diff --git a/inst/doc/Rplots.pdf b/inst/doc/Rplots.pdf
index dc7ac7eddfbb8e32e39cca8105fe152c0a9a55b4..bb8b51ec39b0bab8f47cf41032ea4647c6dc9ecf 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 6790de9889de7b81ae39c88880ec3a53900a7088..6e8f3ef14e00469b4f2db5e874fcaaf2bd5991e2 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 %
-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 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}
+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 %
+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}
diff --git a/inst/doc/dataRetrieval-fig1.pdf b/inst/doc/dataRetrieval-fig1.pdf
index dace22f63fd4321be0c2579653878c82bdfb002f..a746b606097eaf41bddab435b55ddbb3840bc48f 100644
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diff --git a/inst/doc/dataRetrieval-fig2.pdf b/inst/doc/dataRetrieval-fig2.pdf
index a610a9a17165f17822005a0c024191e546c5a092..4feb498e13c477e33b770023c9eb5e9cb4d5ae19 100644
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diff --git a/inst/doc/dataRetrieval-fig3.pdf b/inst/doc/dataRetrieval-fig3.pdf
index 0b9f14e7d9e50e7cce8c6a15b388fc6428019eb1..60cab61d164cf5c760ec246e2672e962d9eb24f7 100644
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diff --git a/inst/doc/dataRetrieval.Rnw b/inst/doc/dataRetrieval.Rnw
index 13936034ac29b639611638d8e01d8e7100ec7e8b..d04331b67205dc320bb0f69cd5dbc6a920cc2a51 100644
--- a/inst/doc/dataRetrieval.Rnw
+++ b/inst/doc/dataRetrieval.Rnw
@@ -360,7 +360,6 @@ startDate <- "1964-01-01"
endDate <- "2013-01-01"
Daily <- getDVData(siteNumber, "00060", startDate, endDate,interactive=FALSE)
-summary(Daily)
@
Details of the Daily dataframe are listed below:
@@ -368,9 +367,10 @@ Details of the Daily dataframe are listed below:
<<label=colNamesDaily, echo=FALSE,results=tex>>=
ColumnName <- c("Date", "Q", "Julian","Month","Day","DecYear","MonthSeq","Qualifier","i","LogQ","Q7","Q30")
Type <- c("Date", "number", "number","integer","integer","number","integer","string","integer","number","number","number")
-Description <- c("Date", "Discharge in cms", "Number of days since January 1, 1850", "Month of the year [1-12]", "Day of the year [1-366]", "Decimal year", "Number of months since January 1, 1850", "Qualifing code", "Index", "Natural logarithm of Q", "7 day running average of Q", "30 running average of Q")
+Description <- c("Date", "Discharge in cms", "Number of days since January 1, 1850", "Month of the year [1-12]", "Day of the year [1-366]", "Decimal year", "Number of months since January 1, 1850", "Qualifing code", "Index of days from the start of the data frame", "Natural logarithm of Q", "7 day running average of Q", "30 running average of Q")
+Units <- c("date", "cms","days", "months","days","years","months", "character","days","numeric","cms","cms")
-DF <- data.frame(ColumnName,Type,Description)
+DF <- data.frame(ColumnName,Type,Description,Units)
data.table <- xtable(DF,
caption="Daily dataframe")
@@ -388,7 +388,6 @@ The function to obtain sample data from the water quality portal is getSampleDat
<<secondExample>>=
Sample <-getSampleData(siteNumber,parameterCd,
startDate, endDate,interactive=FALSE)
-summary(Sample)
@
Details of the Sample dataframe are listed below:
@@ -396,14 +395,18 @@ Details of the Sample dataframe are listed below:
<<label=colNamesQW, echo=FALSE,results=tex>>=
ColumnName <- c("Date", "ConcLow", "ConcHigh", "Uncen", "ConcAve", "Julian","Month","Day","DecYear","MonthSeq","SinDY","CosDY","Q","LogQ")
Type <- c("Date", "number","number","integer","number", "number","integer","integer","number","integer","number","number","number","number")
-Description <- c("Date", "Lower limit of concentration", "Upper limit of concentration", "Uncensored data (1=true, 0=false)", "Average concentration","Number of days since January 1, 1850", "Month of the year [1-12]", "Day of the year [1-366]", "Decimal year", "Number of months since January 1, 1850", "Sine of ...", "Cosine of ...", "Discharge in cms", "Natural logarithm of flow")
+Description <- c("Date", "Lower limit of concentration", "Upper limit of concentration", "Uncensored data (1=true, 0=false)", "Average concentration","Number of days since January 1, 1850", "Month of the year [1-12]", "Day of the year [1-366]", "Decimal year", "Number of months since January 1, 1850", "Sine of DecYear", "Cosine of DecYear", "Discharge **", "Natural logarithm of flow **")
+Units <- c("date","mg/L","mg/L","integer","mg/L","days","months","days","years","months","numeric","numeric","cms", "numeric")
-DF <- data.frame(ColumnName,Type,Description)
+DF <- data.frame(ColumnName,Type,Description,Units)
data.table <- xtable(DF,
caption="Sample dataframe")
print(data.table, caption.placement="top",floating="FALSE",latex.environments=NULL)
@
+\\
+** Flow columns are populated from data in the Daily dataframe after calling the mergeReport function.
+
In a more complex situation, the Sample data frame will combine all of the measured parameters. An example is provided to explain how the values are combined:
diff --git a/inst/doc/dataRetrieval.log b/inst/doc/dataRetrieval.log
index cc38c50175743a390b540d3c12d60a276eb63341..37783b3dbd862f585e13ed4cc618818f53de28e4 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) 18 FEB 2013 14:20
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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diff --git a/inst/doc/dataRetrieval.pdf b/inst/doc/dataRetrieval.pdf
index be7a221d95381093f61f9243bf7afeeccd405c2e..e5b34631cf2b96dc9b6d3ff70f74f5465e2abff8 100644
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diff --git a/inst/doc/dataRetrieval.synctex.gz b/inst/doc/dataRetrieval.synctex.gz
index 93b780824d723f250956368fe1012c14615748f0..927ffd1d0feb495ae229fb6ad86d21c028bcf44c 100644
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diff --git a/inst/doc/dataRetrieval.tex b/inst/doc/dataRetrieval.tex
index 1c51c3a27291906a91b33717e6b8262172ea91aa..db10cc564a6c9251478d267e91e4224d0c1ee31b 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
-% Mon Feb 18 11:57:57 2013
+% Mon Feb 18 14:20:11 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
-% Mon Feb 18 11:57:57 2013
+% Mon Feb 18 14:20:11 2013
\begin{table}[ht]
\begin{center}
\caption{Commonly found USGS Stat Codes}
@@ -421,56 +421,29 @@ The function to obtain the daily values (discharge in this case) is getDVData.
> startDate <- "1964-01-01"
> endDate <- "2013-01-01"
> Daily <- getDVData(siteNumber, "00060", startDate, endDate,interactive=FALSE)
-> summary(Daily)
\end{Sinput}
-\begin{Soutput}
- Date Q Julian Month
- Min. :1964-01-01 Min. : 0.00991 Min. :41637 Min. : 1.000
- 1st Qu.:1976-04-01 1st Qu.: 0.87782 1st Qu.:46112 1st Qu.: 4.000
- Median :1988-07-02 Median : 2.26535 Median :50586 Median : 7.000
- Mean :1988-07-02 Mean : 4.01787 Mean :50586 Mean : 6.522
- 3rd Qu.:2000-10-01 3rd Qu.: 4.55901 3rd Qu.:55061 3rd Qu.:10.000
- Max. :2013-01-01 Max. :246.35656 Max. :59535 Max. :12.000
-
- Day DecYear MonthSeq Qualifier
- Min. : 1.0 Min. :1964 Min. :1369 Length:17899
- 1st Qu.: 92.0 1st Qu.:1976 1st Qu.:1516 Class :character
- Median :183.0 Median :1989 Median :1663 Mode :character
- Mean :183.1 Mean :1989 Mean :1663
- 3rd Qu.:274.0 3rd Qu.:2001 3rd Qu.:1810
- Max. :366.0 Max. :2013 Max. :1957
-
- i LogQ Q7 Q30
- Min. : 1 Min. :-4.6141 Min. : 0.01808 Min. : 0.09606
- 1st Qu.: 4476 1st Qu.:-0.1303 1st Qu.: 0.92232 1st Qu.: 1.05811
- Median : 8950 Median : 0.8177 Median : 2.45143 Median : 2.83074
- Mean : 8950 Mean : 0.7258 Mean : 4.01655 Mean : 4.01178
- 3rd Qu.:13424 3rd Qu.: 1.5171 3rd Qu.: 4.92309 3rd Qu.: 5.61594
- Max. :17899 Max. : 5.5068 Max. :84.00395 Max. :25.47478
- NA's :6 NA's :29
-\end{Soutput}
\end{Schunk}
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 11:58:08 2013
-\begin{tabular}{rlll}
+% Mon Feb 18 14:20:19 2013
+\begin{tabular}{rllll}
\hline
- & ColumnName & Type & Description \\
+ & ColumnName & Type & Description & Units \\
\hline
-1 & Date & Date & Date \\
- 2 & Q & number & Discharge in cms \\
- 3 & Julian & number & Number of days since January 1, 1850 \\
- 4 & Month & integer & Month of the year [1-12] \\
- 5 & Day & integer & Day of the year [1-366] \\
- 6 & DecYear & number & Decimal year \\
- 7 & MonthSeq & integer & Number of months since January 1, 1850 \\
- 8 & Qualifier & string & Qualifing code \\
- 9 & i & integer & Index \\
- 10 & LogQ & number & Natural logarithm of Q \\
- 11 & Q7 & number & 7 day running average of Q \\
- 12 & Q30 & number & 30 running average of Q \\
+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 \\
\hline
\end{tabular}\\*
@@ -485,59 +458,36 @@ The function to obtain sample data from the water quality portal is getSampleDat
\begin{Sinput}
> Sample <-getSampleData(siteNumber,parameterCd,
startDate, endDate,interactive=FALSE)
-> summary(Sample)
\end{Sinput}
-\begin{Soutput}
- Date ConcLow ConcHigh Uncen
- Min. :1973-06-04 Min. :0.176 Min. :0.050 Min. :0.0000
- 1st Qu.:1989-01-31 1st Qu.:0.900 1st Qu.:0.900 1st Qu.:1.0000
- Median :1995-02-15 Median :1.150 Median :1.150 Median :1.0000
- Mean :1996-04-07 Mean :1.145 Mean :1.143 Mean :0.9984
- 3rd Qu.:2003-08-26 3rd Qu.:1.400 3rd Qu.:1.400 3rd Qu.:1.0000
- Max. :2012-12-18 Max. :2.430 Max. :2.430 Max. :1.0000
- NA's :1
- ConcAve Julian Month Day
- Min. :0.025 Min. :45079 Min. : 1.000 Min. : 2.0
- 1st Qu.:0.900 1st Qu.:50799 1st Qu.: 3.000 1st Qu.: 81.0
- Median :1.150 Median :53005 Median : 6.000 Median :161.0
- Mean :1.143 Mean :53423 Mean : 6.155 Mean :170.7
- 3rd Qu.:1.400 3rd Qu.:56119 3rd Qu.: 9.000 3rd Qu.:261.0
- Max. :2.430 Max. :59521 Max. :12.000 Max. :363.0
-
- DecYear MonthSeq SinDY CosDY
- Min. :1973 Min. :1482 Min. :-1.00000 Min. :-0.99996
- 1st Qu.:1989 1st Qu.:1670 1st Qu.:-0.65358 1st Qu.:-0.66655
- Median :1995 Median :1742 Median : 0.16237 Median : 0.03433
- Mean :1996 Mean :1756 Mean : 0.06474 Mean : 0.02331
- 3rd Qu.:2004 3rd Qu.:1844 3rd Qu.: 0.76785 3rd Qu.: 0.72212
- Max. :2013 Max. :1956 Max. : 0.99985 Max. : 0.99967
-\end{Soutput}
\end{Schunk}
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 11:58:08 2013
-\begin{tabular}{rlll}
+% Mon Feb 18 14:20:20 2013
+\begin{tabular}{rllll}
\hline
- & ColumnName & Type & Description \\
+ & ColumnName & Type & Description & Units \\
\hline
-1 & Date & Date & Date \\
- 2 & ConcLow & number & Lower limit of concentration \\
- 3 & ConcHigh & number & Upper limit of concentration \\
- 4 & Uncen & integer & Uncensored data (1=true, 0=false) \\
- 5 & ConcAve & number & Average concentration \\
- 6 & Julian & number & Number of days since January 1, 1850 \\
- 7 & Month & integer & Month of the year [1-12] \\
- 8 & Day & integer & Day of the year [1-366] \\
- 9 & DecYear & number & Decimal year \\
- 10 & MonthSeq & integer & Number of months since January 1, 1850 \\
- 11 & SinDY & number & Sine of ... \\
- 12 & CosDY & number & Cosine of ... \\
- 13 & Q & number & Discharge in cms \\
- 14 & LogQ & number & Natural logarithm of flow \\
+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 \\
\hline
-\end{tabular}
+\end{tabular}\\
+** Flow columns are populated from data in the Daily dataframe after calling the mergeReport function.
+
+
In a more complex situation, the Sample data frame will combine all of the measured parameters. An example is provided to explain how the values are combined:
%------------------------------------------------------------
@@ -546,7 +496,7 @@ 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
-% Mon Feb 18 11:58:09 2013
+% Mon Feb 18 14:20:20 2013
\begin{tabular}{rllrlrlr}
\hline
& cdate & rdp & dp & rpp & pp & rtp & tp \\
@@ -767,7 +717,7 @@ 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 11:58:09 2013
+% Mon Feb 18 14:20:21 2013
\begin{tabular}{l}
\hline
\hline
@@ -824,7 +774,7 @@ 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 11:58:09 2013
+% Mon Feb 18 14:20:21 2013
\begin{tabular}{l}
\hline
\hline
@@ -872,7 +822,7 @@ OrganizationIdentifier \\
\end{tabular}\\*
\newpage
% latex table generated in R 2.15.2 by xtable 1.7-0 package
-% Mon Feb 18 11:58:09 2013
+% Mon Feb 18 14:20:21 2013
\begin{tabular}{l}
\hline
\hline
diff --git a/inst/doc/dataRetrieval.toc b/inst/doc/dataRetrieval.toc
index a91746bf657cf0e759d3bd5d50c4dc26eeeafea5..bfaf481566ab41db712c569ead361a696e756669 100644
--- a/inst/doc/dataRetrieval.toc
+++ b/inst/doc/dataRetrieval.toc
@@ -11,16 +11,16 @@
\contentsline {section}{\numberline {3}Polished Data: USGS Web Retrieval Examples}{11}{section.3}
\contentsline {subsection}{\numberline {3.1}INFO Data}{11}{subsection.3.1}
\contentsline {subsection}{\numberline {3.2}Daily Data}{12}{subsection.3.2}
-\contentsline {subsection}{\numberline {3.3}Sample Data}{13}{subsection.3.3}
-\contentsline {subsection}{\numberline {3.4}Complex Sample Data Example}{14}{subsection.3.4}
-\contentsline {subsection}{\numberline {3.5}Merge Report}{16}{subsection.3.5}
-\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 {A}Appendix 1: Getting Started}{19}{appendix.A}
-\contentsline {subsection}{\numberline {A.1}New to R?}{19}{subsection.A.1}
-\contentsline {subsection}{\numberline {A.2}R User: Installing dataRetrieval from downloaded binary}{19}{subsection.A.2}
-\contentsline {subsection}{\numberline {A.3}R Developers: Installing dataRetrieval from gitHub}{20}{subsection.A.3}
-\contentsline {section}{\numberline {B}Appendix 2: Columns Names}{22}{appendix.B}
-\contentsline {subsection}{\numberline {B.1}INFO dataframe}{22}{subsection.B.1}
-\contentsline {subsection}{\numberline {B.2}Water Quality Portal}{23}{subsection.B.2}
+\contentsline {subsection}{\numberline {3.3}Sample Data}{12}{subsection.3.3}
+\contentsline {subsection}{\numberline {3.4}Complex Sample Data Example}{13}{subsection.3.4}
+\contentsline {subsection}{\numberline {3.5}Merge Report}{14}{subsection.3.5}
+\contentsline {section}{\numberline {4}Retrieving User-Generated Data Files}{16}{section.4}
+\contentsline {subsection}{\numberline {4.1}getDailyDataFromFile}{16}{subsection.4.1}
+\contentsline {subsection}{\numberline {4.2}getSampleDataFromFile}{17}{subsection.4.2}
+\contentsline {section}{\numberline {A}Appendix 1: Getting Started}{18}{appendix.A}
+\contentsline {subsection}{\numberline {A.1}New to R?}{18}{subsection.A.1}
+\contentsline {subsection}{\numberline {A.2}R User: Installing dataRetrieval from downloaded binary}{18}{subsection.A.2}
+\contentsline {subsection}{\numberline {A.3}R Developers: Installing dataRetrieval from gitHub}{19}{subsection.A.3}
+\contentsline {section}{\numberline {B}Appendix 2: Columns Names}{21}{appendix.B}
+\contentsline {subsection}{\numberline {B.1}INFO dataframe}{21}{subsection.B.1}
+\contentsline {subsection}{\numberline {B.2}Water Quality Portal}{22}{subsection.B.2}