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Commit aa48368a authored by Laura A DeCicco's avatar Laura A DeCicco
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Updating help files.

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inst/doc/Rplots.pdf
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inst/doc/dataRetrieval-fig1.pdf
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inst/doc/dataRetrieval.Rnw
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......@@ -100,6 +100,11 @@ install.packages(
It is a good idea to re-start the R enviornment after installing the package, especially if installing an updated version (that is, restart RStudio). Some users have found it necessary to delete the previous version's package folder before installing newer version of dataRetrieval. If you are experiencing issues after updating a package, trying deleting the package folder - the default location for Windows is something like this: C:/Users/userA/Documents/R/win-library/2.15/dataRetrieval, and the default for a Mac: /Users/userA/Library/R/2.15/library/dataRetrieval. Then, re-install the package using the directions above. Moving to CRAN should solve this problem.
After installing the package, you need to open the library each time you re-start R. This is done with the simple command:
<<openLibraryTest, eval=FALSE>>=
library(dataRetrieval)
@
Using RStudio, you could alternatively click on the checkbox for dataRetrieval in the Packages window.
%------------------------------------------------------------
\subsection{R Developers: Installing dataRetrieval from gitHub}
......@@ -234,7 +239,7 @@ mtext("Discharge [cfs]",side=4,line=3,col="red")
\caption{Temperature and discharge plot of Choptank River.}
\end{figure}
There are occasions where NWIS values are not reported as numbers, instead a common example is "Ice". Any value that cannot be converted to a number will be reported as NA in this package.
There are occasions where NWIS values are not reported as numbers, instead there might be text describing a certain event such as "Ice". Any value that cannot be converted to a number will be reported as NA in this package.
%------------------------------------------------------------
\subsection{USGS Unit Value Retrievals}
......
inst/doc/dataRetrieval.tex
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......@@ -106,6 +106,13 @@ A Mac example looks like this:
It is a good idea to re-start the R enviornment after installing the package, especially if installing an updated version (that is, restart RStudio). Some users have found it necessary to delete the previous version's package folder before installing newer version of dataRetrieval. If you are experiencing issues after updating a package, trying deleting the package folder - the default location for Windows is something like this: C:/Users/userA/Documents/R/win-library/2.15/dataRetrieval, and the default for a Mac: /Users/userA/Library/R/2.15/library/dataRetrieval. Then, re-install the package using the directions above. Moving to CRAN should solve this problem.
After installing the package, you need to open the library each time you re-start R. This is done with the simple command:
\begin{Schunk}
\begin{Sinput}
> library(dataRetrieval)
\end{Sinput}
\end{Schunk}
Using RStudio, you could alternatively click on the checkbox for dataRetrieval in the Packages window.
%------------------------------------------------------------
\subsection{R Developers: Installing dataRetrieval from gitHub}
......@@ -143,7 +150,7 @@ Once the site-ID is known, the next required input for USGS data retrievals is t
Not every station will measure all parameters. The following is a list of commonly measured parameters:
% latex table generated in R 2.15.2 by xtable 1.7-0 package
% Tue Jan 22 16:04:58 2013
% Wed Jan 23 10:35:45 2013
\begin{table}[ht]
\begin{center}
\caption{Commonly found USGS Parameter Codes}
......@@ -166,7 +173,7 @@ For real-time data, the parameter code and site ID will suffice. The USGS store
The most common stat codes are:
% latex table generated in R 2.15.2 by xtable 1.7-0 package
% Tue Jan 22 16:04:58 2013
% Wed Jan 23 10:35:45 2013
\begin{table}[ht]
\begin{center}
\caption{Commonly found USGS Stat Codes}
......@@ -218,7 +225,7 @@ A dataframe is returned that looks like the following:
The structure of the dataframe is:
\begin{Schunk}
\begin{Soutput}
'data.frame': 23763 obs. of 5 variables:
'data.frame': 23764 obs. of 5 variables:
$ agency_cd : chr "USGS" "USGS" "USGS" "USGS" ...
$ site_no : chr "01491000" "01491000" "01491000" "01491000" ...
$ datetime : Date, format: "1948-01-01" "1948-01-02" ...
......@@ -282,252 +289,4 @@ We can also get real-time, instantaneous measurements using the retrieveUnitNWIS
> parameterCd <- "00060" # Discharge in cubic feet per second
> startDate <- as.character(Sys.Date())
> endDate <- as.character(Sys.Date())
> dischargeToday <- retrieveUnitNWISData(siteNumber, parameterCd, startDate, endDate)
\end{Sinput}
\end{Schunk}
Which produces the following dataframe:
\begin{Schunk}
\begin{Soutput}
agency_cd site_no datetime tz_cd X02_00060 X02_00060_cd
1 USGS 01491000 2013-01-22 00:00:00 EST 209 P
2 USGS 01491000 2013-01-22 00:15:00 EST 209 P
3 USGS 01491000 2013-01-22 00:30:00 EST 209 P
4 USGS 01491000 2013-01-22 00:45:00 EST 209 P
5 USGS 01491000 2013-01-22 01:00:00 EST 209 P
6 USGS 01491000 2013-01-22 01:15:00 EST 209 P
\end{Soutput}
\end{Schunk}
The structure of the dataframe is:
\begin{Schunk}
\begin{Soutput}
'data.frame': 66 obs. of 6 variables:
$ agency_cd : chr "USGS" "USGS" "USGS" "USGS" ...
$ site_no : chr "01491000" "01491000" "01491000" "01491000" ...
$ datetime : POSIXct, format: "2013-01-22 00:00:00" "2013-01-22 00:15:00" ...
$ tz_cd : chr "EST" "EST" "EST" "EST" ...
$ X02_00060 : num 209 209 209 209 209 209 211 206 206 206 ...
$ X02_00060_cd: chr "P" "P" "P" "P" ...
\end{Soutput}
\end{Schunk}
Note that time now becomes important, so the dateTime is a POSIXct, and the time zone is included. Data is pulled from \url{http://waterservices.usgs.gov/rest/IV-Test-Tool.html}. There are occasions where NWIS values are not reported as numbers, instead a common example is "Ice". Any value that cannot be converted to a number will be reported as NA in this package.
%------------------------------------------------------------
\subsection{USGS Water Quality Retrievals}
%------------------------------------------------------------
Finally, we can use the dataRetrieval package to get water quality data that is available on the water quality data portal: \url{http://www.waterqualitydata.us/}. The function is getQWData, with the similar input arguments: siteNumber, parameterCd, startDate, endDate, and interactive. The difference is in parameterCd, in this function multiple parameters can be queried using a ";" separator, and setting parameterCd <- "" will return all of the measured observations.
\begin{Schunk}
\begin{Sinput}
> # Using defaults:
> siteNumber <- "01491000" # Site ID for Choptank River near Greensboro, MD
> parameterCd <- "00618;71851" # Dissolved Nitrate parameter codes (one as mg/l as N, one as mg/l)
> startDate <- "1964-06-11"
> endDate <- "2012-12-18"
> dissolvedNitrate <- getQWData(siteNumber, parameterCd, startDate, endDate)
\end{Sinput}
\end{Schunk}
Producing a dataframe with the following columns:
\begin{Schunk}
\begin{Soutput}
[1] "dateTime" "qualifier.71851" "value.71851" "qualifier.00618"
[5] "value.00618"
\end{Soutput}
\end{Schunk}
%------------------------------------------------------------
\subsection{USGS Site Information Retrievals}
%------------------------------------------------------------
To obtain all of the available site information, use the getSiteFileData function:
\begin{Schunk}
\begin{Sinput}
> # Using defaults:
> siteNumber <- "01491000" # Site ID for Choptank River near Greensboro, MD
> ChopTankInfo <- getSiteFileData(siteNumber)
\end{Sinput}
\end{Schunk}
The available data for these for the USGS sites are:
\begin{Schunk}
\begin{Sinput}
> colnames(ChopTankInfo)
\end{Sinput}
\begin{Soutput}
[1] "agency.cd" "site.no" "station.nm"
[4] "site.tp.cd" "lat.va" "long.va"
[7] "dec.lat.va" "dec.long.va" "coord.meth.cd"
[10] "coord.acy.cd" "coord.datum.cd" "dec.coord.datum.cd"
[13] "district.cd" "state.cd" "county.cd"
[16] "country.cd" "land.net.ds" "map.nm"
[19] "map.scale.fc" "alt.va" "alt.meth.cd"
[22] "alt.acy.va" "alt.datum.cd" "huc.cd"
[25] "basin.cd" "topo.cd" "instruments.cd"
[28] "construction.dt" "inventory.dt" "drain.area.va"
[31] "contrib.drain.area.va" "tz.cd" "local.time.fg"
[34] "reliability.cd" "gw.file.cd" "nat.aqfr.cd"
[37] "aqfr.cd" "aqfr.type.cd" "well.depth.va"
[40] "hole.depth.va" "depth.src.cd" "project.no"
[43] "queryTime"
\end{Soutput}
\end{Schunk}
Pulling out a specific example piece of information, in this case station name can be done as follows:
\begin{Schunk}
\begin{Sinput}
> ChopTankInfo$station.nm
\end{Sinput}
\begin{Soutput}
[1] "CHOPTANK RIVER NEAR GREENSBORO, MD"
\end{Soutput}
\end{Schunk}
Site information is obtained from \url{http://waterservices.usgs.gov/rest/Site-Test-Tool.html}
%------------------------------------------------------------
\subsection{USGS Parameter Information Retrievals}
%------------------------------------------------------------
To obtain all of the available information concerning a measured parameter, use the getParameterInfo function:
\begin{Schunk}
\begin{Sinput}
> # Using defaults:
> parameterCd <- "00618"
> parameterINFO <- getParameterInfo(parameterCd)
\end{Sinput}
\end{Schunk}
The available data for these for the USGS sites are:
\begin{Schunk}
\begin{Sinput}
> colnames(parameterINFO)
\end{Sinput}
\begin{Soutput}
[1] "parameter_cd" "parameter_group_nm" "parameter_nm"
[4] "casrn" "srsname" "parameter_units"
\end{Soutput}
\end{Schunk}
Pulling out a specific example piece of information, in this case station name can be done as follows:
\begin{Schunk}
\begin{Sinput}
> parameterINFO$parameter_nm
\end{Sinput}
\begin{Soutput}
[1] "Nitrate, water, filtered, milligrams per liter as nitrogen"
\end{Soutput}
\end{Schunk}
Parameter information is obtained from \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes/}
%------------------------------------------------------------
\section{Polished Data: USGS Web Retrieval Examples}
%------------------------------------------------------------
In this example, we use 3 dataRetrieval functions to get daily streamflow data and inorganic nitrogen sample results, and site information for a USGS gaging station with the ID 06934500. The station is Missouri River at Hermann, MO (which is discovered in the INFO dataset). Rather than see the raw output from NWIS, we will get more polished returned data frames. These data frames were exclusively designed to work with the EGRET R package, however can be very useful for all hydrologic studies.
\begin{Schunk}
\begin{Sinput}
> Daily <- getDVData("06934500","00060","1970-10-01","2011-09-30")
\end{Sinput}
\begin{Soutput}
There are 14975 data points, and 14975 days.
There are 0 zero flow days
If there are any zero discharge days, all days had 0 cubic meters per second added to the discharge value.
\end{Soutput}
\begin{Sinput}
> head(Daily)
\end{Sinput}
\begin{Soutput}
Date Q Julian Month Day DecYear MonthSeq Qualifier i LogQ
1 1970-10-01 3879.408 44102 10 274 1970.747 1450 A 1 8.263438
2 1970-10-02 3454.655 44103 10 275 1970.750 1450 A 2 8.147478
3 1970-10-03 3029.903 44104 10 276 1970.753 1450 A 3 8.016286
4 1970-10-04 2644.793 44105 10 277 1970.755 1450 A 4 7.880348
5 1970-10-05 2293.665 44106 10 278 1970.758 1450 A 5 7.737906
6 1970-10-06 2072.793 44107 10 279 1970.761 1450 A 6 7.636652
Q7 Q30
1 NA NA
2 NA NA
3 NA NA
4 NA NA
5 NA NA
6 NA NA
\end{Soutput}
\begin{Sinput}
> Sample <-getSampleData("06934500","00631","1970-10-01","2011-09-30")
> head(Sample)
\end{Sinput}
\begin{Soutput}
Date ConcLow ConcHigh Uncen ConcAve Julian Month Day DecYear MonthSeq
1 1979-09-26 1.10 1.10 1 1.10 47384 9 269 1979.734 1557
2 1979-10-16 0.42 0.42 1 0.42 47404 10 289 1979.788 1558
3 1979-11-27 2.00 2.00 1 2.00 47446 11 331 1979.903 1559
4 1979-12-18 1.70 1.70 1 1.70 47467 12 352 1979.960 1560
5 1980-01-29 1.30 1.30 1 1.30 47509 1 29 1980.078 1561
6 1980-02-21 1.10 1.10 1 1.10 47532 2 52 1980.141 1562
SinDY CosDY
1 -0.9946999 -0.1028210
2 -0.9712570 0.2380333
3 -0.5724040 0.8199718
4 -0.2463613 0.9691781
5 0.4699767 0.8826788
6 0.7733507 0.6339785
\end{Soutput}
\begin{Sinput}
> INFO <-getMetaData("06934500","00631", interactive=FALSE)
> colnames(INFO)
\end{Sinput}
\begin{Soutput}
[1] "agency.cd" "site.no" "station.nm"
[4] "site.tp.cd" "lat.va" "long.va"
[7] "dec.lat.va" "dec.long.va" "coord.meth.cd"
[10] "coord.acy.cd" "coord.datum.cd" "dec.coord.datum.cd"
[13] "district.cd" "state.cd" "county.cd"
[16] "country.cd" "map.nm" "map.scale.fc"
[19] "alt.va" "alt.meth.cd" "alt.acy.va"
[22] "alt.datum.cd" "huc.cd" "basin.cd"
[25] "topo.cd" "construction.dt" "inventory.dt"
[28] "drain.area.va" "contrib.drain.area.va" "tz.cd"
[31] "local.time.fg" "reliability.cd" "project.no"
[34] "queryTime" "drainSqKm" "staAbbrev"
[37] "param.nm" "param.units" "paramShortName"
[40] "paramNumber" "constitAbbrev"
\end{Soutput}
\begin{Sinput}
> INFO$station.nm
\end{Sinput}
\begin{Soutput}
[1] "Missouri River at Hermann, MO"
\end{Soutput}
\begin{Sinput}
> Sample <- mergeReport()
\end{Sinput}
\begin{Soutput}
Discharge Record is 14975 days long, which is 41 years
First day of the discharge record is 1970-10-01 and last day is 2011-09-30
The water quality record has 437 samples
The first sample is from 1979-09-26 and the last sample is from 2011-09-29
Discharge: Minimum, mean and maximum 394 2660 20900
Concentration: Minimum, mean and maximum 0.02 1.3 4.2
Percentage of the sample values that are censored is 1.4 %
\end{Soutput}
\end{Schunk}
\newpage
%------------------------------------------------------------
% BIBLIO
%------------------------------------------------------------
\begin{thebibliography}{10}
\bibitem{HirschI}
Helsel, D.R. and R. M. Hirsch, 2002. Statistical Methods in Water Resources Techniques of Water Resources Investigations, Book 4, chapter A3. U.S. Geological Survey. 522 pages. \url{http://pubs.usgs.gov/twri/twri4a3/}
\bibitem{HirschII}
Hirsch, R. M., Moyer, D. L. and Archfield, S. A. (2010), Weighted Regressions on Time, Discharge, and Season (WRTDS), with an Application to Chesapeake Bay River Inputs. JAWRA Journal of the American Water Resources Association, 46: 857-880. doi: 10.1111/j.1752-1688.2010.00482.x \url{http://onlinelibrary.wiley.com/doi/10.1111/j.1752-1688.2010.00482.x/full}
\bibitem{HirschIII}
Sprague, L. A., Hirsch, R. M., and Aulenbach, B. T. (2011), Nitrate in the Mississippi River and Its Tributaries, 1980 to 2008: Are We Making Progress? Environmental Science \& Technology, 45 (17): 7209-7216. doi: 10.1021/es201221s \url{http://pubs.acs.org/doi/abs/10.1021/es201221s}
\end{thebibliography}
\end{document}
\end{document}
> dischargeToday <- retrieveUnitNWISData(siteNumber, parameterCd, startDate, endDate)
\ No newline at end of file
man/getQWData.Rd
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\name{getQWData}
\alias{getQWData}
\title{Data Import for USGS NWIS Water Quality Data}
\title{Raw Data Import for USGS NWIS Water Quality Data}
\usage{
getQWData(siteNumber, ParameterCd, StartDate, EndDate,
interactive = TRUE)
......@@ -41,9 +41,9 @@
}
\examples{
# These examples require an internet connection to run
rawSample <- getQWData('01594440','01075', '1985-01-01', '1985-03-31')
rawSampleAll <- getQWData('05114000','', '1985-01-01', '1985-03-31')
rawSampleSelect <- getQWData('05114000','00915;00931', '1985-01-01', '1985-04-30', interactive=FALSE)
rawProcessedSample <- getQWData('01594440','01075', '1985-01-01', '1985-03-31')
rawProcessedSampleAll <- getQWData('05114000','', '1985-01-01', '1985-03-31')
rawProcessedSampleSelect <- getQWData('05114000','00915;00931', '1985-01-01', '1985-04-30', interactive=FALSE)
}
\keyword{USGS}
\keyword{data}
......
man/getRawQWData.Rd 0 → 100644
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− 0
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\name{getRawQWData}
\alias{getRawQWData}
\title{Raw Data Import for USGS NWIS Water Quality Data}
\usage{
getRawQWData(siteNumber, ParameterCd, StartDate, EndDate,
interactive = TRUE)
}
\arguments{
\item{siteNumber}{string USGS site number. This is
usually an 8 digit number}
\item{ParameterCd}{string USGS parameter code. This is
usually an 5 digit number. Multiple parameter codes can
be inputted with a ';' separator. Leaving this blank
will return all of the measured values during the
specified time period.}
\item{StartDate}{string starting date for data retrieval
in the form YYYY-MM-DD.}
\item{EndDate}{string ending date for data retrieval in
the form YYYY-MM-DD.}
\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)
}
\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}
}
\examples{
# These examples require an internet connection to run
rawSample <- getRawQWData('01594440','01075', '1985-01-01', '1985-03-31')
rawSampleAll <- getRawQWData('05114000','', '1985-01-01', '1985-03-31')
rawSampleSelect <- getRawQWData('05114000','00915;00931', '1985-01-01', '1985-04-30', interactive=FALSE)
}
\keyword{USGS}
\keyword{data}
\keyword{import}
\keyword{service}
\keyword{web}
man/processQWData.Rd 0 → 100644
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\name{processQWData}
\alias{processQWData}
\title{Processing of USGS NWIS Water Quality Data}
\usage{
processQWData(data)
}
\arguments{
\item{data}{dataframe from}
}
\value{
data dataframe with first column dateTime, and at least
one qualifier and value columns (subsequent
qualifier/value columns could follow depending on the
number of parameter codes)
}
\description{
Processes water quality portal data. This function looks
at detection limit and detection conditions to determine
if a value is left censored or not. Censored values are
given the qualifier "<". The dataframe is also converted
from a long to wide format.
}
\examples{
# These examples require an internet connection to run
rawSample <- getRawQWData('01594440','01075', '1985-01-01', '1985-03-31')
rawSampleSelect <- processQWData(rawSample)
}
\keyword{USGS}
\keyword{data}
\keyword{import}
\keyword{service}
\keyword{web}
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