diff --git a/inst/doc/Rplots.pdf b/inst/doc/Rplots.pdf
index 7285c41a9ddffcf938bf8e33bdafdcc4279c7790..2913bf1792129727f0507fda6af833776f4c252a 100644
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diff --git a/inst/doc/dataRetrieval-concordance.tex b/inst/doc/dataRetrieval-concordance.tex
index 207689982033dc26f92213225fe925f39a89507f..6b2389b758f2b08b698a880960c73445b2d3196e 100644
--- a/inst/doc/dataRetrieval-concordance.tex
+++ b/inst/doc/dataRetrieval-concordance.tex
@@ -8,6 +8,6 @@
1 -4 1 8 8 1 1 3 2 0 1 1 12 0 1 2 13 1 1 2 4 0 1 2 7 1 1 2 1 0 3 1 1 2 %
1 1 29 0 1 2 2 1 1 10 18 0 1 2 8 1 1 3 2 0 1 1 28 0 1 2 2 1 1 10 20 0 1 %
2 7 1 1 14 12 0 1 2 7 1 1 2 17 0 1 3 5 1 1 2 1 0 5 1 11 0 1 1 9 0 1 2 %
-30 1 1 2 1 0 3 1 12 0 1 2 15 1 1 2 1 0 3 1 19 0 1 2 19 1 1 3 5 0 1 2 2 %
-1 1 4 6 0 1 2 2 1 1 4 6 0 1 2 3 1 1 2 4 0 1 2 6 1 1 2 1 0 1 1 3 0 1 2 1 %
-1 1 2 4 0 1 2 8 1 1 5 46 0 1 2 8 1 1 6 45 0 1 2 1 1 1 6 27 0 1 2 20 1}
+30 1 1 2 1 0 2 1 3 0 1 2 15 1 1 2 1 0 2 1 3 0 1 2 19 1 1 3 5 0 1 2 2 1 %
+1 4 6 0 1 2 2 1 1 4 6 0 1 2 3 1 1 2 4 0 1 2 6 1 1 2 1 0 1 1 3 0 1 2 1 1 %
+1 2 4 0 1 2 8 1 1 5 46 0 1 2 8 1 1 6 45 0 1 2 1 1 1 6 27 0 1 2 20 1}
diff --git a/inst/doc/dataRetrieval-fig1.pdf b/inst/doc/dataRetrieval-fig1.pdf
index 6fb3d4edcc9e0414580dfce9604659ebd6e0ecf5..9a0332d24c6739a779e8d8dda669298811ee6246 100644
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diff --git a/inst/doc/dataRetrieval-fig2.pdf b/inst/doc/dataRetrieval-fig2.pdf
index bf3474e1c7a45bc7a40d6723dbffac300e229b1c..47657759268de785b958d924a4ca8a3dbde7c68c 100644
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diff --git a/inst/doc/dataRetrieval-fig3.pdf b/inst/doc/dataRetrieval-fig3.pdf
index bed84055de8148bb20da558460fb727d69e5ffb1..c79bc31ac6c84aad60e51b88e350dd2e8ef1547f 100644
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diff --git a/inst/doc/dataRetrieval.Rnw b/inst/doc/dataRetrieval.Rnw
index a89c773889a611c620a0311f9dd5f29490c3ae0a..cf5cb8a07ae0aee3acab5c76267e6b89516e328d 100644
--- a/inst/doc/dataRetrieval.Rnw
+++ b/inst/doc/dataRetrieval.Rnw
@@ -479,11 +479,10 @@ date Qdaily
\end{verbatim}
The call to open this file, convert the flow to cubic meters per second, and populate the Daily data frame would be:
-<<openDaily, eval = TRUE>>=
+<<openDaily, eval = FALSE>>=
fileName <- "ChoptankRiverFlow.txt"
-filePath <- "~/RData/"
+filePath <- "C:/RData/"
Daily <- getDailyDataFromFile(filePath,fileName,separator="\t",interactive=FALSE)
-head(Daily)
@
%------------------------------------------------------------
@@ -501,11 +500,10 @@ cdate;remarkCode;Nitrate
...
\end{verbatim}
The call to open this file, and populate the Sample dataframe would be:
-<<openSample, eval = TRUE>>=
+<<openSample, eval = FALSE>>=
fileName <- "ChoptankRiverNitrate.csv"
filePath <- "C:/RData/"
Sample <- getSampleDataFromFile(filePath,fileName,separator=",",interactive=FALSE)
-head(Sample)
@
diff --git a/inst/doc/dataRetrieval.log b/inst/doc/dataRetrieval.log
index b9cbb4a336b39fafd80b98fd57ca7c77ea3800d0..cd112c788bbd1b9e35ec263283331e7e888ed2db 100644
--- a/inst/doc/dataRetrieval.log
+++ b/inst/doc/dataRetrieval.log
@@ -1,4 +1,4 @@
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+This is pdfTeX, Version 3.1415926-2.3-1.40.12 (MiKTeX 2.9) (preloaded format=pdflatex 2012.1.6) 15 FEB 2013 13:18
entering extended mode
**dataRetrieval.tex
(D:\LADData\RCode\dataRetrieval\inst\doc\dataRetrieval.tex
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\T1/aer/m/n/10.95 library/2.15/dataRetrieval, and the de-fault for a Mac: /User
s/userA/Library/R/2.15/library/dataRetrieval.
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+Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 910.
+Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 910.
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diff --git a/inst/doc/dataRetrieval.pdf b/inst/doc/dataRetrieval.pdf
index 9eac4a773573a61de180d60417bc5d58a70c1bbe..cd3524c62a84fbb37f12aa79955a3db6e03be7b4 100644
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diff --git a/inst/doc/dataRetrieval.synctex.gz b/inst/doc/dataRetrieval.synctex.gz
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diff --git a/inst/doc/dataRetrieval.tex b/inst/doc/dataRetrieval.tex
index d763f0d7d0366afbcac3938fcaa91d3f66d211a0..e7f3d6cc9de8017e4145e19e24fc1734dfa56c38 100644
--- a/inst/doc/dataRetrieval.tex
+++ b/inst/doc/dataRetrieval.tex
@@ -79,7 +79,7 @@ Once the site-ID is known, the next required input for USGS data retrievals is t
% latex table generated in R 2.15.2 by xtable 1.7-0 package
-% Fri Feb 15 11:39:15 2013
+% Fri Feb 15 13:18:37 2013
\begin{table}[ht]
\begin{center}
\caption{Commonly found USGS Parameter Codes}
@@ -102,7 +102,7 @@ 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
-% Fri Feb 15 11:39:15 2013
+% Fri Feb 15 13:18:37 2013
\begin{table}[ht]
\begin{center}
\caption{Commonly found USGS Stat Codes}
@@ -448,7 +448,7 @@ The function to obtain the daily values (discharge in this case) is getDVData.
Details of the Daily dataframe are listed below:
% latex table generated in R 2.15.2 by xtable 1.7-0 package
-% Fri Feb 15 11:39:24 2013
+% Fri Feb 15 13:18:45 2013
\begin{tabular}{rlll}
\hline
& ColumnName & Type & Description \\
@@ -511,7 +511,7 @@ The function to obtain sample data from the water quality portal is getSampleDat
Details of the Sample dataframe are listed below:
% latex table generated in R 2.15.2 by xtable 1.7-0 package
-% Fri Feb 15 11:39:25 2013
+% Fri Feb 15 13:18:46 2013
\begin{tabular}{rlll}
\hline
& ColumnName & Type & Description \\
@@ -540,7 +540,7 @@ In a more complex situation, the Sample data frame will combine all of the measu
As an example, let us say that in 2004 and earlier, we computed a total phosphorus (tp) as the sum of dissolved phosphorus (dp) and particulate phosphorus (pp). Form 2005 and onward, we have direct measurements of total phosphorus (tp). A small subset of this fictional data looks like this:
% latex table generated in R 2.15.2 by xtable 1.7-0 package
-% Fri Feb 15 11:39:25 2013
+% Fri Feb 15 13:18:46 2013
\begin{tabular}{rllrlrlr}
\hline
& cdate & rdp & dp & rpp & pp & rtp & tp \\
@@ -646,19 +646,9 @@ The call to open this file, convert the flow to cubic meters per second, and pop
\begin{Schunk}
\begin{Sinput}
> fileName <- "ChoptankRiverFlow.txt"
-> filePath <- "~/RData/"
+> filePath <- "C:/RData/"
> Daily <- getDailyDataFromFile(filePath,fileName,separator="\t",interactive=FALSE)
-> head(Daily)
\end{Sinput}
-\begin{Soutput}
- Date Q Julian Month Day DecYear MonthSeq i LogQ Q7 Q30
-1 1999-10-01 0.08579729 54694 10 274 1999.747 1798 1 -2.455768 NA NA
-2 1999-10-02 0.06815672 54695 10 275 1999.750 1798 2 -2.685945 NA NA
-3 1999-10-03 0.06094013 54696 10 276 1999.753 1798 3 -2.797863 NA NA
-4 1999-10-04 0.06094013 54697 10 277 1999.755 1798 4 -2.797863 NA NA
-5 1999-10-05 0.09060835 54698 10 278 1999.758 1798 5 -2.401209 NA NA
-6 1999-10-06 0.07858069 54699 10 279 1999.761 1798 6 -2.543629 NA NA
-\end{Soutput}
\end{Schunk}
%------------------------------------------------------------
@@ -681,24 +671,7 @@ The call to open this file, and populate the Sample dataframe would be:
> fileName <- "ChoptankRiverNitrate.csv"
> filePath <- "C:/RData/"
> Sample <- getSampleDataFromFile(filePath,fileName,separator=",",interactive=FALSE)
-> head(Sample)
\end{Sinput}
-\begin{Soutput}
- Date ConcLow ConcHigh Uncen ConcAve Julian Month Day DecYear MonthSeq
-1 1999-10-07 1.40 1.40 1 1.400 54700 10 280 1999.764 1798
-2 1999-11-04 NA 0.99 0 0.495 54728 11 308 1999.840 1799
-3 1999-12-03 1.42 1.42 1 1.420 54757 12 337 1999.919 1800
-4 2000-01-04 1.59 1.59 1 1.590 54789 1 4 2000.010 1801
-5 2000-02-03 1.54 1.54 1 1.540 54819 2 34 2000.092 1802
-6 2000-02-15 1.37 1.37 1 1.370 54831 2 46 2000.124 1802
- SinDY CosDY
-1 -0.99631836 0.0857305
-2 -0.84377556 0.5366962
-3 -0.48505985 0.8744810
-4 0.06004896 0.9981954
-5 0.54391895 0.8391378
-6 0.70406552 0.7101350
-\end{Soutput}
\end{Schunk}
@@ -785,7 +758,7 @@ To then open the library, simply type:
%------------------------------------------------------------
% latex table generated in R 2.15.2 by xtable 1.7-0 package
-% Fri Feb 15 11:39:26 2013
+% Fri Feb 15 13:18:46 2013
\begin{tabular}{l}
\hline
\hline
@@ -841,7 +814,7 @@ agency.cd \\
There are 62 columns returned from the water quality portal.
% latex table generated in R 2.15.2 by xtable 1.7-0 package
-% Fri Feb 15 11:39:26 2013
+% Fri Feb 15 13:18:46 2013
\begin{tabular}{l}
\hline
\hline
@@ -889,7 +862,7 @@ OrganizationIdentifier \\
\end{tabular}\\*
\newpage
% latex table generated in R 2.15.2 by xtable 1.7-0 package
-% Fri Feb 15 11:39:26 2013
+% Fri Feb 15 13:18:46 2013
\begin{tabular}{l}
\hline
\hline
diff --git a/inst/doc/dataRetrieval.toc b/inst/doc/dataRetrieval.toc
index 1569bacd9907aecb8b3d96f625a7332bf6f2666a..169b6f44445f3e85646f827ac2e4db5a2d3e05bc 100644
--- a/inst/doc/dataRetrieval.toc
+++ b/inst/doc/dataRetrieval.toc
@@ -17,10 +17,10 @@
\contentsline {section}{\numberline {4}Retrieving User-Generated Data Files}{17}{section.4}
\contentsline {subsection}{\numberline {4.1}getDailyDataFromFile}{17}{subsection.4.1}
\contentsline {subsection}{\numberline {4.2}getSampleDataFromFile}{18}{subsection.4.2}
-\contentsline {section}{\numberline {5}Appendix 1: Getting Started}{20}{section.5}
-\contentsline {subsection}{\numberline {5.1}New to R?}{20}{subsection.5.1}
-\contentsline {subsection}{\numberline {5.2}R User: Installing dataRetrieval from downloaded binary}{20}{subsection.5.2}
-\contentsline {subsection}{\numberline {5.3}R Developers: Installing dataRetrieval from gitHub}{21}{subsection.5.3}
-\contentsline {section}{\numberline {6}Appendix 2: Columns Names}{23}{section.6}
-\contentsline {subsection}{\numberline {6.1}INFO dataframe}{23}{subsection.6.1}
-\contentsline {subsection}{\numberline {6.2}Water Quality Portal}{24}{subsection.6.2}
+\contentsline {section}{\numberline {5}Appendix 1: Getting Started}{19}{section.5}
+\contentsline {subsection}{\numberline {5.1}New to R?}{19}{subsection.5.1}
+\contentsline {subsection}{\numberline {5.2}R User: Installing dataRetrieval from downloaded binary}{19}{subsection.5.2}
+\contentsline {subsection}{\numberline {5.3}R Developers: Installing dataRetrieval from gitHub}{20}{subsection.5.3}
+\contentsline {section}{\numberline {6}Appendix 2: Columns Names}{22}{section.6}
+\contentsline {subsection}{\numberline {6.1}INFO dataframe}{22}{subsection.6.1}
+\contentsline {subsection}{\numberline {6.2}Water Quality Portal}{23}{subsection.6.2}