diff --git a/R/compressData.r b/R/compressData.r index 095d6a15..89a9dca1 100644 --- 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$ConcHigh),] + # + # if (nrow(flaggedData2) > 0){ + # WarningMessage <- paste("Deleted", nrow(flaggedData2), "rows of data because the high concentration was reported lower than the low concentration, the program is unable to interpret that result and is therefore deleting it.") + # warning(WarningMessage) + # if (verbose){ + # cat("Deleted Rows:\n") + # print(flaggedData2) + # } + #} return(returnDataFrame) } diff --git a/R/populateConcentrations.r b/R/populateConcentrations.r index 582e1d70..d437e219 100644 --- a/R/populateConcentrations.r +++ b/R/populateConcentrations.r @@ -14,9 +14,10 @@ populateConcentrations <- function(rawData){ # rawData is a dataframe with valu concentrationColumns <- as.data.frame(matrix(ncol=3,nrow=length(rawData$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 index 38461e71..5fc40e35 100644 --- 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) }