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28 commits ahead of main branch for Erik to accept #168

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8b0bde9
Updating code after EPA internal review part 2
m-pennino Sep 26, 2024
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Updating code after EPA internal review part 4
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Updating code after EPA internal review part 5
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Updating code after EPA internal review part 6
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Updating code after EPA internal review part 7
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Updating code after EPA internal review part 8
m-pennino Sep 26, 2024
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Updating code after EPA internal review part 9
m-pennino Sep 26, 2024
90f9625
Updating code after EPA internal review part 10
m-pennino Sep 26, 2024
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Updating code after EPA internal review part 11
m-pennino Sep 26, 2024
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Updating code after EPA internal review part 12
m-pennino Sep 26, 2024
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Updating code after EPA internal review part 13
m-pennino Sep 26, 2024
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Updating code after EPA internal review part 14
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Updating code after EPA internal review part 15
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Updating code after EPA internal review part 16
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m-pennino Dec 17, 2024
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Updated config files to better locate thresholds
m-pennino Dec 17, 2024
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leppott Feb 11, 2025
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m-pennino Apr 8, 2025
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Merge branch 'main' of https://github.com/USEPA/ContDataQC
m-pennino Apr 8, 2025
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41 changes: 21 additions & 20 deletions inst/shiny-examples/ContDataQC/www/Config.R
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Expand Up @@ -14,6 +14,7 @@
# 20150928
# 20170323, add 3 parameters (Cond, DO, pH)
# 20210106, replace gageheight with waterlevel
# 20230828, updated were QC flag test thresholds, Jen
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ok

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# User defined variable names for input data
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -409,7 +410,7 @@ ContData.env$myFlagVal.Order <- c(ContData.env$myFlagVal.Pass
### Examines values as outliers versus threholds
### if value >= Hi or <= Lo then flagged as "Fail"
ContData.env$myThresh.Gross.Fail.Hi.WaterTemp <- 30
ContData.env$myThresh.Gross.Fail.Lo.WaterTemp <- -2
ContData.env$myThresh.Gross.Fail.Lo.WaterTemp <- -1
ContData.env$myThresh.Gross.Fail.Hi.AirTemp <- 38
ContData.env$myThresh.Gross.Fail.Lo.AirTemp <- -25
ContData.env$myThresh.Gross.Fail.Hi.AirBP <- 15
Expand All @@ -422,9 +423,9 @@ ContData.env$myThresh.Gross.Fail.Hi.Discharge <- 10^5 # dependent upon stream
ContData.env$myThresh.Gross.Fail.Lo.Discharge <- -1 # dependent upon stream size
ContData.env$myThresh.Gross.Fail.Hi.Cond <- 1500 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Lo.Cond <- 10 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Hi.DO <- 20 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.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 <- 20 # 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
Expand All @@ -442,7 +443,7 @@ ContData.env$myThresh.Gross.Fail.Lo.Salinity <- 2
### Examines values as outliers versus threholds
### if value >= Hi or <= Lo then flagged as "Suspect"
ContData.env$myThresh.Gross.Suspect.Hi.WaterTemp <- 25
ContData.env$myThresh.Gross.Suspect.Lo.WaterTemp <- -0.1
ContData.env$myThresh.Gross.Suspect.Lo.WaterTemp <- -0.5
ContData.env$myThresh.Gross.Suspect.Hi.AirTemp <- 35
ContData.env$myThresh.Gross.Suspect.Lo.AirTemp <- -23
ContData.env$myThresh.Gross.Suspect.Hi.AirBP <- 14.8
Expand All @@ -455,10 +456,10 @@ ContData.env$myThresh.Gross.Suspect.Hi.Discharge <- 10^3 # dependent upon str
ContData.env$myThresh.Gross.Suspect.Lo.Discharge <- -1 # dependent upon stream size
ContData.env$myThresh.Gross.Suspect.Hi.Cond <- 1200 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Lo.Cond <- 20 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Hi.DO <- 18 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Hi.DO <- 16 # this threshold has not been closely evaluated
ContData.env$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$myThresh.Gross.Suspect.Lo.DO.adj <- 2 # this threshold has not been closely evaluated
ContData.env$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
Expand All @@ -476,8 +477,8 @@ ContData.env$myThresh.Gross.Suspect.Lo.Salinity <- 3
### Examines difference between consecutive measurements
### if delta >= Hi then flagged as "Fail"
### if delta >= Lo then flagged as "Suspect"
ContData.env$myThresh.Spike.Hi.WaterTemp <- 1.5
ContData.env$myThresh.Spike.Lo.WaterTemp <- 1
ContData.env$myThresh.Spike.Hi.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
Expand All @@ -490,10 +491,10 @@ ContData.env$myThresh.Spike.Hi.Discharge <- 10^4 # dependent upon stream size
ContData.env$myThresh.Spike.Lo.Discharge <- 10^3 # dependent upon stream size
ContData.env$myThresh.Spike.Hi.Cond <- 10 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Lo.Cond <- 5 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Hi.DO <- 10 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Lo.DO <- 5 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Hi.DO.adj <- 10 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Lo.DO.adj <- 5 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Hi.DO <- 4 # this threshold has not been closely evaluated
ContData.env$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$myThresh.Spike.Hi.pH <- 10 # this threshold has not been closely evaluated
Expand All @@ -510,7 +511,7 @@ ContData.env$myThresh.Spike.Lo.Salinity <- 3
## Rate of Change (relative change)
### Examines SD over "period" and difference in consecutive values
### If delta >= SD.number * SD then flagged as "Suspect"
ContData.env$myDefault.RoC.SD.number <- 3
ContData.env$myDefault.RoC.SD.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$myDefault.RoC.SD.period
Expand Down Expand Up @@ -550,11 +551,11 @@ ContData.env$myThresh.RoC.SD.period.Salinity <- ContData.env$myDefault.RoC.S
ContData.env$myDefault.Flat.Hi <- 30 # maximum is myThresh.Flat.MaxComp
ContData.env$myDefault.Flat.Lo <- 15
ContData.env$myDefault.Flat.Tolerance <- 0.01 # set to one sigdig less than measurements. Check with fivenum(x)
ContData.env$myThresh.Flat.Hi.WaterTemp <- 30
ContData.env$myThresh.Flat.Lo.WaterTemp <- 20
ContData.env$myThresh.Flat.Hi.WaterTemp <- 100
ContData.env$myThresh.Flat.Lo.WaterTemp <- 60
ContData.env$myThresh.Flat.Tolerance.WaterTemp <- 0.01
ContData.env$myThresh.Flat.Hi.AirTemp <- 20
ContData.env$myThresh.Flat.Lo.AirTemp <- 15
ContData.env$myThresh.Flat.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
Expand All @@ -563,7 +564,7 @@ ContData.env$myThresh.Flat.Hi.WaterP <- 15
ContData.env$myThresh.Flat.Lo.WaterP <- 10
ContData.env$myThresh.Flat.Tolerance.WaterP <- 0.001
ContData.env$myThresh.Flat.Hi.SensorDepth <- 60
ContData.env$myThresh.Flat.Lo.SensorDepth <- 20
ContData.env$myThresh.Flat.Lo.SensorDepth <- 30
ContData.env$myThresh.Flat.Tolerance.SensorDepth <- 0.0
ContData.env$myThresh.Flat.Hi.Discharge <- ContData.env$myDefault.Flat.Hi * 2
ContData.env$myThresh.Flat.Lo.Discharge <- ContData.env$myDefault.Flat.Lo * 2
Expand Down Expand Up @@ -592,8 +593,8 @@ ContData.env$myThresh.Flat.Tolerance.Chlorophylla <- 0.01
ContData.env$myThresh.Flat.Hi.WaterLevel <- ContData.env$myThresh.Flat.Hi.SensorDepth
ContData.env$myThresh.Flat.Lo.WaterLevel <- ContData.env$myThresh.Flat.Lo.SensorDepth
ContData.env$myThresh.Flat.Tolerance.WaterLevel <- ContData.env$myThresh.Flat.Tolerance.SensorDepth
ContData.env$myThresh.Flat.Hi.Salinity <- ContData.env$myThresh.Flat.Hi.SensorDepth * 2
ContData.env$myThresh.Flat.Lo.Salinity <- ContData.env$myThresh.Flat.Lo.SensorDepth * 2
ContData.env$myThresh.Flat.Hi.Salinity <- ContData.env$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$myThresh.Flat.Hi.WaterTemp
Expand Down
41 changes: 21 additions & 20 deletions inst/shiny-examples/ContDataQC/www/Config_Default.R
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
# 20150928
# 20170323, add 3 parameters (Cond, DO, pH)
# 20210106, replace gageheight with waterlevel
# 20230828, updated were QC flag test thresholds, Jen
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# User defined variable names for input data
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -409,7 +410,7 @@ ContData.env$myFlagVal.Order <- c(ContData.env$myFlagVal.Pass
### Examines values as outliers versus threholds
### if value >= Hi or <= Lo then flagged as "Fail"
ContData.env$myThresh.Gross.Fail.Hi.WaterTemp <- 30
ContData.env$myThresh.Gross.Fail.Lo.WaterTemp <- -2
ContData.env$myThresh.Gross.Fail.Lo.WaterTemp <- -1
ContData.env$myThresh.Gross.Fail.Hi.AirTemp <- 38
ContData.env$myThresh.Gross.Fail.Lo.AirTemp <- -25
ContData.env$myThresh.Gross.Fail.Hi.AirBP <- 15
Expand All @@ -422,9 +423,9 @@ ContData.env$myThresh.Gross.Fail.Hi.Discharge <- 10^5 # dependent upon stream
ContData.env$myThresh.Gross.Fail.Lo.Discharge <- -1 # dependent upon stream size
ContData.env$myThresh.Gross.Fail.Hi.Cond <- 1500 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Lo.Cond <- 10 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Hi.DO <- 20 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Hi.DO <- 18 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Lo.DO <- 1 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Fail.Hi.DO.adj <- 20 # this threshold has not been closely evaluated
ContData.env$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$myThresh.Gross.Fail.Lo.DO.pctsat <- -1 # this threshold has not been closely evaluated
Expand All @@ -442,7 +443,7 @@ ContData.env$myThresh.Gross.Fail.Lo.Salinity <- 2
### Examines values as outliers versus threholds
### if value >= Hi or <= Lo then flagged as "Suspect"
ContData.env$myThresh.Gross.Suspect.Hi.WaterTemp <- 25
ContData.env$myThresh.Gross.Suspect.Lo.WaterTemp <- -0.1
ContData.env$myThresh.Gross.Suspect.Lo.WaterTemp <- -0.5
ContData.env$myThresh.Gross.Suspect.Hi.AirTemp <- 35
ContData.env$myThresh.Gross.Suspect.Lo.AirTemp <- -23
ContData.env$myThresh.Gross.Suspect.Hi.AirBP <- 14.8
Expand All @@ -455,10 +456,10 @@ ContData.env$myThresh.Gross.Suspect.Hi.Discharge <- 10^3 # dependent upon str
ContData.env$myThresh.Gross.Suspect.Lo.Discharge <- -1 # dependent upon stream size
ContData.env$myThresh.Gross.Suspect.Hi.Cond <- 1200 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Lo.Cond <- 20 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.Hi.DO <- 18 # this threshold has not been closely evaluated
ContData.env$myThresh.Gross.Suspect.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.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$myThresh.Gross.Suspect.Hi.pH <- 11 # this threshold has not been closely evaluated
Expand All @@ -476,8 +477,8 @@ ContData.env$myThresh.Gross.Suspect.Lo.Salinity <- 3
### Examines difference between consecutive measurements
### if delta >= Hi then flagged as "Fail"
### if delta >= Lo then flagged as "Suspect"
ContData.env$myThresh.Spike.Hi.WaterTemp <- 1.5
ContData.env$myThresh.Spike.Lo.WaterTemp <- 1
ContData.env$myThresh.Spike.Hi.WaterTemp <- 2
ContData.env$myThresh.Spike.Lo.WaterTemp <- 1.5
ContData.env$myThresh.Spike.Hi.AirTemp <- 10
ContData.env$myThresh.Spike.Lo.AirTemp <- 8
ContData.env$myThresh.Spike.Hi.AirBP <- 0.25
Expand All @@ -490,10 +491,10 @@ ContData.env$myThresh.Spike.Hi.Discharge <- 10^4 # dependent upon stream size
ContData.env$myThresh.Spike.Lo.Discharge <- 10^3 # dependent upon stream size
ContData.env$myThresh.Spike.Hi.Cond <- 10 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Lo.Cond <- 5 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Hi.DO <- 10 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Lo.DO <- 5 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Hi.DO.adj <- 10 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Lo.DO.adj <- 5 # this threshold has not been closely evaluated
ContData.env$myThresh.Spike.Hi.DO <- 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
Expand All @@ -510,7 +511,7 @@ ContData.env$myThresh.Spike.Lo.Salinity <- 3
## Rate of Change (relative change)
### Examines SD over "period" and difference in consecutive values
### If delta >= SD.number * SD then flagged as "Suspect"
ContData.env$myDefault.RoC.SD.number <- 3
ContData.env$myDefault.RoC.SD.number <- 6
ContData.env$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
Expand Down Expand Up @@ -550,11 +551,11 @@ ContData.env$myThresh.RoC.SD.period.Salinity <- ContData.env$myDefault.RoC.S
ContData.env$myDefault.Flat.Hi <- 30 # maximum is myThresh.Flat.MaxComp
ContData.env$myDefault.Flat.Lo <- 15
ContData.env$myDefault.Flat.Tolerance <- 0.01 # set to one sigdig less than measurements. Check with fivenum(x)
ContData.env$myThresh.Flat.Hi.WaterTemp <- 30
ContData.env$myThresh.Flat.Lo.WaterTemp <- 20
ContData.env$myThresh.Flat.Hi.WaterTemp <- 100
ContData.env$myThresh.Flat.Lo.WaterTemp <- 60
ContData.env$myThresh.Flat.Tolerance.WaterTemp <- 0.01
ContData.env$myThresh.Flat.Hi.AirTemp <- 20
ContData.env$myThresh.Flat.Lo.AirTemp <- 15
ContData.env$myThresh.Flat.Hi.AirTemp <- 60
ContData.env$myThresh.Flat.Lo.AirTemp <- 30
ContData.env$myThresh.Flat.Tolerance.AirTemp <- 0.01
ContData.env$myThresh.Flat.Hi.AirBP <- 15
ContData.env$myThresh.Flat.Lo.AirBP <- 10
Expand All @@ -563,7 +564,7 @@ ContData.env$myThresh.Flat.Hi.WaterP <- 15
ContData.env$myThresh.Flat.Lo.WaterP <- 10
ContData.env$myThresh.Flat.Tolerance.WaterP <- 0.001
ContData.env$myThresh.Flat.Hi.SensorDepth <- 60
ContData.env$myThresh.Flat.Lo.SensorDepth <- 20
ContData.env$myThresh.Flat.Lo.SensorDepth <- 30
ContData.env$myThresh.Flat.Tolerance.SensorDepth <- 0.0
ContData.env$myThresh.Flat.Hi.Discharge <- ContData.env$myDefault.Flat.Hi * 2
ContData.env$myThresh.Flat.Lo.Discharge <- ContData.env$myDefault.Flat.Lo * 2
Expand Down Expand Up @@ -592,8 +593,8 @@ ContData.env$myThresh.Flat.Tolerance.Chlorophylla <- 0.01
ContData.env$myThresh.Flat.Hi.WaterLevel <- ContData.env$myThresh.Flat.Hi.SensorDepth
ContData.env$myThresh.Flat.Lo.WaterLevel <- ContData.env$myThresh.Flat.Lo.SensorDepth
ContData.env$myThresh.Flat.Tolerance.WaterLevel <- ContData.env$myThresh.Flat.Tolerance.SensorDepth
ContData.env$myThresh.Flat.Hi.Salinity <- ContData.env$myThresh.Flat.Hi.SensorDepth * 2
ContData.env$myThresh.Flat.Lo.Salinity <- ContData.env$myThresh.Flat.Lo.SensorDepth * 2
ContData.env$myThresh.Flat.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
Expand Down
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