diff --git a/inst/doc/Rplots.pdf b/inst/doc/Rplots.pdf
index 8cfa32a2efad1e68c16e7434b3c2535f325bed4b..87cc06778e7a2dcdc35b4a81fc749c8cc2c53ba6 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 6e8f3ef14e00469b4f2db5e874fcaaf2bd5991e2..6886d24a9099f3daf4de0b83890547522476e63a 100644
--- a/inst/doc/dataRetrieval-concordance.tex
+++ b/inst/doc/dataRetrieval-concordance.tex
@@ -6,8 +6,8 @@
6 0 2 2 10 0 1 2 3 1 1 5 4 0 1 1 3 0 1 2 3 1 1 -5 1 9 11 1 1 2 1 0 1 2 %
1 0 2 1 1 3 4 0 1 2 4 1 1 3 2 0 1 1 7 0 1 2 3 1 1 6 5 0 1 1 3 0 1 2 2 1 %
1 -4 1 8 9 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 %
-3 0 1 2 2 1 1 11 18 0 1 2 8 1 1 3 5 0 1 2 2 1 1 11 20 0 1 2 10 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 0 1 2 2 1 1 11 18 0 1 2 8 1 1 3 5 0 1 2 2 1 1 11 20 0 1 2 12 1 1 14 %
+12 0 1 2 9 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 %
2 1 3 0 1 2 15 1 1 2 1 0 2 1 3 0 1 2 21 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 9 %
-1 1 5 46 0 1 2 9 1 1 6 45 0 1 2 1 1 1 6 27 0 1 2 20 1}
+1 1 5 47 0 1 2 9 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 372be6ced8cc3745375323a218045183a8bf2f86..b6b96aa0851bd01fac48f640be6fca02a33d6b01 100644
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diff --git a/inst/doc/dataRetrieval-fig2.pdf b/inst/doc/dataRetrieval-fig2.pdf
index 8d2885501b5abef9c7485ad7b29cac7bbf92392e..1b53b133278ac241a8df73ad1a5603d2b219d939 100644
Binary files a/inst/doc/dataRetrieval-fig2.pdf and b/inst/doc/dataRetrieval-fig2.pdf differ
diff --git a/inst/doc/dataRetrieval-fig3.pdf b/inst/doc/dataRetrieval-fig3.pdf
index 95ebb7677627d2998e2d9086b5c09eb1376c6e8e..c8db8444209c82f118d0e6b2ad42f1cfab5d58ba 100644
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diff --git a/inst/doc/dataRetrieval.Rnw b/inst/doc/dataRetrieval.Rnw
index 2e2ce459ecbdf54b68ba5e9301372f55f8c88a30..0538655a97ae8cc4699b706b633a7e0a6b62b4f9 100644
--- a/inst/doc/dataRetrieval.Rnw
+++ b/inst/doc/dataRetrieval.Rnw
@@ -415,6 +415,8 @@ 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:
+\begin{center}
+
<<label=exampleComplexQW, echo=FALSE,results=tex>>=
cdate <- c("2003-02-15","2003-06-30","2004-09-15","2005-01-30","2005-05-30","2005-10-30")
rdp <- c("", "<","<","","","")
@@ -430,7 +432,9 @@ data.table <- xtable(DF,
caption="Example data")
print(data.table, caption.placement="top",floating="FALSE",latex.environments=NULL,include.rownames=FALSE)
@
-\\*
+
+\end{center}
+
The dataRetrieval package will "add up" all the values in a given row to form the total for that sample. Thus, you only want to enter data that should be added together. 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 suppose to add it in to the values in 2005.
diff --git a/inst/doc/dataRetrieval.log b/inst/doc/dataRetrieval.log
index cf384bbcce4bfeae55e8475d34a6910cf3c37911..fb27b8624169b2ea972b54e47fd5b3240f6af404 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) 18 FEB 2013 14:45
+This is pdfTeX, Version 3.1415926-2.3-1.40.12 (MiKTeX 2.9) (preloaded format=pdflatex 2012.1.6) 18 FEB 2013 16:25
entering extended mode
**dataRetrieval.tex
(D:\LADData\RCode\dataRetrieval\inst\doc\dataRetrieval.tex
@@ -527,11 +527,6 @@ Overfull \vbox (21.68121pt too high) has occurred while \output is active []
[11]
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- []
-
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@@ -541,11 +536,6 @@ Overfull \vbox (21.68121pt too high) has occurred while \output is active []
[12]
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-
- []
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@@ -566,7 +556,7 @@ Overfull \vbox (21.68121pt too high) has occurred while \output is active []
[17]
-Overfull \hbox (63.21521pt too wide) in paragraph at lines 681--682
+Overfull \hbox (63.21521pt too wide) in paragraph at lines 685--686
\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.
[]
@@ -576,7 +566,7 @@ Overfull \vbox (21.68121pt too high) has occurred while \output is active []
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+Underfull \hbox (badness 10000) in paragraph at lines 725--773
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[20]
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+Overfull \vbox (21.66835pt too high) has occurred while \output is active []
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+Underfull \hbox (badness 10000) in paragraph at lines 783--828
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+Underfull \hbox (badness 10000) in paragraph at lines 831--858
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@@ -614,23 +604,23 @@ Overfull \vbox (21.68121pt too high) has occurred while \output is active []
[23]
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+Package atveryend Info: Empty hook `BeforeClearDocument' on input line 875.
Overfull \vbox (21.68121pt too high) has occurred while \output is active []
[24]
-Package atveryend Info: Empty hook `AfterLastShipout' on input line 870.
+Package atveryend Info: Empty hook `AfterLastShipout' on input line 875.
(D:\LADData\RCode\dataRetrieval\inst\doc\dataRetrieval.aux)
-Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 870.
-Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 870.
+Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 875.
+Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 875.
Package rerunfilecheck Info: File `dataRetrieval.out' has not changed.
(rerunfilecheck) Checksum: FEA45D43F3DDF55AFA8755D4D3BFEDB8;1845.
)
Here is how much of TeX's memory you used:
7416 strings out of 494045
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40005 words of font info for 82 fonts, out of 3000000 for 9000
715 hyphenation exceptions out of 8191
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m Files (x86)/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/cmtt10.pfb>
-Output written on dataRetrieval.pdf (24 pages, 301717 bytes).
+Output written on dataRetrieval.pdf (24 pages, 301883 bytes).
PDF statistics:
361 PDF objects out of 1000 (max. 8388607)
60 named destinations out of 1000 (max. 500000)
diff --git a/inst/doc/dataRetrieval.pdf b/inst/doc/dataRetrieval.pdf
index ad3b174246e9774312ea1bcefd3cc22ba4448544..31bdff45cb0560ea1c8f5a3f92c7b5bfc479fca2 100644
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diff --git a/inst/doc/dataRetrieval.synctex.gz b/inst/doc/dataRetrieval.synctex.gz
index 927ffd1d0feb495ae229fb6ad86d21c028bcf44c..f566d857be132f983bc00a6b9644d728a18f76ca 100644
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diff --git a/inst/doc/dataRetrieval.tex b/inst/doc/dataRetrieval.tex
index d250f7b1844e3de33b11b7fee86f68349da0be3e..e54b9d7678fe9cf018cf4f7ca2380a2289036546 100644
--- a/inst/doc/dataRetrieval.tex
+++ b/inst/doc/dataRetrieval.tex
@@ -79,19 +79,19 @@ 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
-% Mon Feb 18 14:45:13 2013
+% Mon Feb 18 16:25:25 2013
\begin{table}[ht]
\begin{center}
\caption{Commonly found USGS Parameter Codes}
-\begin{tabular}{rll}
+\begin{tabular}{ll}
\hline
- & pCode & shortName \\
+pCode & shortName \\
\hline
-1 & 00060 & Discharge [cfs] \\
- 2 & 00065 & Gage height [ft] \\
- 3 & 00010 & Temperature [C] \\
- 4 & 00045 & Precipitation [in] \\
- 5 & 00400 & pH \\
+00060 & Discharge [cfs] \\
+ 00065 & Gage height [ft] \\
+ 00010 & Temperature [C] \\
+ 00045 & Precipitation [in] \\
+ 00400 & pH \\
\hline
\end{tabular}
\end{center}
@@ -102,18 +102,18 @@ 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
-% Mon Feb 18 14:45:13 2013
+% Mon Feb 18 16:25:25 2013
\begin{table}[ht]
\begin{center}
\caption{Commonly found USGS Stat Codes}
-\begin{tabular}{rll}
+\begin{tabular}{ll}
\hline
- & StatCode & shortName \\
+StatCode & shortName \\
\hline
-1 & 00001 & Maximum \\
- 2 & 00002 & Minimum \\
- 3 & 00003 & Mean \\
- 4 & 00008 & Median \\
+00001 & Maximum \\
+ 00002 & Minimum \\
+ 00003 & Mean \\
+ 00008 & Median \\
\hline
\end{tabular}
\end{center}
@@ -427,23 +427,23 @@ 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
-% Mon Feb 18 14:45:22 2013
-\begin{tabular}{rllll}
+% Mon Feb 18 16:25:34 2013
+\begin{tabular}{llll}
\hline
- & ColumnName & Type & Description & Units \\
+ColumnName & Type & Description & Units \\
\hline
-1 & Date & Date & Date & date \\
- 2 & Q & number & Discharge in cms & cms \\
- 3 & Julian & number & Number of days since January 1, 1850 & days \\
- 4 & Month & integer & Month of the year [1-12] & months \\
- 5 & Day & integer & Day of the year [1-366] & days \\
- 6 & DecYear & number & Decimal year & years \\
- 7 & MonthSeq & integer & Number of months since January 1, 1850 & months \\
- 8 & Qualifier & string & Qualifing code & character \\
- 9 & i & integer & Index of days from the start of the data frame & days \\
- 10 & LogQ & number & Natural logarithm of Q & numeric \\
- 11 & Q7 & number & 7 day running average of Q & cms \\
- 12 & Q30 & number & 30 running average of Q & cms \\
+Date & Date & Date & date \\
+ Q & number & Discharge in cms & cms \\
+ Julian & number & Number of days since January 1, 1850 & days \\
+ Month & integer & Month of the year [1-12] & months \\
+ Day & integer & Day of the year [1-366] & days \\
+ DecYear & number & Decimal year & years \\
+ MonthSeq & integer & Number of months since January 1, 1850 & months \\
+ Qualifier & string & Qualifing code & character \\
+ i & integer & Index of days from the start of the data frame & days \\
+ LogQ & number & Natural logarithm of Q & numeric \\
+ Q7 & number & 7 day running average of Q & cms \\
+ Q30 & number & 30 running average of Q & cms \\
\hline
\end{tabular}\\*
@@ -464,25 +464,25 @@ 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
-% Mon Feb 18 14:45:22 2013
-\begin{tabular}{rllll}
+% Mon Feb 18 16:25:35 2013
+\begin{tabular}{llll}
\hline
- & ColumnName & Type & Description & Units \\
+ColumnName & Type & Description & Units \\
\hline
-1 & Date & Date & Date & date \\
- 2 & ConcLow & number & Lower limit of concentration & mg/L \\
- 3 & ConcHigh & number & Upper limit of concentration & mg/L \\
- 4 & Uncen & integer & Uncensored data (1=true, 0=false) & integer \\
- 5 & ConcAve & number & Average concentration & mg/L \\
- 6 & Julian & number & Number of days since January 1, 1850 & days \\
- 7 & Month & integer & Month of the year [1-12] & months \\
- 8 & Day & integer & Day of the year [1-366] & days \\
- 9 & DecYear & number & Decimal year & years \\
- 10 & MonthSeq & integer & Number of months since January 1, 1850 & months \\
- 11 & SinDY & number & Sine of DecYear & numeric \\
- 12 & CosDY & number & Cosine of DecYear & numeric \\
- 13 & Q & number & Discharge ** & cms \\
- 14 & LogQ & number & Natural logarithm of flow ** & numeric \\
+Date & Date & Date & date \\
+ ConcLow & number & Lower limit of concentration & mg/L \\
+ ConcHigh & number & Upper limit of concentration & mg/L \\
+ Uncen & integer & Uncensored data (1=true, 0=false) & integer \\
+ ConcAve & number & Average concentration & mg/L \\
+ Julian & number & Number of days since January 1, 1850 & days \\
+ Month & integer & Month of the year [1-12] & months \\
+ Day & integer & Day of the year [1-366] & days \\
+ DecYear & number & Decimal year & years \\
+ MonthSeq & integer & Number of months since January 1, 1850 & months \\
+ SinDY & number & Sine of DecYear & numeric \\
+ CosDY & number & Cosine of DecYear & numeric \\
+ Q & number & Discharge ** & cms \\
+ LogQ & number & Natural logarithm of flow ** & numeric \\
\hline
\end{tabular}\\
** Flow columns are populated from data in the Daily dataframe after calling the mergeReport function.
@@ -495,20 +495,24 @@ 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:
+\begin{center}
+
% latex table generated in R 2.15.2 by xtable 1.7-0 package
-% Mon Feb 18 14:45:23 2013
-\begin{tabular}{rllrlrlr}
+% Mon Feb 18 16:25:35 2013
+\begin{tabular}{llrlrlr}
\hline
- & cdate & rdp & dp & rpp & pp & rtp & tp \\
+cdate & rdp & dp & rpp & pp & rtp & tp \\
\hline
-1 & 2003-02-15 & & 0.02 & & 0.50 & & \\
- 2 & 2003-06-30 & $<$ & 0.01 & & 0.30 & & \\
- 3 & 2004-09-15 & $<$ & 0.00 & $<$ & 0.20 & & \\
- 4 & 2005-01-30 & & & & & & 0.43 \\
- 5 & 2005-05-30 & & & & & $<$ & 0.05 \\
- 6 & 2005-10-30 & & & & & $<$ & 0.02 \\
+2003-02-15 & & 0.02 & & 0.50 & & \\
+ 2003-06-30 & $<$ & 0.01 & & 0.30 & & \\
+ 2004-09-15 & $<$ & 0.00 & $<$ & 0.20 & & \\
+ 2005-01-30 & & & & & & 0.43 \\
+ 2005-05-30 & & & & & $<$ & 0.05 \\
+ 2005-10-30 & & & & & $<$ & 0.02 \\
\hline
-\end{tabular}\\*
+\end{tabular}
+\end{center}
+
The dataRetrieval package will "add up" all the values in a given row to form the total for that sample. Thus, you only want to enter data that should be added together. 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 suppose to add it in to the values in 2005.
@@ -717,7 +721,7 @@ To then open the library, simply type:
%------------------------------------------------------------
\label{sec:appendix2INFO}
% latex table generated in R 2.15.2 by xtable 1.7-0 package
-% Mon Feb 18 14:45:23 2013
+% Mon Feb 18 16:25:35 2013
\begin{tabular}{l}
\hline
\hline
@@ -756,6 +760,7 @@ agency.cd \\
project.no \\
queryTime \\
drainSqKm \\
+ shortName \\
staAbbrev \\
param.nm \\
param.units \\
@@ -774,7 +779,7 @@ 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
-% Mon Feb 18 14:45:23 2013
+% Mon Feb 18 16:25:35 2013
\begin{tabular}{l}
\hline
\hline
@@ -822,7 +827,7 @@ OrganizationIdentifier \\
\end{tabular}\\*
\newpage
% latex table generated in R 2.15.2 by xtable 1.7-0 package
-% Mon Feb 18 14:45:23 2013
+% Mon Feb 18 16:25:35 2013
\begin{tabular}{l}
\hline
\hline