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

DESCRIPTION

@@ -62,7 +62,8 @@ Depends:
 Imports:
     zoo,
     XML,
-    RCurl
+    RCurl,
+    plyr
 Suggests:
     xtable,
     EGRET,

NAMESPACE

@@ -43,3 +43,4 @@ export(retrieveUnitNWISData)
 import(RCurl)
 import(XML)
 import(zoo)
+importFrom(plyr,rbind.fill.matrix)

R/checkStartEndDate.r

@@ -11,7 +11,7 @@
 #' @examples
 #' startDate <- '1985-01-01'
 #' endDate <- '1990-01-01'
-#' checkStartEndDate(startDate, endDate, interactive = FALSE)
+#' checkStartEndDate(startDate, endDate)
 checkStartEndDate <- function(StartDate, EndDate,interactive=TRUE){
   start <- as.Date("1850-01-01")
   end <- as.Date(Sys.Date())

R/compressData.r

@@ -20,7 +20,7 @@
 #' 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)
 compressData <- function(data, interactive=TRUE){  
   
   data <- as.data.frame(data, stringsAsFactors=FALSE)

R/constructNWISURL.r

@@ -13,7 +13,7 @@
 #' @param format string, can be "tsv" or "xml", and is only applicable for daily and unit value requests.  "tsv" returns results faster, but there is a possiblitiy that an incomplete file is returned without warning. XML is slower, 
 #' but will offer a warning if the file was incomplete (for example, if there was a momentary problem with the internet connection). It is possible to safely use the "tsv" option, 
 #' but the user must carefully check the results to see if the data returns matches what is expected. The default is therefore "xml". 
-#' @param interactive logical Option for interactive mode.  If true, there is user interaction for error handling and data checks.
+#' @param interactive logical Option for interactive mode.  If TRUE, there is user interaction for error handling and data checks.
 #' @keywords data import USGS web service
 #' @return url string
 #' @export
@@ -28,7 +28,7 @@
 #' url_qw <- constructNWISURL(siteNumber,c('01075','00029','00453'),startDate,endDate,'qw')
 #' url_wqp <- constructNWISURL(siteNumber,c('01075','00029','00453'),startDate,endDate,'wqp')
 #' url_daily_tsv <- constructNWISURL(siteNumber,pCode,startDate,endDate,'dv',statCd=c("00003","00001"),format="tsv")
-constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,statCd="00003", format="xml",interactive=FALSE){
+constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,statCd="00003", format="xml",interactive=TRUE){
 
   startDate <- formatCheckDate(startDate, "StartDate", interactive=interactive)
   endDate <- formatCheckDate(endDate, "EndDate", interactive=interactive)

R/formatCheckParameterCd.r

@@ -9,7 +9,7 @@
 #' @export
 #' @examples
 #' pCode <- '01234'
-#' formatCheckParameterCd(pCode, interactive = FALSE)
+#' formatCheckParameterCd(pCode)
 formatCheckParameterCd <- function(ParameterCd, interactive=TRUE){     #checks for a 5 digit number
   
   pCodeReturn <- rep(NA,length(ParameterCd))

R/formatCheckSiteNumber.r

@@ -8,7 +8,7 @@
 #' @export
 #' @examples
 #' site<- '01234567'
-#' formatCheckSiteNumber(site, interactive = FALSE)
+#' formatCheckSiteNumber(site)
 formatCheckSiteNumber <- function(siteNumber, interactive=TRUE){  #checks for a 8 digit number
   if (nchar(siteNumber) != 8){
     if (interactive){

R/getDVData.r

@@ -20,7 +20,7 @@
 #' @seealso \code{\link{retrieveNWISData}}, \code{\link{populateDaily}}
 #' @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')
 getDVData <- function (siteNumber,ParameterCd,StartDate,EndDate,interactive=TRUE,convert=TRUE,format="tsv"){
   data <- retrieveNWISData(siteNumber,ParameterCd,StartDate,EndDate,interactive=interactive,format=format)
   

R/getDataAvailability.r

@@ -9,7 +9,7 @@
 #' @export
 #' @examples
 #' # These examples require an internet connection to run
-#' availableData <- getDataAvailability('05114000',interactive=FALSE)
+#' availableData <- getDataAvailability('05114000')
 getDataAvailability <- function(siteNumber="",interactive=TRUE){
   
   # Checking for 8 digit site ID:

R/getDataFromFile.r

@@ -14,9 +14,9 @@
 #' @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")}
 getDataFromFile <- function (filePath,fileName,hasHeader=TRUE,separator=","){
   totalPath <- paste(filePath,fileName,sep="");  
   tmp <- read.delim(  

R/getMetaData.r

@@ -17,7 +17,7 @@
 #' @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')
 getMetaData <- function(siteNumber="", parameterCd="",interactive=TRUE){
   if (nzchar(siteNumber)){
     INFO <- getSiteFileData(siteNumber,interactive=interactive)

R/getQWData.r

@@ -17,7 +17,7 @@
 #' # 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')
 getQWData <- function(siteNumber,ParameterCd,StartDate,EndDate,interactive=TRUE){
   rawSample <- getRawQWData(siteNumber,ParameterCd,StartDate,EndDate,interactive)
   retval <- processQWData(rawSample)

R/getQWDataFromFile.r

@@ -17,7 +17,7 @@
 #' # 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=";")}
 getQWDataFromFile <- function (filePath,fileName,hasHeader=TRUE,separator=","){
   totalPath <- paste(filePath,fileName,sep="");
   tmp <- read.delim(  

R/getRawQWData.r

@@ -5,7 +5,7 @@
 #' A list of statistic codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
 #'
 #' @param siteNumber string USGS site number.  This is usually an 8 digit number
-#' @param ParameterCd string USGS parameter code.  This is usually an 5 digit number. Multiple parameter codes can be inputted with a ';' separator.  Leaving this blank will return all of the measured values during the specified time period.
+#' @param ParameterCd vector of USGS 5-digit parameter code. Leaving this blank will return all of the measured values during the specified time period.
 #' @param StartDate string starting date for data retrieval in the form YYYY-MM-DD.
 #' @param EndDate string ending date for data retrieval in the form YYYY-MM-DD.
 #' @param interactive logical Option for interactive mode.  If true, there is user interaction for error handling and data checks.
@@ -18,7 +18,7 @@
 #' # These examples require an internet connection to run
 #' rawSample <- getRawQWData('01594440','01075', '1985-01-01', '1985-03-31')
 #' rawSampleAll <- getRawQWData('05114000','', '1985-01-01', '1985-03-31')
-#' rawSampleSelect <- getRawQWData('05114000',c('00915','00931'), '1985-01-01', '1985-04-30', interactive=FALSE)
+#' rawSampleSelect <- getRawQWData('05114000',c('00915','00931'), '1985-01-01', '1985-04-30')
 getRawQWData <- function(siteNumber,ParameterCd,StartDate,EndDate,interactive=TRUE){
 
   url <- constructNWISURL(siteNumber,ParameterCd,StartDate,EndDate,"wqp")

R/getSTORETSampleData.R

@@ -17,8 +17,8 @@
 #' @seealso \code{\link{compressData}}, \code{\link{populateSampleColumns}}
 #' @examples
 #' # These examples require an internet connection to run
-#' Sample_01075 <- getSTORETSampleData('USGS-01594440','Chloride', '', '', interactive=FALSE)
-#' Sample_All <- getSTORETSampleData('WIDNR_WQX-10032762','Specific conductance', '', '', interactive=FALSE)
+#' Sample_01075 <- getSTORETSampleData('USGS-01594440','Chloride', '', '')
+#' Sample_All <- getSTORETSampleData('WIDNR_WQX-10032762','Specific conductance', '', '')
 getSTORETSampleData <- function(siteNumber,characteristicName,StartDate,EndDate,interactive=TRUE){
   data <- getWQPData(siteNumber,characteristicName,StartDate,EndDate,interactive=interactive)
   compressedData <- compressData(data, interactive=interactive)

R/getSampleData.r

@@ -17,9 +17,9 @@
 #' @seealso \code{\link{compressData}}, \code{\link{populateSampleColumns}}
 #' @examples
 #' # These examples require an internet connection to run
-#' Sample_01075 <- getSampleData('01594440','01075', '1985-01-01', '1985-03-31', interactive=FALSE)
-#' Sample_All <- getSampleData('05114000','00915;00931', '1985-01-01', '1985-03-31', interactive=FALSE)
-#' Sample_Select <- getSampleData('05114000','00915;00931', '', '', interactive=FALSE)
+#' Sample_01075 <- getSampleData('01594440','01075', '1985-01-01', '1985-03-31')
+#' Sample_All <- getSampleData('05114000','00915;00931', '1985-01-01', '1985-03-31')
+#' Sample_Select <- getSampleData('05114000','00915;00931', '', '')
 getSampleData <- function(siteNumber,ParameterCd,StartDate,EndDate,interactive=TRUE){
   data <- getQWData(siteNumber,ParameterCd,StartDate,EndDate,interactive=interactive)
   compressedData <- compressData(data, interactive=interactive)

R/getSampleDataFromFile.r

@@ -16,7 +16,7 @@
 #' # Change the file path and file name to something meaningful:
 #' filePath <- '~/RData/'  # Sample format
 #' fileName <- 'ChoptankRiverNitrate.csv'
-#' #Sample <- getSampleDataFromFile(filePath,fileName, separator=";",interactive=FALSE)
+#' \dontrun{Sample <- getSampleDataFromFile(filePath,fileName, separator=";",interactive=FALSE)}
 getSampleDataFromFile <- function (filePath,fileName,hasHeader=TRUE,separator=",", interactive=TRUE){
   data <- getQWDataFromFile(filePath,fileName,hasHeader=hasHeader,separator=separator)
   compressedData <- compressData(data, interactive=interactive)

R/getSiteFileData.r

@@ -9,7 +9,7 @@
 #' @export
 #' @examples
 #' # These examples require an internet connection to run
-#' siteINFO <- getSiteFileData('05114000',interactive=FALSE)
+#' siteINFO <- getSiteFileData('05114000')
 getSiteFileData <- function(siteNumber="",interactive=TRUE){
   
   # Checking for 8 digit site ID:

R/getWaterML1Data.r

-#' Function to return data from the NWISWeb WaterML1.1 daily values service
+#' Function to return data from the NWISWeb WaterML1.1 service
 #'
 #' This function accepts a url parameter that already contains the desired
 #' NWIS site, parameter code, statistic, startdate and enddate. 

R/getWaterML2Data.r

@@ -6,14 +6,10 @@
 #' @return mergedDF a data frame containing columns agency, site, dateTime, values, and remark codes for all requested combinations
 #' @export
 #' @import XML
-#' @import plyr
+#' @importFrom plyr rbind.fill.matrix
 #' @examples
-#' url <- "http://webvastage6.er.usgs.gov/ogc-swie/wml2/uv/sos?request=GetObservation&featureID=01446500&observedProperty=00065&offering=UNIT&beginPosition=2013-08-20"
-#' dataReturned <- getWaterML2Data(url)
-#' URL2 <- "http://cida-test.er.usgs.gov/ngwmn_cache/sos?REQUEST=GetObservation&featureOfInterest=VW_GWDP_GEOSERVER.USGS.401532085085301"
-#' dataReturned2 <- getWaterML2Data(URL2)
-#' URL3 <- "http://webvastage6.er.usgs.gov/ogc-swie/wml2/dv/sos?request=GetObservation&featureID=435601087432701&observedProperty=00045&beginPosition=2012-01-01&offering=Sum"
-#' dataReturned3 <- getWaterML2Data(URL3)
+#' URL <- "http://webvastage6.er.usgs.gov/ogc-swie/wml2/dv/sos?request=GetObservation&featureID=435601087432701&observedProperty=00045&beginPosition=2012-01-01&offering=Sum"
+#' dataReturned3 <- getWaterML2Data(URL)
 getWaterML2Data <- function(obs_url){
   
   doc <- xmlTreeParse(obs_url, getDTD = FALSE, useInternalNodes = TRUE)
@@ -27,7 +23,7 @@ getWaterML2Data <- function(obs_url){
     setNames(ifelse(nzchar(xmlValue(x)), xmlValue(x), 
                     ifelse("qualifier" == xmlName(x),xpathSApply(x,"./@xlink:title",namespaces = ns),"")), #originally I had the "" as xmlAttr(x) 
              xmlName(x)), namespaces = ns)
-  library(plyr)
+
   DF2 <- do.call(rbind.fill.matrix, lapply(xp, t))
   DF2 <- as.data.frame(DF2,stringsAsFactors=FALSE)
   DF2$time <- gsub(":","",DF2$time)