diff --git a/DESCRIPTION b/DESCRIPTION
index db24faf1fa1a3e4939cb31dc191b911b55bb1139..0d43ad3392dcc7b7f06926de997be2bff60847ae 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -62,7 +62,8 @@ Depends:
Imports:
zoo,
XML,
- RCurl
+ RCurl,
+ plyr
Suggests:
xtable,
EGRET,
diff --git a/NAMESPACE b/NAMESPACE
index a0effc82a4061ca822787666442b9667481b7b04..cfa3034906a489e8501b0b57268d954fae68b2f6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -43,3 +43,4 @@ export(retrieveUnitNWISData)
import(RCurl)
import(XML)
import(zoo)
+importFrom(plyr,rbind.fill.matrix)
diff --git a/R/checkStartEndDate.r b/R/checkStartEndDate.r
index 2e516e0941fd5d7f87597f1a08c890b9a37dd855..28a1c52e3d42b073ba0bdc87212e5a460954189f 100644
--- a/R/checkStartEndDate.r
+++ b/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())
diff --git a/R/compressData.r b/R/compressData.r
index 2be5baef0fb17cfff68bbf07a9515d94608a0339..57cf0bf54095f5f65e8d10240187c60cbbaed52c 100644
--- a/R/compressData.r
+++ b/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)
diff --git a/R/constructNWISURL.r b/R/constructNWISURL.r
index 75f9182878d45033b5c7b6d2646773e6626b1dce..f9695c6cc5e857acc08457ed5a479df96efbec6b 100644
--- a/R/constructNWISURL.r
+++ b/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)
diff --git a/R/formatCheckParameterCd.r b/R/formatCheckParameterCd.r
index 7187c6975d21ed0b40db6103debc556c41a047ee..7a0a0a49d9f123fe44a9e6350412c9a35ae3d3b0 100644
--- a/R/formatCheckParameterCd.r
+++ b/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))
diff --git a/R/formatCheckSiteNumber.r b/R/formatCheckSiteNumber.r
index a335797958172b117ca9bbbb1c9065d8ed787f04..4a8c9d67c3351840ca14d696de450b4ff9b92e27 100644
--- a/R/formatCheckSiteNumber.r
+++ b/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){
diff --git a/R/getDVData.r b/R/getDVData.r
index a3d4ae68b953dfb6570bf3123e4a11e879c4851c..b2b4254a868226bb3a887a4f708f51ae17d90f39 100644
--- a/R/getDVData.r
+++ b/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)
diff --git a/R/getDataAvailability.r b/R/getDataAvailability.r
index 526b6a5287389a366cf919a88c4a0944500b6880..18fae0ccc32a8b513a1a528040a9a5d890ff502e 100644
--- a/R/getDataAvailability.r
+++ b/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:
diff --git a/R/getDataFromFile.r b/R/getDataFromFile.r
index 07476c04ff0d1b4c07d4319b199bd9a5abcc5dc9..edc87ab6a02f2ce7e015828cdf0e64cb88f6efaf 100644
--- a/R/getDataFromFile.r
+++ b/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(
diff --git a/R/getMetaData.r b/R/getMetaData.r
index f18f4fc2f145b77565a8c3c26a81c4609df7220d..e012b8978edaaa69f1cd66ad13d2c39c99b510db 100644
--- a/R/getMetaData.r
+++ b/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)
diff --git a/R/getQWData.r b/R/getQWData.r
index 8d452b3e947aa128a9c50d436710b2c834d82449..28903c4bdd66f26ea5690dab94983af96a20fcf2 100644
--- a/R/getQWData.r
+++ b/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)
diff --git a/R/getQWDataFromFile.r b/R/getQWDataFromFile.r
index e403cbc15c29c722ff6788347add86c08d9949de..c9a40aa22ca82649432dda3e7b4645edce41cd60 100644
--- a/R/getQWDataFromFile.r
+++ b/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(
diff --git a/R/getRawQWData.r b/R/getRawQWData.r
index ec24d52a82901ec7059cb8fc330a362dfa73a220..b0e3b9cad17138a2998cc4d68a6a33855fd451df 100644
--- a/R/getRawQWData.r
+++ b/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")
diff --git a/R/getSTORETSampleData.R b/R/getSTORETSampleData.R
index 79abd67a10a5bf0a31f6adb1a9cc6d11cbd4bf66..0029d140391939a768e0cc7296636fdb2df764de 100644
--- a/R/getSTORETSampleData.R
+++ b/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)
diff --git a/R/getSampleData.r b/R/getSampleData.r
index 3cd6d070d3349a221ac1d8a4a4ad9790276b41e3..ae766ec1c72c9252099555d82295da7eb06680f4 100644
--- a/R/getSampleData.r
+++ b/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)
diff --git a/R/getSampleDataFromFile.r b/R/getSampleDataFromFile.r
index f49ce7aab05c859fa6f17257bb9819cd85fa3b73..9cb560a10e987e6b0e017913ca288448cf1e4cd6 100644
--- a/R/getSampleDataFromFile.r
+++ b/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)
diff --git a/R/getSiteFileData.r b/R/getSiteFileData.r
index d4f67190d19d334f45b219489506e6c7164eb77c..46cf018792e9aa2493f464724d20e00803f71679 100644
--- a/R/getSiteFileData.r
+++ b/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:
diff --git a/R/getWaterML1Data.r b/R/getWaterML1Data.r
index fabca89165fe31d0ac886e04abfc0b21e0efffe0..a1c485cf2ae8d5aac4243302d8a4a0d20c8c3269 100644
--- a/R/getWaterML1Data.r
+++ b/R/getWaterML1Data.r
@@ -1,4 +1,4 @@
-#' 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.
diff --git a/R/getWaterML2Data.r b/R/getWaterML2Data.r
index 4baac2f8e055364f8d675dae8c0c703538fb6cde..60d4c8fad23ce67a92545dfc4789426d083b9770 100644
--- a/R/getWaterML2Data.r
+++ b/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)
diff --git a/R/mergeReport.r b/R/mergeReport.r
index 7db0ebd09062b2018b527cda7fb28ec31e8610b1..0cf0af3e159ba82b2684eff3c5171bce6d4faa40 100644
--- a/R/mergeReport.r
+++ b/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)
diff --git a/R/populateDaily.r b/R/populateDaily.r
index f17163514553287ac67268175e60232c695b09da..9a3d4fff015081f450dc8726a9c67048649434f6 100644
--- a/R/populateDaily.r
+++ b/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$Julian[1])+1
if (interactive){
- cat("There are ", as.character(dataPoints), "data points, and ", as.character(difference), "days.\n")
+ cat("There are", as.character(dataPoints), "data points, and", as.character(difference), "days.\n")
#these next two lines show the user where the gaps in the data are if there are any
n<-nrow(localDaily)
diff --git a/R/populateParameterINFO.r b/R/populateParameterINFO.r
index 75c04c70d64aa913db1ac42184896cae52cacbca..8ef770d6eafff951cdb3a0c6e64200bc95abd699 100644
--- a/R/populateParameterINFO.r
+++ b/R/populateParameterINFO.r
@@ -16,7 +16,7 @@
#' INFO$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){
diff --git a/R/populateSiteINFO.r b/R/populateSiteINFO.r
index 52c4f744756e37978556fae37be2ee9a79b4b8bd..49f8f0e2fb17e306971b452319f004dd8c99f6be 100644
--- a/R/populateSiteINFO.r
+++ b/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)){
diff --git a/R/renameColumns.R b/R/renameColumns.R
index 27f98997080e9465bbfcfc6e348af9b14ba09a69..bf5c68dba4b7a97b3ea8f0168d7a396a75a24b7d 100644
--- a/R/renameColumns.R
+++ b/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)
diff --git a/R/retrieveNWISData.r b/R/retrieveNWISData.r
index ca901e99af4ec228cb0a4ea3bc5b1e152f2946e2..4d8399fab2c67618111ce574b2373096af2ee74a 100644
--- a/R/retrieveNWISData.r
+++ b/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)
diff --git a/R/retrieveNWISqwData.r b/R/retrieveNWISqwData.r
index 7b7010a9e5beb68df852db61bffbdc782e7df420..1e6b7ab5e938050cd30533ee1a0c6cd04c5a1dc0 100644
--- a/R/retrieveNWISqwData.r
+++ b/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){
diff --git a/R/retrieveUnitNWISData.r b/R/retrieveUnitNWISData.r
index b40b98af8782385be37af169c21dd4e1117cbae4..f2130d26909c1868510f2755ba29447325249673 100644
--- a/R/retrieveUnitNWISData.r
+++ b/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)
diff --git a/inst/doc/dataRetrieval.pdf b/inst/doc/dataRetrieval.pdf
index 9c3efd6b32f4a2d216c164cb05d1d4fe3a4e04f8..1def98857083c27b2beccf76cabc2af7c6078832 100644
Binary files a/inst/doc/dataRetrieval.pdf and b/inst/doc/dataRetrieval.pdf differ
diff --git a/man/checkStartEndDate.Rd b/man/checkStartEndDate.Rd
index 892f64cca9c0ad84ad4ad691484ae396ed210d2e..ce5da41b9ff354cc6a75844912f837221ac37adb 100644
--- a/man/checkStartEndDate.Rd
+++ b/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}
diff --git a/man/compressData.Rd b/man/compressData.Rd
index 92d9134d44d9369c41a427c163d614c96601a8d5..143dbcc72c6db7959e9542ad30dd7800b2b225ab 100644
--- a/man/compressData.Rd
+++ b/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}
diff --git a/man/constructNWISURL.Rd b/man/constructNWISURL.Rd
index d27f4d78cc64771dabe636f541ce83bf84e2d358..69e70cecc0627af3f24b0a861b11b7e1e4c33264 100644
--- a/man/constructNWISURL.Rd
+++ b/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{
diff --git a/man/formatCheckParameterCd.Rd b/man/formatCheckParameterCd.Rd
index d1574546ed4940e46494b4c4bbd46bacce0da90e..a506bd85e0ba4eda3d47c926635ed44c98a33fb8 100644
--- a/man/formatCheckParameterCd.Rd
+++ b/man/formatCheckParameterCd.Rd
@@ -21,7 +21,7 @@
}
\examples{
pCode <- '01234'
-formatCheckParameterCd(pCode, interactive = FALSE)
+formatCheckParameterCd(pCode)
}
\keyword{WRTDS}
\keyword{flow}
diff --git a/man/formatCheckSiteNumber.Rd b/man/formatCheckSiteNumber.Rd
index 5d8b42cd9e9cb3a8d96bdf4d70ac01ec0fbe8a03..2f16232501e4729fb68393c7cbb60ff70116ad3b 100644
--- a/man/formatCheckSiteNumber.Rd
+++ b/man/formatCheckSiteNumber.Rd
@@ -20,7 +20,7 @@
}
\examples{
site<- '01234567'
-formatCheckSiteNumber(site, interactive = FALSE)
+formatCheckSiteNumber(site)
}
\keyword{WRTDS}
\keyword{flow}
diff --git a/man/getDVData.Rd b/man/getDVData.Rd
index 89c721c68e85843950c7fb0fe53685004d4a2264..e4a61195d1b730cc87bb7d713dcf80d013e08b3d 100644
--- a/man/getDVData.Rd
+++ b/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}},
diff --git a/man/getDataAvailability.Rd b/man/getDataAvailability.Rd
index 97d8982836502c506edd289ce9441bce879eb365..4c45fe760d625a04f65b4243a4bca5882f5abd91 100644
--- a/man/getDataAvailability.Rd
+++ b/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}
diff --git a/man/getDataFromFile.Rd b/man/getDataFromFile.Rd
index 6d772bcf24750ac0310a71fe9293e8cf4287bea0..7ec446f59216b6173dead3192e11d6cd46fb0a08 100644
--- a/man/getDataFromFile.Rd
+++ b/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}
diff --git a/man/getMetaData.Rd b/man/getMetaData.Rd
index fb57f7d818c177f9756645238dada84569867e04..91ae02d37af2334be85e06624148abed504efe14 100644
--- a/man/getMetaData.Rd
+++ b/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}
diff --git a/man/getQWData.Rd b/man/getQWData.Rd
index 8348de8d5e2cd018928e1498e8d0ce37842488d7..70f7885ccba58ef2dd0f5a29dcd5e4d5f2481bbf 100644
--- a/man/getQWData.Rd
+++ b/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}
diff --git a/man/getQWDataFromFile.Rd b/man/getQWDataFromFile.Rd
index c25fa7a47ff0d1c6805bb7beaaf381de7a0a152a..1303449e53bd8b0d45a379c661ae17f392bf6d38 100644
--- a/man/getQWDataFromFile.Rd
+++ b/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}
diff --git a/man/getRawQWData.Rd b/man/getRawQWData.Rd
index 738023e62faec1f5e19e3f7973eb04b875e5d7d0..b1aaccf3f4ba98c5ba10aa23757614e4391ceb92 100644
--- a/man/getRawQWData.Rd
+++ b/man/getRawQWData.Rd
@@ -9,11 +9,9 @@
\item{siteNumber}{string USGS site number. This is
usually an 8 digit number}
- \item{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.}
+ \item{ParameterCd}{vector of USGS 5-digit parameter code.
+ Leaving this blank will return all of the measured values
+ during the specified time period.}
\item{StartDate}{string starting date for data retrieval
in the form YYYY-MM-DD.}
@@ -43,7 +41,7 @@
# 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')
}
\keyword{USGS}
\keyword{data}
diff --git a/man/getSTORETSampleData.Rd b/man/getSTORETSampleData.Rd
index a1fc936e537dcb5235c44d9582da57eb0dad1fa3..5fe9a4d79738ad6db7a43422ef8e43a398527567 100644
--- a/man/getSTORETSampleData.Rd
+++ b/man/getSTORETSampleData.Rd
@@ -37,8 +37,8 @@
}
\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', '', '')
}
\seealso{
\code{\link{compressData}},
diff --git a/man/getSampleData.Rd b/man/getSampleData.Rd
index f8fc6db8dd5b2a7f164977fe2e1c287b8eefcb84..aa83390b01f2f112a4441e86fe4491d60803de99 100644
--- a/man/getSampleData.Rd
+++ b/man/getSampleData.Rd
@@ -38,9 +38,9 @@
}
\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', '', '')
}
\seealso{
\code{\link{compressData}},
diff --git a/man/getSampleDataFromFile.Rd b/man/getSampleDataFromFile.Rd
index f295b54c36bbffe76ecd4934edde2f67b6531f51..41907f997828a77f8393939512736290ebaf77f7 100644
--- a/man/getSampleDataFromFile.Rd
+++ b/man/getSampleDataFromFile.Rd
@@ -33,7 +33,7 @@
# 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)}
}
\keyword{USGS}
\keyword{WRTDS}
diff --git a/man/getSiteFileData.Rd b/man/getSiteFileData.Rd
index 37a7d14a54aa31799bcb74be2ebf6e8137323eac..56f3fdff84903dc5f704b46179269f3660fb5867 100644
--- a/man/getSiteFileData.Rd
+++ b/man/getSiteFileData.Rd
@@ -22,7 +22,7 @@
}
\examples{
# These examples require an internet connection to run
-siteINFO <- getSiteFileData('05114000',interactive=FALSE)
+siteINFO <- getSiteFileData('05114000')
}
\keyword{USGS}
\keyword{data}
diff --git a/man/getWaterML1Data.Rd b/man/getWaterML1Data.Rd
index eb259185e93590ebfa75b838e470ccda90d010bd..5f62dc79ab951e77d2905b2a4d2f9d4de1046c8c 100644
--- a/man/getWaterML1Data.Rd
+++ b/man/getWaterML1Data.Rd
@@ -1,6 +1,6 @@
\name{getWaterML1Data}
\alias{getWaterML1Data}
-\title{Function to return data from the NWISWeb WaterML1.1 daily values service}
+\title{Function to return data from the NWISWeb WaterML1.1 service}
\usage{
getWaterML1Data(obs_url)
}
diff --git a/man/getWaterML2Data.Rd b/man/getWaterML2Data.Rd
index 3e7611bd1d4516cc91bb914fb33339def82b452d..0c747e83688d3d298d09a95f8f61be2809265d1d 100644
--- a/man/getWaterML2Data.Rd
+++ b/man/getWaterML2Data.Rd
@@ -18,7 +18,7 @@
getObservation
}
\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(urlMulti)
+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)
}
diff --git a/man/mergeReport.Rd b/man/mergeReport.Rd
index 5efff9d3878cddc49ca7a82527a2ece4d08a4f52..f66466308fd52d95f367657fb9bddeb9162702c2 100644
--- a/man/mergeReport.Rd
+++ b/man/mergeReport.Rd
@@ -25,9 +25,9 @@
}
\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()
}
\seealso{
\code{\link{getDVData}},
diff --git a/man/populateDaily.Rd b/man/populateDaily.Rd
index 5722f563c0cd546c3c1cb92f01026ffb4690c6a3..17b7ddd74e351dadf310ac4ee1cfb9747b4d99b8 100644
--- a/man/populateDaily.Rd
+++ b/man/populateDaily.Rd
@@ -28,7 +28,7 @@ dateTime <- c('1985-01-01', '1985-01-02', '1985-01-03')
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)
}
\author{
Robert M. Hirsch \email{rhirsch@usgs.gov}
diff --git a/man/populateParameterINFO.Rd b/man/populateParameterINFO.Rd
index bcc0acb9ce87acb77333428a1d5dfa000a5111f8..695a65d08d98375adf4e338e4a7702e89c251143 100644
--- a/man/populateParameterINFO.Rd
+++ b/man/populateParameterINFO.Rd
@@ -31,6 +31,6 @@ INFO$param.nm <- parameterData$parameter_nm
INFO$param.units <- parameterData$parameter_units
INFO$paramShortName <- parameterData$srsname
INFO$paramNumber <- parameterData$parameter_cd
-INFO <- populateParameterINFO(parameterCd,interactive=FALSE)
+INFO <- populateParameterINFO(parameterCd)
}
diff --git a/man/populateSiteINFO.Rd b/man/populateSiteINFO.Rd
index 7603aa9645780c95fe4ed5b4983f8c9964f4722c..ac90811d19a6ba630d697f101d24b3bba1f015f6 100644
--- a/man/populateSiteINFO.Rd
+++ b/man/populateSiteINFO.Rd
@@ -25,6 +25,6 @@
#This example requires an internet connection to run
INFO <- getSiteFileData('01594440')
siteNumber <- "01594440"
-siteINFO <- populateSiteINFO(INFO, siteNumber,interactive=FALSE)
+siteINFO <- populateSiteINFO(INFO, siteNumber)
}
diff --git a/man/renameColumns.Rd b/man/renameColumns.Rd
index 1f68f8287b74f95468fbcb9c74310e07a0d7cbb0..d1900410d08d1d33d24f8f46306a63c10d1ecf85 100644
--- a/man/renameColumns.Rd
+++ b/man/renameColumns.Rd
@@ -15,20 +15,9 @@
Rename columns coming back from NWIS data retrievals
}
\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)
}
\keyword{USGS}
\keyword{data}
diff --git a/man/retrieveNWISData.Rd b/man/retrieveNWISData.Rd
index 8d7ce45c0360d221dbd8763fce7246cdd8c34e95..43181ce116c3620cc2d8267233d4065e37a3e1ed 100644
--- a/man/retrieveNWISData.Rd
+++ b/man/retrieveNWISData.Rd
@@ -56,9 +56,9 @@ startDate <- '2012-01-01'
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'))
}
\keyword{USGS}
\keyword{data}
diff --git a/man/retrieveNWISqwData.Rd b/man/retrieveNWISqwData.Rd
index 254045c748b2520c03b207a717b6a2034639f995..48e5fd6e9cfdc928c83d4c8a0e10a7d4245d2c8c 100644
--- a/man/retrieveNWISqwData.Rd
+++ b/man/retrieveNWISqwData.Rd
@@ -41,7 +41,7 @@ rawNWISqwData <- retrieveNWISqwData(siteNumber,pCodes,startDate,endDate)
# 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)
}
\keyword{USGS}
diff --git a/man/retrieveUnitNWISData.Rd b/man/retrieveUnitNWISData.Rd
index f69c1294191c97249a6426057aab6a3daa315659..05e4bd29288ce6e2318022fa2f8bba1d78be1f2a 100644
--- a/man/retrieveUnitNWISData.Rd
+++ b/man/retrieveUnitNWISData.Rd
@@ -51,8 +51,8 @@ ParameterCd <- '00060'
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")
}
\keyword{USGS}
\keyword{data}
diff --git a/vignettes/dataRetrieval-concordance.tex b/vignettes/dataRetrieval-concordance.tex
index 01bedc0b2020a711a149b2b72d000e6f9e94a837..ebbc1fc7a7fb60fa965678258b10a88cda7e4020 100644
--- a/vignettes/dataRetrieval-concordance.tex
+++ b/vignettes/dataRetrieval-concordance.tex
@@ -1,9 +1,9 @@
\Sconcordance{concordance:dataRetrieval.tex:dataRetrieval.Rnw:%
-1 49 1 55 0 1 6 11 1 1 5 41 1 10 0 16 1 9 0 21 1 5 0 %
-6 1 8 0 14 1 42 0 17 1 4 0 15 1 6 0 16 1 10 0 5 1 8 0 %
-20 1 5 0 16 1 4 0 21 1 10 0 20 1 5 0 4 1 18 0 29 1 9 %
-0 10 1 10 0 14 1 21 0 19 1 5 0 19 1 5 0 17 1 8 0 14 1 %
+1 49 1 50 0 1 6 11 1 1 5 41 1 10 0 16 1 9 0 21 1 5 0 %
+6 1 8 0 14 1 42 0 17 1 3 0 15 1 6 0 16 1 10 0 5 1 8 0 %
+20 1 3 0 18 1 1 0 21 1 9 0 20 1 4 0 4 1 18 0 29 1 6 0 %
+10 1 10 0 14 1 21 0 19 1 5 0 19 1 5 0 17 1 8 0 14 1 %
15 0 16 1 5 0 9 1 5 0 62 1 6 0 14 1 17 0 36 1 5 0 24 %
-1 5 0 20 1 38 0 13 1 10 0 22 1 5 0 5 1 13 0 10 1 5 0 %
-7 1 5 0 16 1 51 0 15 1 49 0 7 1 32 0 24 1 19 0 8 1 5 %
+1 5 0 20 1 37 0 13 1 10 0 22 1 5 0 5 1 13 0 10 1 5 0 %
+7 1 5 0 16 1 51 0 15 1 49 0 7 1 32 0 24 1 18 0 8 1 5 %
0 56 1}
diff --git a/vignettes/dataRetrieval.Rnw b/vignettes/dataRetrieval.Rnw
index 82de5232f8cb84cf72abb2dde05ba3ecbd508326..2d28f5b4c8fad9de9380de0508d59de671fe0e0b 100644
--- a/vignettes/dataRetrieval.Rnw
+++ b/vignettes/dataRetrieval.Rnw
@@ -256,6 +256,8 @@ endDate <- "2012-05-01"
temperatureAndFlow <- retrieveNWISData(siteNumber, parameterCd,
startDate, endDate, StatCd=statCd)
+temperatureAndFlow <- renameColumns(temperatureAndFlow)
+
@
Daily data is pulled from \url{http://waterservices.usgs.gov/rest/DV-Test-Tool.html}.
@@ -264,14 +266,14 @@ An example of plotting the above data (Figure \ref{fig:getNWIStemperaturePlot}):
<<getNWIStemperaturePlot, echo=TRUE, fig.cap="Temperature and discharge plot of Choptank River in 2012.",out.width='1\\linewidth',out.height='1\\linewidth',fig.show='hold'>>=
par(mar=c(5,5,5,5))
-colnames <- names(temperatureAndFlow)
+
with(temperatureAndFlow, plot(
- datetime, get(colnames[6]),
+ datetime, Temperature_water_01,
xlab="Date",ylab="Temperature [C]"
))
par(new=TRUE)
with(temperatureAndFlow, plot(
- get(colnames[3]), get(colnames[8]),
+ datetime, Stream_flow_mean_daily,
col="red",type="l",xaxt="n",yaxt="n",xlab="",ylab="",axes=FALSE
))
axis(4,col="red",col.axis="red")
diff --git a/vignettes/dataRetrieval.log b/vignettes/dataRetrieval.log
index 4002811f19e51483ba099632eeb9fcadfbf46a4b..bc8b26a1d159677b0656e34aa3b7ec6eae6195f2 100644
--- a/vignettes/dataRetrieval.log
+++ b/vignettes/dataRetrieval.log
@@ -1,4 +1,4 @@
-This is pdfTeX, Version 3.1415926-2.3-1.40.12 (MiKTeX 2.9) (preloaded format=pdflatex 2012.1.6) 1 AUG 2013 16:23
+This is pdfTeX, Version 3.1415926-2.3-1.40.12 (MiKTeX 2.9) (preloaded format=pdflatex 2012.1.6) 4 SEP 2013 12:54
entering extended mode
**dataRetrieval.tex
(D:\LADData\RCode\dataRetrieval\vignettes\dataRetrieval.tex
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[][]$\OT1/pcr/m/n/10.95 http : / / nwis . waterdata . usgs . gov / nwis / help
/ ?read _ file = stat&format = table$[]
[]
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[]\OT1/ptm/m/n/10.95 Site in-for-ma-tion is ob-tained from []$\OT1/pcr/m/n/10.9
5 http : / / waterservices . usgs . gov / rest / Site-[]Test-[]Tool .$
[]
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[] \OT1/pcr/m/n
/10.95 parameter_nm[]
[]
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+Overfull \hbox (57.81561pt too wide) in paragraph at lines 282--282
[]\OT1/pcr/m/n/10.95 1 Location in cross section, distance from right bank loo
king upstream, feet[]
[]
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+Overfull \hbox (57.81561pt too wide) in paragraph at lines 282--282
[]\OT1/pcr/m/n/10.95 2
Stream width, feet[]
[]
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[]\OT1/pcr/m/n/10.95 3 Sampl
e accounting number[]
[]
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[]\OT1/pcr/m/n/10.95 4 Location in cross section, distance from left bank looki
ng downstream, feet[]
[]
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+Overfull \hbox (57.81561pt too wide) in paragraph at lines 282--282
[]\OT1/pcr/m/n/10.95 5 Temperature, wat
er, degrees Celsius[]
[]
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[]\OT1/pcr/m/n/10.95 6 Temperature, wat
er, degrees Celsius[]
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[]
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\OT1/ptm/m/n/10.95 There are ad-di-tional data sets avail-able on the Wa-ter Qu
al-ity Data Por-tal ([]$\OT1/pcr/m/n/10.95 http : / / www . waterqualitydata .$
[]
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+]\OT1/pcr/m/n/10.95 (siteNumber,[][]"00060"[][],startDate,endDate,[][]\TS1/pcr/
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[] \OT1/pcr/m/n/10.95 First day of the discharge record is 2000-01-01 and last
day is 2013-01-01[]
[]
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[] \OT1/pcr/m/n/10.95 The first sample is from 2000-01-04 and the last sample i
s from 2012-12-18[]
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[] \OT1/pcr/m/n/10.95 Sample1 <- localSample[!duplicated(localSample[c("DecYea
r","ConcHigh")]),][]
[]
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+[][]\OT1/pcr/b/n/10.95 install.packages[][]\OT1/pcr/m/n/10.95 ([][]"dataRetriev
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+urce"[][])[][]
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\OT1/ptm/m/n/10.95 C:/Users/userA/Documents/R/win-library/2.15/dataRetrieval, a
nd the de-fault for a Mac: /Users/userA/Library/R/2.15/library/dataRetrieval.
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[29
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+Overfull \hbox (11.82567pt too wide) in paragraph at lines 1267--1267
[]\OT1/pcr/m/n/10.95 Suspended sediment concentration (SSC) 1980-10-01 1991-09-
30 3651 mg/l[]
[]
-<table1.png, id=348, 554.07pt x 125.71968pt>
+<table1.png, id=349, 554.07pt x 125.71968pt>
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+Underfull \hbox (badness 1983) in paragraph at lines 1302--1303
[]\OT1/ptm/m/n/10.95 Hirsch, R. M., Moyer, D. L. and Arch-field, S. A. (2010),
Weighted Re-gres-sions on
[]
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+Underfull \hbox (badness 1221) in paragraph at lines 1302--1303
\OT1/ptm/m/n/10.95 Time, Dis-charge, and Sea-son (WRTDS), with an Ap-pli-ca-tio
n to Chesa-peake Bay River
[]
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+Underfull \hbox (badness 2443) in paragraph at lines 1302--1303
\OT1/ptm/m/n/10.95 In-puts. JAWRA Jour-nal of the Amer-i-can Wa-ter Re-sources
As-so-ci-a-tion, 46: 857-880.
[]
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+Underfull \hbox (badness 3690) in paragraph at lines 1302--1303
\OT1/ptm/m/n/10.95 doi: 10.1111/j.1752-1688.2010.00482.x []$\OT1/pcr/m/n/10.95
http : / / onlinelibrary . wiley . com / doi /$
[]
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+times/utmr8a.pfb><C:/Program Files (x86)/MiKTeX 2.9/fonts/type1/urw/times/utmri
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+Output written on dataRetrieval.pdf (31 pages, 288145 bytes).
PDF statistics:
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+ 429 PDF objects out of 1000 (max. 8388607)
88 named destinations out of 1000 (max. 500000)
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diff --git a/vignettes/dataRetrieval.pdf b/vignettes/dataRetrieval.pdf
index 9c3efd6b32f4a2d216c164cb05d1d4fe3a4e04f8..1def98857083c27b2beccf76cabc2af7c6078832 100644
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diff --git a/vignettes/dataRetrieval.synctex.gz b/vignettes/dataRetrieval.synctex.gz
index afdb961fab745cec75a2b4700d648096d1b1a811..3305ddaeab67e20944babfcb89aef5ff1940aed0 100644
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diff --git a/vignettes/dataRetrieval.tex b/vignettes/dataRetrieval.tex
index 4248bde759bed6ac0665bec36b8635eb607641c1..a39a5b7458beef5930e714cfa358fd3eccc76b3f 100644
--- a/vignettes/dataRetrieval.tex
+++ b/vignettes/dataRetrieval.tex
@@ -5,7 +5,7 @@
%\VignetteImports{zoo, XML, RCurl}
%\VignettePackage{dataRetrieval}
-\documentclass[a4paper,11pt]{article}\usepackage{graphicx, color}
+\documentclass[a4paper,11pt]{article}\usepackage[]{graphicx}\usepackage[]{color}
%% maxwidth is the original width if it is less than linewidth
%% otherwise use linewidth (to make sure the graphics do not exceed the margin)
\makeatletter
@@ -18,21 +18,16 @@
}
\makeatother
-\definecolor{fgcolor}{rgb}{0.2, 0.2, 0.2}
-\newcommand{\hlnumber}[1]{\textcolor[rgb]{0,0,0}{#1}}%
-\newcommand{\hlfunctioncall}[1]{\textcolor[rgb]{0.501960784313725,0,0.329411764705882}{\textbf{#1}}}%
-\newcommand{\hlstring}[1]{\textcolor[rgb]{0.6,0.6,1}{#1}}%
-\newcommand{\hlkeyword}[1]{\textcolor[rgb]{0,0,0}{\textbf{#1}}}%
-\newcommand{\hlargument}[1]{\textcolor[rgb]{0.690196078431373,0.250980392156863,0.0196078431372549}{#1}}%
-\newcommand{\hlcomment}[1]{\textcolor[rgb]{0.180392156862745,0.6,0.341176470588235}{#1}}%
-\newcommand{\hlroxygencomment}[1]{\textcolor[rgb]{0.43921568627451,0.47843137254902,0.701960784313725}{#1}}%
-\newcommand{\hlformalargs}[1]{\textcolor[rgb]{0.690196078431373,0.250980392156863,0.0196078431372549}{#1}}%
-\newcommand{\hleqformalargs}[1]{\textcolor[rgb]{0.690196078431373,0.250980392156863,0.0196078431372549}{#1}}%
-\newcommand{\hlassignement}[1]{\textcolor[rgb]{0,0,0}{\textbf{#1}}}%
-\newcommand{\hlpackage}[1]{\textcolor[rgb]{0.588235294117647,0.709803921568627,0.145098039215686}{#1}}%
-\newcommand{\hlslot}[1]{\textit{#1}}%
-\newcommand{\hlsymbol}[1]{\textcolor[rgb]{0,0,0}{#1}}%
-\newcommand{\hlprompt}[1]{\textcolor[rgb]{0.2,0.2,0.2}{#1}}%
+\definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345}
+\newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}%
+\newcommand{\hlstr}[1]{\textcolor[rgb]{0.192,0.494,0.8}{#1}}%
+\newcommand{\hlcom}[1]{\textcolor[rgb]{0.678,0.584,0.686}{\textit{#1}}}%
+\newcommand{\hlopt}[1]{\textcolor[rgb]{0,0,0}{#1}}%
+\newcommand{\hlstd}[1]{\textcolor[rgb]{0.345,0.345,0.345}{#1}}%
+\newcommand{\hlkwa}[1]{\textcolor[rgb]{0.161,0.373,0.58}{\textbf{#1}}}%
+\newcommand{\hlkwb}[1]{\textcolor[rgb]{0.69,0.353,0.396}{#1}}%
+\newcommand{\hlkwc}[1]{\textcolor[rgb]{0.333,0.667,0.333}{#1}}%
+\newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}%
\usepackage{framed}
\makeatletter
@@ -148,7 +143,7 @@ Not every station will measure all parameters. A short list of commonly measured
% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Thu Aug 01 16:23:09 2013
+% Wed Sep 04 12:53:33 2013
\begin{table}[ht]
\centering
\begin{tabular}{rll}
@@ -174,7 +169,7 @@ For real-time data, the parameter code and site ID will suffice. For most varia
Some common stat codes are shown in Table \ref{tab:stat}.
% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Thu Aug 01 16:23:09 2013
+% Wed Sep 04 12:53:33 2013
\begin{table}[ht]
\centering
\begin{tabular}{rll}
@@ -210,10 +205,10 @@ Use the getSiteFileData function to obtain all of the information available for
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlfunctioncall{library}(dataRetrieval)
-\hlcomment{# Site ID for Choptank River near Greensboro, MD}
-siteNumber <- \hlstring{"01491000"}
-ChoptankInfo <- \hlfunctioncall{getSiteFileData}(siteNumber)
+\hlkwd{library}\hlstd{(dataRetrieval)}
+\hlcom{# Site ID for Choptank River near Greensboro, MD}
+\hlstd{siteNumber} \hlkwb{<-} \hlstr{"01491000"}
+\hlstd{ChoptankInfo} \hlkwb{<-} \hlkwd{getSiteFileData}\hlstd{(siteNumber)}
\end{alltt}
\end{kframe}
\end{knitrout}
@@ -224,7 +219,7 @@ A list of the available columns are found in Appendix \ref{sec:appendix2INFO}: I
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-ChoptankInfo$station.nm
+\hlstd{ChoptankInfo}\hlopt{$}\hlstd{station.nm}
\end{alltt}
\begin{verbatim}
[1] "CHOPTANK RIVER NEAR GREENSBORO, MD"
@@ -244,9 +239,9 @@ To find out the available data at a particular USGS site, including measured par
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlcomment{# Continuing from the previous example:}
-ChoptankAvailableData <- \hlfunctioncall{getDataAvailability}(siteNumber)
-\hlfunctioncall{head}(ChoptankAvailableData)
+\hlcom{# Continuing from the previous example:}
+\hlstd{ChoptankAvailableData} \hlkwb{<-} \hlkwd{getDataAvailability}\hlstd{(siteNumber)}
+\hlkwd{head}\hlstd{(ChoptankAvailableData)}
\end{alltt}
\begin{verbatim}
parameter_cd statCd startDate endDate count service
@@ -297,21 +292,20 @@ It is also possible to only request parameter information for a subset of variab
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlcomment{# Continuing from the previous example:}
-\hlcomment{# This pulls out just the daily data:}
-ChoptankDailyData <- \hlfunctioncall{subset}(ChoptankAvailableData,
- \hlstring{"dv"} == service)
-
-\hlcomment{# This pulls out the mean:}
-ChoptankDailyData <- \hlfunctioncall{subset}(ChoptankDailyData,
- \hlstring{"00003"} == statCd)
+\hlcom{# Continuing from the previous example:}
+\hlcom{# This pulls out just the daily data:}
+\hlstd{ChoptankDailyData} \hlkwb{<-} \hlkwd{subset}\hlstd{(ChoptankAvailableData,}
+ \hlstr{"dv"} \hlopt{==} \hlstd{service)}
+\hlcom{# This pulls out the mean:}
+\hlstd{ChoptankDailyData} \hlkwb{<-} \hlkwd{subset}\hlstd{(ChoptankDailyData,}
+ \hlstr{"00003"} \hlopt{==} \hlstd{statCd)}
\end{alltt}
\end{kframe}
\end{knitrout}
% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Thu Aug 01 16:23:12 2013
+% Wed Sep 04 12:53:38 2013
\begin{table}[ht]
\centering
\begin{tabular}{rlllll}
@@ -319,7 +313,7 @@ ChoptankDailyData <- \hlfunctioncall{subset}(ChoptankDailyData,
& shortName & Start & End & Count & Units \\
\hline
1 & Temperature, water & 2010-10-01 & 2012-05-09 & 529 & deg C \\
- 2 & Stream flow, mean. daily & 1948-01-01 & 2013-07-31 & 23954 & cfs \\
+ 2 & Stream flow, mean. daily & 1948-01-01 & 2013-09-03 & 23988 & ft3/s \\
3 & Specific conductance & 2010-10-01 & 2012-05-09 & 527 & uS/cm @25C \\
4 & Suspended sediment concentration (SSC) & 1980-10-01 & 1991-09-30 & 3651 & mg/l \\
5 & Suspended sediment discharge & 1980-10-01 & 1991-09-30 & 3652 & tons/day \\
@@ -343,10 +337,10 @@ To obtain all of the available information concerning a measured parameter, use
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlcomment{# Using defaults:}
-parameterCd <- \hlstring{"00618"}
-parameterINFO <- \hlfunctioncall{getParameterInfo}(parameterCd)
-\hlfunctioncall{colnames}(parameterINFO)
+\hlcom{# Using defaults:}
+\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00618"}
+\hlstd{parameterINFO} \hlkwb{<-} \hlkwd{getParameterInfo}\hlstd{(parameterCd)}
+\hlkwd{colnames}\hlstd{(parameterINFO)}
\end{alltt}
\begin{verbatim}
[1] "parameter_cd" "parameter_group_nm"
@@ -361,7 +355,7 @@ Pulling out a specific example piece of information, in this case parameter name
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-parameterINFO$parameter_nm
+\hlstd{parameterINFO}\hlopt{$}\hlstd{parameter_nm}
\end{alltt}
\begin{verbatim}
[1] "Nitrate, water, filtered, milligrams per liter as nitrogen"
@@ -382,14 +376,12 @@ The dates (start and end) need to be in the format \texttt{"}YYYY-MM-DD\texttt{"
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-
-\hlcomment{# Continuing with our Choptank River example}
-parameterCd <- \hlstring{"00060"} # \hlfunctioncall{Discharge} (cfs)
-startDate <- \hlstring{""} # Will request earliest date
-endDate <- \hlstring{""} # Will request latest date
-
-discharge <- \hlfunctioncall{retrieveNWISData}(siteNumber,
- parameterCd, startDate, endDate)
+\hlcom{# Continuing with our Choptank River example}
+\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00060"} \hlcom{# Discharge (cfs)}
+\hlstd{startDate} \hlkwb{<-} \hlstr{""} \hlcom{# Will request earliest date}
+\hlstd{endDate} \hlkwb{<-} \hlstr{""} \hlcom{# Will request latest date}
+\hlstd{discharge} \hlkwb{<-} \hlkwd{retrieveNWISData}\hlstd{(siteNumber,}
+ \hlstd{parameterCd, startDate, endDate)}
\end{alltt}
\end{kframe}
\end{knitrout}
@@ -402,14 +394,13 @@ Another example that doesn't use the defaults would be a request for mean and ma
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-
-parameterCd <- \hlfunctioncall{c}(\hlstring{"00010"},\hlstring{"00060"}) # Temperature and discharge
-statCd <- \hlfunctioncall{c}(\hlstring{"00001"},\hlstring{"00003"}) # Mean and maximum
-startDate <- \hlstring{"2012-01-01"}
-endDate <- \hlstring{"2012-05-01"}
-
-temperatureAndFlow <- \hlfunctioncall{retrieveNWISData}(siteNumber, parameterCd,
- startDate, endDate, StatCd=statCd)
+\hlstd{parameterCd} \hlkwb{<-} \hlkwd{c}\hlstd{(}\hlstr{"00010"}\hlstd{,}\hlstr{"00060"}\hlstd{)} \hlcom{# Temperature and discharge}
+\hlstd{statCd} \hlkwb{<-} \hlkwd{c}\hlstd{(}\hlstr{"00001"}\hlstd{,}\hlstr{"00003"}\hlstd{)} \hlcom{# Mean and maximum}
+\hlstd{startDate} \hlkwb{<-} \hlstr{"2012-01-01"}
+\hlstd{endDate} \hlkwb{<-} \hlstr{"2012-05-01"}
+\hlstd{temperatureAndFlow} \hlkwb{<-} \hlkwd{retrieveNWISData}\hlstd{(siteNumber, parameterCd,}
+ \hlstd{startDate, endDate,} \hlkwc{StatCd}\hlstd{=statCd)}
+\hlstd{temperatureAndFlow} \hlkwb{<-} \hlkwd{renameColumns}\hlstd{(temperatureAndFlow)}
\end{alltt}
\end{kframe}
\end{knitrout}
@@ -422,20 +413,19 @@ An example of plotting the above data (Figure \ref{fig:getNWIStemperaturePlot}):
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlfunctioncall{par}(mar=\hlfunctioncall{c}(5,5,5,5))
-colnames <- \hlfunctioncall{names}(temperatureAndFlow)
-\hlfunctioncall{with}(temperatureAndFlow, \hlfunctioncall{plot}(
- datetime, \hlfunctioncall{get}(colnames[6]),
- xlab=\hlstring{"Date"},ylab=\hlstring{"Temperature [C]"}
- ))
-\hlfunctioncall{par}(new=TRUE)
-\hlfunctioncall{with}(temperatureAndFlow, \hlfunctioncall{plot}(
- \hlfunctioncall{get}(colnames[3]), \hlfunctioncall{get}(colnames[8]),
- col=\hlstring{"red"},type=\hlstring{"l"},xaxt=\hlstring{"n"},yaxt=\hlstring{"n"},xlab=\hlstring{""},ylab=\hlstring{""},axes=FALSE
- ))
-\hlfunctioncall{axis}(4,col=\hlstring{"red"},col.axis=\hlstring{"red"})
-\hlfunctioncall{mtext}(\hlstring{"Discharge [cfs]"},side=4,line=3,col=\hlstring{"red"})
-\hlfunctioncall{title}(\hlfunctioncall{paste}(ChoptankInfo$station.nm,\hlstring{"2012"},sep=\hlstring{" "}))
+\hlkwd{par}\hlstd{(}\hlkwc{mar}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{5}\hlstd{,}\hlnum{5}\hlstd{,}\hlnum{5}\hlstd{,}\hlnum{5}\hlstd{))}
+\hlkwd{with}\hlstd{(temperatureAndFlow,} \hlkwd{plot}\hlstd{(}
+ \hlstd{datetime, Temperature_water_01,}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"Date"}\hlstd{,}\hlkwc{ylab}\hlstd{=}\hlstr{"Temperature [C]"}
+ \hlstd{))}
+\hlkwd{par}\hlstd{(}\hlkwc{new}\hlstd{=}\hlnum{TRUE}\hlstd{)}
+\hlkwd{with}\hlstd{(temperatureAndFlow,} \hlkwd{plot}\hlstd{(}
+ \hlstd{datetime, Stream_flow_mean_daily,}
+ \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,}\hlkwc{type}\hlstd{=}\hlstr{"l"}\hlstd{,}\hlkwc{xaxt}\hlstd{=}\hlstr{"n"}\hlstd{,}\hlkwc{yaxt}\hlstd{=}\hlstr{"n"}\hlstd{,}\hlkwc{xlab}\hlstd{=}\hlstr{""}\hlstd{,}\hlkwc{ylab}\hlstd{=}\hlstr{""}\hlstd{,}\hlkwc{axes}\hlstd{=}\hlnum{FALSE}
+ \hlstd{))}
+\hlkwd{axis}\hlstd{(}\hlnum{4}\hlstd{,}\hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,}\hlkwc{col.axis}\hlstd{=}\hlstr{"red"}\hlstd{)}
+\hlkwd{mtext}\hlstd{(}\hlstr{"Discharge [cfs]"}\hlstd{,}\hlkwc{side}\hlstd{=}\hlnum{4}\hlstd{,}\hlkwc{line}\hlstd{=}\hlnum{3}\hlstd{,}\hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{)}
+\hlkwd{title}\hlstd{(}\hlkwd{paste}\hlstd{(ChoptankInfo}\hlopt{$}\hlstd{station.nm,}\hlstr{"2012"}\hlstd{,}\hlkwc{sep}\hlstd{=}\hlstr{" "}\hlstd{))}
\end{alltt}
\end{kframe}\begin{figure}[]
@@ -460,12 +450,11 @@ Any data that are collected at regular time intervals (such as 15-minute or hour
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-
-parameterCd <- \hlstring{"00060"} # \hlfunctioncall{Discharge} (cfs)
-startDate <- \hlstring{"2012-05-12"}
-endDate <- \hlstring{"2012-05-13"}
-dischargeToday <- \hlfunctioncall{retrieveUnitNWISData}(siteNumber, parameterCd,
- startDate, endDate)
+\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00060"} \hlcom{# Discharge (cfs)}
+\hlstd{startDate} \hlkwb{<-} \hlstr{"2012-05-12"}
+\hlstd{endDate} \hlkwb{<-} \hlstr{"2012-05-13"}
+\hlstd{dischargeToday} \hlkwb{<-} \hlkwd{retrieveUnitNWISData}\hlstd{(siteNumber, parameterCd,}
+ \hlstd{startDate, endDate)}
\end{alltt}
\end{kframe}
\end{knitrout}
@@ -510,22 +499,19 @@ To get USGS water quality data from water samples collected at the streamgage (a
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-
-\hlcomment{# Dissolved Nitrate parameter codes:}
-parameterCd <- \hlfunctioncall{c}(\hlstring{"00618"},\hlstring{"71851"})
-startDate <- \hlstring{"1979-10-11"}
-endDate <- \hlstring{"2012-12-18"}
-
-dissolvedNitrate <- \hlfunctioncall{getRawQWData}(siteNumber, parameterCd,
- startDate, endDate)
-
-dissolvedNitrateSimple <- \hlfunctioncall{getQWData}(siteNumber, parameterCd,
- startDate, endDate)
-\hlfunctioncall{names}(dissolvedNitrateSimple)
+\hlcom{# Dissolved Nitrate parameter codes:}
+\hlstd{parameterCd} \hlkwb{<-} \hlkwd{c}\hlstd{(}\hlstr{"00618"}\hlstd{,}\hlstr{"71851"}\hlstd{)}
+\hlstd{startDate} \hlkwb{<-} \hlstr{"1979-10-11"}
+\hlstd{endDate} \hlkwb{<-} \hlstr{"2012-12-18"}
+\hlstd{dissolvedNitrate} \hlkwb{<-} \hlkwd{getRawQWData}\hlstd{(siteNumber, parameterCd,}
+ \hlstd{startDate, endDate)}
+\hlstd{dissolvedNitrateSimple} \hlkwb{<-} \hlkwd{getQWData}\hlstd{(siteNumber, parameterCd,}
+ \hlstd{startDate, endDate)}
+\hlkwd{names}\hlstd{(dissolvedNitrateSimple)}
\end{alltt}
\begin{verbatim}
-[1] "dateTime" "qualifier.71851" "value.71851"
-[4] "qualifier.00618" "value.00618"
+[1] "dateTime" "qualifier.00618" "value.00618"
+[4] "qualifier.71851" "value.71851"
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -535,12 +521,12 @@ Note that in this dataframe, datetime is imported as Dates (no times are include
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlfunctioncall{with}(dissolvedNitrateSimple, \hlfunctioncall{plot}(
- dateTime, value.00618,
- xlab=\hlstring{"Date"},ylab = \hlfunctioncall{paste}(parameterINFO$srsname,
- \hlstring{"["},parameterINFO$parameter_units,\hlstring{"]"})
- ))
-\hlfunctioncall{title}(ChoptankInfo$station.nm)
+\hlkwd{with}\hlstd{(dissolvedNitrateSimple,} \hlkwd{plot}\hlstd{(}
+ \hlstd{dateTime, value.00618,}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"Date"}\hlstd{,}\hlkwc{ylab} \hlstd{=} \hlkwd{paste}\hlstd{(parameterINFO}\hlopt{$}\hlstd{srsname,}
+ \hlstr{"["}\hlstd{,parameterINFO}\hlopt{$}\hlstd{parameter_units,}\hlstr{"]"}\hlstd{)}
+ \hlstd{))}
+\hlkwd{title}\hlstd{(ChoptankInfo}\hlopt{$}\hlstd{station.nm)}
\end{alltt}
\end{kframe}\begin{figure}[]
@@ -562,9 +548,9 @@ There are additional data sets available on the Water Quality Data Portal (\url{
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-specificCond <- \hlfunctioncall{getWQPData}(\hlstring{'WIDNR_WQX-10032762'},
- \hlstring{'Specific conductance'}, \hlstring{''}, \hlstring{''})
-\hlfunctioncall{head}(specificCond)
+\hlstd{specificCond} \hlkwb{<-} \hlkwd{getWQPData}\hlstd{(}\hlstr{'WIDNR_WQX-10032762'}\hlstd{,}
+ \hlstr{'Specific conductance'}\hlstd{,} \hlstr{''}\hlstd{,} \hlstr{''}\hlstd{)}
+\hlkwd{head}\hlstd{(specificCond)}
\end{alltt}
\begin{verbatim}
dateTime qualifier.Specific conductance
@@ -597,14 +583,14 @@ There may be times when you might be interested in seeing the URL (web address)
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlcomment{# Dissolved Nitrate parameter codes:}
-pCode <- \hlfunctioncall{c}(\hlstring{"00618"},\hlstring{"71851"})
-startDate <- \hlstring{"1964-06-11"}
-endDate <- \hlstring{"2012-12-18"}
-url_qw <- \hlfunctioncall{constructNWISURL}(siteNumber,pCode,startDate,endDate,\hlstring{'qw'})
-url_dv <- \hlfunctioncall{constructNWISURL}(siteNumber,\hlstring{"00060"},startDate,endDate,
- \hlstring{'dv'},statCd=\hlstring{"00003"})
-url_uv <- \hlfunctioncall{constructNWISURL}(siteNumber,\hlstring{"00060"},startDate,endDate,\hlstring{'uv'})
+\hlcom{# Dissolved Nitrate parameter codes:}
+\hlstd{pCode} \hlkwb{<-} \hlkwd{c}\hlstd{(}\hlstr{"00618"}\hlstd{,}\hlstr{"71851"}\hlstd{)}
+\hlstd{startDate} \hlkwb{<-} \hlstr{"1964-06-11"}
+\hlstd{endDate} \hlkwb{<-} \hlstr{"2012-12-18"}
+\hlstd{url_qw} \hlkwb{<-} \hlkwd{constructNWISURL}\hlstd{(siteNumber,pCode,startDate,endDate,}\hlstr{'qw'}\hlstd{)}
+\hlstd{url_dv} \hlkwb{<-} \hlkwd{constructNWISURL}\hlstd{(siteNumber,}\hlstr{"00060"}\hlstd{,startDate,endDate,}
+ \hlstr{'dv'}\hlstd{,}\hlkwc{statCd}\hlstd{=}\hlstr{"00003"}\hlstd{)}
+\hlstd{url_uv} \hlkwb{<-} \hlkwd{constructNWISURL}\hlstd{(siteNumber,}\hlstr{"00060"}\hlstd{,startDate,endDate,}\hlstr{'uv'}\hlstd{)}
\end{alltt}
\end{kframe}
\end{knitrout}
@@ -627,8 +613,8 @@ The function to obtain metadata, or data about the streamgage and measured param
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-parameterCd <- \hlstring{"00618"}
-INFO <-\hlfunctioncall{getMetaData}(siteNumber,parameterCd, interactive=FALSE)
+\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00618"}
+\hlstd{INFO} \hlkwb{<-}\hlkwd{getMetaData}\hlstd{(siteNumber,parameterCd,} \hlkwc{interactive}\hlstd{=}\hlnum{FALSE}\hlstd{)}
\end{alltt}
\end{kframe}
\end{knitrout}
@@ -646,14 +632,14 @@ The function to obtain the daily values (discharge in this case) is getDVData.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-siteNumber <- \hlstring{"01491000"}
-startDate <- \hlstring{"2000-01-01"}
-endDate <- \hlstring{"2013-01-01"}
-\hlcomment{# This call will get NWIS (cfs) data , and convert it to cms:}
-Daily <- \hlfunctioncall{getDVData}(siteNumber, \hlstring{"00060"}, startDate, endDate)
+\hlstd{siteNumber} \hlkwb{<-} \hlstr{"01491000"}
+\hlstd{startDate} \hlkwb{<-} \hlstr{"2000-01-01"}
+\hlstd{endDate} \hlkwb{<-} \hlstr{"2013-01-01"}
+\hlcom{# This call will get NWIS (cfs) data , and convert it to cms:}
+\hlstd{Daily} \hlkwb{<-} \hlkwd{getDVData}\hlstd{(siteNumber,} \hlstr{"00060"}\hlstd{, startDate, endDate)}
\end{alltt}
\begin{verbatim}
-There are 4750 data points, and 4750 days.
+There are 4750 data points, and 4750 days.
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -662,7 +648,7 @@ There are 4750 data points, and 4750 days.
Details of the Daily dataframe are listed below:
% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Thu Aug 01 16:23:22 2013
+% Wed Sep 04 12:53:59 2013
\begin{table}[ht]
\centering
\begin{tabular}{rllll}
@@ -701,9 +687,9 @@ The function to obtain USGS sample data from the water quality portal is getSamp
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-parameterCd <- \hlstring{"00618"}
-Sample <-\hlfunctioncall{getSampleData}(siteNumber,parameterCd,
- startDate, endDate)
+\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00618"}
+\hlstd{Sample} \hlkwb{<-}\hlkwd{getSampleData}\hlstd{(siteNumber,parameterCd,}
+ \hlstd{startDate, endDate)}
\end{alltt}
\end{kframe}
\end{knitrout}
@@ -714,10 +700,10 @@ The function to obtain STORET sample data from the water quality portal is getST
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-site <- \hlstring{'WIDNR_WQX-10032762'}
-characteristicName <- \hlstring{'Specific conductance'}
-Sample <-\hlfunctioncall{getSTORETSampleData}(site,characteristicName,
- startDate, endDate)
+\hlstd{site} \hlkwb{<-} \hlstr{'WIDNR_WQX-10032762'}
+\hlstd{characteristicName} \hlkwb{<-} \hlstr{'Specific conductance'}
+\hlstd{Sample} \hlkwb{<-}\hlkwd{getSTORETSampleData}\hlstd{(site,characteristicName,}
+ \hlstd{startDate, endDate)}
\end{alltt}
\end{kframe}
\end{knitrout}
@@ -771,7 +757,7 @@ As an example to understand how the dataRetrieval package handles a more complex
\begin{center}
% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Thu Aug 01 16:23:24 2013
+% Wed Sep 04 12:54:01 2013
\begin{table}[ht]
\centering
\begin{tabular}{rllrlrlr}
@@ -854,10 +840,10 @@ The call to open this file, convert the discharge to cubic meters per second, an
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-fileName <- \hlstring{"ChoptankRiverFlow.txt"}
-filePath <- \hlstring{"C:/RData/"}
-Daily <- \hlfunctioncall{getDailyDataFromFile}(filePath,fileName,
- separator=\hlstring{"\textbackslash{}t"})
+\hlstd{fileName} \hlkwb{<-} \hlstr{"ChoptankRiverFlow.txt"}
+\hlstd{filePath} \hlkwb{<-} \hlstr{"C:/RData/"}
+\hlstd{Daily} \hlkwb{<-} \hlkwd{getDailyDataFromFile}\hlstd{(filePath,fileName,}
+ \hlkwc{separator}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
\end{alltt}
\end{kframe}
\end{knitrout}
@@ -883,10 +869,10 @@ The call to open this file, and populate the Sample dataframe would be:
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-fileName <- \hlstring{"ChoptankRiverNitrate.csv"}
-filePath <- \hlstring{"C:/RData/"}
-Sample <- \hlfunctioncall{getSampleDataFromFile}(filePath,fileName,
- separator=\hlstring{","})
+\hlstd{fileName} \hlkwb{<-} \hlstr{"ChoptankRiverNitrate.csv"}
+\hlstd{filePath} \hlkwb{<-} \hlstr{"C:/RData/"}
+\hlstd{Sample} \hlkwb{<-} \hlkwd{getSampleDataFromFile}\hlstd{(filePath,fileName,}
+ \hlkwc{separator}\hlstd{=}\hlstr{","}\hlstd{)}
\end{alltt}
\end{kframe}
\end{knitrout}
@@ -903,19 +889,18 @@ Finally, there is a function called mergeReport that will look at both the Daily
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-siteNumber <- \hlstring{"01491000"}
-parameterCd <- \hlstring{"00631"} # Nitrate
-startDate <- \hlstring{"2000-01-01"}
-endDate <- \hlstring{"2013-01-01"}
-
-Daily <- \hlfunctioncall{getDVData}(siteNumber, \hlstring{"00060"}, startDate, endDate)
+\hlstd{siteNumber} \hlkwb{<-} \hlstr{"01491000"}
+\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00631"} \hlcom{# Nitrate}
+\hlstd{startDate} \hlkwb{<-} \hlstr{"2000-01-01"}
+\hlstd{endDate} \hlkwb{<-} \hlstr{"2013-01-01"}
+\hlstd{Daily} \hlkwb{<-} \hlkwd{getDVData}\hlstd{(siteNumber,} \hlstr{"00060"}\hlstd{, startDate, endDate)}
\end{alltt}
\begin{verbatim}
-There are 4750 data points, and 4750 days.
+There are 4750 data points, and 4750 days.
\end{verbatim}
\begin{alltt}
-Sample <- \hlfunctioncall{getSampleData}(siteNumber,parameterCd, startDate, endDate)
-Sample <- \hlfunctioncall{mergeReport}()
+\hlstd{Sample} \hlkwb{<-} \hlkwd{getSampleData}\hlstd{(siteNumber,parameterCd, startDate, endDate)}
+\hlstd{Sample} \hlkwb{<-} \hlkwd{mergeReport}\hlstd{()}
\end{alltt}
\begin{verbatim}
@@ -928,7 +913,7 @@ Sample <- \hlfunctioncall{mergeReport}()
Percentage of the sample values that are censored is 0 %
\end{verbatim}
\begin{alltt}
-\hlfunctioncall{head}(Sample)
+\hlkwd{head}\hlstd{(Sample)}
\end{alltt}
\begin{verbatim}
Date ConcLow ConcHigh Uncen ConcAve Julian Month
@@ -960,9 +945,9 @@ As has been mentioned, the data is specifically formatted to be used with the EG
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlcomment{# Continuing Choptank example from the previous sections}
-\hlfunctioncall{library}(EGRET)
-\hlfunctioncall{multiPlotDataOverview}()
+\hlcom{# Continuing Choptank example from the previous sections}
+\hlkwd{library}\hlstd{(EGRET)}
+\hlkwd{multiPlotDataOverview}\hlstd{()}
\end{alltt}
\end{kframe}\begin{figure}[]
@@ -994,7 +979,7 @@ At any time, you can get information about any function in R by typing a questio
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-?removeDuplicates
+\hlopt{?}\hlstd{removeDuplicates}
\end{alltt}
\end{kframe}
\end{knitrout}
@@ -1004,7 +989,7 @@ To see the raw code for a particular code, type the name of the function:
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-removeDuplicates
+\hlstd{removeDuplicates}
\end{alltt}
\begin{verbatim}
function(localSample=Sample) {
@@ -1026,8 +1011,8 @@ Before installing dataRetrieval, the zoo packages must be installed from CRAN:
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlfunctioncall{install.packages}(\hlstring{"zoo"})
-\hlfunctioncall{install.packages}(\hlstring{"dataRetrieval"}, repos=\hlstring{"http://usgs-r.github.com"}, type=\hlstring{"source"})
+\hlkwd{install.packages}\hlstd{(}\hlstr{"zoo"}\hlstd{)}
+\hlkwd{install.packages}\hlstd{(}\hlstr{"dataRetrieval"}\hlstd{,} \hlkwc{repos}\hlstd{=}\hlstr{"http://usgs-r.github.com"}\hlstd{,} \hlkwc{type}\hlstd{=}\hlstr{"source"}\hlstd{)}
\end{alltt}
\end{kframe}
\end{knitrout}
@@ -1039,7 +1024,7 @@ After installing the package, you need to open the library each time you re-star
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlfunctioncall{library}(dataRetrieval)
+\hlkwd{library}\hlstd{(dataRetrieval)}
\end{alltt}
\end{kframe}
\end{knitrout}
@@ -1056,7 +1041,7 @@ After installing the package, you need to open the library each time you re-star
%------------------------------------------------------------
% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Thu Aug 01 16:23:26 2013
+% Wed Sep 04 12:54:04 2013
\begin{table}[ht]
\centering
\begin{tabular}{rl}
@@ -1122,7 +1107,7 @@ After installing the package, you need to open the library each time you re-star
There are 62 columns returned from the water quality portal.
% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Thu Aug 01 16:23:26 2013
+% Wed Sep 04 12:54:04 2013
\begin{table}[ht]
\centering
\begin{tabular}{rl}
@@ -1179,7 +1164,7 @@ There are 62 columns returned from the water quality portal.
\FloatBarrier
% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Thu Aug 01 16:23:26 2013
+% Wed Sep 04 12:54:04 2013
\begin{table}[ht]
\centering
\begin{tabular}{rl}
@@ -1226,19 +1211,18 @@ There are a few steps that are required in order to create a table in a Microsof
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-availableData <- \hlfunctioncall{getDataAvailability}(siteNumber)
-dailyData <- availableData[\hlstring{"dv"} == availableData$service,]
-dailyData <- dailyData[\hlstring{"00003"} == dailyData$statCd,]
-
-tableData <- \hlfunctioncall{with}(dailyData,
- \hlfunctioncall{data.frame}(
- shortName=srsname,
- Start=startDate,
- End=endDate,
- Count=count,
- Units=parameter_units)
- )
-tableData
+\hlstd{availableData} \hlkwb{<-} \hlkwd{getDataAvailability}\hlstd{(siteNumber)}
+\hlstd{dailyData} \hlkwb{<-} \hlstd{availableData[}\hlstr{"dv"} \hlopt{==} \hlstd{availableData}\hlopt{$}\hlstd{service,]}
+\hlstd{dailyData} \hlkwb{<-} \hlstd{dailyData[}\hlstr{"00003"} \hlopt{==} \hlstd{dailyData}\hlopt{$}\hlstd{statCd,]}
+\hlstd{tableData} \hlkwb{<-} \hlkwd{with}\hlstd{(dailyData,}
+ \hlkwd{data.frame}\hlstd{(}
+ \hlkwc{shortName}\hlstd{=srsname,}
+ \hlkwc{Start}\hlstd{=startDate,}
+ \hlkwc{End}\hlstd{=endDate,}
+ \hlkwc{Count}\hlstd{=count,}
+ \hlkwc{Units}\hlstd{=parameter_units)}
+ \hlstd{)}
+\hlstd{tableData}
\end{alltt}
\begin{verbatim}
shortName Start
@@ -1249,7 +1233,7 @@ tableData
5 Suspended sediment discharge 1980-10-01
End Count Units
1 2012-05-09 529 deg C
-2 2013-07-31 23954 cfs
+2 2013-09-03 23988 ft3/s
3 2012-05-09 527 uS/cm @25C
4 1991-09-30 3651 mg/l
5 1991-09-30 3652 tons/day
@@ -1264,8 +1248,8 @@ First, save the dataframe as a tab delimited file (you don't want to use comma d
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlfunctioncall{write.table}(tableData, file=\hlstring{"tableData.tsv"},sep=\hlstring{"\textbackslash{}t"},
- row.names = FALSE,quote=FALSE)
+\hlkwd{write.table}\hlstd{(tableData,} \hlkwc{file}\hlstd{=}\hlstr{"tableData.tsv"}\hlstd{,}\hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{,}
+ \hlkwc{row.names} \hlstd{=} \hlnum{FALSE}\hlstd{,}\hlkwc{quote}\hlstd{=}\hlnum{FALSE}\hlstd{)}
\end{alltt}
\end{kframe}
\end{knitrout}
diff --git a/vignettes/figure/egretEx.pdf b/vignettes/figure/egretEx.pdf
index abea195b57302f3f31613fec67458ca0ba9e306f..c87255f3930e3fe52f3edeb2d6ab6e64c040483e 100644
Binary files a/vignettes/figure/egretEx.pdf and b/vignettes/figure/egretEx.pdf differ
diff --git a/vignettes/figure/getNWIStemperaturePlot.pdf b/vignettes/figure/getNWIStemperaturePlot.pdf
index 9ed9ce86f465f8b9e72fa78b6e7c4544bfc3b4b0..94b837efafd84e0a04937a5c203de8a0f0302fa7 100644
Binary files a/vignettes/figure/getNWIStemperaturePlot.pdf and b/vignettes/figure/getNWIStemperaturePlot.pdf differ
diff --git a/vignettes/figure/getQWtemperaturePlot.pdf b/vignettes/figure/getQWtemperaturePlot.pdf
index dd10677a2b3c7827775300fbbc193066db98cb9c..170c9fa2481bbb9eff18433cea0892e2dbd2fad5 100644
Binary files a/vignettes/figure/getQWtemperaturePlot.pdf and b/vignettes/figure/getQWtemperaturePlot.pdf differ