diff --git a/inst/doc/Rplots.pdf b/inst/doc/Rplots.pdf
index 06e77e86c0e6d801b89584514681073a0d00fa04..f89943c6c9998bd81ff086aa30371d31b2710560 100644
Binary files a/inst/doc/Rplots.pdf and b/inst/doc/Rplots.pdf differ
diff --git a/inst/doc/dataRetrieval-concordance.tex b/inst/doc/dataRetrieval-concordance.tex
index dec73fe01f2498d39fc4f0a7e4390dac694e528d..6666b7b667561fba80b016bbd472f5700fae6068 100644
--- a/inst/doc/dataRetrieval-concordance.tex
+++ b/inst/doc/dataRetrieval-concordance.tex
@@ -3,7 +3,7 @@
3 0 1 2 2 1 1 2 7 0 1 2 7 1 1 3 2 0 1 1 12 0 1 2 5 1 1 4 3 0 1 3 1 0 1 %
3 7 0 1 3 4 0 1 2 2 1 1 8 7 0 1 4 1 0 1 2 21 0 1 2 7 1 1 3 2 0 2 1 7 0 %
1 2 1 1 1 2 7 0 1 2 9 1 1 4 2 0 2 1 1 2 3 0 1 2 4 1 1 3 1 0 3 1 1 3 5 0 %
-1 3 4 1 1 2 1 0 1 4 3 0 1 1 1 4 3 0 3 1 3 0 1 2 3 1 1 -5 1 9 14 1 1 2 1 %
+1 3 4 1 1 2 1 0 1 4 3 0 1 1 1 4 3 0 3 1 3 0 1 2 3 1 1 -5 1 9 14 1 1 3 1 %
0 1 1 1 2 1 0 1 3 5 0 2 2 10 0 1 2 3 1 1 2 1 0 1 4 3 0 1 1 4 0 1 3 3 1 %
1 -6 1 10 12 1 1 4 2 0 2 1 1 3 1 0 1 3 1 0 1 1 7 0 1 2 1 1 1 6 5 0 1 1 %
3 0 1 2 2 1 1 -4 1 8 11 1 1 3 2 0 1 1 12 0 1 2 8 1 1 3 2 0 5 1 3 0 1 2 %
@@ -11,6 +11,6 @@
9 1 1 3 5 0 1 2 2 1 1 12 24 0 1 2 11 1 1 14 12 0 1 2 9 1 1 2 17 0 1 3 %
28 1 1 2 1 0 2 1 3 0 1 2 16 1 1 2 1 0 2 1 3 0 1 2 7 1 1 2 1 0 3 1 1 2 2 %
1 11 0 1 1 19 0 1 2 6 1 1 3 2 0 1 1 3 0 1 2 3 1 1 -5 1 9 21 1 1 2 4 0 1 %
-2 1 1 1 2 12 0 1 2 6 1 1 2 1 0 1 1 3 0 1 2 3 1 1 2 4 0 1 2 7 1 1 2 1 0 %
+2 1 1 1 2 13 0 1 2 6 1 1 2 1 0 1 1 3 0 1 2 3 1 1 2 4 0 1 2 7 1 1 2 1 0 %
1 1 3 0 1 2 1 1 1 2 4 0 1 2 10 1 1 5 47 0 1 2 9 1 1 6 45 0 1 2 2 1 1 6 %
27 0 1 2 8 1 1 2 1 0 4 1 1 9 10 0 1 2 3 1 1 3 5 0 1 2 53 1}
diff --git a/inst/doc/dataRetrieval-fig1.pdf b/inst/doc/dataRetrieval-fig1.pdf
index 70dbab89e72a19d1c107d1e2b284dfe433e23b39..d38cc3f7d338173b4fede7d83ea296eb39549a54 100644
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diff --git a/inst/doc/dataRetrieval-fig2.pdf b/inst/doc/dataRetrieval-fig2.pdf
index d05927f1b89356b1fe4dc5e996dd24ef80f422c5..457fdbf881ecbe72594efb99cd0f7f8ea812726a 100644
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diff --git a/inst/doc/dataRetrieval-fig3.pdf b/inst/doc/dataRetrieval-fig3.pdf
index 13609b4ad33d666daab44857d10aca9ab600f2d5..b968a0353aeea257da49be83cd9e7e0a2d0c7120 100644
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diff --git a/inst/doc/dataRetrieval-figegretEx.pdf b/inst/doc/dataRetrieval-figegretEx.pdf
index eabd34090461d3ee4db8bff18c5ba52555cae604..9107ee822299fdbd74b9c13ad8f25e0910fea734 100644
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diff --git a/inst/doc/dataRetrieval.Rnw b/inst/doc/dataRetrieval.Rnw
index fdc171bbd9f8f8cf6e53b565308afc1ec0cc38b6..a92f5947bfd6a56788a3cc14de45b9d77645a18e 100644
--- a/inst/doc/dataRetrieval.Rnw
+++ b/inst/doc/dataRetrieval.Rnw
@@ -294,6 +294,7 @@ There are occasions where NWIS values are not reported as numbers, instead there
Any data that are collected at regular time intervals (such as 15-minute or hourly) are known as \texttt{"}Unit Values\texttt{"} - 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 retrieveUnitNWISData. Some of these Unit Values are available for the past several years, and some are only available for a recent time period such as 120 days or a year. Here is an example of a retrieval of such data.
<<label=getNWISUnit, echo=TRUE>>=
+
parameterCd <- "00060" # Discharge (cfs)
startDate <- "2012-05-12"
# or use (yesterday): startDate <- as.character(Sys.Date()-1)
@@ -433,7 +434,7 @@ The function to obtain the daily values (discharge in this case) is getDVData.
<<firstExample>>=
siteNumber <- "01491000"
-startDate <- "1964-01-01"
+startDate <- "2000-01-01"
endDate <- "2013-01-01"
# This call will get NWIS data that is in cfs, and convert it
# to cms since we didn't override the default in the convert argument:
@@ -592,7 +593,7 @@ Finally, there is a function called mergeReport that will look at both the Daily
<<mergeExample>>=
siteNumber <- "01491000"
parameterCd <- "00631" # Nitrate
-startDate <- "1964-01-01"
+startDate <- "2000-01-01"
endDate <- "2013-01-01"
Daily <- getDVData(siteNumber, "00060", startDate, endDate,interactive=FALSE)
diff --git a/inst/doc/dataRetrieval.log b/inst/doc/dataRetrieval.log
index b7d83422ac3be2c326cf83ca27312ad3448b0d5e..bd5264a91ece8f62c83bf2cce7988bef00d4caa9 100644
--- a/inst/doc/dataRetrieval.log
+++ b/inst/doc/dataRetrieval.log
@@ -1,4 +1,4 @@
-This is pdfTeX, Version 3.1415926-2.3-1.40.12 (MiKTeX 2.9) (preloaded format=pdflatex 2012.1.6) 28 MAR 2013 14:05
+This is pdfTeX, Version 3.1415926-2.3-1.40.12 (MiKTeX 2.9) (preloaded format=pdflatex 2012.1.6) 29 MAR 2013 11:54
entering extended mode
**dataRetrieval.tex
(D:\LADData\RCode\dataRetrieval\inst\doc\dataRetrieval.tex
@@ -646,14 +646,14 @@ Overfull \vbox (21.68121pt too high) has occurred while \output is active []
] <table1.png, id=357, 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 1068.
+Package pdftex.def Info: table1.png used on input line 1069.
(pdftex.def) Requested size: 358.46039pt x 81.33507pt.
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
[28 <D:/LADData/RCode/dataRetrieval/inst/doc/table1.png>]
-Package atveryend Info: Empty hook `BeforeClearDocument' on input line 1090.
+Package atveryend Info: Empty hook `BeforeClearDocument' on input line 1091.
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
@@ -661,10 +661,10 @@ Overfull \vbox (21.68121pt too high) has occurred while \output is active []
[29
]
-Package atveryend Info: Empty hook `AfterLastShipout' on input line 1090.
+Package atveryend Info: Empty hook `AfterLastShipout' on input line 1091.
(D:\LADData\RCode\dataRetrieval\inst\doc\dataRetrieval.aux)
-Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 1090.
-Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 1090.
+Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 1091.
+Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 1091.
Package rerunfilecheck Info: File `dataRetrieval.out' has not changed.
(rerunfilecheck) Checksum: 3B1480473EC95CC4090ED48BB3268644;2119.
@@ -691,7 +691,7 @@ Files (x86)/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/cmr9.pfb><C:/Program File
s (x86)/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/cmsltt10.pfb><C:/Program File
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(x86)/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/cmtt10.pfb>
-Output written on dataRetrieval.pdf (29 pages, 469489 bytes).
+Output written on dataRetrieval.pdf (29 pages, 396461 bytes).
PDF statistics:
451 PDF objects out of 1000 (max. 8388607)
83 named destinations out of 1000 (max. 500000)
diff --git a/inst/doc/dataRetrieval.pdf b/inst/doc/dataRetrieval.pdf
index 2e7205efc29d66ab8b775b770400b32c4066f6f6..e0c1728450a249837d079a027a92318998d50466 100644
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diff --git a/inst/doc/dataRetrieval.synctex.gz b/inst/doc/dataRetrieval.synctex.gz
index 7caadbef7b28a24e6ee263d38c3a4920feaaf1f4..cf8d8ad619f649286ae06d33da940301cd63d4a4 100644
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diff --git a/inst/doc/dataRetrieval.tex b/inst/doc/dataRetrieval.tex
index c47b3e55dddaf4cf31a6b8cfb8b88429e063e692..89a30536ed4946fc56a7cadd81903ee646de1eb8 100644
--- a/inst/doc/dataRetrieval.tex
+++ b/inst/doc/dataRetrieval.tex
@@ -86,7 +86,7 @@ Not every station will measure all parameters. A short list of commonly measured
% latex table generated in R 2.15.3 by xtable 1.7-1 package
-% Thu Mar 28 14:04:21 2013
+% Fri Mar 29 11:54:02 2013
\begin{table}[!ht]
\centering
\caption{Common USGS Parameter Codes}
@@ -109,7 +109,7 @@ For real-time data, the parameter code and site ID will suffice. For most varia
Some common stat codes are shown in Table \ref{tab:stat}.
% latex table generated in R 2.15.3 by xtable 1.7-1 package
-% Thu Mar 28 14:04:21 2013
+% Fri Mar 29 11:54:02 2013
\begin{table}[!ht]
\centering
\caption{Commonly found USGS Stat Codes}
@@ -176,7 +176,7 @@ To find out the available data at a particular USGS site, including measured par
2 00010 00001 1988-10-01 2012-06-24 940 dv
3 00010 00002 2010-10-01 2012-06-24 575 dv
4 00010 00003 2010-10-01 2012-06-24 575 dv
-5 00060 00003 1948-01-01 2013-03-27 23828 dv
+5 00060 00003 1948-01-01 2013-03-28 23829 dv
6 00095 00001 2010-10-01 2012-06-24 551 dv
7 00095 00002 2010-10-01 2012-06-24 551 dv
\end{Soutput}
@@ -224,7 +224,7 @@ The daily data at the Choptank River site can be displayed in a \LaTeX table usi
caption.placement="top",include.rownames=FALSE)
\end{Sinput}
% latex table generated in R 2.15.3 by xtable 1.7-1 package
-% Thu Mar 28 14:04:26 2013
+% Fri Mar 29 11:54:09 2013
\begin{table}[ht]
\centering
\caption{Daily mean data availabile at the Choptank River}
@@ -234,7 +234,7 @@ The daily data at the Choptank River site can be displayed in a \LaTeX table usi
shortName & Start & End & Count & Units \\
\hline
Temperature, water & 2010-10-01 & 2012-06-24 & 575 & deg C \\
- Stream flow, mean. daily & 1948-01-01 & 2013-03-27 & 23828 & cfs \\
+ Stream flow, mean. daily & 1948-01-01 & 2013-03-28 & 23829 & cfs \\
Specific conductance & 2010-10-01 & 2012-06-24 & 551 & uS/cm @25C \\
Suspended sediment concentration (SSC) & 1980-10-01 & 1991-09-30 & 3651 & mg/l \\
Suspended sediment discharge & 1980-10-01 & 1991-09-30 & 3652 & tons/day \\
@@ -517,7 +517,7 @@ The function to obtain the daily values (discharge in this case) is getDVData.
\begin{Schunk}
\begin{Sinput}
> siteNumber <- "01491000"
-> startDate <- "1964-01-01"
+> startDate <- "2000-01-01"
> endDate <- "2013-01-01"
> # This call will get NWIS data that is in cfs, and convert it
> # to cms since we didn't override the default in the convert argument:
@@ -528,7 +528,7 @@ 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 2.15.3 by xtable 1.7-1 package
-% Thu Mar 28 14:04:42 2013
+% Fri Mar 29 11:54:18 2013
\begin{tabular}{llll}
\hline
ColumnName & Type & Description & Units \\
@@ -566,7 +566,7 @@ 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 2.15.3 by xtable 1.7-1 package
-% Thu Mar 28 14:04:43 2013
+% Fri Mar 29 11:54:19 2013
\begin{table}[!ht]
\centering
\caption{Sample dataframe}
@@ -603,7 +603,7 @@ As an example to understand how the dataRetrieval package handles a more complex
\begin{center}
% latex table generated in R 2.15.3 by xtable 1.7-1 package
-% Thu Mar 28 14:04:43 2013
+% Fri Mar 29 11:54:19 2013
\begin{tabular}{llrlrlr}
\hline
cdate & rdp & dp & rpp & pp & rtp & tp \\
@@ -715,39 +715,39 @@ Finally, there is a function called mergeReport that will look at both the Daily
\begin{Sinput}
> siteNumber <- "01491000"
> parameterCd <- "00631" # Nitrate
-> startDate <- "1964-01-01"
+> startDate <- "2000-01-01"
> endDate <- "2013-01-01"
> Daily <- getDVData(siteNumber, "00060", startDate, endDate,interactive=FALSE)
> Sample <- getSampleData(siteNumber,parameterCd, startDate, endDate, interactive=FALSE)
> Sample <- mergeReport()
\end{Sinput}
\begin{Soutput}
- Discharge Record is 17899 days long, which is 49 years
- First day of the discharge record is 1964-01-01 and last day is 2013-01-01
- The water quality record has 627 samples
- The first sample is from 1973-06-04 and the last sample is from 2012-12-18
- Discharge: Minimum, mean and maximum 0.00991 4.02 246
- Concentration: Minimum, mean and maximum 0.05 1.1 2.4
- Percentage of the sample values that are censored is 0.16 %
+ Discharge Record is 4750 days long, which is 13 years
+ First day of the discharge record is 2000-01-01 and last day is 2013-01-01
+ The water quality record has 220 samples
+ The first sample is from 2000-01-04 and the last sample is from 2012-12-18
+ Discharge: Minimum, mean and maximum 0.00991 4.55 246
+ Concentration: Minimum, mean and maximum 0.2 1.3 2.4
+ Percentage of the sample values that are censored is 0 %
\end{Soutput}
\begin{Sinput}
> head(Sample)
\end{Sinput}
\begin{Soutput}
Date ConcLow ConcHigh Uncen ConcAve Julian Month Day DecYear MonthSeq
-1 1973-06-04 1.30 1.30 1 1.30 45079 6 155 1973.422 1482
-2 1979-09-25 0.52 0.52 1 0.52 47383 9 268 1979.731 1557
-3 1979-10-24 0.62 0.62 1 0.62 47412 10 297 1979.810 1558
-4 1979-12-05 1.40 1.40 1 1.40 47454 12 339 1979.925 1560
-5 1979-12-21 1.20 1.20 1 1.20 47470 12 355 1979.969 1560
-6 1980-01-24 0.84 0.84 1 0.84 47504 1 24 1980.064 1561
- SinDY CosDY Q LogQ
-1 0.4699767 -0.8826788 3.341388 1.206386
-2 -0.9927882 -0.1198812 4.275844 1.452981
-3 -0.9295235 0.3687629 2.944952 1.080093
-4 -0.4547551 0.8906165 3.086536 1.127050
-5 -0.1961425 0.9805754 3.058219 1.117833
-6 0.3925740 0.9197204 9.089708 2.207143
+1 2000-01-04 1.59 1.59 1 1.59 54789 1 4 2000.010 1801
+2 2000-02-03 1.54 1.54 1 1.54 54819 2 34 2000.092 1802
+3 2000-02-15 1.37 1.37 1 1.37 54831 2 46 2000.124 1802
+4 2000-02-19 1.24 1.24 1 1.24 54835 2 50 2000.135 1802
+5 2000-03-23 0.52 0.52 1 0.52 54868 3 83 2000.225 1803
+6 2000-06-05 1.11 1.11 1 1.11 54942 6 157 2000.428 1806
+ SinDY CosDY Q LogQ
+1 0.06004896 0.9981954 2.746734 1.0104126
+2 0.54391895 0.8391378 3.936042 1.3701756
+3 0.70406552 0.7101350 10.845352 2.3837366
+4 0.75113193 0.6601521 15.517632 2.7419769
+5 0.98808790 0.1538906 56.916861 4.0415916
+6 0.43939951 -0.8982918 1.812278 0.5945847
\end{Soutput}
\end{Schunk}
@@ -803,10 +803,11 @@ To see the raw code for a particular code, type the name of the function:
> removeDuplicates
\end{Sinput}
\begin{Soutput}
-function(localSample=Sample) {
- Sample1 <- localSample[!duplicated(localSample[c("DecYear","ConcHigh")]),]
-
- return(Sample1)
+function (localSample = Sample)
+{
+ Sample1 <- localSample[!duplicated(localSample[c("DecYear",
+ "ConcHigh")]), ]
+ return(Sample1)
}
<environment: namespace:dataRetrieval>
\end{Soutput}
@@ -866,7 +867,7 @@ To then open the library, simply type:
%------------------------------------------------------------
% latex table generated in R 2.15.3 by xtable 1.7-1 package
-% Thu Mar 28 14:04:54 2013
+% Fri Mar 29 11:54:22 2013
\begin{tabular}{l}
\hline
\hline
@@ -924,7 +925,7 @@ agency.cd \\
There are 62 columns returned from the water quality portal.
% latex table generated in R 2.15.3 by xtable 1.7-1 package
-% Thu Mar 28 14:04:54 2013
+% Fri Mar 29 11:54:23 2013
\begin{tabular}{l}
\hline
\hline
@@ -973,7 +974,7 @@ OrganizationIdentifier \\
\FloatBarrier
% latex table generated in R 2.15.3 by xtable 1.7-1 package
-% Thu Mar 28 14:04:54 2013
+% Fri Mar 29 11:54:23 2013
\begin{tabular}{l}
\hline
\hline