= ", val_WaterTemp[7]," deg ",val_WaterTemp[2]," (+/-)") , "NA" , paste0("> ",val_WaterTemp[11] ," consecutive measurements within ",val_WaterTemp[13] ," units of one another")) txt_WaterTemp_S <- c(val_WaterTemp[1] , "Suspect" , paste0("> ",val_WaterTemp[5]," deg ",val_WaterTemp[2] ," or < ",val_WaterTemp[6]," deg ",val_WaterTemp[2]) , paste0(">= ", val_WaterTemp[8]," deg ",val_WaterTemp[2]," (+/-)") , paste0(">= ",val_WaterTemp[9]," standard deviations within " ,val_WaterTemp[10]," hours") , paste0("> ",val_WaterTemp[12] ," consecutive measurements within ",val_WaterTemp[13] ," units of one another")) # AirTemp nam_AirTemp <- c("myLab.AirTemp" #1 , "myUnits.AirTemp" #2 , "myThresh.Gross.Fail.Hi.AirTemp" #3 , "myThresh.Gross.Fail.Lo.AirTemp" #4 , "myThresh.Gross.Suspect.Hi.AirTemp" #5 , "myThresh.Gross.Suspect.Lo.AirTemp" #6 , "myThresh.Spike.Hi.AirTemp" #7 , "myThresh.Spike.Lo.AirTemp" #8 , "myThresh.RoC.SD.number.AirTemp" #9 , "myThresh.RoC.SD.period.AirTemp" #10 , "myThresh.Flat.Hi.AirTemp" #11 , "myThresh.Flat.Lo.AirTemp" #12 , "myThresh.Flat.Tolerance.AirTemp" #13 ) val_AirTemp <- mget(nam_AirTemp, envir=ContData.env) txt_AirTemp_F <- c(val_AirTemp[1] , "Fail" , paste0("> ",val_AirTemp[3]," deg ",val_AirTemp[2] ," or < ",val_AirTemp[4]," deg ",val_AirTemp[2]) , paste0(">= ", val_AirTemp[7]," deg ",val_AirTemp[2]," (+/-)") , "NA" , paste0("> ",val_AirTemp[11] ," consecutive measurements within ",val_AirTemp[13] ," units of one another")) txt_AirTemp_S <- c(val_AirTemp[1] , "Suspect" , paste0("> ",val_AirTemp[5]," deg ",val_AirTemp[2] ," or < ",val_AirTemp[6]," deg ",val_AirTemp[2]) , paste0(">= ", val_AirTemp[8]," deg ",val_AirTemp[2]," (+/-)") , paste0(">= ",val_AirTemp[9]," standard deviations within " ,val_AirTemp[10]," hours") , paste0("> ",val_AirTemp[12] ," consecutive measurements within ",val_AirTemp[13] ," units of one another")) # WaterP nam_WaterP <- c("myLab.WaterP" #1 , "myUnits.WaterP" #2 , "myThresh.Gross.Fail.Hi.WaterP" #3 , "myThresh.Gross.Fail.Lo.WaterP" #4 , "myThresh.Gross.Suspect.Hi.WaterP" #5 , "myThresh.Gross.Suspect.Lo.WaterP" #6 , "myThresh.Spike.Hi.WaterP" #7 , "myThresh.Spike.Lo.WaterP" #8 , "myThresh.RoC.SD.number.WaterP" #9 , "myThresh.RoC.SD.period.WaterP" #10 , "myThresh.Flat.Hi.WaterP" #11 , "myThresh.Flat.Lo.WaterP" #12 , "myThresh.Flat.Tolerance.WaterP" #13 ) val_WaterP <- mget(nam_WaterP, envir=ContData.env) txt_WaterP_F <- c(val_WaterP[1] , "Fail" , paste0("> ",val_WaterP[3]," ",val_WaterP[2] ," or < ",val_WaterP[4]," ",val_WaterP[2]) , paste0(">= ", val_WaterP[7]," ",val_WaterP[2]," (+/-)") , "NA" , paste0("> ",val_WaterP[11] ," consecutive measurements within ",val_WaterP[13] ," units of one another")) txt_WaterP_S <- c(val_WaterP[1] , "Suspect" , paste0("> ",val_WaterP[5]," ",val_WaterP[2] ," or < ",val_WaterP[6]," ",val_WaterP[2]) , paste0(">= ", val_WaterP[8]," ",val_WaterP[2]," (+/-)") , paste0(">= ",val_WaterP[9]," standard deviations within " ,val_WaterP[10]," hours") , paste0("> ",val_WaterP[12] ," consecutive measurements within ",val_WaterP[13] ," units of one another")) # AirBP nam_AirBP <- c("myLab.AirBP" #1 , "myUnits.AirBP" #2 , "myThresh.Gross.Fail.Hi.AirBP" #3 , "myThresh.Gross.Fail.Lo.AirBP" #4 , "myThresh.Gross.Suspect.Hi.AirBP" #5 , "myThresh.Gross.Suspect.Lo.AirBP" #6 , "myThresh.Spike.Hi.AirBP" #7 , "myThresh.Spike.Lo.AirBP" #8 , "myThresh.RoC.SD.number.AirBP" #9 , "myThresh.RoC.SD.period.AirBP" #10 , "myThresh.Flat.Hi.AirBP" #11 , "myThresh.Flat.Lo.AirBP" #12 , "myThresh.Flat.Tolerance.AirBP" #13 ) val_AirBP <- mget(nam_AirBP, envir=ContData.env) txt_AirBP_F <- c(val_AirBP[1] , "Fail" , paste0("> ",val_AirBP[3]," ",val_AirBP[2] ," or < ",val_AirBP[4]," ",val_AirBP[2]) , paste0(">= ", val_AirBP[7]," ",val_AirBP[2]," (+/-)") , "NA" , paste0("> ",val_AirBP[11] ," consecutive measurements within ",val_AirBP[13] ," units of one another")) txt_AirBP_S <- c(val_AirBP[1] , "Suspect" , paste0("> ",val_AirBP[5]," ",val_AirBP[2] ," or < ",val_AirBP[6]," ",val_AirBP[2]) , paste0(">= ", val_AirBP[8]," ",val_AirBP[2]," (+/-)") , paste0(">= ",val_AirBP[9]," standard deviations within " ,val_AirBP[10]," hours") , paste0("> ",val_AirBP[12] ," consecutive measurements within ",val_AirBP[13] ," units of one another")) # SensorDepth nam_SensorDepth <- c("myLab.SensorDepth" #1 , "myUnits.SensorDepth" #2 , "myThresh.Gross.Fail.Hi.SensorDepth" #3 , "myThresh.Gross.Fail.Lo.SensorDepth" #4 , "myThresh.Gross.Suspect.Hi.SensorDepth" #5 , "myThresh.Gross.Suspect.Lo.SensorDepth" #6 , "myThresh.Spike.Hi.SensorDepth" #7 , "myThresh.Spike.Lo.SensorDepth" #8 , "myThresh.RoC.SD.number.SensorDepth" #9 , "myThresh.RoC.SD.period.SensorDepth" #10 , "myThresh.Flat.Hi.SensorDepth" #11 , "myThresh.Flat.Lo.SensorDepth" #12 , "myThresh.Flat.Tolerance.SensorDepth" #13 ) val_SensorDepth <- mget(nam_SensorDepth, envir=ContData.env) txt_SensorDepth_F <- c(val_SensorDepth[1] , "Fail" , paste0("> ",val_SensorDepth[3]," ",val_SensorDepth[2] ," or < ",val_SensorDepth[4]," ",val_SensorDepth[2]) , paste0(">= ", val_SensorDepth[7]," ",val_SensorDepth[2]," (+/-)") , "NA" , paste0("> ",val_SensorDepth[11] ," consecutive measurements within ",val_SensorDepth[13] ," units of one another")) txt_SensorDepth_S <- c(val_SensorDepth[1] , "Suspect" , paste0("> ",val_SensorDepth[5]," ",val_SensorDepth[2] ," or < ",val_SensorDepth[6]," ",val_SensorDepth[2]) , paste0(">= ", val_SensorDepth[8]," ",val_SensorDepth[2]," (+/-)") , paste0(">= ",val_SensorDepth[9]," standard deviations within " ,val_SensorDepth[10]," hours") , paste0("> ",val_SensorDepth[12] ," consecutive measurements within ",val_SensorDepth[13] ," units of one another")) # Discharge nam_Discharge <- c("myLab.Discharge" #1 , "myUnits.Discharge" #2 , "myThresh.Gross.Fail.Hi.Discharge" #3 , "myThresh.Gross.Fail.Lo.Discharge" #4 , "myThresh.Gross.Suspect.Hi.Discharge" #5 , "myThresh.Gross.Suspect.Lo.Discharge" #6 , "myThresh.Spike.Hi.Discharge" #7 , "myThresh.Spike.Lo.Discharge" #8 , "myThresh.RoC.SD.number.Discharge" #9 , "myThresh.RoC.SD.period.Discharge" #10 , "myThresh.Flat.Hi.Discharge" #11 , "myThresh.Flat.Lo.Discharge" #12 , "myThresh.Flat.Tolerance.Discharge" #13 ) val_Discharge <- mget(nam_Discharge, envir=ContData.env) txt_Discharge_F <- c(val_Discharge[1] , "Fail" , paste0("> ",val_Discharge[3]," ",val_Discharge[2] ," or < ",val_Discharge[4]," ",val_Discharge[2]) , paste0(">= ", val_Discharge[7]," ",val_Discharge[2]," (+/-)") , "NA" , paste0("> ",val_Discharge[11] ," consecutive measurements within ",val_Discharge[13] ," units of one another")) txt_Discharge_S <- c(val_Discharge[1] , "Suspect" , paste0("> ",val_Discharge[5]," ",val_Discharge[2] ," or < ",val_Discharge[6]," ",val_Discharge[2]) , paste0(">= ", val_Discharge[8]," ",val_Discharge[2]," (+/-)") , paste0(">= ",val_Discharge[9]," standard deviations within " ,val_Discharge[10]," hours") , paste0("> ",val_Discharge[12] ," consecutive measurements within ",val_Discharge[13] ," units of one another")) # WaterLevel nam_WaterLevel <- c("myLab.WaterLevel" #1 , "myUnits.WaterLevel" #2 , "myThresh.Gross.Fail.Hi.WaterLevel" #3 , "myThresh.Gross.Fail.Lo.WaterLevel" #4 , "myThresh.Gross.Suspect.Hi.WaterLevel" #5 , "myThresh.Gross.Suspect.Lo.WaterLevel" #6 , "myThresh.Spike.Hi.WaterLevel" #7 -removed , "myThresh.Spike.Lo.WaterLevel" #8 - removed , "myThresh.RoC.SD.number.WaterLevel" #9 - 7 , "myThresh.RoC.SD.period.WaterLevel" #10 - 8 , "myThresh.Flat.Hi.WaterLevel" #11 - 9 , "myThresh.Flat.Lo.WaterLevel" #12 - 10 , "myThresh.Flat.Tolerance.WaterLevel" #13 - 11 ) val_WaterLevel <- mget(nam_WaterLevel, envir=ContData.env) txt_WaterLevel_F <- c(val_WaterLevel[1] , "Fail" , paste0("> ",val_WaterLevel[3]," ",val_WaterLevel[2] ," or < ",val_WaterLevel[4]," ",val_WaterLevel[2]) , "NA" , "NA" , paste0("> ",val_WaterLevel[9] ," consecutive measurements within ",val_WaterLevel[11] ," units of one another")) txt_WaterLevel_S <- c(val_WaterLevel[1] , "Suspect" , paste0("> ",val_WaterLevel[5]," ",val_WaterLevel[2] ," or < ",val_WaterLevel[6]," ",val_WaterLevel[2]) , "NA" , paste0(">= ",val_WaterLevel[7]," standard deviations within " ,val_WaterLevel[8]," hours") , paste0("> ",val_WaterLevel[10] ," consecutive measurements within ",val_WaterLevel[11] ," units of one another")) # Cond nam_Cond <- c("myLab.Cond" #1 , "myUnits.Cond" #2 , "myThresh.Gross.Fail.Hi.Cond" #3 , "myThresh.Gross.Fail.Lo.Cond" #4 , "myThresh.Gross.Suspect.Hi.Cond" #5 , "myThresh.Gross.Suspect.Lo.Cond" #6 , "myThresh.Spike.Hi.Cond" #7 , "myThresh.Spike.Lo.Cond" #8 , "myThresh.RoC.SD.number.Cond" #9 , "myThresh.RoC.SD.period.Cond" #10 , "myThresh.Flat.Hi.Cond" #11 , "myThresh.Flat.Lo.Cond" #12 , "myThresh.Flat.Tolerance.Cond" #13 ) val_Cond <- mget(nam_Cond, envir=ContData.env) txt_Cond_F <- c(val_Cond[1] , "Fail" , paste0("> ",val_Cond[3]," ",val_Cond[2] ," or < ",val_Cond[4]," ",val_Cond[2]) , paste0(">= ", val_Cond[7]," ",val_Cond[2]," (+/-)") , "NA" , paste0("> ",val_Cond[11] ," consecutive measurements within ",val_Cond[13] ," units of one another")) txt_Cond_S <- c(val_Cond[1] , "Suspect" , paste0("> ",val_Cond[5]," ",val_Cond[2] ," or < ",val_Cond[6]," ",val_Cond[2]) , paste0(">= ", val_Cond[8]," ",val_Cond[2]," (+/-)") , paste0(">= ",val_Cond[9]," standard deviations within " ,val_Cond[10]," hours") , paste0("> ",val_Cond[12] ," consecutive measurements within ",val_Cond[13] ," units of one another")) # DO nam_DO <- c("myLab.DO" #1 , "myUnits.DO" #2 , "myThresh.Gross.Fail.Hi.DO" #3 , "myThresh.Gross.Fail.Lo.DO" #4 , "myThresh.Gross.Suspect.Hi.DO" #5 , "myThresh.Gross.Suspect.Lo.DO" #6 , "myThresh.Spike.Hi.DO" #7 , "myThresh.Spike.Lo.DO" #8 , "myThresh.RoC.SD.number.DO" #9 , "myThresh.RoC.SD.period.DO" #10 , "myThresh.Flat.Hi.DO" #11 , "myThresh.Flat.Lo.DO" #12 , "myThresh.Flat.Tolerance.DO" #13 ) val_DO <- mget(nam_DO, envir=ContData.env) txt_DO_F <- c(val_DO[1] , "Fail" , paste0("> ",val_DO[3]," ",val_DO[2] ," or < ",val_DO[4]," ",val_DO[2]) , paste0(">= ", val_DO[7]," ",val_DO[2]," (+/-)") , "NA" , paste0("> ",val_DO[11] ," consecutive measurements within ",val_DO[13] ," units of one another")) txt_DO_S <- c(val_DO[1] , "Suspect" , paste0("> ",val_DO[5]," ",val_DO[2] ," or < ",val_DO[6]," ",val_DO[2]) , paste0(">= ", val_DO[8]," ",val_DO[2]," (+/-)") , paste0(">= ",val_DO[9]," standard deviations within " ,val_DO[10]," hours") , paste0("> ",val_DO[12] ," consecutive measurements within ",val_DO[13] ," units of one another")) # DO.adj nam_DO.adj <- c("myLab.DO.adj" #1 , "myUnits.DO.adj" #2 , "myThresh.Gross.Fail.Hi.DO.adj" #3 , "myThresh.Gross.Fail.Lo.DO.adj" #4 , "myThresh.Gross.Suspect.Hi.DO.adj" #5 , "myThresh.Gross.Suspect.Lo.DO.adj" #6 , "myThresh.Spike.Hi.DO.adj" #7 , "myThresh.Spike.Lo.DO.adj" #8 , "myThresh.RoC.SD.number.DO.adj" #9 , "myThresh.RoC.SD.period.DO.adj" #10 , "myThresh.Flat.Hi.DO.adj" #11 , "myThresh.Flat.Lo.DO.adj" #12 , "myThresh.Flat.Tolerance.DO.adj" #13 ) val_DO.adj <- mget(nam_DO.adj, envir=ContData.env) txt_DO.adj_F <- c(val_DO.adj[1] , "Fail" , paste0("> ",val_DO.adj[3]," ",val_DO.adj[2] ," or < ",val_DO.adj[4]," ",val_DO.adj[2]) , paste0(">= ", val_DO.adj[7]," ",val_DO.adj[2]," (+/-)") , "NA" , paste0("> ",val_DO.adj[11] ," consecutive measurements within ",val_DO.adj[13] ," units of one another")) txt_DO.adj_S <- c(val_DO.adj[1] , "Suspect" , paste0("> ",val_DO.adj[5]," ",val_DO.adj[2] ," or < ",val_DO.adj[6]," ",val_DO.adj[2]) , paste0(">= ", val_DO.adj[8]," ",val_DO.adj[2]," (+/-)") , paste0(">= ",val_DO[9]," standard deviations within " ,val_DO[10]," hours") , paste0("> ",val_DO[12] ," consecutive measurements within ",val_DO.adj[13] ," units of one another")) # DO.pctsat nam_DO.pctsat <- c("myLab.DO.pctsat" #1 , "myUnits.DO.pctsat" #2 , "myThresh.Gross.Fail.Hi.DO.pctsat" #3 , "myThresh.Gross.Fail.Lo.DO.pctsat" #4 , "myThresh.Gross.Suspect.Hi.DO.pctsat" #5 , "myThresh.Gross.Suspect.Lo.DO.pctsat" #6 , "myThresh.Spike.Hi.DO.pctsat" #7 , "myThresh.Spike.Lo.DO.pctsat" #8 , "myThresh.RoC.SD.number.DO.pctsat" #9 , "myThresh.RoC.SD.period.DO.pctsat" #10 , "myThresh.Flat.Hi.DO.pctsat" #11 , "myThresh.Flat.Lo.DO.pctsat" #12 , "myThresh.Flat.Tolerance.DO.pctsat" #13 ) val_DO.pctsat <- mget(nam_DO.pctsat, envir=ContData.env) txt_DO.pctsat_F <- c(val_DO.pctsat[1] , "Fail" , paste0("> ",val_DO.pctsat[3]," ",val_DO.pctsat[2] ," or < ",val_DO.pctsat[4]," ",val_DO.pctsat[2]) , paste0(">= ", val_DO.pctsat[7]," ",val_DO.pctsat[2]," (+/-)") , "NA" , paste0("> ",val_DO.pctsat[11] ," consecutive measurements within ",val_DO.pctsat[13] ," units of one another")) txt_DO.pctsat_S <- c(val_DO.pctsat[1] , "Suspect" , paste0("> ",val_DO.pctsat[5]," ",val_DO.pctsat[2] ," or < ",val_DO.pctsat[6]," ",val_DO.pctsat[2]) , paste0(">= ", val_DO.pctsat[8]," ",val_DO.pctsat[2]," (+/-)") , paste0(">= ",val_DO.pctsat[9]," standard deviations within " ,val_DO.pctsat[10]," hours") , paste0("> ",val_DO.pctsat[12] ," consecutive measurements within ",val_DO.pctsat[13] ," units of one another")) # pH nam_pH <- c("myLab.pH" #1 , "myUnits.pH" #2 , "myThresh.Gross.Fail.Hi.pH" #3 , "myThresh.Gross.Fail.Lo.pH" #4 , "myThresh.Gross.Suspect.Hi.pH" #5 , "myThresh.Gross.Suspect.Lo.pH" #6 , "myThresh.Spike.Hi.pH" #7 , "myThresh.Spike.Lo.pH" #8 , "myThresh.RoC.SD.number.pH" #9 , "myThresh.RoC.SD.period.pH" #10 , "myThresh.Flat.Hi.pH" #11 , "myThresh.Flat.Lo.pH" #12 , "myThresh.Flat.Tolerance.pH" #13 ) val_pH <- mget(nam_pH, envir=ContData.env) txt_pH_F <- c(val_pH[1] , "Fail" , paste0("> ",val_pH[3]," ",val_pH[2] ," or < ",val_pH[4]," ",val_pH[2]) , paste0(">= ", val_pH[7]," ",val_pH[2]," (+/-)") , "NA" , paste0("> ",val_pH[11] ," consecutive measurements within ",val_pH[13] ," units of one another")) txt_pH_S <- c(val_pH[1] , "Suspect" , paste0("> ",val_pH[5]," ",val_pH[2] ," or < ",val_pH[6]," ",val_pH[2]) , paste0(">= ", val_pH[8]," ",val_pH[2]," (+/-)") , paste0(">= ",val_pH[9]," standard deviations within " ,val_pH[10]," hours") , paste0("> ",val_pH[12] ," consecutive measurements within ",val_pH[13] ," units of one another")) # Turbidity nam_Turbidity <- c("myLab.Turbidity" #1 , "myUnits.Turbidity" #2 , "myThresh.Gross.Fail.Hi.Turbidity" #3 , "myThresh.Gross.Fail.Lo.Turbidity" #4 , "myThresh.Gross.Suspect.Hi.Turbidity" #5 , "myThresh.Gross.Suspect.Lo.Turbidity" #6 , "myThresh.Spike.Hi.Turbidity" #7 , "myThresh.Spike.Lo.Turbidity" #8 , "myThresh.RoC.SD.number.Turbidity" #9 , "myThresh.RoC.SD.period.Turbidity" #10 , "myThresh.Flat.Hi.Turbidity" #11 , "myThresh.Flat.Lo.Turbidity" #12 , "myThresh.Flat.Tolerance.Turbidity" #13 ) val_Turbidity <- mget(nam_Turbidity, envir=ContData.env) txt_Turbidity_F <- c(val_Turbidity[1] , "Fail" , paste0("> ",val_Turbidity[3]," ",val_Turbidity[2] ," or < ",val_Turbidity[4]," ",val_Turbidity[2]) , paste0(">= ", val_Turbidity[7]," ",val_Turbidity[2]," (+/-)") , "NA" , paste0("> ",val_Turbidity[11] ," consecutive measurements within ",val_Turbidity[13] ," units of one another")) txt_Turbidity_S <- c(val_Turbidity[1] , "Suspect" , paste0("> ",val_Turbidity[5]," ",val_Turbidity[2] ," or < ",val_Turbidity[6]," ",val_Turbidity[2]) , paste0(">= ", val_Turbidity[8]," ",val_Turbidity[2]," (+/-)") , paste0(">= ",val_Turbidity[9]," standard deviations within " ,val_Turbidity[10]," hours") , paste0("> ",val_Turbidity[12] ," consecutive measurements within ",val_Turbidity[13] ," units of one another")) # Chlorophylla nam_Chlorophylla <- c("myLab.Chlorophylla" #1 , "myUnits.Chlorophylla" #2 , "myThresh.Gross.Fail.Hi.Chlorophylla" #3 , "myThresh.Gross.Fail.Lo.Chlorophylla" #4 , "myThresh.Gross.Suspect.Hi.Chlorophylla" #5 , "myThresh.Gross.Suspect.Lo.Chlorophylla" #6 , "myThresh.Spike.Hi.Chlorophylla" #7 , "myThresh.Spike.Lo.Chlorophylla" #8 , "myThresh.RoC.SD.number.Chlorophylla" #9 , "myThresh.RoC.SD.period.Chlorophylla" #10 , "myThresh.Flat.Hi.Chlorophylla" #11 , "myThresh.Flat.Lo.Chlorophylla" #12 , "myThresh.Flat.Tolerance.Chlorophylla" #13 ) val_Chlorophylla <- mget(nam_Chlorophylla, envir=ContData.env) txt_Chlorophylla_F <- c(val_Chlorophylla[1] , "Fail" , paste0("> ",val_Chlorophylla[3]," ",val_Chlorophylla[2] ," or < ",val_Chlorophylla[4]," ",val_Chlorophylla[2]) , paste0(">= ", val_Chlorophylla[7]," ",val_Chlorophylla[2]," (+/-)") , "NA" , paste0("> ",val_Chlorophylla[11] ," consecutive measurements within ",val_Chlorophylla[13] ," units of one another")) txt_Chlorophylla_S <- c(val_Chlorophylla[1] , "Suspect" , paste0("> ",val_Chlorophylla[5]," ",val_Chlorophylla[2] ," or < ",val_Chlorophylla[6]," ",val_Chlorophylla[2]) , paste0(">= ", val_Chlorophylla[8]," ",val_Chlorophylla[2]," (+/-)") , paste0(">= ",val_Chlorophylla[9]," standard deviations within " ,val_Chlorophylla[10]," hours") , paste0("> ",val_Chlorophylla[12] ," consecutive measurements within ",val_Chlorophylla[13] ," units of one another")) ## Salinity nam_Salinity <- c("myLab.Salinity" #1 , "myUnits.Salinity" #2 , "myThresh.Gross.Fail.Hi.Salinity" #3 , "myThresh.Gross.Fail.Lo.Salinity" #4 , "myThresh.Gross.Suspect.Hi.Salinity" #5 , "myThresh.Gross.Suspect.Lo.Salinity" #6 , "myThresh.Spike.Hi.Salinity" #7 , "myThresh.Spike.Lo.Salinity" #8 , "myThresh.RoC.SD.number.Salinity" #9 , "myThresh.RoC.SD.period.Salinity" #10 , "myThresh.Flat.Hi.Salinity" #11 , "myThresh.Flat.Lo.Salinity" #12 , "myThresh.Flat.Tolerance.Salinity" #13 ) val_Salinity <- mget(nam_Salinity, envir=ContData.env) txt_Salinity_F <- c(val_Salinity[1] , "Fail" , paste0("> ",val_Salinity[3]," ",val_Salinity[2] ," or < ",val_Salinity[4]," ",val_Salinity[2]) , paste0(">= ", val_Salinity[7]," ",val_Salinity[2]," (+/-)") , "NA" , paste0("> ",val_Salinity[11] ," consecutive measurements within ",val_Salinity[13] ," units of one another")) txt_Salinity_S <- c(val_Salinity[1] , "Suspect" , paste0("> ",val_Salinity[5]," ",val_Salinity[2] ," or < ",val_Salinity[6]," ",val_Salinity[2]) , paste0(">= ", val_Salinity[8]," ",val_Salinity[2]," (+/-)") , paste0(">= ",val_Salinity[9]," standard deviations within " ,val_Salinity[10]," hours") , paste0("> ",val_Salinity[12] ," consecutive measurements within ",val_Salinity[13] ," units of one another")) # Create Table df_Env <- data.frame(rbind(txt_WaterTemp_F, txt_WaterTemp_S , txt_AirTemp_F, txt_AirTemp_S , txt_WaterP_F, txt_WaterP_S , txt_AirBP_F, txt_AirBP_S , txt_SensorDepth_F, txt_SensorDepth_S , txt_WaterLevel_F, txt_WaterLevel_S , txt_Discharge_F, txt_Discharge_S , txt_Cond_F, txt_Cond_S , txt_DO_F, txt_DO_S , txt_DO.adj_F, txt_DO.adj_S , txt_DO.pctsat_F, txt_DO.pctsat_S , txt_pH_F, txt_pH_S , txt_Turbidity_F, txt_Turbidity_S , txt_Chlorophylla_F, txt_Chlorophylla_S , txt_Salinity_F, txt_Salinity_S ) , row.names = NULL) names(df_Env) <- txt_header knitr::kable(df_Env, caption = kbl_caption)
All Settings, Alphabetical
All settings listed by name in alphabetical order with values.
# sapply(ls(ContData.env), function(x) get(x, envir=ContData.env)) kbl_caption <- "Thresholds, ALL, Alphabetical" env_Nam <- ls(ContData.env) env_Val <- mget(env_Nam, envir=ContData.env) df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL) names(df_Env) <- c("Names", "Values") knitr::kable(df_Env, caption = kbl_caption)
All Settings, Categories
All settings by category listed by name with values.
The order presented here is the order in the config file.
Column Names
- Acceptable column names for the data
- Units
- Logger Fields
- Parameters as appear in logger files
- Plot Labels
kbl_caption <- "Thresholds, Column Names" env_Nam <- c("myDelim" , "myName.SiteID" , "myName.Date" , "myName.Time" , "myName.DateTime" , "myUnits.AirTemp" , "myUnits.WaterTemp" , "myUnits.AirBP" , "myUnits.WaterP" , "myUnits.SensorDepth" , "myUnits.WaterLevel" , "myUnits.Discharge" , "myUnits.Cond" , "myUnits.DO" , "myUnits.DO.adj" , "myUnits.DO.pctsat" , "myUnits.pH" , "myUnits.Turbidity" , "myUnits.Chlorophylla" , "myUnits.Salinity" , "myName.RowID.Water" , "myName.LoggerID.Water" , "myName.RowID.Air" , "myName.LoggerID.Air" , "myName.WaterTemp" , "myName.AirTemp" , "myName.WaterP" , "myName.AirBP" , "myName.SensorDepth" , "myName.WaterLevel" , "myName.Discharge" , "myName.Cond" , "myName.DO" , "myName.DO.adj" , "myName.DO.pctsat" , "myName.pH" , "myName.Turbidity" , "myName.Chlorophylla" , "myName.Salinity" , "myLab.WaterTemp" , "myLab.AirTemp" , "myLab.Date" , "myLab.DateTime" , "myLab.WaterP" , "myLab.AirBP" , "myLab.SensorDepth" , "myLab.WaterLevel" , "myLab.Temp.BOTH" , "myLab.Discharge" , "myLab.Cond" , "myLab.DO" , "myLab.DO.adj" , "myLab.DO.pctsat" , "myLab.pH" , "myLab.Turbidity" , "myLab.Chlorophylla" , "myLab.Salinity" ) env_Val <- mget(env_Nam, envir=ContData.env) df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL) names(df_Env) <- c("Names", "Values") knitr::kable(df_Env, caption = kbl_caption)
Discrete Measurements
- Discrete, Names
- Discrete, Labels
kbl_caption <- "Thresholds, Discrete Measurements" env_Nam <- c("myPrefix.Discrete" , "myName.Discrete.WaterTemp" , "myName.Discrete.AirTemp" , "myName.Discrete.WaterP" , "myName.Discrete.AirBP" , "myName.Discrete.SensorDepth" , "myName.Discrete.WaterLevel" , "myName.Discrete.Discharge" , "myName.Discrete.Cond" , "myName.Discrete.DO" , "myName.Discrete.DO.adj" , "myName.Discrete.DO.pctsat" , "myName.Discrete.pH" , "myName.Discrete.Turbidity" , "myName.Discrete.Chlorophylla" , "myName.Discrete.Salinity" , "myLab.Discrete.WaterTemp" , "myLab.Discrete.AirTemp" , "myLab.Discrete.WaterP" , "myLab.Discrete.AirBP" , "myLab.Discrete.SensorDepth" , "myLab.Discrete.Discharge" , "myLab.Discrete.WaterLevel" , "myLab.Discrete.Cond" , "myLab.Discrete.DO" , "myLab.Discrete.DO.adj" , "myLab.Discrete.DO.pctsat" , "myLab.Discrete.pH" , "myLab.Discrete.Turbidity" , "myLab.Discrete.Chlorophylla" , "myLab.Discrete.Salinity" ) env_Val <- mget(env_Nam, envir=ContData.env) df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL) names(df_Env) <- c("Names", "Values") knitr::kable(df_Env, caption = kbl_caption)
Automated QC Stuff
- data type/stages
kbl_caption <- "Thresholds, Automated QC Stuff" env_Nam <- c("myDataQuality.Raw" , "myDataQuality.QCauto" , "myDataQuality.QCmanual" , "myDataQuality.Final" , "myDataQuality.Aggregated" ) env_Val <- mget(env_Nam, envir=ContData.env) df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL) names(df_Env) <- c("Names", "Values") knitr::kable(df_Env, caption = kbl_caption)
Directory Names
kbl_caption <- "Thresholds, Directory Names" env_Nam <- c("myName.Dir.1Raw" , "myName.Dir.2QC" , "myName.Dir.3Agg" , "myName.Dir.4Stats" ) env_Val <- mget(env_Nam, envir=ContData.env) df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL) names(df_Env) <- c("Names", "Values") knitr::kable(df_Env, caption = kbl_caption)
Data Fields
- Field Names
- Field Labels for plots
kbl_caption <- "Thresholds, Data Fields" env_Nam <- c("myNames.DataFields" , "myNames.DataFields.Lab" , "myNames.DataFields.Col" ) env_Val <- mget(env_Nam, envir=ContData.env) df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL) names(df_Env) <- c("Names", "Values") knitr::kable(df_Env, caption = kbl_caption)
Data Quality Flag Values
kbl_caption <- "Thresholds, Data Quality Flag Values" env_Nam <- c("myFlagVal.Pass" , "myFlagVal.NotEval" , "myFlagVal.Suspect" , "myFlagVal.Fail" , "myFlagVal.NoData" , "myFlagVal.Order" ) env_Val <- mget(env_Nam, envir=ContData.env) df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL) names(df_Env) <- c("Names", "Values") knitr::kable(df_Env, caption = kbl_caption)
QC Tests and Calculations
Parameters grouped by type of QC check.
Gross Min/Max, Fail (equipment)
Examines values as outliers versus threholds.
- if value >= Hi or <= Lo then flagged as "Fail"
kbl_caption <- "Thresholds, QC Tests and Calculations, Gross Min/Max, Fail (equipment)" env_Nam <- c("myThresh.Gross.Fail.Hi.WaterTemp" , "myThresh.Gross.Fail.Lo.WaterTemp" , "myThresh.Gross.Fail.Hi.AirTemp" , "myThresh.Gross.Fail.Lo.AirTemp" , "myThresh.Gross.Fail.Hi.WaterP" , "myThresh.Gross.Fail.Lo.WaterP" , "myThresh.Gross.Fail.Hi.AirBP" , "myThresh.Gross.Fail.Lo.AirBP" , "myThresh.Gross.Fail.Hi.SensorDepth" , "myThresh.Gross.Fail.Lo.SensorDepth" , "myThresh.Gross.Fail.Hi.WaterLevel" , "myThresh.Gross.Fail.Lo.WaterLevel" , "myThresh.Gross.Fail.Hi.Discharge" , "myThresh.Gross.Fail.Lo.Discharge" , "myThresh.Gross.Fail.Hi.Cond" , "myThresh.Gross.Fail.Lo.Cond" , "myThresh.Gross.Fail.Hi.DO" , "myThresh.Gross.Fail.Lo.DO" , "myThresh.Gross.Fail.Hi.DO.adj" , "myThresh.Gross.Fail.Lo.DO.adj" , "myThresh.Gross.Fail.Hi.DO.pctsat" , "myThresh.Gross.Fail.Lo.DO.pctsat" , "myThresh.Gross.Fail.Hi.pH" , "myThresh.Gross.Fail.Lo.pH" , "myThresh.Gross.Fail.Hi.Turbidity" , "myThresh.Gross.Fail.Lo.Turbidity" , "myThresh.Gross.Fail.Hi.Chlorophylla" , "myThresh.Gross.Fail.Lo.Chlorophylla" , "myThresh.Gross.Fail.Hi.Salinity" , "myThresh.Gross.Fail.Lo.Salinity" ) env_Val <- mget(env_Nam, envir=ContData.env) df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL) names(df_Env) <- c("Names", "Values") knitr::kable(df_Env, caption = kbl_caption)
Gross Min/Max, Suspect (extreme)
Examines values as outliers versus threholds.
- if value >= Hi or <= Lo then flagged as "Suspect"
kbl_caption <- "Thresholds, QC Tests and Calculations, Gross Min/Max, Fail (equipment)" env_Nam <- c("myThresh.Gross.Suspect.Hi.WaterTemp" , "myThresh.Gross.Suspect.Lo.WaterTemp" , "myThresh.Gross.Suspect.Hi.AirTemp" , "myThresh.Gross.Suspect.Lo.AirTemp" , "myThresh.Gross.Suspect.Hi.WaterP" , "myThresh.Gross.Suspect.Lo.WaterP" , "myThresh.Gross.Suspect.Hi.AirBP" , "myThresh.Gross.Suspect.Lo.AirBP" , "myThresh.Gross.Suspect.Hi.SensorDepth" , "myThresh.Gross.Suspect.Lo.SensorDepth" , "myThresh.Gross.Suspect.Hi.WaterLevel" , "myThresh.Gross.Suspect.Lo.WaterLevel" , "myThresh.Gross.Suspect.Hi.Discharge" , "myThresh.Gross.Suspect.Lo.Discharge" , "myThresh.Gross.Suspect.Hi.Cond" , "myThresh.Gross.Suspect.Lo.Cond" , "myThresh.Gross.Suspect.Hi.DO" , "myThresh.Gross.Suspect.Lo.DO" , "myThresh.Gross.Suspect.Hi.DO.adj" , "myThresh.Gross.Suspect.Lo.DO.adj" , "myThresh.Gross.Suspect.Hi.DO.pctsat" , "myThresh.Gross.Suspect.Lo.DO.pctsat" , "myThresh.Gross.Suspect.Hi.pH" , "myThresh.Gross.Suspect.Lo.pH" , "myThresh.Gross.Suspect.Hi.Turbidity" , "myThresh.Gross.Suspect.Lo.Turbidity" , "myThresh.Gross.Suspect.Hi.Chlorophylla" , "myThresh.Gross.Suspect.Lo.Chlorophylla" , "myThresh.Gross.Suspect.Hi.Salinity" , "myThresh.Gross.Suspect.Lo.Salinity" ) env_Val <- mget(env_Nam, envir=ContData.env) df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL) names(df_Env) <- c("Names", "Values") knitr::kable(df_Env, caption = kbl_caption)
Spike thresholds (absolute change)
Examines difference between consecutive measurements.
- if delta >= Hi then flagged as "Fail"
- if delta >= Lo then flagged as "Suspect"
kbl_caption <- "Thresholds, QC Tests and Calculations, Spike thresholds (absolute change)" env_Nam <- c("myThresh.Spike.Hi.WaterTemp" , "myThresh.Spike.Lo.WaterTemp" , "myThresh.Spike.Hi.AirTemp" , "myThresh.Spike.Lo.AirTemp" , "myThresh.Spike.Hi.WaterP" , "myThresh.Spike.Lo.WaterP" , "myThresh.Spike.Hi.AirBP" , "myThresh.Spike.Lo.AirBP" , "myThresh.Spike.Hi.SensorDepth" , "myThresh.Spike.Lo.SensorDepth" , "myThresh.Spike.Hi.WaterLevel" , "myThresh.Spike.Lo.WaterLevel" , "myThresh.Spike.Hi.Discharge" , "myThresh.Spike.Lo.Discharge" , "myThresh.Spike.Hi.Cond" , "myThresh.Spike.Lo.Cond" , "myThresh.Spike.Hi.DO" , "myThresh.Spike.Lo.DO" , "myThresh.Spike.Hi.DO.adj" , "myThresh.Spike.Lo.DO.adj" , "myThresh.Spike.Hi.DO.pctsat" , "myThresh.Spike.Lo.DO.pctsat" , "myThresh.Spike.Hi.pH" , "myThresh.Spike.Lo.pH" , "myThresh.Spike.Hi.Turbidity" , "myThresh.Spike.Lo.Turbidity" , "myThresh.Spike.Hi.Chlorophylla" , "myThresh.Spike.Lo.Chlorophylla" , "myThresh.Spike.Hi.Salinity" , "myThresh.Spike.Lo.Salinity" ) env_Val <- mget(env_Nam, envir=ContData.env) df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL) names(df_Env) <- c("Names", "Values") knitr::kable(df_Env, caption = kbl_caption)
Rate of Change (relative change)
Examines Standard Deviation (SD) over "period" and difference in consecutive values.
- If delta >= SD.number * SD then flagged as "Suspect"
kbl_caption <- "Thresholds, QC Tests and Calculations, Rate of Change (relative change)" env_Nam <- c("myDefault.RoC.SD.number" , "myDefault.RoC.SD.period" , "myThresh.RoC.SD.number.WaterTemp" , "myThresh.RoC.SD.period.WaterTemp" , "myThresh.RoC.SD.number.AirTemp" , "myThresh.RoC.SD.period.AirTemp" , "myThresh.RoC.SD.number.WaterP" , "myThresh.RoC.SD.period.WaterP" , "myThresh.RoC.SD.number.AirBP" , "myThresh.RoC.SD.period.AirBP" , "myThresh.RoC.SD.number.SensorDepth" , "myThresh.RoC.SD.period.SensorDepth" , "myThresh.RoC.SD.number.WaterLevel" , "myThresh.RoC.SD.period.WaterLevel" , "myThresh.RoC.SD.number.Discharge" , "myThresh.RoC.SD.period.Discharge" , "myThresh.RoC.SD.number.Cond" , "myThresh.RoC.SD.period.Cond" , "myThresh.RoC.SD.number.DO" , "myThresh.RoC.SD.period.DO" , "myThresh.RoC.SD.number.DO.adj" , "myThresh.RoC.SD.period.DO.adj" , "myThresh.RoC.SD.number.DO.pctsat" , "myThresh.RoC.SD.period.DO.pctsat" , "myThresh.RoC.SD.number.pH" , "myThresh.RoC.SD.period.pH" , "myThresh.RoC.SD.number.Turbidity" , "myThresh.RoC.SD.period.Turbidity" , "myThresh.RoC.SD.number.Chlorophylla" , "myThresh.RoC.SD.period.Chlorophylla" , "myThresh.RoC.SD.number.Salinity" , "myThresh.RoC.SD.period.Salinity" ) env_Val <- mget(env_Nam, envir=ContData.env) df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL) names(df_Env) <- c("Names", "Values") knitr::kable(df_Env, caption = kbl_caption)
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"
kbl_caption <- "Thresholds, QC Tests and Calculations, No Change (flat-line)" env_Nam <- c("myDefault.Flat.Hi" , "myDefault.Flat.Lo" , "myDefault.Flat.Tolerance" , "myThresh.Flat.Hi.WaterTemp" , "myThresh.Flat.Lo.WaterTemp" , "myThresh.Flat.Tolerance.WaterTemp" , "myThresh.Flat.Hi.AirTemp" , "myThresh.Flat.Lo.AirTemp" , "myThresh.Flat.Tolerance.AirTemp" , "myThresh.Flat.Hi.WaterP" , "myThresh.Flat.Lo.WaterP" , "myThresh.Flat.Tolerance.WaterP" , "myThresh.Flat.Hi.AirBP" , "myThresh.Flat.Lo.AirBP" , "myThresh.Flat.Tolerance.AirBP" , "myThresh.Flat.Hi.SensorDepth" , "myThresh.Flat.Lo.SensorDepth" , "myThresh.Flat.Tolerance.SensorDepth" , "myThresh.Flat.Hi.WaterLevel" , "myThresh.Flat.Lo.WaterLevel" , "myThresh.Flat.Tolerance.WaterLevel" , "myThresh.Flat.Hi.Discharge" , "myThresh.Flat.Lo.Discharge" , "myThresh.Flat.Tolerance.Discharge" , "myThresh.Flat.Hi.Cond" , "myThresh.Flat.Lo.Cond" , "myThresh.Flat.Tolerance.Cond" , "myThresh.Flat.Hi.DO" , "myThresh.Flat.Lo.DO" , "myThresh.Flat.Tolerance.DO" , "myThresh.Flat.Hi.DO.adj" , "myThresh.Flat.Lo.DO.adj" , "myThresh.Flat.Tolerance.DO.adj" , "myThresh.Flat.Hi.DO.pctsat" , "myThresh.Flat.Lo.DO.pctsat" , "myThresh.Flat.Tolerance.DO.pctsat" , "myThresh.Flat.Hi.pH" , "myThresh.Flat.Lo.pH" , "myThresh.Flat.Tolerance.pH" , "myThresh.Flat.Hi.Turbidity" , "myThresh.Flat.Lo.Turbidity" , "myThresh.Flat.Tolerance.Turbidity" , "myThresh.Flat.Hi.Chlorophylla" , "myThresh.Flat.Lo.Chlorophylla" , "myThresh.Flat.Tolerance.Chlorophylla" , "myThresh.Flat.Hi.Salinity" , "myThresh.Flat.Lo.Salinity" , "myThresh.Flat.Tolerance.Salinity" , "myThresh.Flat.MaxComp" ) env_Val <- mget(env_Nam, envir=ContData.env) df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL) names(df_Env) <- c("Names", "Values") knitr::kable(df_Env, caption = kbl_caption)
Data Fields with Flags
- flag labels
- Data Quality Test Names
kbl_caption <- "Thresholds, Data Fields with Flags" env_Nam <- c("myName.Flag" , "myNames.Cols4Flags" , "myNames.Flags" , "myName.Flag.DateTime" , "myName.Flag.WaterTemp" , "myName.Flag.AirTemp" , "myName.Flag.WaterP" , "myName.Flag.AirBP" , "myName.Flag.SensorDepth" , "myName.Flag.WaterLevel" , "myName.Flag.Discharge" , "myName.Flag.Cond" , "myName.Flag.DO" , "myName.Flag.DO.adj" , "myName.Flag.DO.pctsat" , "myName.Flag.pH" , "myName.Flag.Turbidity" , "myName.Flag.Chlorophylla" , "myName.Flag.Salinity" , "myNames.QCTests" , "myNames.QCCalcs" ) env_Val <- mget(env_Nam, envir=ContData.env) df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL) names(df_Env) <- c("Names", "Values") knitr::kable(df_Env, caption = kbl_caption)
Exceedance Values for Statistics
Exceedance values for stats (default to Gross-Suspect-Hi value)
kbl_caption <- "Thresholds, Exceedance Values for Statistics" env_Nam <- c("myExceed.WaterTemp" , "myExceed.AirTemp" , "myExceed.SensorDepth" ) env_Val <- mget(env_Nam, envir=ContData.env) df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL) names(df_Env) <- c("Names", "Values") knitr::kable(df_Env, caption = kbl_caption)
Date and Time Formats
- Date and Time Formats
- Time zone
kbl_caption <- "Thresholds, Date and Time Formats" env_Nam <- c("myFormat.Date" , "myFormat.Time" , "myFormat.DateTime" , "DateRange.Start.Default" , "DateRange.End.Default" , "myTZ" ) env_Val <- mget(env_Nam, envir=ContData.env) df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL) names(df_Env) <- c("Names", "Values") knitr::kable(df_Env, caption = kbl_caption)
Time Frames
- Time Frames (MM-DD)
- Time Frame Names
- for summary stats
kbl_caption <- "Thresholds, Time Frames" env_Nam <- c("myTimeFrame.Annual.Start" , "myTimeFrame.Annual.End" , "myTimeFrame.WaterYear.Start" , "myTimeFrame.Season.Spring.Start" , "myTimeFrame.Season.Summer.Start" , "myTimeFrame.Season.Fall.Start" , "myTimeFrame.Season.Winter.Start" , "myName.Yr" , "myName.YrMo" , "myName.Mo" , "myName.MoDa" , "myName.JuDa" , "myName.Day" , "myName.Season" , "myName.YrSeason" , "myNames.Fields.TimePeriods" ) env_Val <- mget(env_Nam, envir=ContData.env) df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL) names(df_Env) <- c("Names", "Values") knitr::kable(df_Env, caption = kbl_caption)
Exclude Trigger
Trigger for Stats to exclude (TRUE) or include (FALSE) where flag = "fail"
kbl_caption <- "Thresholds, Exclude Trigger" env_Nam <- c("myStats.Fails.Exclude" ) env_Val <- mget(env_Nam, envir=ContData.env) df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL) names(df_Env) <- c("Names", "Values") knitr::kable(df_Env, caption = kbl_caption)
Report Format
Default report format output.
kbl_caption <- "Thresholds, Report Format" env_Nam <- c("myReport.Format" #, "myReport.Dir" ) env_Val <- mget(env_Nam, envir=ContData.env) df_Env <- data.frame(cbind(env_Nam, env_Val), row.names = NULL) names(df_Env) <- c("Names", "Values") knitr::kable(df_Env, caption = kbl_caption)
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