Merge 0a7647b into 1cfadd9

DOI-USGS · Oct 16, 2017 · fd3a2ce · fd3a2ce
2 parents 1cfadd9 + 0a7647b
commit fd3a2ce
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Showing 3 changed files with 19 additions and 17 deletions.
diff --git a/R/compressData.r b/R/compressData.r
@@ -68,7 +68,7 @@ compressData <- function(data, verbose = TRUE, interactive=NULL){
   returnDataFrame$ConcLow <- as.numeric(lowConcentration)
   returnDataFrame$ConcHigh <- as.numeric(highConcentration)
   Uncen1<-ifelse(returnDataFrame$ConcLow==returnDataFrame$ConcHigh,1,0)
-  returnDataFrame$Uncen<-ifelse(is.na(returnDataFrame$ConcLow),0,Uncen1)
+  returnDataFrame$Uncen<-ifelse(is.na(returnDataFrame$ConcLow)|is.na(returnDataFrame$ConcHigh),0,Uncen1)
 
   flaggedData1 <- returnDataFrame[(returnDataFrame$ConcLow == 0 & returnDataFrame$ConcHigh == 0),]
   returnDataFrame <- returnDataFrame[!(returnDataFrame$ConcLow == 0 & returnDataFrame$ConcHigh == 0),]
@@ -82,17 +82,17 @@ compressData <- function(data, verbose = TRUE, interactive=NULL){
     }
   }
 
-  flaggedData2 <- returnDataFrame[(returnDataFrame$ConcLow > returnDataFrame$ConcHigh),]
-  returnDataFrame <- returnDataFrame[(returnDataFrame$ConcLow <= returnDataFrame$ConcHigh),]
-
-  if (nrow(flaggedData2) > 0){
-    WarningMessage <- paste("Deleted", nrow(flaggedData2), "rows of data because the high concentration was reported lower than the low concentration, the program is unable to interpret that result and is therefore deleting it.")    
-    warning(WarningMessage)
-    if (verbose){
-      cat("Deleted Rows:\n")
-      print(flaggedData2)
-    }
-  }
+  # flaggedData2 <- returnDataFrame[(returnDataFrame$ConcLow > returnDataFrame$ConcHigh),]
+  # returnDataFrame <- returnDataFrame[(returnDataFrame$ConcLow <= returnDataFrame$ConcHigh),]
+  # 
+  # if (nrow(flaggedData2) > 0){
+  #   WarningMessage <- paste("Deleted", nrow(flaggedData2), "rows of data because the high concentration was reported lower than the low concentration, the program is unable to interpret that result and is therefore deleting it.")    
+  #   warning(WarningMessage)
+  #   if (verbose){
+  #     cat("Deleted Rows:\n")
+  #     print(flaggedData2)
+  #   }
+  #}
 
   return(returnDataFrame)
 }
diff --git a/R/populateConcentrations.r b/R/populateConcentrations.r
@@ -14,9 +14,10 @@ populateConcentrations <- function(rawData){  # rawData is a dataframe with valu
   concentrationColumns <- as.data.frame(matrix(ncol=3,nrow=length(rawData$value)))
   colnames(concentrationColumns) <- c('ConcLow','ConcHigh','Uncen')  
   concentrationColumns$ConcLow <- as.numeric(ifelse((rawData$code!="<" | is.na(rawData$code)),rawData$value,0))
-  concentrationColumns$ConcHigh <- as.numeric(rawData$value)
+  concentrationColumns$ConcHigh <- as.numeric(ifelse((rawData$code != ">" | is.na(rawData$code)), rawData$value, 0))
   tempConcLow<-ifelse((rawData$code!="<" | is.na(rawData$code)),rawData$value,0)
-  concentrationColumns$Uncen <- ifelse(tempConcLow==0,0,1)  
+  tempConcHigh <- ifelse((rawData$code != ">" | is.na(rawData$code)), rawData$value, 0)
+  concentrationColumns$Uncen <- ifelse(tempConcLow == 0 | tempConcHigh == 0, 0, 1)
   #Add if value = NA?
   return (concentrationColumns)  # returns ConcLow, ConcHigh, Uncen (0 if censored, 1 if uncensored)
 }
diff --git a/R/populateSampleColumns.r b/R/populateSampleColumns.r
@@ -19,14 +19,15 @@ populateSampleColumns <- function(rawData){  # rawData is a dataframe with dateT
   Sample$ConcLow <- rawData$ConcLow
   Sample$ConcHigh <- rawData$ConcHigh
   Sample$Uncen <- rawData$Uncen
-  Sample$ConcAve <- (Sample$ConcLow+Sample$ConcHigh)/2
+  Sample$ConcAve <- ifelse(Sample$ConcHigh == 0, Sample$ConcLow*1.5, (Sample$ConcLow + Sample$ConcHigh)/2)
   Sample$ConcLow <- ifelse((rawData$ConcLow == 0.0 & rawData$Uncen == 0),NA,rawData$ConcLow)
+  Sample$ConcHigh <- ifelse((rawData$ConcHigh == 0 & rawData$Uncen == 0), NA, rawData$ConcHigh)
 
   dateFrame <- populateDateColumns(rawData$dateTime)
   Sample <- cbind(Sample, dateFrame[,-1])
 
   Sample$SinDY <- sin(2*pi*Sample$DecYear)
   Sample$CosDY <- cos(2*pi*Sample$DecYear)
-  Sample2 <- subset(Sample, (!is.na(Sample$ConcHigh)))  # Was just ConcHigh.....
-  return (Sample2)  
+  # Sample2 <- subset(Sample, (!is.na(Sample$ConcHigh)))  # Was just ConcHigh.....
+  return (Sample)  
 }