diff --git a/NAMESPACE b/NAMESPACE
index 0a98d2bf9c9d85c35e406542ce00371798c987c7..74920c94e566ee84bbda77120cd7d706466c407b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -8,7 +8,6 @@ export(dataOverview)
export(dateFormatCheck)
export(formatCheckDate)
export(formatCheckParameterCd)
-export(formatCheckSiteNumber)
export(getDVData)
export(getDailyDataFromFile)
export(getDataAvailability)
diff --git a/R/constructNWISURL.r b/R/constructNWISURL.r
index d638f8d5fbc3965c18a0373c99711abd4d362c60..7b3e72279dbd672e99487e5f3d207c67c9150b95 100644
--- a/R/constructNWISURL.r
+++ b/R/constructNWISURL.r
@@ -89,8 +89,7 @@ constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,st
}
},
wqp = {
- siteNumber <- formatCheckSiteNumber(siteNumber, interactive=interactive)
-
+
#Check for pcode:
if(all(nchar(parameterCd) == 5)){
suppressWarnings(pCodeLogic <- all(!is.na(as.numeric(parameterCd))))
@@ -122,8 +121,7 @@ constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,st
"&countrycode=US&mimeType=tsv",sep = "")
},
{ # this will be either dv or uv
- siteNumber <- formatCheckSiteNumber(siteNumber, interactive=interactive)
-
+
# Check for 5 digit parameter code:
if(length(parameterCd)>1){
parameterCd <- paste(parameterCd, collapse=",")
@@ -145,8 +143,6 @@ constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,st
} else {
warning("non-supported format requested, please choose xml or tsv")
}
-
-
url <- paste(baseURL,"/?site=",siteNumber, "&ParameterCd=",parameterCd, "&format=", format, sep = "")
diff --git a/R/dateFormatCheck.r b/R/dateFormatCheck.r
index f01570bd58d8d00e3904ec230e15e1471b2e8c02..c3f9dbdf3858a14b51d145347446955280f5b3f1 100644
--- a/R/dateFormatCheck.r
+++ b/R/dateFormatCheck.r
@@ -9,6 +9,8 @@
#' @examples
#' date <- '1985-01-01'
#' dateFormatCheck(date)
+#' dateWrong <- '1999/1/7'
+#' dateFormatCheck(dateWrong)
dateFormatCheck <- function(date){ # checks for the format YYYY-MM-DD
parts <- strsplit(date,"-",fixed=TRUE)
condition <- FALSE
diff --git a/R/formatCheckSiteNumber.r b/R/formatCheckSiteNumber.r
deleted file mode 100644
index d673a4be2befa8d366bd907db5ab1213c93696bc..0000000000000000000000000000000000000000
--- a/R/formatCheckSiteNumber.r
+++ /dev/null
@@ -1,25 +0,0 @@
-#' formatCheckSiteNumber
-#'
-#' Checks that the site code is at least 8 digits. If not, it confirms with the user.
-#' @param siteNumber string to check
-#' @param interactive logical Option for interactive mode. If true, there is user interaction for error handling and data checks.
-#' @keywords WRTDS flow
-#' @return siteNumber string
-#' @export
-#' @examples
-#' site<- '01234567'
-#' formatCheckSiteNumber(site)
-formatCheckSiteNumber <- function(siteNumber, interactive=TRUE){ #checks for a 8 digit number
- if (nchar(siteNumber) < 8){
- if (interactive){
- cat("Most common USGS site numbers are at least 8 digits long, you entered a ", nchar(siteNumber), "digit number = ", siteNumber , ".\n")
- cat("If you would like to change the site id, enter it here (no quotes), otherwise hit return:\n")
- tempSiteID <- readline()
- if (nzchar(tempSiteID)) siteNumber <- tempSiteID
- } else {
- warningMessage <- paste("Most common USGS site numbers are at least 8 digits long, you entered ", siteNumber , ".", sep="")
- warning(warningMessage)
- }
- }
- return(siteNumber)
-}
diff --git a/R/getDataAvailability.r b/R/getDataAvailability.r
index a54f9651c4e1ac7c300352d405ab29e2985fdcaf..a217d83a4ef13bf0c1aedeaa0d7142f2c4e0e3a0 100644
--- a/R/getDataAvailability.r
+++ b/R/getDataAvailability.r
@@ -11,9 +11,12 @@
#' # These examples require an internet connection to run
#' availableData <- getDataAvailability('05114000')
#' # To find just unit value ('instantaneous') data:
-#' uvData <- availableData <- getDataAvailability('05114000',type="uv")
+#' uvData <- getDataAvailability('05114000',type="uv")
+#' uvDataMulti <- getDataAvailability(c('05114000','09423350'),type="uv")
getDataAvailability <- function(siteNumber,type=c("uv","dv","qw")){
+ siteNumber <- paste(siteNumber,collapse=",")
+
urlSitefile <- paste("http://waterservices.usgs.gov/nwis/site/?format=rdb&seriesCatalogOutput=true&sites=",siteNumber,sep = "")
doc = tryCatch({
diff --git a/R/getMetaData.r b/R/getMetaData.r
index a4761240f0a4b9f461577cc397d254bdf7d01b32..9793e2e311c4ff868dc93261c845774b03fb4589 100644
--- a/R/getMetaData.r
+++ b/R/getMetaData.r
@@ -20,7 +20,7 @@
#' INFO <- getMetaData('05114000','00010')
getMetaData <- function(siteNumber="", parameterCd="",interactive=TRUE){
if (nzchar(siteNumber)){
- INFO <- getSiteFileData(siteNumber,interactive=interactive)
+ INFO <- getSiteFileData(siteNumber)
} else {
INFO <- as.data.frame(matrix(ncol = 2, nrow = 1))
names(INFO) <- c('site.no', 'shortName')
diff --git a/R/getNWISSites.R b/R/getNWISSites.R
index 1b720c3806bff87ab94c41b16830d5f6d2138f92..9d756c7c0618a8d4d9e256c9d22f77168cc3a442 100644
--- a/R/getNWISSites.R
+++ b/R/getNWISSites.R
@@ -18,7 +18,7 @@ getNWISSites <- function(...){
urlCall <- paste(paste(names(values),values,sep="="),collapse="&")
- baseURL <- "http://waterservices.usgs.gov/nwis/site/?format=rdb&siteOutput=expanded&"
+ baseURL <- "http://waterservices.usgs.gov/nwis/site/?format=rdb&"
urlCall <- paste(baseURL,
urlCall,sep = "")
diff --git a/R/getQWDataFromFile.r b/R/getQWDataFromFile.r
index c9a40aa22ca82649432dda3e7b4645edce41cd60..c005ea65ecc643250ba409a905605f3316e8bb93 100644
--- a/R/getQWDataFromFile.r
+++ b/R/getQWDataFromFile.r
@@ -15,11 +15,12 @@
#' @examples
#' # Examples of how to use getQWDataFromFile:
#' # Change the file path and file name to something meaningful:
-#' filePath <- '~/RData/' # Sample format
+#' filePath <- system.file("extdata", package="dataRetrieval")
+#' filePath <- paste(filePath,"/",sep="")
#' fileName <- 'ChoptankRiverNitrate.csv'
-#' \dontrun{rawSampleData <- getQWDataFromFile(filePath,fileName, separator=";")}
+#' rawSampleData <- getQWDataFromFile(filePath,fileName, separator=";")
getQWDataFromFile <- function (filePath,fileName,hasHeader=TRUE,separator=","){
- totalPath <- paste(filePath,fileName,sep="");
+ totalPath <- paste(filePath,fileName,sep="")
tmp <- read.delim(
totalPath,
header = hasHeader,
@@ -29,5 +30,17 @@ getQWDataFromFile <- function (filePath,fileName,hasHeader=TRUE,separator=","){
comment.char="#")
retval <- as.data.frame(tmp, stringsAsFactors=FALSE)
- return (retval)
+ names(retval)[1:3] <- c("dateTime","code","value")
+
+ if(dateFormatCheck(retval$dateTime[1])){
+ retval$dateTime <- as.Date(retval$dateTime)
+
+ compressedData <- compressData(retval)
+ Sample <- populateSampleColumns(compressedData)
+ return (Sample)
+ } else {
+ warning("Please adjust date formatting to 'YYYY-MM-DD'")
+ return(NA)
+ }
+
}
diff --git a/R/getRDB1Data.r b/R/getRDB1Data.r
index 3bb264d60333cab989dea8d0fb2bca9ad29125bc..c6e8ce718904895ef6a171db84ca333f23c565e5 100644
--- a/R/getRDB1Data.r
+++ b/R/getRDB1Data.r
@@ -62,8 +62,10 @@ getRDB1Data <- function(obs_url,asDateTime=FALSE){
data <- data[findRowsWithHeaderInfo,]
}
-
- if(sum(regexpr('d$', dataType) > 0) > 0){
+
+ data[,grep('n$', dataType)] <- suppressWarnings(sapply(data[,grep('n$', dataType)], function(x) as.numeric(x)))
+
+ if(length(grep('d$', dataType)) > 0){
if (asDateTime){
timeZoneLibrary <- setNames(c("America/New_York","America/New_York","America/Chicago","America/Chicago",
@@ -82,22 +84,17 @@ getRDB1Data <- function(obs_url,asDateTime=FALSE){
for(i in additionalTZs){
data[timeZone == i,regexpr('d$', dataType) > 0] <- as.POSIXct(data[,regexpr('d$', dataType) > 0], "%Y-%m-%d %H:%M", tz = i)
}
-
-# for(i in seq_along(row.names(data))){
-# data[i,regexpr('d$', dataType) > 0] <- as.POSIXct(data[i,regexpr('d$', dataType) > 0], "%Y-%m-%d %H:%M", tz = timeZone[i])
-# }
}
} else {
- data[,regexpr('d$', dataType) > 0] <- as.Date(data[,regexpr('d$', dataType) > 0])
+ for (i in grep('d$', dataType)){
+ data[,i] <- as.Date(data[,i])
+ }
+
+
}
}
- if (sum(regexpr('n$', dataType) > 0) > 0){
- tempDF <- data[,which(regexpr('n$', dataType) > 0)]
- tempDF <- suppressWarnings(sapply(tempDF, function(x) as.numeric(x)))
- data[,which(regexpr('n$', dataType) > 0)] <- tempDF
- }
row.names(data) <- NULL
return(data)
} else {
diff --git a/R/getSiteFileData.r b/R/getSiteFileData.r
index 228a49c701f56fcdadd9d442482d132b006b9418..c8f71f56145d1e6ba5c502119308cd61fd102091 100644
--- a/R/getSiteFileData.r
+++ b/R/getSiteFileData.r
@@ -3,18 +3,16 @@
#' Imports data from USGS site file site. This function gets data from here: \url{http://waterservices.usgs.gov/}
#'
#' @param siteNumber string USGS site number. This is usually an 8 digit number
-#' @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 retval dataframe with all information found in the expanded site file
#' @export
#' @examples
#' # These examples require an internet connection to run
#' siteINFO <- getSiteFileData('05114000')
-getSiteFileData <- function(siteNumber="",interactive=TRUE){
-
- # Checking for 8 digit site ID:
- siteNumber <- formatCheckSiteNumber(siteNumber, interactive=interactive)
+#' siteINFOMulti <- getSiteFileData(c('05114000','09423350'))
+getSiteFileData <- function(siteNumber){
+ siteNumber <- paste(siteNumber,collapse=",")
urlSitefile <- paste("http://waterservices.usgs.gov/nwis/site/?format=rdb&siteOutput=Expanded&sites=",siteNumber,sep = "")
doc = tryCatch({
diff --git a/data/ChoptankRiverNitrate.csv b/data/ChoptankRiverNitrate.csv
index d24d64fccc92f215cbe517fc3a8503a68da2af07..dbe882ea77d4f2238f20ec9d5e18642a52c80e38 100644
--- a/data/ChoptankRiverNitrate.csv
+++ b/data/ChoptankRiverNitrate.csv
@@ -1,205 +1,8 @@
cdate;remarkCode;Nitrate
-10/7/1999;;1.4
-11/4/1999;;0.99
-12/3/1999;;1.42
-1/4/2000;;1.59
-2/3/2000;;1.54
-2/15/2000;;1.37
-2/19/2000;;1.24
-3/23/2000;;0.52
-6/5/2000;;1.11
-7/5/2000;;0.9
-7/27/2000;;0.89
-8/3/2000;;0.69
-8/15/2000;;0.78
-8/15/2000;;0.5
-9/5/2000;;0.44
-9/13/2000;;1.09
-10/4/2000;;1.27
-11/7/2000;;1.41
-12/4/2000;;1.29
-12/18/2000;;0.64
-1/3/2001;;1.81
-1/20/2001;;1.36
-2/6/2001;;1.23
-3/8/2001;;1.34
-3/22/2001;;0.58
-4/4/2001;;1.35
-5/3/2001;;1.24
-5/31/2001;;1.27
-6/18/2001;;0.64
-7/2/2001;;1.42
-8/1/2001;;1.55
-9/10/2001;;1.5
-10/3/2001;;1.51
-11/6/2001;;1.16
-12/5/2001;;1.38
-1/8/2002;;1.76
-2/5/2002;;1.47
-3/12/2002;;1.13
-3/18/2002;;0.97
-3/27/2002;;1.24
-4/5/2002;;0.73
-5/3/2002;;0.65
-6/7/2002;;0.96
-7/10/2002;;1.01
-7/24/2002;;1.28
-8/1/2002;;1.26
-8/29/2002;;1.53
-9/6/2002;;1.06
-10/1/2002;;1.23
-10/11/2002;;0.97
-10/31/2002;;1.17
-11/7/2002;;1.38
-11/13/2002;;0.9
-12/4/2002;;2.09
-12/12/2002;;1.48
-1/2/2003;;1.41
-1/13/2003;;2
-2/5/2003;;1.76
-2/24/2003;;0.76
-3/26/2003;;1.27
-4/10/2003;;0.97
-4/16/2003;;1.18
-5/13/2003;;1.27
-5/27/2003;;0.85
-6/24/2003;;0.87
-7/17/2003;;1.05
-8/5/2003;;1.28
-9/16/2003;;0.39
-10/9/2003;;1.6
-10/28/2003;;1.51
-11/7/2003;;0.43
-11/17/2003;;1.42
-12/9/2003;;1.44
-1/14/2004;;2.17
-2/12/2004;;1.43
-3/3/2004;;1.54
-4/7/2004;;1.18
-4/14/2004;;0.75
-5/12/2004;;1.13
-6/1/2004;;1.67
-7/7/2004;;1.1
-8/3/2004;;0.98
-9/7/2004;;1.15
-10/6/2004;;1.28
-11/1/2004;;0.94
-11/30/2004;;0.86
-12/7/2004;;1.42
-1/4/2005;;1.49
-2/15/2005;;1.63
-3/22/2005;;1.38
-3/25/2005;;1.04
-4/4/2005;;0.6
-4/19/2005;;1.54
-5/17/2005;;1.38
-6/1/2005;;1.37
-7/6/2005;;1.32
-8/3/2005;;1.18
-9/12/2005;;1.23
-10/10/2005;;0.74
-11/9/2005;;1.46
-12/8/2005;;1.72
-1/4/2006;;1.17
-1/10/2006;;1.93
-1/24/2006;;0.98
-2/6/2006;;1.7
-3/9/2006;;1.87
-4/18/2006;;1.18
-4/23/2006;;1.15
-5/11/2006;;1.33
-6/7/2006;;1.34
-6/26/2006;;1.14
-7/12/2006;;1.29
-8/8/2006;;1.51
-9/5/2006;;0.96
-10/3/2006;;1.75
-11/7/2006;;1.75
-11/9/2006;;1.25
-11/14/2006;;0.62
-12/11/2006;;2.17
-1/2/2007;;1.1
-1/9/2007;;0.56
-2/13/2007;;2.36
-3/6/2007;;1.52
-4/10/2007;;1.37
-4/13/2007;;1.14
-4/18/2007;;0.87
-5/10/2007;;1.59
-6/4/2007;;1.35
-7/5/2007;;1.46
-8/27/2007;;1.68
-9/10/2007;;1.58
-10/2/2007;;1.66
-10/25/2007;;1.06
-11/15/2007;;1.66
-12/3/2007;;1.42
-12/17/2007;;1.29
-1/4/2008;;1.74
-2/6/2008;;1.58
-2/14/2008;;1.46
-3/5/2008;;1.59
-3/9/2008;;0.6
-4/10/2008;;1.25
-5/12/2008;;0.93
-5/13/2008;;0.69
-6/5/2008;;1.29
-7/8/2008;;1.27
-8/6/2008;;1.69
-9/3/2008;;2.14
-9/8/2008;;1.43
-10/1/2008;;1.64
-10/27/2008;;1.56
-10/29/2008;;1.36
-11/6/2008;;1.12
-12/2/2008;;1.62
-12/12/2008;;1.4
-1/8/2009;;1.66
-2/2/2009;;1.86
-3/12/2009;;1.18
-3/30/2009;;0.96
-4/15/2009;;0.95
-5/4/2009;;1.04
-6/1/2009;;1.22
-6/11/2009;;0.72
-7/6/2009;;1.29
-8/12/2009;;1.49
-8/24/2009;;0.31
-9/8/2009;;1.54
-10/5/2009;;1.55
-10/29/2009;;0.3
-11/9/2009;;1.59
-11/14/2009;;0.57
-12/3/2009;;1.08
-12/10/2009;;0.31
-1/12/2010;;2.43
-1/26/2010;;0.84
-3/9/2010;;1.6
-3/15/2010;;0.69
-4/8/2010;;1.25
-4/27/2010;;1.21
-5/6/2010;;1.54
-5/19/2010;;1.36
-6/4/2010;;1.43
-7/8/2010;;1.51
-7/12/2010;;1.02
-7/14/2010;;1.13
-8/2/2010;;1.46
-9/1/2010;;1.78
-10/1/2010;;0.74
-10/1/2010;;0.75
-10/13/2010;;1.81
-12/8/2010;;1.74
-1/10/2011;;1.8
-2/3/2011;;0.94
-3/1/2011;;1.18
-3/7/2011;;0.97
-4/13/2011;;0.99
-4/18/2011;;0.57
-5/16/2011;;1.23
-6/14/2011;;1.74
-7/13/2011;;1.39
-8/9/2011;;1.54
-8/15/2011;;0.92
-9/8/2011;;0.78
-9/29/2011;;0.8
+1999-10-07;;1.4
+1999-11-04;;0.99
+1999-12-30;;1.42
+2000-01-04;;1.59
+2000-02-03;;1.54
+2000-02-15;;1.37
+2000-02-19;;1.24
diff --git a/inst/extdata/ChoptankRiverNitrate.csv b/inst/extdata/ChoptankRiverNitrate.csv
index d24d64fccc92f215cbe517fc3a8503a68da2af07..dbe882ea77d4f2238f20ec9d5e18642a52c80e38 100644
--- a/inst/extdata/ChoptankRiverNitrate.csv
+++ b/inst/extdata/ChoptankRiverNitrate.csv
@@ -1,205 +1,8 @@
cdate;remarkCode;Nitrate
-10/7/1999;;1.4
-11/4/1999;;0.99
-12/3/1999;;1.42
-1/4/2000;;1.59
-2/3/2000;;1.54
-2/15/2000;;1.37
-2/19/2000;;1.24
-3/23/2000;;0.52
-6/5/2000;;1.11
-7/5/2000;;0.9
-7/27/2000;;0.89
-8/3/2000;;0.69
-8/15/2000;;0.78
-8/15/2000;;0.5
-9/5/2000;;0.44
-9/13/2000;;1.09
-10/4/2000;;1.27
-11/7/2000;;1.41
-12/4/2000;;1.29
-12/18/2000;;0.64
-1/3/2001;;1.81
-1/20/2001;;1.36
-2/6/2001;;1.23
-3/8/2001;;1.34
-3/22/2001;;0.58
-4/4/2001;;1.35
-5/3/2001;;1.24
-5/31/2001;;1.27
-6/18/2001;;0.64
-7/2/2001;;1.42
-8/1/2001;;1.55
-9/10/2001;;1.5
-10/3/2001;;1.51
-11/6/2001;;1.16
-12/5/2001;;1.38
-1/8/2002;;1.76
-2/5/2002;;1.47
-3/12/2002;;1.13
-3/18/2002;;0.97
-3/27/2002;;1.24
-4/5/2002;;0.73
-5/3/2002;;0.65
-6/7/2002;;0.96
-7/10/2002;;1.01
-7/24/2002;;1.28
-8/1/2002;;1.26
-8/29/2002;;1.53
-9/6/2002;;1.06
-10/1/2002;;1.23
-10/11/2002;;0.97
-10/31/2002;;1.17
-11/7/2002;;1.38
-11/13/2002;;0.9
-12/4/2002;;2.09
-12/12/2002;;1.48
-1/2/2003;;1.41
-1/13/2003;;2
-2/5/2003;;1.76
-2/24/2003;;0.76
-3/26/2003;;1.27
-4/10/2003;;0.97
-4/16/2003;;1.18
-5/13/2003;;1.27
-5/27/2003;;0.85
-6/24/2003;;0.87
-7/17/2003;;1.05
-8/5/2003;;1.28
-9/16/2003;;0.39
-10/9/2003;;1.6
-10/28/2003;;1.51
-11/7/2003;;0.43
-11/17/2003;;1.42
-12/9/2003;;1.44
-1/14/2004;;2.17
-2/12/2004;;1.43
-3/3/2004;;1.54
-4/7/2004;;1.18
-4/14/2004;;0.75
-5/12/2004;;1.13
-6/1/2004;;1.67
-7/7/2004;;1.1
-8/3/2004;;0.98
-9/7/2004;;1.15
-10/6/2004;;1.28
-11/1/2004;;0.94
-11/30/2004;;0.86
-12/7/2004;;1.42
-1/4/2005;;1.49
-2/15/2005;;1.63
-3/22/2005;;1.38
-3/25/2005;;1.04
-4/4/2005;;0.6
-4/19/2005;;1.54
-5/17/2005;;1.38
-6/1/2005;;1.37
-7/6/2005;;1.32
-8/3/2005;;1.18
-9/12/2005;;1.23
-10/10/2005;;0.74
-11/9/2005;;1.46
-12/8/2005;;1.72
-1/4/2006;;1.17
-1/10/2006;;1.93
-1/24/2006;;0.98
-2/6/2006;;1.7
-3/9/2006;;1.87
-4/18/2006;;1.18
-4/23/2006;;1.15
-5/11/2006;;1.33
-6/7/2006;;1.34
-6/26/2006;;1.14
-7/12/2006;;1.29
-8/8/2006;;1.51
-9/5/2006;;0.96
-10/3/2006;;1.75
-11/7/2006;;1.75
-11/9/2006;;1.25
-11/14/2006;;0.62
-12/11/2006;;2.17
-1/2/2007;;1.1
-1/9/2007;;0.56
-2/13/2007;;2.36
-3/6/2007;;1.52
-4/10/2007;;1.37
-4/13/2007;;1.14
-4/18/2007;;0.87
-5/10/2007;;1.59
-6/4/2007;;1.35
-7/5/2007;;1.46
-8/27/2007;;1.68
-9/10/2007;;1.58
-10/2/2007;;1.66
-10/25/2007;;1.06
-11/15/2007;;1.66
-12/3/2007;;1.42
-12/17/2007;;1.29
-1/4/2008;;1.74
-2/6/2008;;1.58
-2/14/2008;;1.46
-3/5/2008;;1.59
-3/9/2008;;0.6
-4/10/2008;;1.25
-5/12/2008;;0.93
-5/13/2008;;0.69
-6/5/2008;;1.29
-7/8/2008;;1.27
-8/6/2008;;1.69
-9/3/2008;;2.14
-9/8/2008;;1.43
-10/1/2008;;1.64
-10/27/2008;;1.56
-10/29/2008;;1.36
-11/6/2008;;1.12
-12/2/2008;;1.62
-12/12/2008;;1.4
-1/8/2009;;1.66
-2/2/2009;;1.86
-3/12/2009;;1.18
-3/30/2009;;0.96
-4/15/2009;;0.95
-5/4/2009;;1.04
-6/1/2009;;1.22
-6/11/2009;;0.72
-7/6/2009;;1.29
-8/12/2009;;1.49
-8/24/2009;;0.31
-9/8/2009;;1.54
-10/5/2009;;1.55
-10/29/2009;;0.3
-11/9/2009;;1.59
-11/14/2009;;0.57
-12/3/2009;;1.08
-12/10/2009;;0.31
-1/12/2010;;2.43
-1/26/2010;;0.84
-3/9/2010;;1.6
-3/15/2010;;0.69
-4/8/2010;;1.25
-4/27/2010;;1.21
-5/6/2010;;1.54
-5/19/2010;;1.36
-6/4/2010;;1.43
-7/8/2010;;1.51
-7/12/2010;;1.02
-7/14/2010;;1.13
-8/2/2010;;1.46
-9/1/2010;;1.78
-10/1/2010;;0.74
-10/1/2010;;0.75
-10/13/2010;;1.81
-12/8/2010;;1.74
-1/10/2011;;1.8
-2/3/2011;;0.94
-3/1/2011;;1.18
-3/7/2011;;0.97
-4/13/2011;;0.99
-4/18/2011;;0.57
-5/16/2011;;1.23
-6/14/2011;;1.74
-7/13/2011;;1.39
-8/9/2011;;1.54
-8/15/2011;;0.92
-9/8/2011;;0.78
-9/29/2011;;0.8
+1999-10-07;;1.4
+1999-11-04;;0.99
+1999-12-30;;1.42
+2000-01-04;;1.59
+2000-02-03;;1.54
+2000-02-15;;1.37
+2000-02-19;;1.24
diff --git a/man/dateFormatCheck.Rd b/man/dateFormatCheck.Rd
index ece1a7ee6004fa7534bdd87731916c2e231267ed..5800f638b3e0f91691724019061fc454b7f5613f 100644
--- a/man/dateFormatCheck.Rd
+++ b/man/dateFormatCheck.Rd
@@ -17,6 +17,8 @@ Checks to see if format is YYYY-MM-DD. Also performs a few other date checks.
\examples{
date <- '1985-01-01'
dateFormatCheck(date)
+dateWrong <- '1999/1/7'
+dateFormatCheck(dateWrong)
}
\keyword{WRTDS}
\keyword{flow}
diff --git a/man/formatCheckSiteNumber.Rd b/man/formatCheckSiteNumber.Rd
deleted file mode 100644
index 120e99d07e527a64cb0c63f0b01c65324ed438b1..0000000000000000000000000000000000000000
--- a/man/formatCheckSiteNumber.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{formatCheckSiteNumber}
-\alias{formatCheckSiteNumber}
-\title{formatCheckSiteNumber}
-\usage{
-formatCheckSiteNumber(siteNumber, interactive = TRUE)
-}
-\arguments{
-\item{siteNumber}{string to check}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-siteNumber string
-}
-\description{
-Checks that the site code is at least 8 digits. If not, it confirms with the user.
-}
-\examples{
-site<- '01234567'
-formatCheckSiteNumber(site)
-}
-\keyword{WRTDS}
-\keyword{flow}
-
diff --git a/man/getDataAvailability.Rd b/man/getDataAvailability.Rd
index 3e6e214702d7fc5e12f59ca255f1783104079035..805ccf8849b0acdf49348cf83413ef1ee9d9258e 100644
--- a/man/getDataAvailability.Rd
+++ b/man/getDataAvailability.Rd
@@ -20,7 +20,8 @@ Imports a table of available parameters, period of record, and count.
# These examples require an internet connection to run
availableData <- getDataAvailability('05114000')
# To find just unit value ('instantaneous') data:
-uvData <- availableData <- getDataAvailability('05114000',type="uv")
+uvData <- getDataAvailability('05114000',type="uv")
+uvDataMulti <- getDataAvailability(c('05114000','09423350'),type="uv")
}
\keyword{USGS}
\keyword{data}
diff --git a/man/getQWDataFromFile.Rd b/man/getQWDataFromFile.Rd
index cc00e2c25d6fe354baed86a6079df6063b6ec5f4..4817423c35c02776c47686aa4a72c2995fbce6ae 100644
--- a/man/getQWDataFromFile.Rd
+++ b/man/getQWDataFromFile.Rd
@@ -26,9 +26,10 @@ be a remark column preceeding.
\examples{
# Examples of how to use getQWDataFromFile:
# Change the file path and file name to something meaningful:
-filePath <- '~/RData/' # Sample format
+filePath <- system.file("extdata", package="dataRetrieval")
+filePath <- paste(filePath,"/",sep="")
fileName <- 'ChoptankRiverNitrate.csv'
-\dontrun{rawSampleData <- getQWDataFromFile(filePath,fileName, separator=";")}
+rawSampleData <- getQWDataFromFile(filePath,fileName, separator=";")
}
\keyword{data}
\keyword{file}
diff --git a/man/getSiteFileData.Rd b/man/getSiteFileData.Rd
index 510251a333e62c267c560b20df6ae5aae1ecacc8..6affa0fc76f9340e427f37c43b2dac813bf53e12 100644
--- a/man/getSiteFileData.Rd
+++ b/man/getSiteFileData.Rd
@@ -3,12 +3,10 @@
\alias{getSiteFileData}
\title{USGS Site File Data Retrieval}
\usage{
-getSiteFileData(siteNumber = "", interactive = TRUE)
+getSiteFileData(siteNumber)
}
\arguments{
\item{siteNumber}{string USGS site number. This is usually an 8 digit number}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
}
\value{
retval dataframe with all information found in the expanded site file
@@ -19,6 +17,7 @@ Imports data from USGS site file site. This function gets data from here: \url{h
\examples{
# These examples require an internet connection to run
siteINFO <- getSiteFileData('05114000')
+siteINFOMulti <- getSiteFileData(c('05114000','09423350'))
}
\keyword{USGS}
\keyword{data}
diff --git a/vignettes/dataRetrieval-concordance.tex b/vignettes/dataRetrieval-concordance.tex
index a7ff1f2180c6f5c1817cd311b3d1af91dd01f43c..c30df2de1f939d12dfcc4addeed47cb367388f51 100644
--- a/vignettes/dataRetrieval-concordance.tex
+++ b/vignettes/dataRetrieval-concordance.tex
@@ -1,9 +1,9 @@
\Sconcordance{concordance:dataRetrieval.tex:dataRetrieval.Rnw:%
-1 126 1 49 0 1 7 15 1 1 14 55 1 3 0 36 1 2 0 11 1 24 %
+1 127 1 49 0 1 7 15 1 1 14 55 1 3 0 36 1 2 0 11 1 24 %
0 24 1 3 0 23 1 3 0 6 1 7 0 18 1 3 0 25 1 1 0 17 1 9 %
0 6 1 7 0 21 1 8 0 16 1 2 0 11 1 23 0 21 1 9 0 20 1 3 %
0 6 1 17 0 27 1 6 0 11 1 9 0 15 1 12 0 19 1 4 0 21 1 %
4 0 17 1 7 0 22 1 8 0 19 1 4 0 9 1 4 0 78 1 1 2 9 1 1 %
-4 4 1 20 0 44 1 4 0 32 1 4 0 21 1 4 0 21 1 37 0 13 1 %
+4 4 1 20 0 44 1 4 0 30 1 4 0 22 1 4 0 21 1 37 0 13 1 %
9 0 94 1 4 0 9 1 13 0 13 1 4 0 14 1 4 0 5 1 4 0 23 1 %
18 0 8 1 4 0 55 1}
diff --git a/vignettes/dataRetrieval.Rnw b/vignettes/dataRetrieval.Rnw
index 3d6b42c173382c08a142a6a72f6b873d9b52269a..e20955c89472a3539281a31606b2bb380775d505 100644
--- a/vignettes/dataRetrieval.Rnw
+++ b/vignettes/dataRetrieval.Rnw
@@ -23,7 +23,7 @@
\usepackage{csquotes}
\usepackage{setspace}
-\doublespacing
+% \doublespacing
\renewcommand{\topfraction}{0.85}
\renewcommand{\textfraction}{0.1}
@@ -33,7 +33,8 @@
\usepackage{mathptmx}% Times Roman font
\usepackage[scaled=.90]{helvet}% Helvetica, served as a model for arial
-\usepackage{indentfirst}
+% \usepackage{indentfirst}
+% \setlength\parindent{20pt}
\setlength{\parskip}{0pt}
\usepackage{courier}
@@ -99,7 +100,7 @@
singlelinecheck=false
}
-\setlength\parindent{20pt}
+
\textwidth=6.2in
\textheight=8.5in
@@ -757,7 +758,7 @@ Finally, qUnit is a numeric argument that defines the discharge units used in th
So, if you have a file called \enquote{ChoptankRiverFlow.txt} located in a folder called \enquote{RData} on the C drive (this example is for the Windows\textregistered\ operating systems), and the file is structured as follows (tab-separated):
-\singlespacing
+% \singlespacing
\begin{verbatim}
date Qdaily
10/1/1999 107
@@ -768,7 +769,7 @@ date Qdaily
10/6/1999 98
...
\end{verbatim}
-\doublespacing
+% \doublespacing
The call to open this file, convert the discharge to cubic meters per second, and populate the Daily data frame would be:
<<openDaily, eval = FALSE>>=
@@ -787,7 +788,6 @@ Microsoft\textregistered\ Excel files can be a bit tricky to import into R direc
\label{sec:SampleFile}
%------------------------------------------------------------
-\doublespacing
The \texttt{getSampleDataFromFile} function will import a user-generated file and populate the Sample dataframe. The difference between sample data and discharge data is that the code requires a third column that contains a remark code, either blank or \verb@"<"@, which will tell the program that the data were \enquote{left-censored} (or, below the detection limit of the sensor). Therefore, the data must be in the form: date, remark, value. An example of a comma-delimited file is:
\singlespacing
@@ -800,7 +800,6 @@ cdate;remarkCode;Nitrate
2/3/2000,,1.54
...
\end{verbatim}
-\doublespacing
The call to open this file, and populate the Sample dataframe is:
<<openSample, eval = FALSE>>=
@@ -823,7 +822,8 @@ date rdp dp rpp pp rtp tp
2005-10-30 < 0.020
...
\end{verbatim}
-\doublespacing
+
+
<<openSample2, eval = FALSE>>=
fileName <- "ChoptankPhosphorus.txt"
filePath <- "C:/RData/"
diff --git a/vignettes/dataRetrieval.lof b/vignettes/dataRetrieval.lof
index 8ac527e5dae3d03e3e021d3ca84816bae57aa58a..603352223e668078ae445cfb60e567cf294ec38b 100644
--- a/vignettes/dataRetrieval.lof
+++ b/vignettes/dataRetrieval.lof
@@ -1,7 +1,7 @@
\select@language {american}
-\contentsline {figure}{\numberline {1}{\ignorespaces Temperature and discharge plot of Choptank River in 2012}}{11}{figure.caption.4}
-\contentsline {figure}{\numberline {2}{\ignorespaces Nitrate plot of Choptank River}}{14}{figure.caption.5}
-\contentsline {figure}{\numberline {3}{\ignorespaces Default multiPlotDataOverview}}{26}{figure.caption.10}
-\contentsline {figure}{\numberline {4}{\ignorespaces A simple R help file\relax }}{30}{figure.caption.14}
-\contentsline {figure}{\numberline {5}{\ignorespaces A simple table produced in Microsoft\textregistered \ Excel. Additional formatting will be requried, for example converting u to $\mu $ \relax }}{33}{figure.caption.15}
+\contentsline {figure}{\numberline {1}{\ignorespaces Temperature and discharge plot of Choptank River in 2012}}{10}{figure.caption.4}
+\contentsline {figure}{\numberline {2}{\ignorespaces Nitrate plot of Choptank River}}{13}{figure.caption.5}
+\contentsline {figure}{\numberline {3}{\ignorespaces Default multiPlotDataOverview}}{23}{figure.caption.10}
+\contentsline {figure}{\numberline {4}{\ignorespaces A simple R help file\relax }}{27}{figure.caption.14}
+\contentsline {figure}{\numberline {5}{\ignorespaces A simple table produced in Microsoft\textregistered \ Excel. Additional formatting will be requried, for example converting u to $\mu $ \relax }}{30}{figure.caption.15}
\contentsfinish
diff --git a/vignettes/dataRetrieval.log b/vignettes/dataRetrieval.log
index 815c8cec36ef1f415c819d72ed43b8bfebb6dbdb..34e622c2d5d5fa501f5705896d6824243d1752b1 100644
--- a/vignettes/dataRetrieval.log
+++ b/vignettes/dataRetrieval.log
@@ -1,4 +1,4 @@
-This is pdfTeX, Version 3.1415926-2.5-1.40.14 (MiKTeX 2.9) (preloaded format=pdflatex 2014.8.7) 11 SEP 2014 16:26
+This is pdfTeX, Version 3.1415926-2.5-1.40.14 (MiKTeX 2.9) (preloaded format=pdflatex 2014.8.7) 17 SEP 2014 13:24
entering extended mode
**dataRetrieval.tex
(D:\LADData\RCode\dataRetrieval\vignettes\dataRetrieval.tex
@@ -427,9 +427,6 @@ LaTeX Info: Redefining \hbar on input line 50.
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\psnfss\helvet.sty"
Package: helvet 2005/04/12 PSNFSS-v9.2a (WaS)
)
-("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\tools\indentfirst.sty"
-Package: indentfirst 1995/11/23 v1.03 Indent first paragraph (DPC)
-)
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\psnfss\courier.sty"
Package: courier 2005/04/12 PSNFSS-v9.2a (WaS)
)
@@ -540,29 +537,29 @@ Package csquotes Info: Adjusting default style.
Package csquotes Info: Redefining alias 'default' -> 'american'.
(D:\LADData\RCode\dataRetrieval\vignettes\dataRetrieval.aux)
-LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 174.
-LaTeX Font Info: ... okay on input line 174.
-LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 174.
-LaTeX Font Info: ... okay on input line 174.
-LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 174.
-LaTeX Font Info: ... okay on input line 174.
-LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 174.
-LaTeX Font Info: ... okay on input line 174.
-LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 174.
-LaTeX Font Info: ... okay on input line 174.
-LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 174.
-LaTeX Font Info: ... okay on input line 174.
-LaTeX Font Info: Checking defaults for PD1/pdf/m/n on input line 174.
-LaTeX Font Info: ... okay on input line 174.
-LaTeX Font Info: Checking defaults for TS1/cmr/m/n on input line 174.
-LaTeX Font Info: Try loading font information for TS1+cmr on input line 174.
+LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 175.
+LaTeX Font Info: ... okay on input line 175.
+LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 175.
+LaTeX Font Info: ... okay on input line 175.
+LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 175.
+LaTeX Font Info: ... okay on input line 175.
+LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 175.
+LaTeX Font Info: ... okay on input line 175.
+LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 175.
+LaTeX Font Info: ... okay on input line 175.
+LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 175.
+LaTeX Font Info: ... okay on input line 175.
+LaTeX Font Info: Checking defaults for PD1/pdf/m/n on input line 175.
+LaTeX Font Info: ... okay on input line 175.
+LaTeX Font Info: Checking defaults for TS1/cmr/m/n on input line 175.
+LaTeX Font Info: Try loading font information for TS1+cmr on input line 175.
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\base\ts1cmr.fd"
File: ts1cmr.fd 1999/05/25 v2.5h Standard LaTeX font definitions
)
-LaTeX Font Info: ... okay on input line 174.
-LaTeX Font Info: Try loading font information for OT1+ptm on input line 174.
+LaTeX Font Info: ... okay on input line 175.
+LaTeX Font Info: Try loading font information for OT1+ptm on input line 175.
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\psnfss\ot1ptm.fd"
@@ -583,7 +580,7 @@ File: ot1ptm.fd 2001/06/04 font definitions for OT1/ptm.
\everyMPtoPDFconversion=\toks25
)
\AtBeginShipoutBox=\box32
-Package hyperref Info: Link coloring OFF on input line 174.
+Package hyperref Info: Link coloring OFF on input line 175.
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\hyperref\nameref.sty"
Package: nameref 2012/10/27 v2.43 Cross-referencing by name of section
@@ -592,9 +589,9 @@ Package: gettitlestring 2010/12/03 v1.4 Cleanup title references (HO)
)
\c@section@level=\count138
)
-LaTeX Info: Redefining \ref on input line 174.
-LaTeX Info: Redefining \pageref on input line 174.
-LaTeX Info: Redefining \nameref on input line 174.
+LaTeX Info: Redefining \ref on input line 175.
+LaTeX Info: Redefining \pageref on input line 175.
+LaTeX Info: Redefining \nameref on input line 175.
(D:\LADData\RCode\dataRetrieval\vignettes\dataRetrieval.out)
(D:\LADData\RCode\dataRetrieval\vignettes\dataRetrieval.out)
@@ -603,36 +600,30 @@ Package caption Info: Begin \AtBeginDocument code.
Package caption Info: subfig package v1.3 is loaded.
Package caption Info: threeparttable package is loaded.
Package caption Info: End \AtBeginDocument code.
-LaTeX Font Info: Try loading font information for OT1+phv on input line 194.
+LaTeX Font Info: Try loading font information for OT1+phv on input line 195.
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\psnfss\ot1phv.fd"
File: ot1phv.fd 2001/06/04 scalable font definitions for OT1/phv.
)
LaTeX Font Info: Font shape `OT1/phv/m/n' will be
-(Font) scaled to size 18.66588pt on input line 194.
+(Font) scaled to size 18.66588pt on input line 195.
LaTeX Font Info: Font shape `OT1/phv/bx/n' in size <20.74> not available
-(Font) Font shape `OT1/phv/b/n' tried instead on input line 194.
+(Font) Font shape `OT1/phv/b/n' tried instead on input line 195.
LaTeX Font Info: Font shape `OT1/phv/b/n' will be
-(Font) scaled to size 18.66588pt on input line 194.
+(Font) scaled to size 18.66588pt on input line 195.
LaTeX Font Info: Font shape `OT1/phv/m/n' will be
-(Font) scaled to size 9.85492pt on input line 196.
+(Font) scaled to size 9.85492pt on input line 197.
LaTeX Font Info: Font shape `OT1/phv/bx/n' in size <10.95> not available
-(Font) Font shape `OT1/phv/b/n' tried instead on input line 204.
+(Font) Font shape `OT1/phv/b/n' tried instead on input line 205.
LaTeX Font Info: Font shape `OT1/phv/b/n' will be
-(Font) scaled to size 9.85492pt on input line 204.
+(Font) scaled to size 9.85492pt on input line 205.
LaTeX Font Info: Font shape `OT1/phv/bx/n' in size <17.28> not available
-(Font) Font shape `OT1/phv/b/n' tried instead on input line 204.
+(Font) Font shape `OT1/phv/b/n' tried instead on input line 205.
LaTeX Font Info: Font shape `OT1/phv/b/n' will be
-(Font) scaled to size 15.55188pt on input line 204.
+(Font) scaled to size 15.55188pt on input line 205.
(D:\LADData\RCode\dataRetrieval\vignettes\dataRetrieval.toc
-Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-
-
-[1
-
-{C:/Users/ldecicco/AppData/Local/MiKTeX/2.9/pdftex/config/pdftex.map}]
LaTeX Font Info: Try loading font information for TS1+ptm on input line 27.
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\psnfss\ts1ptm.fd"
@@ -683,6 +674,12 @@ LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <6> not available
\tf@lof=\write5
(D:\LADData\RCode\dataRetrieval\vignettes\dataRetrieval.lot
+Overfull \vbox (21.68121pt too high) has occurred while \output is active []
+
+
+[1
+
+{C:/Users/ldecicco/AppData/Local/MiKTeX/2.9/pdftex/config/pdftex.map}]
Overfull \hbox (1.53842pt too wide) in paragraph at lines 4--4
[]|\OT1/phv/b/n/10.95 Table| | [][]\OT1/phv/m/n/10.95 Daily mean data avail-ab
ile at the Chop-tank River near Greens-boro, MD. [Some columns
@@ -695,18 +692,18 @@ Overfull \vbox (21.68121pt too high) has occurred while \output is active []
[2]
-Package color Info: Redefining color shadecolor on input line 223.
-LaTeX Font Info: Try loading font information for OT1+pcr on input line 224.
+Package color Info: Redefining color shadecolor on input line 224.
+LaTeX Font Info: Try loading font information for OT1+pcr on input line 225.
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\psnfss\ot1pcr.fd"
File: ot1pcr.fd 2001/06/04 font definitions for OT1/pcr.
)
LaTeX Font Info: Font shape `OT1/pcr/bx/n' in size <10.95> not available
-(Font) Font shape `OT1/pcr/b/n' tried instead on input line 225.
+(Font) Font shape `OT1/pcr/b/n' tried instead on input line 226.
LaTeX Font Info: Font shape `OT1/pcr/m/it' in size <10.95> not available
-(Font) Font shape `OT1/pcr/m/sl' tried instead on input line 226.
+(Font) Font shape `OT1/pcr/m/sl' tried instead on input line 227.
-Underfull \vbox (badness 10000) detected at line 249
+Overfull \vbox (0.53902pt too high) detected at line 250
[]
@@ -714,127 +711,127 @@ Overfull \vbox (21.68121pt too high) has occurred while \output is active []
[3]
-Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-
-
-[4]
LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <9> not available
-(Font) Font shape `OT1/ptm/b/n' tried instead on input line 275.
+(Font) Font shape `OT1/ptm/b/n' tried instead on input line 276.
LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <7> not available
-(Font) Font shape `OT1/ptm/b/n' tried instead on input line 275.
+(Font) Font shape `OT1/ptm/b/n' tried instead on input line 276.
LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <5> not available
-(Font) Font shape `OT1/ptm/b/n' tried instead on input line 275.
+(Font) Font shape `OT1/ptm/b/n' tried instead on input line 276.
LaTeX Font Info: Font shape `OT1/phv/bx/n' in size <9> not available
-(Font) Font shape `OT1/phv/b/n' tried instead on input line 277.
+(Font) Font shape `OT1/phv/b/n' tried instead on input line 278.
LaTeX Font Info: Font shape `OT1/phv/b/n' will be
-(Font) scaled to size 8.09995pt on input line 277.
-Package color Info: Redefining color shadecolor on input line 293.
+(Font) scaled to size 8.09995pt on input line 278.
+Package color Info: Redefining color shadecolor on input line 294.
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[5]
+[4]
LaTeX Font Info: Font shape `OT1/phv/bx/n' in size <14.4> not available
-(Font) Font shape `OT1/phv/b/n' tried instead on input line 357.
+(Font) Font shape `OT1/phv/b/n' tried instead on input line 358.
LaTeX Font Info: Font shape `OT1/phv/b/n' will be
-(Font) scaled to size 12.9599pt on input line 357.
+(Font) scaled to size 12.9599pt on input line 358.
LaTeX Font Info: Font shape `OT1/phv/m/n' will be
-(Font) scaled to size 10.79993pt on input line 362.
-Package color Info: Redefining color shadecolor on input line 369.
-Package color Info: Redefining color shadecolor on input line 381.
+(Font) scaled to size 10.79993pt on input line 363.
+Package color Info: Redefining color shadecolor on input line 370.
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[6]
-Package color Info: Redefining color shadecolor on input line 401.
+[5]
+Package color Info: Redefining color shadecolor on input line 382.
+Package color Info: Redefining color shadecolor on input line 402.
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[7]
-Overfull \hbox (36.60727pt too wide) in paragraph at lines 446--447
-[]\OT1/ptm/m/n/10.95 To ob-tain all of the avail-able in-for-ma-tion con-cern-i
-ng a mea-sured pa-ram-e-ter, use the \OT1/pcr/m/n/10.95 getParameterInfo
+[6]
+Overfull \hbox (16.60727pt too wide) in paragraph at lines 447--448
+\OT1/ptm/m/n/10.95 To ob-tain all of the avail-able in-for-ma-tion con-cern-ing
+ a mea-sured pa-ram-e-ter, use the \OT1/pcr/m/n/10.95 getParameterInfo
[]
-Package color Info: Redefining color shadecolor on input line 449.
-Package color Info: Redefining color shadecolor on input line 467.
+Package color Info: Redefining color shadecolor on input line 450.
+Package color Info: Redefining color shadecolor on input line 468.
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[8]
-Package color Info: Redefining color shadecolor on input line 487.
-Package color Info: Redefining color shadecolor on input line 511.
-Package color Info: Redefining color shadecolor on input line 529.
+[7]
+Package color Info: Redefining color shadecolor on input line 488.
+Package color Info: Redefining color shadecolor on input line 512.
+Package color Info: Redefining color shadecolor on input line 530.
+
+Underfull \vbox (badness 10000) detected at line 556
+ []
+
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[9]
-Package color Info: Redefining color shadecolor on input line 561.
+[8]
+Package color Info: Redefining color shadecolor on input line 562.
LaTeX Warning: No positions in optional float specifier.
- Default added (so using `tbp') on input line 580.
+ Default added (so using `tbp') on input line 581.
-<figure/getNWIStemperaturePlot.pdf, id=270, 505.89pt x 505.89pt>
+<figure/getNWIStemperaturePlot.pdf, id=266, 505.89pt x 505.89pt>
File: figure/getNWIStemperaturePlot.pdf Graphic file (type pdf)
<use figure/getNWIStemperaturePlot.pdf>
Package pdftex.def Info: figure/getNWIStemperaturePlot.pdf used on input line 5
-82.
+83.
(pdftex.def) Requested size: 448.07928pt x 448.07928pt.
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[10]
+[9]
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[11 <D:/LADData/RCode/dataRetrieval/vignettes/figure/getNWIStemperaturePlot.pdf
+[10 <D:/LADData/RCode/dataRetrieval/vignettes/figure/getNWIStemperaturePlot.pdf
>]
-Package color Info: Redefining color shadecolor on input line 600.
-Package color Info: Redefining color shadecolor on input line 614.
+Package color Info: Redefining color shadecolor on input line 601.
+Package color Info: Redefining color shadecolor on input line 615.
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[12]
-Package color Info: Redefining color shadecolor on input line 649.
-Package color Info: Redefining color shadecolor on input line 670.
+[11]
+Package color Info: Redefining color shadecolor on input line 650.
+Package color Info: Redefining color shadecolor on input line 671.
LaTeX Warning: No positions in optional float specifier.
- Default added (so using `tbp') on input line 679.
+ Default added (so using `tbp') on input line 680.
-<figure/getQWtemperaturePlot.pdf, id=291, 505.89pt x 505.89pt>
+<figure/getQWtemperaturePlot.pdf, id=287, 505.89pt x 505.89pt>
File: figure/getQWtemperaturePlot.pdf Graphic file (type pdf)
<use figure/getQWtemperaturePlot.pdf>
-Package pdftex.def Info: figure/getQWtemperaturePlot.pdf used on input line 681
+Package pdftex.def Info: figure/getQWtemperaturePlot.pdf used on input line 682
.
(pdftex.def) Requested size: 448.07378pt x 448.07928pt.
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[13]
+[12]
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[14 <D:/LADData/RCode/dataRetrieval/vignettes/figure/getQWtemperaturePlot.pdf>]
-Package color Info: Redefining color shadecolor on input line 697.
-LaTeX Font Info: Try loading font information for TS1+pcr on input line 699.
+[13 <D:/LADData/RCode/dataRetrieval/vignettes/figure/getQWtemperaturePlot.pdf>]
+Package color Info: Redefining color shadecolor on input line 698.
+LaTeX Font Info: Try loading font information for TS1+pcr on input line 700.
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\psnfss\ts1pcr.fd"
File: ts1pcr.fd 2001/06/04 font definitions for TS1/pcr.
)
-Package color Info: Redefining color shadecolor on input line 723.
+Package color Info: Redefining color shadecolor on input line 724.
-Overfull \hbox (5.25568pt too wide) in paragraph at lines 732--732
+Overfull \hbox (5.25568pt too wide) in paragraph at lines 733--733
[][]\OT1/pcr/m/n/10.95 url_uv[] []<-[] []\OT1/pcr/b/n/10.95 constructNWISURL[][
]\OT1/pcr/m/n/10.95 (siteNumber,[][]"00060"[][],startDate,endDate,[][]\TS1/pcr/
m/n/10.95 '\OT1/pcr/m/n/10.95 uv\TS1/pcr/m/n/10.95 '[][]\OT1/pcr/m/n/10.95 )[][
@@ -845,61 +842,68 @@ m/n/10.95 '\OT1/pcr/m/n/10.95 uv\TS1/pcr/m/n/10.95 '[][]\OT1/pcr/m/n/10.95 )[][
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[15]
-Package color Info: Redefining color shadecolor on input line 754.
-
-Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-
+[14]
+Overfull \hbox (14.57181pt too wide) in paragraph at lines 752--753
+\OT1/ptm/m/n/10.95 ters. This func-tion com-bines \OT1/pcr/m/n/10.95 getSiteFil
+eData \OT1/ptm/m/n/10.95 and \OT1/pcr/m/n/10.95 getParameterInfo\OT1/ptm/m/n/10
+.95 , pro-duc-ing one dataframe
+ []
-[16]
-Package color Info: Redefining color shadecolor on input line 772.
+Package color Info: Redefining color shadecolor on input line 755.
+Package color Info: Redefining color shadecolor on input line 773.
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[17]
-Package color Info: Redefining color shadecolor on input line 830.
-Package color Info: Redefining color shadecolor on input line 842.
+[15]
+Package color Info: Redefining color shadecolor on input line 831.
+Package color Info: Redefining color shadecolor on input line 843.
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[18]
+[16]
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[19]
-Overfull \vbox (21.68121pt too high) has occurred while \output is active []
+[17]
+Package color Info: Redefining color shadecolor on input line 943.
+Underfull \vbox (badness 10000) detected at line 963
+ []
-[20]
-Package color Info: Redefining color shadecolor on input line 942.
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[21]
-Package color Info: Redefining color shadecolor on input line 1003.
-
+[18]
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[22]
-LaTeX Font Info: Try loading font information for OMS+pcr on input line 1008
+[19]
+Package color Info: Redefining color shadecolor on input line 1004.
+LaTeX Font Info: Try loading font information for OMS+pcr on input line 1009
.
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\psnfss\omspcr.fd"
File: omspcr.fd
)
LaTeX Font Info: Font shape `OMS/pcr/m/n' in size <10.95> not available
-(Font) Font shape `OMS/cmsy/m/n' tried instead on input line 1008.
+(Font) Font shape `OMS/cmsy/m/n' tried instead on input line 1009.
-Package color Info: Redefining color shadecolor on input line 1039.
+Package color Info: Redefining color shadecolor on input line 1038.
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[23]
+[20]
Package color Info: Redefining color shadecolor on input line 1064.
+
+Overfull \hbox (0.56488pt too wide) in paragraph at lines 1080--1081
+\OT1/ptm/m/n/10.95 Finally, there is a func-tion called \OT1/pcr/m/n/10.95 merg
+eReport \OT1/ptm/m/n/10.95 that will look at both the Daily and Sam-ple datafra
+me,
+ []
+
Package color Info: Redefining color shadecolor on input line 1084.
Overfull \hbox (44.67563pt too wide) in paragraph at lines 1109--1109
@@ -917,14 +921,14 @@ s from 2012-12-18[]
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[24]
+[21]
Package color Info: Redefining color shadecolor on input line 1140.
LaTeX Warning: No positions in optional float specifier.
Default added (so using `tbp') on input line 1146.
-<figure/egretEx.pdf, id=368, 505.89pt x 505.89pt>
+<figure/egretEx.pdf, id=356, 505.89pt x 505.89pt>
File: figure/egretEx.pdf Graphic file (type pdf)
<use figure/egretEx.pdf>
Package pdftex.def Info: figure/egretEx.pdf used on input line 1148.
@@ -933,24 +937,24 @@ Package pdftex.def Info: figure/egretEx.pdf used on input line 1148.
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[25]
+[22]
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[26 <D:/LADData/RCode/dataRetrieval/vignettes/figure/egretEx.pdf>]
+[23 <D:/LADData/RCode/dataRetrieval/vignettes/figure/egretEx.pdf>]
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[27
+[24
]
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[28]
+[25]
Package color Info: Redefining color shadecolor on input line 1245.
Package color Info: Redefining color shadecolor on input line 1258.
- <Rhelp.png, id=398, 433.62pt x 395.22656pt>
+ <Rhelp.png, id=386, 433.62pt x 395.22656pt>
File: Rhelp.png Graphic file (type png)
<use Rhelp.png>
Package pdftex.def Info: Rhelp.png used on input line 1277.
@@ -960,13 +964,13 @@ Package color Info: Redefining color shadecolor on input line 1284.
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[29
+[26
]
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[30 <D:/LADData/RCode/dataRetrieval/vignettes/Rhelp.png>]
+[27 <D:/LADData/RCode/dataRetrieval/vignettes/Rhelp.png>]
Package color Info: Redefining color shadecolor on input line 1299.
Package color Info: Redefining color shadecolor on input line 1311.
LaTeX Font Info: Font shape `TS1/phv/bx/n' in size <17.28> not available
@@ -978,7 +982,7 @@ Package color Info: Redefining color shadecolor on input line 1326.
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[31
+[28
]
Package color Info: Redefining color shadecolor on input line 1363.
@@ -988,11 +992,7 @@ Overfull \hbox (11.82567pt too wide) in paragraph at lines 1380--1380
30 3651 mg/l[]
[]
-
-Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-
-
-[32] <table1.png, id=422, 554.07pt x 125.71968pt>
+<table1.png, id=401, 554.07pt x 125.71968pt>
File: table1.png Graphic file (type png)
<use table1.png>
Package pdftex.def Info: table1.png used on input line 1399.
@@ -1001,7 +1001,11 @@ Package pdftex.def Info: table1.png used on input line 1399.
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
-[33 <D:/LADData/RCode/dataRetrieval/vignettes/table1.png>]
+[29]
+Overfull \vbox (21.68121pt too high) has occurred while \output is active []
+
+
+[30 <D:/LADData/RCode/dataRetrieval/vignettes/table1.png>]
Package atveryend Info: Empty hook `BeforeClearDocument' on input line 1424.
Package atveryend Info: Empty hook `AfterLastShipout' on input line 1424.
@@ -1014,13 +1018,13 @@ Package rerunfilecheck Info: File `dataRetrieval.out' has not changed.
Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 1424.
)
Here is how much of TeX's memory you used:
- 9967 strings out of 493921
- 149101 string characters out of 3144868
- 249602 words of memory out of 3000000
- 12963 multiletter control sequences out of 15000+200000
+ 9958 strings out of 493921
+ 148881 string characters out of 3144868
+ 249537 words of memory out of 3000000
+ 12960 multiletter control sequences out of 15000+200000
47347 words of font info for 96 fonts, out of 3000000 for 9000
841 hyphenation exceptions out of 8191
- 44i,15n,42p,957b,506s stack positions out of 5000i,500n,10000p,200000b,50000s
+ 44i,15n,42p,957b,504s stack positions out of 5000i,500n,10000p,200000b,50000s
{C:/Program Files (x86)/MiKTeX 2.9/fonts/enc/dvips/fontname/8r.enc}<C:/Progra
m Files (x86)/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/cmmi10.pfb><C:/Program
Files (x86)/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/cmsy10.pfb><C:/Program Fi
@@ -1032,9 +1036,9 @@ rw/helvetic/uhvr8a.pfb><C:/Users/ldecicco/AppData/Roaming/MiKTeX/2.9/fonts/type
1/urw/symbol/usyr.pfb><C:/Program Files (x86)/MiKTeX 2.9/fonts/type1/urw/times/
utmr8a.pfb><C:/Program Files (x86)/MiKTeX 2.9/fonts/type1/urw/times/utmri8a.pfb
>
-Output written on dataRetrieval.pdf (33 pages, 339117 bytes).
+Output written on dataRetrieval.pdf (30 pages, 336019 bytes).
PDF statistics:
- 486 PDF objects out of 1000 (max. 8388607)
- 84 named destinations out of 1000 (max. 500000)
+ 473 PDF objects out of 1000 (max. 8388607)
+ 81 named destinations out of 1000 (max. 500000)
234 words of extra memory for PDF output out of 10000 (max. 10000000)
diff --git a/vignettes/dataRetrieval.lot b/vignettes/dataRetrieval.lot
index d77d60e5b3acbacf827bf913c5de4f2eaba7ef2a..47ede036fecb200f86521bf8ffe04ef7bc918967 100644
--- a/vignettes/dataRetrieval.lot
+++ b/vignettes/dataRetrieval.lot
@@ -1,10 +1,10 @@
\select@language {american}
-\contentsline {table}{\numberline {1}{\ignorespaces Common USGS Parameter Codes\relax }}{5}{table.caption.1}
-\contentsline {table}{\numberline {2}{\ignorespaces Commonly used USGS Stat Codes\relax }}{6}{table.caption.2}
+\contentsline {table}{\numberline {1}{\ignorespaces Common USGS Parameter Codes\relax }}{4}{table.caption.1}
+\contentsline {table}{\numberline {2}{\ignorespaces Commonly used USGS Stat Codes\relax }}{5}{table.caption.2}
\contentsline {table}{\numberline {3}{\ignorespaces Daily mean data availabile at the Choptank River near Greensboro, MD. [Some columns deleted for space considerations]\relax }}{7}{table.caption.3}
-\contentsline {table}{\numberline {4}{\ignorespaces Daily dataframe\relax }}{17}{table.caption.6}
-\contentsline {table}{\numberline {5}{\ignorespaces Sample dataframe\relax }}{19}{table.caption.8}
-\contentsline {table}{\numberline {6}{\ignorespaces Example data\relax }}{20}{table.caption.9}
-\contentsline {table}{\numberline {7}{\ignorespaces dataRetrieval functions\relax }}{28}{table.caption.12}
-\contentsline {table}{\numberline {8}{\ignorespaces dataRetrieval miscellaneous functions\relax }}{28}{table.caption.13}
+\contentsline {table}{\numberline {4}{\ignorespaces Daily dataframe\relax }}{16}{table.caption.6}
+\contentsline {table}{\numberline {5}{\ignorespaces Sample dataframe\relax }}{17}{table.caption.8}
+\contentsline {table}{\numberline {6}{\ignorespaces Example data\relax }}{18}{table.caption.9}
+\contentsline {table}{\numberline {7}{\ignorespaces dataRetrieval functions\relax }}{25}{table.caption.12}
+\contentsline {table}{\numberline {8}{\ignorespaces dataRetrieval miscellaneous functions\relax }}{25}{table.caption.13}
\contentsfinish
diff --git a/vignettes/dataRetrieval.pdf b/vignettes/dataRetrieval.pdf
index 224629c85bd99569fe02ed9e0368084695e25e2e..3e2f6fe6727e496958a515722f8aa57a0d0b7604 100644
Binary files a/vignettes/dataRetrieval.pdf and b/vignettes/dataRetrieval.pdf differ
diff --git a/vignettes/dataRetrieval.synctex.gz b/vignettes/dataRetrieval.synctex.gz
index 31fdac390ca8e5e489ec463ee55b7e3470b27078..4c84db1325afc21abe57ec6f737aa062fd0c8ff0 100644
Binary files a/vignettes/dataRetrieval.synctex.gz and b/vignettes/dataRetrieval.synctex.gz differ
diff --git a/vignettes/dataRetrieval.tex b/vignettes/dataRetrieval.tex
index 4f84b9b192baed5048709f1d44f11d62c8223d8b..166bff7f3cca8a55095c31c97d833b8af129529d 100644
--- a/vignettes/dataRetrieval.tex
+++ b/vignettes/dataRetrieval.tex
@@ -72,7 +72,7 @@
\usepackage{csquotes}
\usepackage{setspace}
-\doublespacing
+% \doublespacing
\renewcommand{\topfraction}{0.85}
\renewcommand{\textfraction}{0.1}
@@ -82,7 +82,8 @@
\usepackage{mathptmx}% Times Roman font
\usepackage[scaled=.90]{helvet}% Helvetica, served as a model for arial
-\usepackage{indentfirst}
+% \usepackage{indentfirst}
+% \setlength\parindent{20pt}
\setlength{\parskip}{0pt}
\usepackage{courier}
@@ -148,7 +149,7 @@
singlelinecheck=false
}
-\setlength\parindent{20pt}
+
\textwidth=6.2in
\textheight=8.5in
@@ -266,8 +267,8 @@ Once the site-ID (siteNumber) is known, the next required input for USGS data re
Not every station will measure all parameters. A short list of commonly measured parameters is shown in Table \ref{tab:params}.
-% latex table generated in R 3.1.1 by xtable 1.7-3 package
-% Thu Sep 11 16:26:30 2014
+% latex table generated in R 3.1.1 by xtable 1.7-4 package
+% Wed Sep 17 13:24:06 2014
\begin{table}[ht]
\caption{Common USGS Parameter Codes}
\label{tab:params}
@@ -329,8 +330,8 @@ For unit values data (sensor data measured at regular time intervals such as 15
Some common codes are shown in Table \ref{tab:stat}.
-% latex table generated in R 3.1.1 by xtable 1.7-3 package
-% Thu Sep 11 16:26:31 2014
+% latex table generated in R 3.1.1 by xtable 1.7-4 package
+% Wed Sep 17 13:24:07 2014
\begin{table}[ht]
\caption{Commonly used USGS Stat Codes}
\label{tab:stat}
@@ -410,8 +411,8 @@ To discover what data is available for a particular USGS site, including measure
\end{knitrout}
-% latex table generated in R 3.1.1 by xtable 1.7-3 package
-% Thu Sep 11 16:26:32 2014
+% latex table generated in R 3.1.1 by xtable 1.7-4 package
+% Wed Sep 17 13:24:07 2014
\begin{table}[ht]
\caption{Daily mean data availabile at the Choptank River near Greensboro, MD. [Some columns deleted for space considerations]}
\label{tab:gda}
@@ -423,7 +424,7 @@ To discover what data is available for a particular USGS site, including measure
& Temperature, water & 1988-10-01 & 2012-05-09 & 894 & deg C \\
[5pt] & Temperature, water & 2010-10-01 & 2012-05-09 & 529 & deg C \\
[5pt] & Temperature, water & 2010-10-01 & 2012-05-09 & 529 & deg C \\
- [5pt] & Stream flow, mean. daily & 1948-01-01 & 2014-09-10 & 24360 & ft$^3$/s \\
+ [5pt] & Stream flow, mean. daily & 1948-01-01 & 2014-09-16 & 24366 & ft$^3$/s \\
[5pt] & Specific conductance & 2010-10-01 & 2012-05-09 & 527 & uS/cm @25C \\
[5pt] & Specific conductance & 2010-10-01 & 2012-05-09 & 527 & uS/cm @25C \\
[5pt] & Specific conductance & 2010-10-01 & 2012-05-09 & 527 & uS/cm @25C \\
@@ -785,8 +786,8 @@ There are 4750 data points, and 4750 days.
-% latex table generated in R 3.1.1 by xtable 1.7-3 package
-% Thu Sep 11 16:26:44 2014
+% latex table generated in R 3.1.1 by xtable 1.7-4 package
+% Wed Sep 17 13:24:23 2014
\begin{table}[ht]
\caption{Daily dataframe}
\label{tab:DailyDF1}
@@ -906,8 +907,8 @@ To illustrate how the dataRetrieval package handles a more complex censoring pro
-% latex table generated in R 3.1.1 by xtable 1.7-3 package
-% Thu Sep 11 16:26:45 2014
+% latex table generated in R 3.1.1 by xtable 1.7-4 package
+% Wed Sep 17 13:24:25 2014
\begin{table}[ht]
\caption{Example data}
\label{tab:exampleComplexQW}
@@ -985,7 +986,7 @@ Finally, qUnit is a numeric argument that defines the discharge units used in th
So, if you have a file called \enquote{ChoptankRiverFlow.txt} located in a folder called \enquote{RData} on the C drive (this example is for the Windows\textregistered\ operating systems), and the file is structured as follows (tab-separated):
-\singlespacing
+% \singlespacing
\begin{verbatim}
date Qdaily
10/1/1999 107
@@ -996,7 +997,7 @@ date Qdaily
10/6/1999 98
...
\end{verbatim}
-\doublespacing
+% \doublespacing
The call to open this file, convert the discharge to cubic meters per second, and populate the Daily data frame would be:
\begin{knitrout}
@@ -1019,7 +1020,6 @@ Microsoft\textregistered\ Excel files can be a bit tricky to import into R direc
\label{sec:SampleFile}
%------------------------------------------------------------
-\doublespacing
The \texttt{getSampleDataFromFile} function will import a user-generated file and populate the Sample dataframe. The difference between sample data and discharge data is that the code requires a third column that contains a remark code, either blank or \verb@"<"@, which will tell the program that the data were \enquote{left-censored} (or, below the detection limit of the sensor). Therefore, the data must be in the form: date, remark, value. An example of a comma-delimited file is:
\singlespacing
@@ -1032,7 +1032,6 @@ cdate;remarkCode;Nitrate
2/3/2000,,1.54
...
\end{verbatim}
-\doublespacing
The call to open this file, and populate the Sample dataframe is:
\begin{knitrout}
@@ -1059,7 +1058,8 @@ date rdp dp rpp pp rtp tp
2005-10-30 < 0.020
...
\end{verbatim}
-\doublespacing
+
+
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
@@ -1348,7 +1348,7 @@ There are a few steps that are required in order to create a table in Microsoft\
5 Suspended sediment discharge 1980-10-01
End Count Units
1 2012-05-09 529 deg C
-2 2014-09-10 24360 ft3/s
+2 2014-09-16 24366 ft3/s
3 2012-05-09 527 uS/cm @25C
4 1991-09-30 3651 mg/l
5 1991-09-30 3652 tons/day
diff --git a/vignettes/dataRetrieval.toc b/vignettes/dataRetrieval.toc
index da70f97eb48c23c9ad26c21a0136d5440889e0e0..ba00912a81727dfab78c593237beb430f2856331 100644
--- a/vignettes/dataRetrieval.toc
+++ b/vignettes/dataRetrieval.toc
@@ -3,26 +3,26 @@
\contentsline {section}{\numberline {2}General USGS Web Retrievals}{4}{section.2}
\contentsline {subsection}{\numberline {2.1}Site Information}{6}{subsection.2.1}
\contentsline {subsubsection}{\numberline {2.1.1}getSiteFileData}{6}{subsubsection.2.1.1}
-\contentsline {subsubsection}{\numberline {2.1.2}getDataAvailability}{7}{subsubsection.2.1.2}
-\contentsline {subsection}{\numberline {2.2}Parameter Information}{8}{subsection.2.2}
-\contentsline {subsection}{\numberline {2.3}Daily Values}{8}{subsection.2.3}
-\contentsline {subsection}{\numberline {2.4}Unit Values}{12}{subsection.2.4}
-\contentsline {subsection}{\numberline {2.5}Water Quality Values}{13}{subsection.2.5}
-\contentsline {subsection}{\numberline {2.6}STORET Water Quality Retrievals}{15}{subsection.2.6}
-\contentsline {subsection}{\numberline {2.7}URL Construction}{15}{subsection.2.7}
-\contentsline {section}{\numberline {3}Data Retrievals Structured For Use In The EGRET Package}{16}{section.3}
-\contentsline {subsection}{\numberline {3.1}INFO Data}{16}{subsection.3.1}
-\contentsline {subsection}{\numberline {3.2}Daily Data}{17}{subsection.3.2}
-\contentsline {subsection}{\numberline {3.3}Sample Data}{18}{subsection.3.3}
-\contentsline {subsection}{\numberline {3.4}Censored Values: Summation Explanation}{19}{subsection.3.4}
-\contentsline {subsection}{\numberline {3.5}User-Generated Data Files}{21}{subsection.3.5}
-\contentsline {subsubsection}{\numberline {3.5.1}getDailyDataFromFile}{21}{subsubsection.3.5.1}
-\contentsline {subsubsection}{\numberline {3.5.2}getSampleDataFromFile}{23}{subsubsection.3.5.2}
-\contentsline {subsection}{\numberline {3.6}Merge Report}{24}{subsection.3.6}
-\contentsline {subsection}{\numberline {3.7}EGRET Plots}{25}{subsection.3.7}
-\contentsline {section}{\numberline {4}Summary}{27}{section.4}
-\contentsline {section}{\numberline {5}Getting Started in R}{29}{section.5}
-\contentsline {subsection}{\numberline {5.1}New to R?}{29}{subsection.5.1}
-\contentsline {subsection}{\numberline {5.2}R User: Installing dataRetrieval}{31}{subsection.5.2}
-\contentsline {section}{\numberline {6}Creating tables in Microsoft\textregistered \ software from R}{31}{section.6}
+\contentsline {subsubsection}{\numberline {2.1.2}getDataAvailability}{6}{subsubsection.2.1.2}
+\contentsline {subsection}{\numberline {2.2}Parameter Information}{7}{subsection.2.2}
+\contentsline {subsection}{\numberline {2.3}Daily Values}{7}{subsection.2.3}
+\contentsline {subsection}{\numberline {2.4}Unit Values}{11}{subsection.2.4}
+\contentsline {subsection}{\numberline {2.5}Water Quality Values}{12}{subsection.2.5}
+\contentsline {subsection}{\numberline {2.6}STORET Water Quality Retrievals}{14}{subsection.2.6}
+\contentsline {subsection}{\numberline {2.7}URL Construction}{14}{subsection.2.7}
+\contentsline {section}{\numberline {3}Data Retrievals Structured For Use In The EGRET Package}{14}{section.3}
+\contentsline {subsection}{\numberline {3.1}INFO Data}{15}{subsection.3.1}
+\contentsline {subsection}{\numberline {3.2}Daily Data}{15}{subsection.3.2}
+\contentsline {subsection}{\numberline {3.3}Sample Data}{16}{subsection.3.3}
+\contentsline {subsection}{\numberline {3.4}Censored Values: Summation Explanation}{17}{subsection.3.4}
+\contentsline {subsection}{\numberline {3.5}User-Generated Data Files}{19}{subsection.3.5}
+\contentsline {subsubsection}{\numberline {3.5.1}getDailyDataFromFile}{19}{subsubsection.3.5.1}
+\contentsline {subsubsection}{\numberline {3.5.2}getSampleDataFromFile}{20}{subsubsection.3.5.2}
+\contentsline {subsection}{\numberline {3.6}Merge Report}{21}{subsection.3.6}
+\contentsline {subsection}{\numberline {3.7}EGRET Plots}{22}{subsection.3.7}
+\contentsline {section}{\numberline {4}Summary}{24}{section.4}
+\contentsline {section}{\numberline {5}Getting Started in R}{26}{section.5}
+\contentsline {subsection}{\numberline {5.1}New to R?}{26}{subsection.5.1}
+\contentsline {subsection}{\numberline {5.2}R User: Installing dataRetrieval}{28}{subsection.5.2}
+\contentsline {section}{\numberline {6}Creating tables in Microsoft\textregistered \ software from R}{28}{section.6}
\contentsfinish
diff --git a/vignettes/figure/egretEx.pdf b/vignettes/figure/egretEx.pdf
index 5e59040b2d1c145403793b103e16359c0676f2e7..f9e10dbe7322b8d1b3cd964958f97c12634b2f13 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 c1565924c0db4faaf6152dac05de61a2982fcf54..149cc770fe05638855b82d35caf2b2ccb591fd9c 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 0e723813845d5095beed2e7471c2975e3f631ec4..c64bce1537517b940d5cafa06673f38f5b7872e0 100644
Binary files a/vignettes/figure/getQWtemperaturePlot.pdf and b/vignettes/figure/getQWtemperaturePlot.pdf differ