diff --git a/DESCRIPTION b/DESCRIPTION
index 30925fcbb8a41824dbd0c09758037f9d16116c8c..b2c8a69f22f63a5ad12640fc331ec8b58acaaf18 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: dataRetrieval
Type: Package
Title: Retrieval functions for hydrologic data
Version: 1.3.3
-Date: 2014-08-04
+Date: 2014-09-12
Author: Robert M. Hirsch, Laura De Cicco
Maintainer: Laura De Cicco <ldecicco@usgs.gov>
Description: Collection of functions to help retrieve USGS data from either web
diff --git a/NAMESPACE b/NAMESPACE
index ae86ab235dd98080bc95ce3978f1aa0f677a25ee..f1d2b6d2a24a646aa5a176b6dfe5be2b2e29933b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,6 @@
# Generated by roxygen2 (4.0.2): do not edit by hand
+export(basicWQPData)
export(checkStartEndDate)
export(compressData)
export(constructNWISURL)
diff --git a/R/basicWQPData.R b/R/basicWQPData.R
new file mode 100644
index 0000000000000000000000000000000000000000..d23328a53c16eb7089c6db8b234bf284ead38176
--- /dev/null
+++ b/R/basicWQPData.R
@@ -0,0 +1,111 @@
+#' Basic Water Quality Portal Data grabber
+#'
+#' Imports data from the Water Quality Portal based on a specified url.
+#'
+#' @param url string URL to Water Quality Portal#' @keywords data import USGS web service
+#' @return retval dataframe raw data returned from the Water Quality Portal. Additionally, a POSIXct dateTime column is supplied for
+#' start and end times.
+#' @export
+#' @import RCurl
+#' @examples
+#' # These examples require an internet connection to run
+#' rawSampleURL <- constructNWISURL('USGS-01594440','01075', '1985-01-01', '1985-03-31',"wqp")
+#' rawSample <- basicWQPData(rawSampleURL)
+basicWQPData <- function(url){
+
+ h <- basicHeaderGatherer()
+
+ retval = tryCatch({
+ doc <- getURL(url, headerfunction = h$update)
+
+ }, warning = function(w) {
+ message(paste("URL caused a warning:", url))
+ message(w)
+ }, error = function(e) {
+ message(paste("URL does not seem to exist:", url))
+ message(e)
+ return(NA)
+ })
+
+ if(h$value()["Content-Type"] == "text/tab-separated-values;charset=UTF-8"){
+
+ numToBeReturned <- as.numeric(h$value()["Total-Result-Count"])
+
+ if (!is.na(numToBeReturned) | numToBeReturned != 0){
+
+
+ namesData <- read.delim(textConnection(doc), header = TRUE, quote="\"",
+ dec=".", sep='\t',
+ colClasses='character',
+ fill = TRUE,nrow=1)
+ classColumns <- setNames(rep('character',ncol(namesData)),names(namesData))
+ classColumns["ActivityStartDate"] <- "Date"
+
+ classColumns[grep("MeasureValue",names(classColumns))] <- NA
+
+ retval <- read.delim(textConnection(doc), header = TRUE, quote="\"",
+ dec=".", sep='\t',
+ colClasses=as.character(classColumns),
+ fill = TRUE)
+ actualNumReturned <- nrow(retval)
+
+ retval[,names(which(sapply(retval[,grep("MeasureValue",names(retval))], function(x)all(is.na(x)))))] <- ""
+
+ if(actualNumReturned != numToBeReturned) warning(numToBeReturned, " sample results were expected, ", actualNumReturned, " were returned")
+
+ timeZoneLibrary <- setNames(c("America/New_York","America/New_York","America/Chicago","America/Chicago",
+ "America/Denver","America/Denver","America/Los_Angeles","America/Los_Angeles",
+ "America/Anchorage","America/Anchorage","America/Honolulu","America/Honolulu"),
+ c("EST","EDT","CST","CDT","MST","MDT","PST","PDT","AKST","AKDT","HAST","HST"))
+ timeZoneStart <- as.character(timeZoneLibrary[retval$ActivityStartTime.TimeZoneCode])
+ timeZoneEnd <- as.character(timeZoneLibrary[retval$ActivityEndTime.TimeZoneCode])
+
+ if(any(!is.na(timeZoneStart))){
+ if(length(unique(timeZoneStart)) == 1){
+ retval$ActivityStartDateTime <- with(retval, as.POSIXct(paste(ActivityStartDate, ActivityStartTime.Time),format="%Y-%m-%d %H:%M:%S", tz=unique(timeZoneStart)))
+ } else {
+ warning("Mixed time zone information")
+ if(any(is.na(timeZoneStart))){
+ warning("Missing time zone information, all dateTimes default to user's local time")
+ retval$ActivityStartDateTime <- with(retval, as.POSIXct(paste(ActivityStartDate, ActivityStartTime.Time), format="%Y-%m-%d %H:%M:%S"),tz=Sys.timezone())
+ } else {
+ for(i in seq_along(row.names(retval))){
+ timeZone <- timeZoneStart[i]
+ retval$ActivityStartDateTime[i] <- with(retval, as.POSIXct(paste(ActivityStartDate[i], ActivityStartTime.Time[i]), format="%Y-%m-%d %H:%M:%S",tz=timeZone))
+ }
+ }
+ }
+ }
+
+ if(any(!is.na(timeZoneEnd))){
+ if(length(unique(timeZoneEnd)) == 1){
+ retval$ActivityEndDateTime <- with(retval, as.POSIXct(paste(ActivityEndDate, ActivityEndTime.Time), format="%Y-%m-%d %H:%M:%S",tz=unique(timeZoneEnd)))
+ } else {
+ warning("Mixed time zone information")
+ if(any(is.na(timeZoneEnd))){
+ warning("Missing time zone information, all dateTimes default to user's local time")
+ retval$ActivityEndDateTime <- with(retval, as.POSIXct(paste(ActivityEndDate, ActivityEndTime.Time), format="%Y-%m-%d %H:%M:%S"), tz=Sys.timezone())
+ } else {
+ for(i in seq_along(row.names(retval))){
+ retval$ActivityEndDateTime[i] <- with(retval, as.POSIXct(paste(ActivityEndDate[i], ActivityEndTime.Time[i]), format="%Y-%m-%d %H:%M:%S",tz=timeZoneEnd[i]))
+ }
+ }
+ }
+ }
+
+ if(any(retval$ActivityEndDate != "")){
+ retval$ActivityEndDate <- as.Date(retval$ActivityEndDate)
+ }
+
+ return(retval)
+
+ } else {
+ warning("No data to retrieve")
+ return(NA)
+ }
+ } else {
+ message(paste("URL caused an error:", url))
+ message("Content-Type=",h$value()["Content-Type"])
+ return(NA)
+ }
+}
\ No newline at end of file
diff --git a/R/getGeneralWQPData.R b/R/getGeneralWQPData.R
index 3e7eb95f47316200c8cf590a0a79a4f1ed01bcf0..4faf41f2c250cf3e906b59b797fecb8d151b30a2 100644
--- a/R/getGeneralWQPData.R
+++ b/R/getGeneralWQPData.R
@@ -30,45 +30,7 @@ getGeneralWQPData <- function(...){
urlCall <- paste(baseURL,
urlCall,
"&mimeType=tsv",sep = "")
-
- doc = tryCatch({
- h <- basicHeaderGatherer()
- doc <- getURL(urlCall, headerfunction = h$update)
-
- }, warning = function(w) {
- message(paste("URL caused a warning:", urlCall))
- message(w)
- }, error = function(e) {
- message(paste("URL does not seem to exist:", urlCall))
- message(e)
- return(NA)
- })
-
- if(h$value()["Content-Type"] == "text/tab-separated-values;charset=UTF-8"){
-
- numToBeReturned <- as.numeric(h$value()["Total-Result-Count"])
-
- if (!is.na(numToBeReturned) | numToBeReturned != 0){
- retval <- read.delim(textConnection(doc), header = TRUE, quote="\"",
- dec=".", sep='\t',
- colClasses=c('character'),
- fill = TRUE)
-
- actualNumReturned <- nrow(retval)
-
- if(actualNumReturned != numToBeReturned) warning(numToBeReturned, " sample results were expected, ", actualNumReturned, " were returned")
-
- return(retval)
- } else {
- warning(paste("No data to retrieve from",urlCall))
- return(NA)
- }
-
- } else {
- message(paste("URL caused an error:", urlCall))
- message("Content-Type=",h$value()["Content-Type"])
- return(NA)
- }
-
+ retVal <- basicWQPData(urlCall)
+ return(retVal)
}
\ No newline at end of file
diff --git a/R/getRawQWData.r b/R/getRawQWData.r
index 3b748d0bf2a6cb0b489cc10ed9477c047ba4820d..a491059d3a909188ab2980205bb766376c2070f3 100644
--- a/R/getRawQWData.r
+++ b/R/getRawQWData.r
@@ -1,17 +1,16 @@
-#' Raw Data Import for USGS NWIS Water Quality Data
+#' Raw Data Import for Water Quality Portal
#'
-#' Imports data from NWIS web service. This function gets the data from here: \url{http://www.waterqualitydata.us}
-#' A list of parameter codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes/}
-#' A list of statistic codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
+#' Imports data from the Water Quality Portal. This function gets the data from here: \url{http://www.waterqualitydata.us}
#'
-#' @param siteNumber string USGS site number. This is usually an 8 digit number
-#' @param parameterCd vector of USGS 5-digit parameter code or string of characteristicNames. Leaving this blank will return all of the measured values during the specified time period.
+#' @param siteNumber string site number. This needs to include the full agency code prefix.
+#' @param parameterCd vector of USGS 5-digit parameter code or string of characteristicNames.
+#' 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.
#' @keywords data import USGS web service
-#' @return retval dataframe with first column dateTime, and at least one qualifier and value columns
-#' (subsequent qualifier/value columns could follow depending on requested parameter codes)
+#' @return retval dataframe raw data returned from the Water Quality Portal. Additionally, a POSIXct dateTime column is supplied for
+#' start and end times.
#' @export
#' @import RCurl
#' @examples
@@ -23,44 +22,7 @@
retrieveWQPqwData <- function(siteNumber,parameterCd,startDate,endDate,interactive=TRUE){
url <- constructNWISURL(siteNumber,parameterCd,startDate,endDate,"wqp",interactive=interactive)
-
- retval = tryCatch({
- h <- basicHeaderGatherer()
- doc <- getURL(url, headerfunction = h$update)
-
- }, warning = function(w) {
- message(paste("URL caused a warning:", url))
- message(w)
- }, error = function(e) {
- message(paste("URL does not seem to exist:", url))
- message(e)
- return(NA)
- })
-
- if(h$value()["Content-Type"] == "text/tab-separated-values;charset=UTF-8"){
-
- numToBeReturned <- as.numeric(h$value()["Total-Result-Count"])
-
- if (!is.na(numToBeReturned) | numToBeReturned != 0){
-
- retval <- read.delim(textConnection(doc), header = TRUE, quote="\"",
- dec=".", sep='\t',
- colClasses=c('character'),
- fill = TRUE)
- actualNumReturned <- nrow(retval)
-
- if(actualNumReturned != numToBeReturned) warning(numToBeReturned, " sample results were expected, ", actualNumReturned, " were returned")
-
- return(retval)
-
- } else {
- warning("No data to retrieve")
- return(NA)
- }
- } else {
- message(paste("URL caused an error:", url))
- message("Content-Type=",h$value()["Content-Type"])
- return(NA)
- }
+ retVal <- basicWQPData(url)
+ return(retVal)
}
diff --git a/R/processQWData.r b/R/processQWData.r
index 2779b108d6647559f381bab592affd327e030d01..e6f696f98135e6eb1540056d3b93a8d6e1055e4e 100644
--- a/R/processQWData.r
+++ b/R/processQWData.r
@@ -24,7 +24,7 @@ processQWData <- function(data,pCode=TRUE){
test <- data.frame(data$USGSPCode)
# test$dateTime <- as.POSIXct(strptime(paste(data$ActivityStartDate,data$ActivityStartTime.Time,sep=" "), "%Y-%m-%d %H:%M:%S"))
- test$dateTime <- as.Date(data$ActivityStartDate, "%Y-%m-%d")
+ test$dateTime <- data$ActivityStartDate
originalLength <- nrow(test)
test$qualifier <- qualifier
diff --git a/man/basicWQPData.Rd b/man/basicWQPData.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..d7a1768157e0ff9094822ed6de9e8454db8f551d
--- /dev/null
+++ b/man/basicWQPData.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2 (4.0.2): do not edit by hand
+\name{basicWQPData}
+\alias{basicWQPData}
+\title{Basic Water Quality Portal Data grabber}
+\usage{
+basicWQPData(url)
+}
+\arguments{
+\item{url}{string URL to Water Quality Portal#'}
+}
+\value{
+retval dataframe raw data returned from the Water Quality Portal. Additionally, a POSIXct dateTime column is supplied for
+start and end times.
+}
+\description{
+Imports data from the Water Quality Portal based on a specified url.
+}
+\examples{
+# These examples require an internet connection to run
+rawSampleURL <- constructNWISURL('USGS-01594440','01075', '1985-01-01', '1985-03-31',"wqp")
+rawSample <- basicWQPData(rawSampleURL)
+}
+\keyword{USGS}
+\keyword{data}
+\keyword{import}
+\keyword{service}
+\keyword{web}
+
diff --git a/man/retrieveWQPqwData.Rd b/man/retrieveWQPqwData.Rd
index 79b0c0ce34dc4d7c02a7b4c9c89a42ba46e16888..e79341e04b5daae51c77f0178278bec9fcf3ed9b 100644
--- a/man/retrieveWQPqwData.Rd
+++ b/man/retrieveWQPqwData.Rd
@@ -1,15 +1,16 @@
% Generated by roxygen2 (4.0.2): do not edit by hand
\name{retrieveWQPqwData}
\alias{retrieveWQPqwData}
-\title{Raw Data Import for USGS NWIS Water Quality Data}
+\title{Raw Data Import for Water Quality Portal}
\usage{
retrieveWQPqwData(siteNumber, parameterCd, startDate, endDate,
interactive = TRUE)
}
\arguments{
-\item{siteNumber}{string USGS site number. This is usually an 8 digit number}
+\item{siteNumber}{string site number. This needs to include the full agency code prefix.}
-\item{parameterCd}{vector of USGS 5-digit parameter code or string of characteristicNames. Leaving this blank will return all of the measured values during the specified time period.}
+\item{parameterCd}{vector of USGS 5-digit parameter code or string of characteristicNames.
+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.}
@@ -18,13 +19,11 @@ retrieveWQPqwData(siteNumber, parameterCd, startDate, endDate,
\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
}
\value{
-retval dataframe with first column dateTime, and at least one qualifier and value columns
-(subsequent qualifier/value columns could follow depending on requested parameter codes)
+retval dataframe raw data returned from the Water Quality Portal. Additionally, a POSIXct dateTime column is supplied for
+start and end times.
}
\description{
-Imports data from NWIS web service. This function gets the data from here: \url{http://www.waterqualitydata.us}
-A list of parameter codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes/}
-A list of statistic codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
+Imports data from the Water Quality Portal. This function gets the data from here: \url{http://www.waterqualitydata.us}
}
\examples{
# These examples require an internet connection to run
diff --git a/vignettes/dataRetrieval-concordance.tex b/vignettes/dataRetrieval-concordance.tex
index 736487217ae60d1ed15be3ce99edb7b45484af60..a7ff1f2180c6f5c1817cd311b3d1af91dd01f43c 100644
--- a/vignettes/dataRetrieval-concordance.tex
+++ b/vignettes/dataRetrieval-concordance.tex
@@ -2,8 +2,8 @@
1 126 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 10 0 11 1 10 0 15 1 13 0 21 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 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}
+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 %
+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 e55acad915fb25420750e39587aa3fae11db123c..3d6b42c173382c08a142a6a72f6b873d9b52269a 100644
--- a/vignettes/dataRetrieval.Rnw
+++ b/vignettes/dataRetrieval.Rnw
@@ -228,7 +228,7 @@ In this section, five examples of Web retrievals document how to get raw data. T
% %------------------------------------------------------------
The USGS organizes hydrologic data in a standard structure. Streamgages are located throughout the United States, and each streamgage has a unique ID. Often (but not always), these ID's are 8 digits. The first step to finding data is discovering this 8-digit ID. There are many ways to do this, one is the National Water Information System: Mapper \url{http://maps.waterdata.usgs.gov/mapper/index.html}.
-Once the site-ID is known, the next required input for USGS data retrievals is the \enquote{parameter code}. This is a 5-digit code that specifies the measured parameter being requested. For example, parameter code 00631 represents \enquote{Nitrate plus nitrite, water, filtered, milligrams per liter as nitrogen}, with units of \enquote{mg/l as N}. A complete list of possible USGS parameter codes can be found at \url{http://nwis.waterdata.usgs.gov/usa/nwis/pmcodes?help}.
+Once the site-ID (siteNumber) is known, the next required input for USGS data retrievals is the \enquote{parameter code}. This is a 5-digit code that specifies the measured parameter being requested. For example, parameter code 00631 represents \enquote{Nitrate plus nitrite, water, filtered, milligrams per liter as nitrogen}, with units of \enquote{mg/l as N}. A complete list of possible USGS parameter codes can be found at \url{http://nwis.waterdata.usgs.gov/usa/nwis/pmcodes?help}.
Not every station will measure all parameters. A short list of commonly measured parameters is shown in Table \ref{tab:params}.
@@ -526,12 +526,10 @@ There are additional water quality data sets available from the Water Quality Da
<<label=getQWData, echo=TRUE>>=
specificCond <- getWQPData('WIDNR_WQX-10032762',
- 'Specific conductance','','')
+ 'Specific conductance','2011-05-01','2011-09-30')
head(specificCond)
@
-There are
-
\FloatBarrier
%------------------------------------------------------------
\subsection{URL Construction}
diff --git a/vignettes/dataRetrieval.lof b/vignettes/dataRetrieval.lof
index 1d5933e2ec1907e8710ffb92fea21554da3c3123..8ac527e5dae3d03e3e021d3ca84816bae57aa58a 100644
--- a/vignettes/dataRetrieval.lof
+++ b/vignettes/dataRetrieval.lof
@@ -1,6 +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 Default multiPlotDataOverview}}{25}{figure.caption.9}
-\contentsline {figure}{\numberline {3}{\ignorespaces A simple R help file\relax }}{29}{figure.caption.13}
-\contentsline {figure}{\numberline {4}{\ignorespaces A simple table produced in Microsoft\textregistered \ Excel. Additional formatting will be requried, for example converting u to $\mu $ \relax }}{32}{figure.caption.14}
+\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}
\contentsfinish
diff --git a/vignettes/dataRetrieval.log b/vignettes/dataRetrieval.log
index 4e4456e65d3e76d510caa9b3cac562e21c35a0a6..815c8cec36ef1f415c819d72ed43b8bfebb6dbdb 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) 9 SEP 2014 12:49
+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
entering extended mode
**dataRetrieval.tex
(D:\LADData\RCode\dataRetrieval\vignettes\dataRetrieval.tex
@@ -649,36 +649,36 @@ LaTeX Font Info: Font shape `TS1/phv/m/n' will be
\tf@toc=\write4
(D:\LADData\RCode\dataRetrieval\vignettes\dataRetrieval.lof
-LaTeX Font Info: Try loading font information for OT1+ztmcm on input line 5.
+LaTeX Font Info: Try loading font information for OT1+ztmcm on input line 6.
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\psnfss\ot1ztmcm.fd"
File: ot1ztmcm.fd 2000/01/03 Fontinst v1.801 font definitions for OT1/ztmcm.
)
-LaTeX Font Info: Try loading font information for OML+ztmcm on input line 5.
+LaTeX Font Info: Try loading font information for OML+ztmcm on input line 6.
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\psnfss\omlztmcm.fd"
File: omlztmcm.fd 2000/01/03 Fontinst v1.801 font definitions for OML/ztmcm.
)
-LaTeX Font Info: Try loading font information for OMS+ztmcm on input line 5.
+LaTeX Font Info: Try loading font information for OMS+ztmcm on input line 6.
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\psnfss\omsztmcm.fd"
File: omsztmcm.fd 2000/01/03 Fontinst v1.801 font definitions for OMS/ztmcm.
)
-LaTeX Font Info: Try loading font information for OMX+ztmcm on input line 5.
+LaTeX Font Info: Try loading font information for OMX+ztmcm on input line 6.
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\psnfss\omxztmcm.fd"
File: omxztmcm.fd 2000/01/03 Fontinst v1.801 font definitions for OMX/ztmcm.
)
LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <10.95> not available
-(Font) Font shape `OT1/ptm/b/n' tried instead on input line 5.
+(Font) Font shape `OT1/ptm/b/n' tried instead on input line 6.
LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <8> not available
-(Font) Font shape `OT1/ptm/b/n' tried instead on input line 5.
+(Font) Font shape `OT1/ptm/b/n' tried instead on input line 6.
LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <6> not available
-(Font) Font shape `OT1/ptm/b/n' tried instead on input line 5.
+(Font) Font shape `OT1/ptm/b/n' tried instead on input line 6.
)
\tf@lof=\write5
@@ -779,7 +779,7 @@ Package color Info: Redefining color shadecolor on input line 561.
LaTeX Warning: No positions in optional float specifier.
Default added (so using `tbp') on input line 580.
-<figure/getNWIStemperaturePlot.pdf, id=268, 505.89pt x 505.89pt>
+<figure/getNWIStemperaturePlot.pdf, id=270, 505.89pt x 505.89pt>
File: figure/getNWIStemperaturePlot.pdf Graphic file (type pdf)
<use figure/getNWIStemperaturePlot.pdf>
@@ -804,21 +804,37 @@ 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 674.
+Package color Info: Redefining color shadecolor on input line 670.
+
+
+LaTeX Warning: No positions in optional float specifier.
+ Default added (so using `tbp') on input line 679.
+
+<figure/getQWtemperaturePlot.pdf, id=291, 505.89pt x 505.89pt>
+File: figure/getQWtemperaturePlot.pdf Graphic file (type pdf)
+
+<use figure/getQWtemperaturePlot.pdf>
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[][]\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 )[][
@@ -829,26 +845,22 @@ m/n/10.95 '\OT1/pcr/m/n/10.95 uv\TS1/pcr/m/n/10.95 '[][]\OT1/pcr/m/n/10.95 )[][
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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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+Overfull \hbox (44.67563pt too wide) in paragraph at lines 1109--1109
[] \OT1/pcr/m/n/10.95 The first sample is from 2000-01-04 and the last sample i
s from 2012-12-18[]
[]
@@ -901,73 +917,73 @@ s from 2012-12-18[]
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[]\OT1/pcr/m/n/10.95 Suspended sediment concentration (SSC) 1980-10-01 1991-09-
30 3651 mg/l[]
[]
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File: table1.png Graphic file (type png)
<use table1.png>
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(rerunfilecheck) Checksum: 09D57CF47C75A1B38FC38F889C2C3F6D;1818.
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diff --git a/vignettes/dataRetrieval.lot b/vignettes/dataRetrieval.lot
index 491563a0adeb2de6a68217e80188dcfd22454364..d77d60e5b3acbacf827bf913c5de4f2eaba7ef2a 100644
--- a/vignettes/dataRetrieval.lot
+++ b/vignettes/dataRetrieval.lot
@@ -2,9 +2,9 @@
\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 {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 }}{16}{table.caption.5}
-\contentsline {table}{\numberline {5}{\ignorespaces Sample dataframe\relax }}{18}{table.caption.7}
-\contentsline {table}{\numberline {6}{\ignorespaces Example data\relax }}{19}{table.caption.8}
-\contentsline {table}{\numberline {7}{\ignorespaces dataRetrieval functions\relax }}{27}{table.caption.11}
-\contentsline {table}{\numberline {8}{\ignorespaces dataRetrieval miscellaneous functions\relax }}{27}{table.caption.12}
+\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}
\contentsfinish
diff --git a/vignettes/dataRetrieval.pdf b/vignettes/dataRetrieval.pdf
index cd1118d0a36edfe818ed08d7f3eb97b4942f8a3e..224629c85bd99569fe02ed9e0368084695e25e2e 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 5954facaaeb66dd69dcaccae9275f762775f2b49..31fdac390ca8e5e489ec463ee55b7e3470b27078 100644
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diff --git a/vignettes/dataRetrieval.tex b/vignettes/dataRetrieval.tex
index fc9a852b6e1bf6e029db44278463e04e66199104..4f84b9b192baed5048709f1d44f11d62c8223d8b 100644
--- a/vignettes/dataRetrieval.tex
+++ b/vignettes/dataRetrieval.tex
@@ -261,13 +261,13 @@ In this section, five examples of Web retrievals document how to get raw data. T
% %------------------------------------------------------------
The USGS organizes hydrologic data in a standard structure. Streamgages are located throughout the United States, and each streamgage has a unique ID. Often (but not always), these ID's are 8 digits. The first step to finding data is discovering this 8-digit ID. There are many ways to do this, one is the National Water Information System: Mapper \url{http://maps.waterdata.usgs.gov/mapper/index.html}.
-Once the site-ID is known, the next required input for USGS data retrievals is the \enquote{parameter code}. This is a 5-digit code that specifies the measured parameter being requested. For example, parameter code 00631 represents \enquote{Nitrate plus nitrite, water, filtered, milligrams per liter as nitrogen}, with units of \enquote{mg/l as N}. A complete list of possible USGS parameter codes can be found at \url{http://nwis.waterdata.usgs.gov/usa/nwis/pmcodes?help}.
+Once the site-ID (siteNumber) is known, the next required input for USGS data retrievals is the \enquote{parameter code}. This is a 5-digit code that specifies the measured parameter being requested. For example, parameter code 00631 represents \enquote{Nitrate plus nitrite, water, filtered, milligrams per liter as nitrogen}, with units of \enquote{mg/l as N}. A complete list of possible USGS parameter codes can be found at \url{http://nwis.waterdata.usgs.gov/usa/nwis/pmcodes?help}.
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
-% Tue Sep 09 12:48:00 2014
+% Thu Sep 11 16:26:30 2014
\begin{table}[ht]
\caption{Common USGS Parameter Codes}
\label{tab:params}
@@ -330,7 +330,7 @@ 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
-% Tue Sep 09 12:48:01 2014
+% Thu Sep 11 16:26:31 2014
\begin{table}[ht]
\caption{Commonly used USGS Stat Codes}
\label{tab:stat}
@@ -411,7 +411,7 @@ To discover what data is available for a particular USGS site, including measure
% latex table generated in R 3.1.1 by xtable 1.7-3 package
-% Tue Sep 09 12:48:02 2014
+% Thu Sep 11 16:26:32 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 +423,7 @@ 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 & 2014-09-08 & 24358 & ft$^3$/s \\
+ [5pt] & Stream flow, mean. daily & 1948-01-01 & 2014-09-10 & 24360 & 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 \\
@@ -613,20 +613,20 @@ The retrieval produces the following dataframe:
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{verbatim}
- agency site dateTime tz_cd X02_00060_00011
-1 USGS 01491000 2012-05-12 00:00:00 EST 83
-2 USGS 01491000 2012-05-12 00:15:00 EST 83
-3 USGS 01491000 2012-05-12 00:30:00 EST 83
-4 USGS 01491000 2012-05-12 00:45:00 EST 83
-5 USGS 01491000 2012-05-12 01:00:00 EST 85
-6 USGS 01491000 2012-05-12 01:15:00 EST 83
- X02_00060_00011_cd
-1 A
-2 A
-3 A
-4 A
-5 A
-6 A
+ agency_cd site_no datetime tz_cd
+1 USGS 01491000 2012-05-12 00:00:00 EST
+2 USGS 01491000 2012-05-12 00:15:00 EST
+3 USGS 01491000 2012-05-12 00:30:00 EST
+4 USGS 01491000 2012-05-12 00:45:00 EST
+5 USGS 01491000 2012-05-12 01:00:00 EST
+6 USGS 01491000 2012-05-12 01:15:00 EST
+ X02_00060_00011 X02_00060_00011_cd
+1 83 A
+2 83 A
+3 83 A
+4 83 A
+5 85 A
+6 83 A
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -655,17 +655,13 @@ To get USGS water quality data from water samples collected at the streamgage or
\hlstd{dissolvedNitrate} \hlkwb{<-} \hlkwd{retrieveNWISqwData}\hlstd{(siteNumber, parameterCd,}
\hlstd{startDate, endDate)}
-\end{alltt}
-
-
-{\ttfamily\noindent\color{warningcolor}{Warning: cannot open: HTTP status was '0 (nil)'}}
-
-{\ttfamily\noindent\bfseries\color{errorcolor}{Error: cannot open the connection}}\begin{alltt}
\hlkwd{names}\hlstd{(dissolvedNitrate)}
\end{alltt}
-
-
-{\ttfamily\noindent\bfseries\color{errorcolor}{Error: object 'dissolvedNitrate' not found}}\end{kframe}
+\begin{verbatim}
+[1] "dateTime" "site" "qualifier_00618"
+[4] "value_00618" "qualifier_71851" "value_71851"
+\end{verbatim}
+\end{kframe}
\end{knitrout}
% Note that in this \enquote{simple} dataframe, datetime is imported as Dates (no times are included), and the qualifier is either blank or \verb@"<"@ signifying a censored value. A plotting example is shown in Figure \ref{fig:getQWtemperaturePlot}.
@@ -678,15 +674,14 @@ To get USGS water quality data from water samples collected at the streamgage or
\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{))}
-\end{alltt}
-
-
-{\ttfamily\noindent\bfseries\color{errorcolor}{Error: object 'dissolvedNitrate' not found}}\begin{alltt}
\hlkwd{title}\hlstd{(ChoptankInfo}\hlopt{$}\hlstd{station.nm)}
\end{alltt}
+\end{kframe}\begin{figure}[]
+
+\includegraphics[width=\maxwidth]{figure/getQWtemperaturePlot} \caption[Nitrate plot of Choptank River]{Nitrate plot of Choptank River.\label{fig:getQWtemperaturePlot}}
+\end{figure}
-{\ttfamily\noindent\bfseries\color{errorcolor}{Error: plot.new has not been called yet}}\end{kframe}
\end{knitrout}
\FloatBarrier
@@ -702,23 +697,20 @@ There are additional water quality data sets available from the Water Quality Da
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{specificCond} \hlkwb{<-} \hlkwd{getWQPData}\hlstd{(}\hlstr{'WIDNR_WQX-10032762'}\hlstd{,}
- \hlstr{'Specific conductance'}\hlstd{,}\hlstr{''}\hlstd{,}\hlstr{''}\hlstd{)}
+ \hlstr{'Specific conductance'}\hlstd{,}\hlstr{'2011-05-01'}\hlstd{,}\hlstr{'2011-09-30'}\hlstd{)}
\hlkwd{head}\hlstd{(specificCond)}
\end{alltt}
\begin{verbatim}
dateTime qualifier. value.
-1 2011-02-14 1360
-2 2011-02-17 1930
-3 2011-03-03 1240
-4 2011-03-10 1480
-5 2011-03-29 1130
-6 2011-04-07 1200
+1 2011-05-09 1000
+2 2011-06-05 800
+3 2011-07-06 860
+4 2011-08-08 471
+5 2011-09-11 750
\end{verbatim}
\end{kframe}
\end{knitrout}
-There are
-
\FloatBarrier
%------------------------------------------------------------
\subsection{URL Construction}
@@ -794,7 +786,7 @@ There are 4750 data points, and 4750 days.
% latex table generated in R 3.1.1 by xtable 1.7-3 package
-% Tue Sep 09 12:49:17 2014
+% Thu Sep 11 16:26:44 2014
\begin{table}[ht]
\caption{Daily dataframe}
\label{tab:DailyDF1}
@@ -915,7 +907,7 @@ 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
-% Tue Sep 09 12:49:44 2014
+% Thu Sep 11 16:26:45 2014
\begin{table}[ht]
\caption{Example data}
\label{tab:exampleComplexQW}
@@ -1356,7 +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 2014-09-08 24358 ft3/s
+2 2014-09-10 24360 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 92d62142883ddf708dd4e64ac133b8529dc9e89c..da70f97eb48c23c9ad26c21a0136d5440889e0e0 100644
--- a/vignettes/dataRetrieval.toc
+++ b/vignettes/dataRetrieval.toc
@@ -8,21 +8,21 @@
\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}{13}{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}{15}{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}{17}{subsection.3.3}
-\contentsline {subsection}{\numberline {3.4}Censored Values: Summation Explanation}{18}{subsection.3.4}
-\contentsline {subsection}{\numberline {3.5}User-Generated Data Files}{20}{subsection.3.5}
-\contentsline {subsubsection}{\numberline {3.5.1}getDailyDataFromFile}{20}{subsubsection.3.5.1}
-\contentsline {subsubsection}{\numberline {3.5.2}getSampleDataFromFile}{22}{subsubsection.3.5.2}
-\contentsline {subsection}{\numberline {3.6}Merge Report}{23}{subsection.3.6}
-\contentsline {subsection}{\numberline {3.7}EGRET Plots}{24}{subsection.3.7}
-\contentsline {section}{\numberline {4}Summary}{26}{section.4}
-\contentsline {section}{\numberline {5}Getting Started in R}{28}{section.5}
-\contentsline {subsection}{\numberline {5.1}New to R?}{28}{subsection.5.1}
-\contentsline {subsection}{\numberline {5.2}R User: Installing dataRetrieval}{30}{subsection.5.2}
-\contentsline {section}{\numberline {6}Creating tables in Microsoft\textregistered \ software from R}{30}{section.6}
+\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}
\contentsfinish
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