Health impacts of waterborne microbes: Difference between revisions

Latest revision as of 10:10, 11 September 2019

This page is a knowledge crystal of subtype variable. The page identifier is Op_en7957
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Question

What are the health impacts of waterborne microbes in drinking water?

Answer

Rationale

Data

Health impacts of waterborne microbes depends on the following parameters:

Exposure to pathogens
- Drinking water consumption
- Concentrations of pathogens in drinking water

Calculations

RCode

Daily cold tap water use of Finns

+ Show code - Hide code

# This is code Op_en7957/consumption on page [[Health impacts of waterborne microbes]]
library(OpasnetUtils)

Wateruse = Ovariable("Wateruse", data = data.frame(WateruseResult = 1153))

objects.store(Wateruse)
cat("Ovariable Wateruse saved. \n")

+ Show code - Hide code

# This is code Op_en7957/rawconsumption in page [[Health impacts of waterborne microbes]]
library(OpasnetUtils)

RawConsumption <- Ovariable("RawConsumption",
                            dependencies = data.frame(Name = c("Wateruse"), Ident = c("Op_en7957/consumption")),
                            formula = function(...){
                              return(2 / 3 * Wateruse / 1000)  # 2/3 consumed unboiled. Converted into liters.
                            }
)

objects.store(RawConsumption)
cat("Ovariable RawConsumption saved. \n")

Log decrease of concentration of microbes in drinking water due to water treatment

+ Show code - Hide code

#This is code "Op_en7957/logdecrease" on page [[Health impacts of waterborne microbes]]
library(OpasnetUtils)

	
MicrobeLogDecrease <- Ovariable("MicrobeLogDecrease",
                                dependencies=data.frame(
                                  Name=c("TreatmentEfficiency", "ChlorineEfficiency", "OzoneEfficiency", "UVEfficiency"),
                                  Ident=c("Op_en7954/variable", "Op_en7956/efficiency", "Op_en7955/ozefficiency", "Op_en7955/uvefficiency")
                                ),
                                formula=function(...){
                                  # Calculate the total log decrease of pathogen concentration from treatment methods
                                  MicrobeLogDecrease <- oapply(TreatmentEfficiency, cols="TreatmentMethod", FUN=sum)
                                  # Then sum that with the disinfection methods to get the total microbe log decrease
                                  MicrobeLogDecrease <- MicrobeLogDecrease+ChlorineEfficiency+OzoneEfficiency+UVEfficiency
                                  
                                  return(MicrobeLogDecrease)
                                }


)

objects.store(MicrobeLogDecrease)
cat("Ovariable MicrobeLogDecrease saved. \n")

Pathogen concentration in drinking water

+ Show code - Hide code

#This is code "Op_en7957/pathconcentration" on page [[Health impacts of waterborne microbes]]
library(OpasnetUtils)

TreatedConcentration <- Ovariable("TreatedConcentration", dependencies = data.frame(
                                  Name=c("RawConcentration", "MicrobeLogDecrease"),
                                  Ident=c("Op_en7953/variable", "Op_en7957/logdecrease")
                                  ),
                                  formula = function(...){

                                    # Calculate the concentration of bacteria after treatment from log decrease
                                    out <- RawConcentration * 10 ^(-1*(MicrobeLogDecrease))
                                    
                                    return(out)
                                  })

objects.store(TreatedConcentration)

cat("Ovariable TreatedConcentration saved. \n")

The amount of pathogens an average water consumer is exposed to in a day

+ Show code - Hide code

#This is code "Op_en7957/exposure" on page [[Health impacts of waterborne microbes]]
library(OpasnetUtils)

exposure <- Ovariable("exposure", 
                      dependencies = data.frame(
                        Name = c("TreatedConcentration", "RawConsumption"),
                        Ident = c("Op_en7957/pathconcentration", "Op_en7957/rawconsumption")
                        ),
                      formula = function(...){
                        out <- TreatedConcentration * RawConsumption
                        colnames(out@output)[colnames(out@output) == "Pathogen"] <- "Exposure_agent"
                        return(out)
                      }
)

objects.store(exposure)
cat("Ovariable exposure saved. \n")

@@ Line 28: / Line 28: @@
 Daily cold tap water use of Finns
-<rcode name="consumption">
+<rcode
+       name="consumption"
+       label="Initialize water use"
+       embed=1
+>
 # This is code Op_en7957/consumption on page [[Health impacts of waterborne microbes]]
 library(OpasnetUtils)
@@ Line 34: / Line 38: @@
 Wateruse = Ovariable("Wateruse", data = data.frame(WateruseResult = 1153))
-objects.save(Wateruse)
+objects.store(Wateruse)
+cat("Ovariable Wateruse saved. \n")
-oprint(Wateruse)
 </rcode>
+<rcode
-<rcode name="rawconsumption">
+        name="rawconsumption"
+        label="Initialize raw consumption"
+	embed=1
+>
 # This is code Op_en7957/rawconsumption in page [[Health impacts of waterborne microbes]]
 library(OpasnetUtils)
@@ Line 52: / Line 59: @@
 objects.store(RawConsumption)
+cat("Ovariable RawConsumption saved. \n")
-oprint(RawConsumption)
 </rcode>
-Concentrations of pathogens in drinking water
+Log decrease of concentration of microbes in drinking water due to water treatment
 <rcode
-	name="pathconcentration"
+	name="logdecrease"
-	label="Initialize variable"
+	label="Initialize microbe log decrease"
 	graphics="1"
+	embed=1
 >
-#This is code "Op_en7957/pathconcentration" on page [[Health impacts of waterborne microbes]]
+#This is code "Op_en7957/logdecrease" on page [[Health impacts of waterborne microbes]]
 library(OpasnetUtils)
-dependencies <- data.frame(
-		Name = c("RawConcentration", "Disinfection", "TreatmentEfficiency", "ChlorineEfficiency"),
+MicrobeLogDecrease <- Ovariable("MicrobeLogDecrease",
-		Ident = c("Op_en7953/variable", "Op_en7955/variable", "Op_en7954/variable", "Op_en7956/efficiency")
+                                dependencies=data.frame(
+                                  Name=c("TreatmentEfficiency", "ChlorineEfficiency", "OzoneEfficiency", "UVEfficiency"),
+                                  Ident=c("Op_en7954/variable", "Op_en7956/efficiency", "Op_en7955/ozefficiency", "Op_en7955/uvefficiency")
+                                ),
+                                formula=function(...){
+                                  # Calculate the total log decrease of pathogen concentration from treatment methods
+                                  MicrobeLogDecrease <- oapply(TreatmentEfficiency, cols="TreatmentMethod", FUN=sum)
+                                  # Then sum that with the disinfection methods to get the total microbe log decrease
+                                  MicrobeLogDecrease <- MicrobeLogDecrease+ChlorineEfficiency+OzoneEfficiency+UVEfficiency
+                                  return(MicrobeLogDecrease)
+                                }
 )
-funktio <- function(...) {
+objects.store(MicrobeLogDecrease)
+cat("Ovariable MicrobeLogDecrease saved. \n")
+</rcode>
-	#MicrobeLogDecrease <- combine(Disinfection, TreatmentEfficiency, ChlorineEfficiency, name = "MicrobeLogDecrease")
+Pathogen concentration in drinking water
-	#MicrobeLogDecrease@output[["TreatmentMethod"]][
+<rcode
-	#		MicrobeLogDecrease@output[["MicrobeLogDecreaseSource"]] == "ChlorineEfficiencyF"
+	name="pathconcentration"
-	#] <- "Chlorination"
+	label="Initialize pathogen concentration"
+	graphics="1"
-	#MicrobeLogDecrease <- oapply(MicrobeLogDecrease, cols = c("TreatmentMethod", "ChlorineDoseSource"), FUN = sum, na.rm = TRUE)
+	embed=1
-	# Varo laskemasta kloorausta monesti
+>
+#This is code "Op_en7957/pathconcentration" on page [[Health impacts of waterborne microbes]]
-	#MicrobeLogDecrease@output <- fillna(MicrobeLogDecrease@output, colnames(MicrobeLogDecrease@output)[MicrobeLogDecrease@marginal])
+library(OpasnetUtils)
-	MicrobeLogDecrease <- orbind(Disinfection, TreatmentEfficiency)
+TreatedConcentration <- Ovariable("TreatedConcentration", dependencies = data.frame(
-	MicrobeLogDecrease <- orbind(MicrobeLogDecrease, ChlorineEfficiency)
+                                  Name=c("RawConcentration", "MicrobeLogDecrease"),
+                                  Ident=c("Op_en7953/variable", "Op_en7957/logdecrease")
-	MicrobeLogDecrease <- fillna(MicrobeLogDecrease, grep("Source$", colnames(MicrobeLogDecrease)))
+                                  ),
+                                  formula = function(...){
-	MicrobeLogDecrease$DisinfectionResult[is.na(MicrobeLogDecrease$DisinfectionResult)] <- 0
-	MicrobeLogDecrease$TreatmentEfficiencyResult[is.na(MicrobeLogDecrease$TreatmentEfficiencyResult)] <- 0
-	MicrobeLogDecrease$ChlorineEfficiencyResult[is.na(MicrobeLogDecrease$ChlorineEfficiencyResult)] <- 0
-	MicrobeLogDecrease$MicrobeLogDecreaseResult <- MicrobeLogDecrease$DisinfectionResult +
-			MicrobeLogDecrease$TreatmentEfficiencyResult + MicrobeLogDecrease$ChlorineEfficiencyResult
-	MicrobeLogDecrease <- Ovariable(
-		"MicrobeLogDecrease",
-		dependencies = data.frame(
-			Name = c("Disinfection", "TreatmentEfficiency", "ChlorineEfficiency")
-		),
-		output = MicrobeLogDecrease
-	)
-	MicrobeLogDecrease <- CheckMarginals(MicrobeLogDecrease, verbose = FALSE)
-	MicrobeLogDecrease <- oapply(MicrobeLogDecrease, cols = c("TreatmentMethod"), FUN = sum, na.rm = TRUE)
-	out <- RawConcentration * 10 ^(-1*(MicrobeLogDecrease))
-	return(out@output)
-}
-TreatedConcentration <- Ovariable("TreatedConcentration", dependencies = dependencies, formula = funktio)
+                                    # Calculate the concentration of bacteria after treatment from log decrease
+                                    out <- RawConcentration * 10 ^(-1*(MicrobeLogDecrease))
+                                    return(out)
+                                  })
 objects.store(TreatedConcentration)
+cat("Ovariable TreatedConcentration saved. \n")
 </rcode>
@@ Line 125: / Line 128: @@
 The amount of pathogens an average water consumer is exposed to in a day
-<rcode name="exposure">
+<rcode
+         name="exposure"
+         label="Initialize exposure"
+	 embed=1
+>
 #This is code "Op_en7957/exposure" on page [[Health impacts of waterborne microbes]]
 library(OpasnetUtils)
-Exposure <- Ovariable("Exposure",
+exposure <- Ovariable("exposure",
                        dependencies = data.frame(
                          Name = c("TreatedConcentration", "RawConsumption"),
@@ Line 135: / Line 142: @@
                          ),
                        formula = function(...){
-                         return(TreatedConcentration * RawConcumption)
+                        out <- TreatedConcentration * RawConsumption
+                        colnames(out@output)[colnames(out@output) == "Pathogen"] <- "Exposure_agent"
+                         return(out)
                        }
 )
-objects.store(Exposure)
+objects.store(exposure)
+cat("Ovariable exposure saved. \n")
 </rcode>

Health impacts of waterborne microbes: Difference between revisions

Latest revision as of 10:10, 11 September 2019

Contents

Question

Answer

Rationale

Data

Calculations

RCode

See also

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