Updated examples to not use interactive=FALSE. Rebuilt package.

R/mergeReport.r

@@ -11,9 +11,9 @@
 #' @seealso \code{\link{getDVData}}, \code{\link{populateSampleColumns}}
 #' @examples
 #' # These examples require an internet connection to run
-#' Daily <- getDVData('01594440','00060', '1985-01-01', '1985-03-31', interactive=FALSE)
-#' Sample <- getSampleData('01594440','01075', '1985-01-01', '1985-03-31', interactive=FALSE)
-#' Sample <- mergeReport(interactive=FALSE)
+#' Daily <- getDVData('01594440','00060', '1985-01-01', '1985-03-31')
+#' Sample <- getSampleData('01594440','01075', '1985-01-01', '1985-03-31')
+#' Sample <- mergeReport()
 mergeReport<-function(localDaily = Daily, localSample = Sample, interactive=TRUE){
   if (interactive){
     dataOverview(localDaily, localSample)  

R/populateDaily.r

@@ -16,7 +16,7 @@
 #' value <- c(1,2,3)
 #' code <- c("","","")
 #' dataInput <- data.frame(dateTime, value, code, stringsAsFactors=FALSE)
-#' Daily <- populateDaily(dataInput, 2, interactive=FALSE)
+#' Daily <- populateDaily(dataInput, 2)
 populateDaily <- function(rawData,qConvert,interactive=TRUE){  # rawData is a dataframe with at least dateTime, value, code
   
 #   require(zoo)
@@ -55,12 +55,12 @@ populateDaily <- function(rawData,qConvert,interactive=TRUE){  # rawData is a da
       zeroNums <- length(which(localDaily$Q == 0))
       
       if (negNums > 0) {
-        cat("There were ", as.character(negNums), " negative flow days \n")
+        cat("There were", as.character(negNums), "negative flow days \n")
         cat("Negative values are not supported in the EGRET package\n")
       }
       
       if (zeroNums > 0){
-        cat("There were ", as.character(zeroNums), " zero flow days \n")
+        cat("There were", as.character(zeroNums), "zero flow days \n")
       }
       
       cat("All days had",as.character(qshift),"cms added to the discharge value.\n")
@@ -90,7 +90,7 @@ populateDaily <- function(rawData,qConvert,interactive=TRUE){  # rawData is a da
   dataPoints <- nrow(localDaily)
   difference <- (localDaily$Julian[dataPoints] - localDaily$Julian[1])+1  
   if (interactive){
-    cat("There are ", as.character(dataPoints), "data points, and ", as.character(difference), "days.\n")
+    cat("There are", as.character(dataPoints), "data points, and", as.character(difference), "days.\n")
 
     #these next two lines show the user where the gaps in the data are if there are any
     n<-nrow(localDaily)

R/populateParameterINFO.r

@@ -16,7 +16,7 @@
 #' INFO$param.units <- parameterData$parameter_units
 #' INFO$paramShortName <- parameterData$srsname
 #' INFO$paramNumber <- parameterData$parameter_cd
-#' INFO <- populateParameterINFO(parameterCd,interactive=FALSE)
+#' INFO <- populateParameterINFO(parameterCd)
 populateParameterINFO <- function(parameterCd, localINFO=INFO, interactive=TRUE){
   if (nzchar(parameterCd)){
     if(interactive){

R/populateSiteINFO.r

@@ -11,7 +11,7 @@
 #' #This example requires an internet connection to run
 #' INFO <- getSiteFileData('01594440')
 #' siteNumber <- "01594440"
-#' siteINFO <- populateSiteINFO(INFO, siteNumber,interactive=FALSE)
+#' siteINFO <- populateSiteINFO(INFO, siteNumber)
 populateSiteINFO <- function(INFO, siteNumber,interactive=TRUE){
   if (nzchar(siteNumber)){
     

R/renameColumns.R

@@ -7,20 +7,9 @@
 #' @return rawData dataframe with improved column names
 #' @export
 #' @examples
-#' # These examples require an internet connection to run
-#' siteNumber <- '05114000'
-#' ParameterCd <- c('00060','00065')
-#' StartDate <- as.character(Sys.Date())
-#' EndDate <- as.character(Sys.Date())
-#' # These examples require an internet connection to run
-#' rawData <- retrieveUnitNWISData(siteNumber,ParameterCd,StartDate,EndDate,interactive=FALSE)
-#' rawData <- renameColumns(rawData)
-#' rawData2 <- retrieveNWISData(siteNumber,c("00010","00060","00300"),"2001-01-01","2002-01-01",StatCd=c("00001","00003"),interactive=FALSE)
+#' # This example requires an internet connection to run
+#' rawData2 <- retrieveNWISData(siteNumber,c("00010","00060","00300"),"2001-01-01","2002-01-01",StatCd=c("00001","00003"))
 #' rawData2 <- renameColumns(rawData2)
-#' site <- '04027000'
-#' pCodes <- c("00010","00060","00095","00300","00400","63680")
-#' rawData3 <- retrieveUnitNWISData(site,pCodes,StartDate,EndDate,interactive=FALSE)
-#' rawData3 <- renameColumns(rawData3)
 renameColumns <- function(rawData){
   
   columnNames <- names(rawData)
@@ -62,6 +51,10 @@ renameColumns <- function(rawData){
   dataColCDS <- paste(dataColNames, "_cd")
   columnNames[which(columnNames %in% dataCol_names)] <- dataColNames
   columnNames[which(columnNames %in% dataCol_cds)] <- dataColCDS
+  
+  columnNames <- gsub("[$,. ]","_",columnNames)
+  columnNames <- gsub("__","_",columnNames)
+  
   names(rawData) <- columnNames
   
   return(rawData)

R/retrieveNWISData.r

@@ -23,9 +23,9 @@
 #' endDate <- '2012-06-30'
 #' pCode <- "00060"
 #' rawDailyQ <- retrieveNWISData(siteNumber,pCode, startDate, endDate)
-#' rawDailyTemperature <- retrieveNWISData(siteNumber,'00010', startDate, endDate, StatCd='00001',interactive=FALSE)
-#' rawDailyTemperatureTSV <- retrieveNWISData(siteNumber,'00010', startDate, endDate, StatCd='00001',format="tsv",interactive=FALSE)
-#' rawDailyQAndTempMeanMax <- retrieveNWISData(siteNumber,c('00010','00060'), startDate, endDate, StatCd=c('00001','00003'), interactive=FALSE)
+#' rawDailyTemperature <- retrieveNWISData(siteNumber,'00010', startDate, endDate, StatCd='00001')
+#' rawDailyTemperatureTSV <- retrieveNWISData(siteNumber,'00010', startDate, endDate, StatCd='00001',format="tsv")
+#' rawDailyQAndTempMeanMax <- retrieveNWISData(siteNumber,c('00010','00060'), startDate, endDate, StatCd=c('00001','00003'))
 retrieveNWISData <- function (siteNumber,ParameterCd,StartDate,EndDate,StatCd="00003",format="tsv",interactive=TRUE){  
   
   url <- constructNWISURL(siteNumber,ParameterCd,StartDate,EndDate,"dv",statCd=StatCd,format=format)

R/retrieveNWISqwData.r

@@ -21,7 +21,7 @@
 #' # To get data in Sample dataframe format:
 #' data <- rawNWISqwData[,names(rawNWISqwData) != "site"]
 #' data$dateTime <- as.Date(data$dateTime)
-#' compressedData <- compressData(data, interactive=interactive)
+#' compressedData <- compressData(data)
 #' Sample <- populateSampleColumns(compressedData)
 retrieveNWISqwData <- function (siteNumber,pCodes,startDate,endDate){  
   

R/retrieveUnitNWISData.r

@@ -21,8 +21,8 @@
 #' StartDate <- as.character(Sys.Date())
 #' EndDate <- as.character(Sys.Date())
 #' # These examples require an internet connection to run
-#' rawData <- retrieveUnitNWISData(siteNumber,ParameterCd,StartDate,EndDate,interactive=FALSE)
-#' rawData2 <- retrieveUnitNWISData(siteNumber,ParameterCd,StartDate,EndDate,"tsv",interactive=FALSE)
+#' rawData <- retrieveUnitNWISData(siteNumber,ParameterCd,StartDate,EndDate)
+#' rawData2 <- retrieveUnitNWISData(siteNumber,ParameterCd,StartDate,EndDate,"tsv")
 retrieveUnitNWISData <- function (siteNumber,ParameterCd,StartDate,EndDate,format="xml",interactive=TRUE){  
   
   url <- constructNWISURL(siteNumber,ParameterCd,StartDate,EndDate,"uv",format=format)

man/checkStartEndDate.Rd

@@ -24,7 +24,7 @@
 \examples{
 startDate <- '1985-01-01'
 endDate <- '1990-01-01'
-checkStartEndDate(startDate, endDate, interactive = FALSE)
+checkStartEndDate(startDate, endDate)
 }
 \keyword{WRTDS}
 \keyword{flow}

man/compressData.Rd

@@ -34,7 +34,7 @@ value2 <- c(2,3,4)
 comment3 <- c("","","<")
 value3 <- c(3,4,5)
 dataInput <- data.frame(dateTime, comment1, value1, comment2, value2, comment3, value3, stringsAsFactors=FALSE)
-compressData(dataInput, interactive=FALSE)
+compressData(dataInput)
 }
 \keyword{WRTDS}
 \keyword{flow}

man/constructNWISURL.Rd

@@ -4,7 +4,7 @@
 \usage{
   constructNWISURL(siteNumber, parameterCd, startDate,
     endDate, service, statCd = "00003", format = "xml",
-    interactive = FALSE)
+    interactive = TRUE)
 }
 \arguments{
   \item{siteNumber}{string or vector of strings USGS site
@@ -40,7 +40,7 @@
   expected. The default is therefore "xml".}
 
   \item{interactive}{logical Option for interactive mode.
-  If true, there is user interaction for error handling and
+  If TRUE, there is user interaction for error handling and
   data checks.}
 }
 \value{

man/formatCheckParameterCd.Rd

@@ -21,7 +21,7 @@
 }
 \examples{
 pCode <- '01234'
-formatCheckParameterCd(pCode, interactive = FALSE)
+formatCheckParameterCd(pCode)
 }
 \keyword{WRTDS}
 \keyword{flow}

man/formatCheckSiteNumber.Rd

@@ -20,7 +20,7 @@
 }
 \examples{
 site<- '01234567'
-formatCheckSiteNumber(site, interactive = FALSE)
+formatCheckSiteNumber(site)
 }
 \keyword{WRTDS}
 \keyword{flow}

man/getDVData.Rd

@@ -51,7 +51,7 @@
 }
 \examples{
 # These examples require an internet connection to run
-Daily <- getDVData('01594440','00060', '1985-01-01', '1985-03-31', interactive=FALSE)
+Daily <- getDVData('01594440','00060', '1985-01-01', '1985-03-31')
 }
 \seealso{
   \code{\link{retrieveNWISData}},

man/getDataAvailability.Rd

@@ -23,7 +23,7 @@
 }
 \examples{
 # These examples require an internet connection to run
-availableData <- getDataAvailability('05114000',interactive=FALSE)
+availableData <- getDataAvailability('05114000')
 }
 \keyword{USGS}
 \keyword{data}

man/getDataFromFile.Rd

@@ -29,9 +29,9 @@
 \examples{
 # Examples of how to use getDataFromFile:
 # Change the file path and file name to something meaningful:
-#filePath <- '~/RData/'  # Sample format
+filePath <- '~/RData/'  # Sample format
 fileName <- 'ChoptankRiverFlow.txt'
-#getDataFromFile(filePath,fileName, separator="\\t")
+\dontrun{getDataFromFile(filePath,fileName, separator="\\t")}
 }
 \keyword{data}
 \keyword{file}

man/getMetaData.Rd

@@ -37,7 +37,7 @@
 \examples{
 # These examples require an internet connection to run
 # Automatically gets information about site 05114000 and temperature, no interaction with user
-INFO <- getMetaData('05114000','00010',interactive=FALSE)
+INFO <- getMetaData('05114000','00010')
 }
 \keyword{USGS}
 \keyword{WRTDS}

man/getQWData.Rd

@@ -44,7 +44,7 @@
 # These examples require an internet connection to run
 rawProcessedSample <- getQWData('01594440','01075', '1985-01-01', '1985-03-31')
 rawProcessedSampleAll <- getQWData('05114000','', '1985-01-01', '1985-03-31')
-rawProcessedSampleSelect <- getQWData('05114000','00915;00931', '1985-01-01', '1985-04-30', interactive=FALSE)
+rawProcessedSampleSelect <- getQWData('05114000','00915;00931', '1985-01-01', '1985-04-30')
 }
 \keyword{USGS}
 \keyword{data}

man/getQWDataFromFile.Rd

@@ -33,7 +33,7 @@
 # Change the file path and file name to something meaningful:
 filePath <- '~/RData/'  # Sample format
 fileName <- 'ChoptankRiverNitrate.csv'
-#rawSampleData <- getQWDataFromFile(filePath,fileName, separator=";")
+\dontrun{rawSampleData <- getQWDataFromFile(filePath,fileName, separator=";")}
 }
 \keyword{data}
 \keyword{file}