diff --git a/vignettes/dataRetrieval-concordance.tex b/vignettes/dataRetrieval-concordance.tex
index 6c049207280a631800833b12426de7a62aaf9832..4c9c14712f612496a3609dbe58d84413073e4f60 100644
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+\contentsline {figure}{\numberline {4}{\ignorespaces A simple R help file\relax }}{30}{figure.caption.14}
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diff --git a/vignettes/dataRetrieval.log b/vignettes/dataRetrieval.log
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[]|\OT1/phv/b/n/10.95 Table| | [][]\OT1/phv/m/n/10.95 Daily mean data avail-ab
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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 )[][
@@ -831,22 +841,26 @@ 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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[] \OT1/pcr/m/n/10.95 The first sample is from 2000-01-04 and the last sample i
s from 2012-12-18[]
[]
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[] \OT1/pcr/m/n/10.95 Sample1 <- localSample[!duplicated(localSample[c("DecYea
r","ConcHigh")]),][]
[]
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[]\OT1/pcr/m/n/10.95 Suspended sediment concentration (SSC) 1980-10-01 1991-09-
30 3651 mg/l[]
[]
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diff --git a/vignettes/dataRetrieval.lot b/vignettes/dataRetrieval.lot
index b3fc11f5e7f66063666043ac55440bbf7e4bceec..164c696eb71c96951282ed9ca0ab2b9248da1276 100644
--- a/vignettes/dataRetrieval.lot
+++ b/vignettes/dataRetrieval.lot
@@ -3,8 +3,8 @@
\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 }}{18}{table.caption.6}
-\contentsline {table}{\numberline {5}{\ignorespaces Sample dataframe\relax }}{20}{table.caption.8}
-\contentsline {table}{\numberline {6}{\ignorespaces Example data\relax }}{21}{table.caption.9}
-\contentsline {table}{\numberline {7}{\ignorespaces dataRetrieval functions\relax }}{29}{table.caption.12}
-\contentsline {table}{\numberline {8}{\ignorespaces dataRetrieval miscellaneous functions\relax }}{29}{table.caption.13}
+\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 51d9e77bc289b99b354da5848c59e47315242c14..ac5e5885a40977f288bbb088b839b505230a37f2 100644
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diff --git a/vignettes/dataRetrieval.synctex.gz b/vignettes/dataRetrieval.synctex.gz
index 3fd107c6e1fe5d61cd822fd25ab9321893f82615..1a63eebca98d346fba1a493bf868925e16f68c7f 100644
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diff --git a/vignettes/dataRetrieval.tex b/vignettes/dataRetrieval.tex
index 7904149aff074199778b139c2784dac09234ca79..ce9715cc12d0c519d1431dd0ef3b1c7954e5ac68 100644
--- a/vignettes/dataRetrieval.tex
+++ b/vignettes/dataRetrieval.tex
@@ -229,7 +229,7 @@ A quick workflow for major dataRetrieval functions:
\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00060"}
\hlcom{#Raw daily data:}
-\hlstd{rawDailyData} \hlkwb{<-} \hlkwd{retrieveNWISData}\hlstd{(siteNumber,parameterCd,}
+\hlstd{rawDailyData} \hlkwb{<-} \hlkwd{retrieveNWISdvData}\hlstd{(siteNumber,parameterCd,}
\hlstr{"1980-01-01"}\hlstd{,}\hlstr{"2010-01-01"}\hlstd{)}
\hlcom{# Data compiled for EGRET analysis}
\hlstd{Daily} \hlkwb{<-} \hlkwd{getDVData}\hlstd{(siteNumber,parameterCd,}
@@ -267,7 +267,7 @@ Not every station will measure all parameters. A short list of commonly measured
% latex table generated in R 3.1.1 by xtable 1.7-3 package
-% Fri Aug 01 16:04:17 2014
+% Sun Aug 03 14:57:17 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
-% Fri Aug 01 16:04:18 2014
+% Sun Aug 03 14:57:19 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
-% Fri Aug 01 16:04:19 2014
+% Sun Aug 03 14:57:20 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 & 2014-07-31 & 24319 & ft$^3$/s \\
+ [5pt] & Stream flow, mean. daily & 1948-01-01 & 2014-08-02 & 24321 & 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 \\
@@ -479,7 +479,7 @@ Parameter information is obtained from \url{http://nwis.waterdata.usgs.gov/nwis/
\subsection{Daily Values}
\label{sec:usgsDaily}
%------------------------------------------------------------
-To obtain daily records of USGS data, use the \texttt{retrieveNWISData} function. The arguments for this function are siteNumber, parameterCd, startDate, endDate, statCd, and a logical (TRUE/FALSE) interactive. There are 2 default arguments: statCd (defaults to \texttt{"}00003\texttt{"}), and interactive (defaults to TRUE). If you want to use the default values, you do not need to list them in the function call. By setting the \texttt{"}interactive\texttt{"} option to FALSE, the operation of the function will advance automatically. It might make more sense to run large batch collections with the interactive option set to FALSE.
+To obtain daily records of USGS data, use the \texttt{retrieveNWISdvData} function. The arguments for this function are siteNumber, parameterCd, startDate, endDate, statCd, and a logical (TRUE/FALSE) interactive. There are 2 default arguments: statCd (defaults to \texttt{"}00003\texttt{"}), and interactive (defaults to TRUE). If you want to use the default values, you do not need to list them in the function call. By setting the \texttt{"}interactive\texttt{"} option to FALSE, the operation of the function will advance automatically. It might make more sense to run large batch collections with the interactive option set to FALSE.
The dates (start and end) must be in the format \texttt{"}YYYY-MM-DD\texttt{"} (note: the user must include the quotes). Setting the start date to \texttt{"}\texttt{"} (no space) will prompt the program to ask for the earliest date, and setting the end date to \texttt{"}\texttt{"} (no space) will prompt for the latest available date.
@@ -491,7 +491,7 @@ The dates (start and end) must be in the format \texttt{"}YYYY-MM-DD\texttt{"} (
\hlstd{startDate} \hlkwb{<-} \hlstr{""} \hlcom{# Will request earliest date}
\hlstd{endDate} \hlkwb{<-} \hlstr{""} \hlcom{# Will request latest date}
-\hlstd{discharge} \hlkwb{<-} \hlkwd{retrieveNWISData}\hlstd{(siteNumber,}
+\hlstd{discharge} \hlkwb{<-} \hlkwd{retrieveNWISdvData}\hlstd{(siteNumber,}
\hlstd{parameterCd, startDate, endDate)}
\hlkwd{names}\hlstd{(discharge)}
\end{alltt}
@@ -515,7 +515,7 @@ Another example that doesn't use the defaults would be a request for mean and ma
\hlstd{startDate} \hlkwb{<-} \hlstr{"2012-01-01"}
\hlstd{endDate} \hlkwb{<-} \hlstr{"2012-05-01"}
-\hlstd{temperatureAndFlow} \hlkwb{<-} \hlkwd{retrieveNWISData}\hlstd{(siteNumber, parameterCd,}
+\hlstd{temperatureAndFlow} \hlkwb{<-} \hlkwd{retrieveNWISdvData}\hlstd{(siteNumber, parameterCd,}
\hlstd{startDate, endDate,} \hlkwc{StatCd}\hlstd{=statCd)}
\end{alltt}
\end{kframe}
@@ -594,7 +594,7 @@ There are occasions where NWIS values are not reported as numbers, instead there
\subsection{Unit Values}
\label{sec:usgsRT}
%------------------------------------------------------------
-Any data collected at regular time intervals (such as 15-minute or hourly) are known as \enquote{unit values}. Many of these are delivered on a real time basis and very recent data (even less than an hour old in many cases) are available through the function \texttt{retrieveUnitNWISData}. Some of these unit values are available for many years, and some are only available for a recent time period such as 120 days. Here is an example of a retrieval of such data.
+Any data collected at regular time intervals (such as 15-minute or hourly) are known as \enquote{unit values}. Many of these are delivered on a real time basis and very recent data (even less than an hour old in many cases) are available through the function \texttt{retrieveNWISunitData}. Some of these unit values are available for many years, and some are only available for a recent time period such as 120 days. Here is an example of a retrieval of such data.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
@@ -602,7 +602,7 @@ Any data collected at regular time intervals (such as 15-minute or hourly) are k
\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00060"} \hlcom{# Discharge (ft3/s)}
\hlstd{startDate} \hlkwb{<-} \hlstr{"2012-05-12"}
\hlstd{endDate} \hlkwb{<-} \hlstr{"2012-05-13"}
-\hlstd{dischargeToday} \hlkwb{<-} \hlkwd{retrieveUnitNWISData}\hlstd{(siteNumber, parameterCd,}
+\hlstd{dischargeToday} \hlkwb{<-} \hlkwd{retrieveNWISunitData}\hlstd{(siteNumber, parameterCd,}
\hlstd{startDate, endDate)}
\end{alltt}
\end{kframe}
@@ -642,7 +642,7 @@ Note that time now becomes important, so the variable datetime is a POSIXct, and
\subsection{Water Quality Values}
\label{sec:usgsWQP}
%------------------------------------------------------------
-To get USGS water quality data from water samples collected at the streamgage or other monitoring site (as distinct from unit values collected through some type of automatic monitor) we can use the function \texttt{retrieveNWISqwData}, with the input arguments: siteNumber, parameterCd, startDate, endDate, and interactive (similar to \texttt{retrieveUnitNWISData} and \texttt{retrieveNWISData}).
+To get USGS water quality data from water samples collected at the streamgage or other monitoring site (as distinct from unit values collected through some type of automatic monitor) we can use the function \texttt{retrieveNWISqwData}, with the input arguments: siteNumber, parameterCd, startDate, endDate, and interactive (similar to \texttt{retrieveNWISunitData} and \texttt{retrieveNWISdvData}).
\begin{knitrout}
@@ -701,20 +701,13 @@ There are additional water quality data sets available from the Water Quality Da
\hlkwd{head}\hlstd{(specificCond)}
\end{alltt}
\begin{verbatim}
- dateTime qualifier.Specific conductance
-1 2011-02-14
-2 2011-02-17
-3 2011-03-03
-4 2011-03-10
-5 2011-03-29
-6 2011-04-07
- value.Specific conductance
-1 1360
-2 1930
-3 1240
-4 1480
-5 1130
-6 1200
+ 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
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -796,7 +789,7 @@ There are 4750 data points, and 4750 days.
% latex table generated in R 3.1.1 by xtable 1.7-3 package
-% Fri Aug 01 16:04:33 2014
+% Sun Aug 03 14:57:39 2014
\begin{table}[ht]
\caption{Daily dataframe}
\label{tab:DailyDF1}
@@ -834,7 +827,7 @@ Notice that the \enquote{Day of the year} column can span from 1 to 366. The 366
\subsection{Sample Data}
\label{Samplesubsection}
%------------------------------------------------------------
-The \texttt{getSampleData} function retrieves USGS sample data from NWIS. The arguments for this function are also siteNumber, ParameterCd, StartDate, EndDate, interactive. These are the same inputs as \texttt{getRawQWData} or \texttt{getQWData} as described in the previous section.
+The \texttt{getSampleData} function retrieves USGS sample data from NWIS. The arguments for this function are also siteNumber, ParameterCd, StartDate, EndDate, interactive. These are the same inputs as \texttt{retrieveWQPqwData} or \texttt{getWQPData} as described in the previous section.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
@@ -917,7 +910,7 @@ 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
-% Fri Aug 01 16:04:34 2014
+% Sun Aug 03 14:57:40 2014
\begin{table}[ht]
\caption{Example data}
\label{tab:exampleComplexQW}
@@ -938,7 +931,7 @@ To illustrate how the dataRetrieval package handles a more complex censoring pro
\end{table}
-The dataRetrieval package will \enquote{add up} all the values in a given row to form the total for that sample when using the Sample dataframe. Thus, you only want to enter data that should be added together. If you want a dataframe with multiple constituents that are not summed, do not use getSampleData, getSTORETSampleData, or getSampleDataFromFile. The raw data functions: \texttt{getWQPData}, \texttt{retrieveNWISqwData}, \texttt{getRawQWData}, \texttt{getQWData} will not sum constituents, but leave them in their individual columns.
+The dataRetrieval package will \enquote{add up} all the values in a given row to form the total for that sample when using the Sample dataframe. Thus, you only want to enter data that should be added together. If you want a dataframe with multiple constituents that are not summed, do not use getSampleData, getSTORETSampleData, or getSampleDataFromFile. The raw data functions: \texttt{getWQPData}, \texttt{retrieveNWISqwData}, \texttt{retrieveWQPqwData}, \texttt{getWQPData} will not sum constituents, but leave them in their individual columns.
For example, we might know the value for dp on 5/30/2005, but we don't want to put it in the table because under the rules of this data set, we are not supposed to add it in to the values in 2005.
@@ -1184,18 +1177,17 @@ Tables \ref{tab:dataRetrievalFunctions1} and \ref{tab:dataRetrievalMisc} summari
\multicolumn{1}{c}{\textbf{\textsf{Function Name}}} &
\multicolumn{1}{c}{\textbf{\textsf{Description}}} \\ [0pt]
\hline
- Daily & \texttt{retrieveNWISData} & Raw USGS daily data \\
+ Daily & \texttt{retrieveNWISdvData} & Raw USGS daily data \\
[5pt]Daily\tnote{1} & \texttt{getDVData} & USGS daily values \\
[5pt]Daily\tnote{1} & \texttt{getDailyDataFromFile} & User generated daily data \\
[5pt]Sample & \texttt{retrieveNWISqwData} & Raw USGS water quality data \\
- [5pt]Sample & \texttt{getRawQWData} & Raw Water Quality Data Portal data \\
+ [5pt]Sample & \texttt{retrieveWQPqwData} & Raw Water Quality Data Portal data \\
[5pt]Sample & \texttt{getQWDataFromFile} & Raw user generated water quality data \\
- [5pt]Sample & \texttt{getQWData} & USGS Water Quality Portal data \\
[5pt]Sample & \texttt{getWQPData} & General Water Quality Portal\\
[5pt]Sample\tnote{1} & \texttt{getSampleData} & USGS water quality data\\
[5pt]Sample\tnote{1} & \texttt{getSTORETSampleData} & STORET Water Quality Data Portal data \\
[5pt]Sample\tnote{1} & \texttt{getSampleDataFromFile} & User generated sample data \\
- [5pt]Unit & \texttt{retrieveUnitNWISData} & Raw USGS instantaneous data \\
+ [5pt]Unit & \texttt{retrieveNWISunitData} & Raw USGS instantaneous data \\
[5pt]Information\tnote{1} & \texttt{getMetaData} & USGS station and parameter code information \\
[5pt]Information & \texttt{getParameterInfo} & USGS parameter code information \\
[5pt]Information & \texttt{getSiteFileData} & USGS station information \\
@@ -1358,7 +1350,7 @@ There are a few steps that are required in order to create a table in a Microsof
5 Suspended sediment discharge 1980-10-01
End Count Units
1 2012-05-09 529 deg C
-2 2014-07-31 24319 ft3/s
+2 2014-08-02 24321 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 f99df5d8d664fb002e519459edeea6301a817f8b..98ce2415db047ab7c18fdacd93bd460a53f01e81 100644
--- a/vignettes/dataRetrieval.toc
+++ b/vignettes/dataRetrieval.toc
@@ -11,18 +11,18 @@
\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}{17}{subsection.3.1}
+\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}{20}{subsection.3.4}
-\contentsline {subsection}{\numberline {3.5}User-Generated Data Files}{22}{subsection.3.5}
-\contentsline {subsubsection}{\numberline {3.5.1}getDailyDataFromFile}{22}{subsubsection.3.5.1}
-\contentsline {subsubsection}{\numberline {3.5.2}getSampleDataFromFile}{24}{subsubsection.3.5.2}
-\contentsline {subsection}{\numberline {3.6}Merge Report}{25}{subsection.3.6}
-\contentsline {subsection}{\numberline {3.7}EGRET Plots}{26}{subsection.3.7}
-\contentsline {section}{\numberline {4}Summary}{28}{section.4}
-\contentsline {section}{\numberline {5}Getting Started in R}{30}{section.5}
-\contentsline {subsection}{\numberline {5.1}New to R?}{30}{subsection.5.1}
-\contentsline {subsection}{\numberline {5.2}R User: Installing dataRetrieval}{32}{subsection.5.2}
-\contentsline {section}{\numberline {6}Creating tables in Microsoft from R}{32}{section.6}
+\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 from R}{31}{section.6}
\contentsfinish
diff --git a/vignettes/figure/egretEx.pdf b/vignettes/figure/egretEx.pdf
index de48f66d0d522be33c0d4ad055cd2b0d45fe3639..633d69d65134cb42a22450528d7e39efd57b7648 100644
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diff --git a/vignettes/figure/getNWIStemperaturePlot.pdf b/vignettes/figure/getNWIStemperaturePlot.pdf
index 5680f7aa85f04fd6755126f02a07cd3f3b5a7829..0aa6f3da9b47fa3f9992e32e2c5884cc76fc1a98 100644
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diff --git a/vignettes/figure/getQWtemperaturePlot.pdf b/vignettes/figure/getQWtemperaturePlot.pdf
index a436b0514b04e8a83abdbe0342d1323b7a62d49f..b9f4ed9ed16bf6eaf7904973414c08394f37f5e7 100644
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