diff --git a/DESCRIPTION b/DESCRIPTION
index d02adb0a7f84b8a9822724e1c9fdf6800d81b26d..30925fcbb8a41824dbd0c09758037f9d16116c8c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: dataRetrieval
Type: Package
Title: Retrieval functions for hydrologic data
-Version: 1.3.2
+Version: 1.3.3
Date: 2014-08-04
Author: Robert M. Hirsch, Laura De Cicco
Maintainer: Laura De Cicco <ldecicco@usgs.gov>
diff --git a/NEWS b/NEWS
index 0c14291543e686b98068355715149c5b7b2c0a74..8308939a2fd7af4ca7829136379e7cb5fe5f4780 100644
--- a/NEWS
+++ b/NEWS
@@ -4,6 +4,7 @@ dataRetrieval 1.3.2
* Deprecated getQWData, updated getWQPData to take either parameter code or characteristic name.
* Changed the name of raw data retrievals to: retrieveNWISqwData, retrieveNWISunitData, retrieveNWISdvData, and retrieveWQPqwData (from: retrieveNWISqwData, retrieveUnitNWISData, retrieveNWISData, getRawQWData)
* Added NA warning to getDVData function
+* Updated mergeReport to allow for Sample data with different measurements taken on the same day
dataRetrieval 1.2.2
diff --git a/R/getGeneralWQPData.R b/R/getGeneralWQPData.R
index 9c178aa5053265c115d6813905b53684a25ee198..f163f623a7bdd04b8d148b918c04013b14f662de 100644
--- a/R/getGeneralWQPData.R
+++ b/R/getGeneralWQPData.R
@@ -9,9 +9,8 @@
#' (subsequent qualifier/value columns could follow depending on requested parameter codes)
#' @export
#' @examples
-#' setInternet2(use=NA)
-#' options(timeout=120)
-#' pHData <- getGeneralWQPData(siteid="USGS-04024315",characteristicName="pH")
+#' nameToUse <- "pH"
+#' pHData <- getGeneralWQPData(siteid="USGS-04024315",characteristicName=nameToUse)
getGeneralWQPData <- function(...){
matchReturn <- match.call()
@@ -22,7 +21,7 @@ getGeneralWQPData <- function(...){
if(!all(names(matchReturn[-1]) %in% options)) warning(matchReturn[!(names(matchReturn[-1]) %in% options)],"is not a valid query parameter to the Water Quality Portal")
- values <- sapply(matchReturn[-1], function(x) URLencode(as.character(paste(x,collapse="",sep=""))))
+ values <- sapply(matchReturn[-1], function(x) URLencode(as.character(paste(eval(x),collapse="",sep=""))))
urlCall <- paste(paste(names(values),values,sep="="),collapse="&")
diff --git a/R/getNWISSites.R b/R/getNWISSites.R
index 78172d2c8e72bb81f7efe3da58cc0f3405b5bd54..1b720c3806bff87ab94c41b16830d5f6d2138f92 100644
--- a/R/getNWISSites.R
+++ b/R/getNWISSites.R
@@ -13,7 +13,7 @@ getNWISSites <- function(...){
matchReturn <- match.call()
- values <- sapply(matchReturn[-1], function(x) URLencode(as.character(paste(x,collapse="",sep=""))))
+ values <- sapply(matchReturn[-1], function(x) URLencode(as.character(paste(eval(x),collapse="",sep=""))))
urlCall <- paste(paste(names(values),values,sep="="),collapse="&")
diff --git a/R/getWQPSites.R b/R/getWQPSites.R
index 73c9e7d75a79796a1593f5511441b1ff9d0b32dc..2cf54c6d36cdf403759ba12d655086152d7d4d09 100644
--- a/R/getWQPSites.R
+++ b/R/getWQPSites.R
@@ -9,13 +9,10 @@
#' (subsequent qualifier/value columns could follow depending on requested parameter codes)
#' @export
#' @examples
-#' setInternet2(use=NA)
-#' options(timeout=120)
-#' \dontrun{sitesList <- getWQPSites(within=10,lat=43.06932,long=-89.4444,characteristicName="pH")
-#' siteListPH <- getWQPSites(characteristicName="pH")}
+#' siteListPH <- getWQPSites(characteristicName="pH", statecode="US:55")
getWQPSites <- function(...){
- matchReturn <- match.call()
+ matchReturn <- match.call(expand.dots = TRUE)
options <- c("bBox","lat","long","within","countrycode","statecode","countycode","siteType","organization",
"siteid","huc","sampleMedia","characteristicType","characteristicName","pCode","activityId",
@@ -23,7 +20,7 @@ getWQPSites <- function(...){
if(!all(names(matchReturn[-1]) %in% options)) warning(matchReturn[!(names(matchReturn[-1]) %in% options)],"is not a valid query parameter to the Water Quality Portal")
- values <- sapply(matchReturn[-1], function(x) URLencode(as.character(paste(x,collapse="",sep=""))))
+ values <- sapply(matchReturn[-1], function(x) URLencode(as.character(paste(eval(x),collapse="",sep=""))))
urlCall <- paste(paste(names(values),values,sep="="),collapse="&")
diff --git a/R/mergeReport.r b/R/mergeReport.r
index 0cf0af3e159ba82b2684eff3c5171bce6d4faa40..aafdcf210fd853ed451136649d719df2685158a9 100644
--- a/R/mergeReport.r
+++ b/R/mergeReport.r
@@ -18,12 +18,8 @@ mergeReport<-function(localDaily = Daily, localSample = Sample, interactive=TRUE
if (interactive){
dataOverview(localDaily, localSample)
}
- julFirst<-localDaily$Julian[1]
- sampleDate<-as.Date(localSample$Date)
- sampleJulian<-as.numeric(julian(sampleDate,origin=as.Date("1850-01-01")))
- sampleIndex <- sampleJulian-julFirst+1
- Q <- localDaily$Q[sampleIndex]
- LogQ<-log(Q)
- newSample<-data.frame(localSample,Q,LogQ)
+
+ newSample <- merge(Daily[,c("Date","Q","LogQ")],Sample,by = "Date",all.y = TRUE)
+
return(newSample)
}
diff --git a/R/populateDateColumns.r b/R/populateDateColumns.r
index 99ac1d3ce67ba1dea9e875a01f4c6c2166a8526a..b6a5cc7d2bb97949c06836d0183b7507e5fb6682 100644
--- a/R/populateDateColumns.r
+++ b/R/populateDateColumns.r
@@ -6,7 +6,7 @@
#' @return DateFrame dataframe
#' @export
#' @examples
-#' dateTime <- c('1984-01-01', '1985-01-02', '1986-01-03')
+#' dateTime <- c('1984-02-28 13:56', '1984-03-01', '1986-03-01')
#' expandedDateDF <- populateDateColumns(dateTime)
populateDateColumns <- function(rawData){ # rawData is a vector of dates
DateFrame <- as.data.frame(matrix(ncol=1,nrow=length(rawData)))
@@ -17,12 +17,25 @@ populateDateColumns <- function(rawData){ # rawData is a vector of dates
DateFrame$Month <- dateTime$mon + 1
DateFrame$Day <- dateTime$yday + 1
year <- dateTime$year + 1900
+ hour <- dateTime$hour
+ minute <- dateTime$min
+
+ if (sum(hour) == 0 & sum(minute) == 0){
+ dateTime$hour <- rep(12,length(dateTime))
+ }
leapOffset <- ifelse((year%%4 == 0) & ((year%%100 != 0) | (year%%400 == 0)), 0,1)
DateFrame$Day[DateFrame$Day > 59] <- DateFrame$Day[DateFrame$Day > 59] + leapOffset[DateFrame$Day > 59]
- DateFrame$DecYear <- year + (DateFrame$Day -0.5)/366
+# DateFrame$DecYear <- year + (DateFrame$Day -0.5)/366
+
+ jan1 <- as.POSIXlt(paste(year,"-01-01",sep=""),format="%Y-%m-%d")
+ jan1NextYear <- as.POSIXlt(paste(year+1,"-01-01",sep=""),format="%Y-%m-%d")
+ decimal <- as.numeric(difftime(dateTime, jan1, units = "secs"))
+ decimal <- decimal/as.numeric(difftime(jan1NextYear, jan1, units = "secs"))
+
+ DateFrame$DecYear <- year + decimal
DateFrame$MonthSeq <- ((year-1850)*12)+DateFrame$Month
return (DateFrame)
diff --git a/inst/doc/dataRetrieval.pdf b/inst/doc/dataRetrieval.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..f62020ecfa6e09995d9db1351c3b6d48346e33b7
Binary files /dev/null and b/inst/doc/dataRetrieval.pdf differ
diff --git a/man/getGeneralWQPData.Rd b/man/getGeneralWQPData.Rd
index 6c9f32562544856b47b22eda04b99bef5e473cfd..f191f404ab752483e3ce5d370dbe97700d63f174 100644
--- a/man/getGeneralWQPData.Rd
+++ b/man/getGeneralWQPData.Rd
@@ -17,9 +17,8 @@ Imports data from Water Quality Portal web service. This function gets the data
because it allows for other agencies rather than the USGS.
}
\examples{
-setInternet2(use=NA)
-options(timeout=120)
-pHData <- getGeneralWQPData(siteid="USGS-04024315",characteristicName="pH")
+nameToUse <- "pH"
+pHData <- getGeneralWQPData(siteid="USGS-04024315",characteristicName=nameToUse)
}
\keyword{WQP}
\keyword{data}
diff --git a/man/getWQPSites.Rd b/man/getWQPSites.Rd
index 357c1f731bac22c2f15e9fe32909edef2c6430fb..4462ad23a1cb9021515e4427a58dcf5b297e8cdb 100644
--- a/man/getWQPSites.Rd
+++ b/man/getWQPSites.Rd
@@ -17,10 +17,7 @@ Returns a list of sites from the Water Quality Portal web service. This function
Arguments to the function should be based on \url{www.waterqualitydata.us/webservices_documentation.jsp}
}
\examples{
-setInternet2(use=NA)
-options(timeout=120)
-\dontrun{sitesList <- getWQPSites(within=10,lat=43.06932,long=-89.4444,characteristicName="pH")
-siteListPH <- getWQPSites(characteristicName="pH")}
+siteListPH <- getWQPSites(characteristicName="pH", statecode="US:55")
}
\keyword{WQP}
\keyword{data}
diff --git a/man/populateDateColumns.Rd b/man/populateDateColumns.Rd
index 8d8f3a447b686c670d31f6f938aaf03d9301dce7..9b5a10f8b0a9865476c2c7b8c342f36ab897a57d 100644
--- a/man/populateDateColumns.Rd
+++ b/man/populateDateColumns.Rd
@@ -15,7 +15,7 @@ DateFrame dataframe
Creates various date columns for WRTDS study.
}
\examples{
-dateTime <- c('1984-01-01', '1985-01-02', '1986-01-03')
+dateTime <- c('1984-02-28 13:56', '1984-03-01', '1986-03-01')
expandedDateDF <- populateDateColumns(dateTime)
}
diff --git a/vignettes/dataRetrieval-concordance.tex b/vignettes/dataRetrieval-concordance.tex
index 4c9c14712f612496a3609dbe58d84413073e4f60..9ddb6dd290d811cff4b497da7a25abced8ca6965 100644
--- a/vignettes/dataRetrieval-concordance.tex
+++ b/vignettes/dataRetrieval-concordance.tex
@@ -5,5 +5,5 @@
0 6 1 17 0 27 1 6 0 11 1 9 0 15 1 13 0 21 1 4 0 21 1 %
4 0 17 1 7 0 22 1 8 0 19 1 4 0 9 1 4 0 78 1 1 2 9 1 1 %
4 4 1 20 0 44 1 4 0 32 1 4 0 21 1 4 0 21 1 37 0 13 1 %
-9 0 94 1 4 0 9 1 12 0 13 1 4 0 14 1 4 0 5 1 4 0 23 1 %
+9 0 94 1 4 0 9 1 13 0 13 1 4 0 14 1 4 0 5 1 4 0 23 1 %
18 0 8 1 4 0 55 1}
diff --git a/vignettes/dataRetrieval.log b/vignettes/dataRetrieval.log
index f053973c87381856b42db677c3a5d80e70ba3e23..105be2591df3c3c3f049d5333ab8169dc829f64f 100644
--- a/vignettes/dataRetrieval.log
+++ b/vignettes/dataRetrieval.log
@@ -1,7 +1,7 @@
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entering extended mode
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Package: framed 2011/10/22 v 0.96: framed or shaded text with page breaks
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Package hyperref Info: Bookmarks ON on input line 4688.
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Package: natbib 2010/09/13 8.31b (PWD, AO)
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Package: subfig 2005/06/28 ver: 1.3 subfig package
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Package: placeins 2005/04/18 v 2.2
-)
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Package: footnote 1997/01/28 1.13 Save footnotes around boxes
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+[11 <D:/LADData/RCode/dataRetrieval/vignettes/figure/getNWIStemperaturePlot.pdf
+>]
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@@ -820,11 +816,10 @@ Overfull \vbox (21.68121pt too high) has occurred while \output is active []
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-[14 <C:/RCodes/dataRetrieval/vignettes/figure/getQWtemperaturePlot.pdf>]
+[14 <D:/LADData/RCode/dataRetrieval/vignettes/figure/getQWtemperaturePlot.pdf>]
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-
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)
@@ -937,7 +932,7 @@ Overfull \vbox (21.68121pt too high) has occurred while \output is active []
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-[26 <C:/RCodes/dataRetrieval/vignettes/figure/egretEx.pdf>]
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[28]
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-
-Overfull \hbox (51.24562pt too wide) in paragraph at lines 1272--1272
-[] \OT1/pcr/m/n/10.95 Sample1 <- localSample[!duplicated(localSample[c("DecYea
-r","ConcHigh")]),][]
- []
-
-<Rhelp.png, id=399, 433.62pt x 395.22656pt>
+ <Rhelp.png, id=399, 433.62pt x 395.22656pt>
File: Rhelp.png Graphic file (type png)
<use Rhelp.png>
-Package pdftex.def Info: Rhelp.png used on input line 1279.
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-[30 <C:/RCodes/dataRetrieval/vignettes/Rhelp.png>]
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[31
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+Overfull \hbox (11.82567pt too wide) in paragraph at lines 1383--1383
[]\OT1/pcr/m/n/10.95 Suspended sediment concentration (SSC) 1980-10-01 1991-09-
30 3651 mg/l[]
[]
@@ -997,27 +986,27 @@ Overfull \vbox (21.68121pt too high) has occurred while \output is active []
[32] <table1.png, id=423, 554.07pt x 125.71968pt>
File: table1.png Graphic file (type png)
<use table1.png>
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+[33 <D:/LADData/RCode/dataRetrieval/vignettes/table1.png>]
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+(D:\LADData\RCode\dataRetrieval\vignettes\dataRetrieval.aux)
+Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 1427.
+Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 1427.
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(rerunfilecheck) Checksum: 0A42302DA34F8DDBBBAD8A2EC505FAF3;1805.
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+Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 1427.
)
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45680 words of font info for 91 fonts, out of 3000000 for 9000
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b>
-Output written on dataRetrieval.pdf (33 pages, 335842 bytes).
+Output written on dataRetrieval.pdf (33 pages, 335831 bytes).
PDF statistics:
484 PDF objects out of 1000 (max. 8388607)
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diff --git a/vignettes/dataRetrieval.pdf b/vignettes/dataRetrieval.pdf
index ac5e5885a40977f288bbb088b839b505230a37f2..ab32ac0ac6810c3430e3bd671e6b9ad7b6106028 100644
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diff --git a/vignettes/dataRetrieval.synctex.gz b/vignettes/dataRetrieval.synctex.gz
index 1a63eebca98d346fba1a493bf868925e16f68c7f..f2742fffb97ddfdbbbc4a0d8fbf026ef220bb2ae 100644
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diff --git a/vignettes/dataRetrieval.tex b/vignettes/dataRetrieval.tex
index ce9715cc12d0c519d1431dd0ef3b1c7954e5ac68..d4710d610fcb823dc5445e34f6257333b9d53bd8 100644
--- a/vignettes/dataRetrieval.tex
+++ b/vignettes/dataRetrieval.tex
@@ -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
-% Sun Aug 03 14:57:17 2014
+% Wed Aug 13 13:07:49 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
-% Sun Aug 03 14:57:19 2014
+% Wed Aug 13 13:07:50 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
-% Sun Aug 03 14:57:20 2014
+% Wed Aug 13 13:07:50 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 & 2014-08-02 & 24321 & ft$^3$/s \\
+ [5pt] & Stream flow, mean. daily & 1948-01-01 & 2014-08-12 & 24331 & ft$^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 \\
@@ -789,7 +789,7 @@ There are 4750 data points, and 4750 days.
% latex table generated in R 3.1.1 by xtable 1.7-3 package
-% Sun Aug 03 14:57:39 2014
+% Wed Aug 13 13:08:05 2014
\begin{table}[ht]
\caption{Daily dataframe}
\label{tab:DailyDF1}
@@ -910,7 +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
-% Sun Aug 03 14:57:40 2014
+% Wed Aug 13 13:08:06 2014
\begin{table}[ht]
\caption{Example data}
\label{tab:exampleComplexQW}
@@ -955,12 +955,12 @@ For the more complex example case, let us say dp is reported as \verb@<@0.01 and
5 2005-05-30 NA 0.050 0 0.0250 56762 5
6 2005-10-30 NA 0.020 0 0.0100 56915 10
Day DecYear MonthSeq SinDY CosDY
-1 46 2003 1838 0.70407 0.7101
-2 182 2003 1842 0.02575 -0.9997
-3 259 2005 1857 -0.96251 -0.2712
-4 30 2005 1861 0.48506 0.8745
-5 151 2005 1865 0.52943 -0.8484
-6 304 2006 1870 -0.87861 0.4775
+1 46 2003 1838 0.70253 0.7117
+2 182 2003 1842 0.03872 -0.9993
+3 259 2005 1857 -0.96134 -0.2754
+4 30 2005 1861 0.48251 0.8759
+5 151 2005 1865 0.54163 -0.8406
+6 304 2006 1870 -0.88205 0.4712
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -1114,20 +1114,20 @@ There are 4750 data points, and 4750 days.
\hlkwd{head}\hlstd{(Sample)}
\end{alltt}
\begin{verbatim}
- Date ConcLow ConcHigh Uncen ConcAve Julian Month
-1 2000-01-04 1.59 1.59 1 1.59 54789 1
-2 2000-02-03 1.54 1.54 1 1.54 54819 2
-3 2000-02-15 1.37 1.37 1 1.37 54831 2
-4 2000-02-19 1.24 1.24 1 1.24 54835 2
-5 2000-03-23 0.52 0.52 1 0.52 54868 3
-6 2000-06-05 1.11 1.11 1 1.11 54942 6
- Day DecYear MonthSeq SinDY CosDY Q LogQ
-1 4 2000 1801 0.06005 0.9982 2.747 1.0104
-2 34 2000 1802 0.54392 0.8391 3.936 1.3702
-3 46 2000 1802 0.70407 0.7101 10.845 2.3837
-4 50 2000 1802 0.75113 0.6602 15.518 2.7420
-5 83 2000 1803 0.98809 0.1539 56.917 4.0416
-6 157 2000 1806 0.43940 -0.8983 1.812 0.5946
+ Date Q LogQ ConcLow ConcHigh Uncen ConcAve
+1 2000-01-04 2.747 1.0104 1.59 1.59 1 1.59
+2 2000-02-03 3.936 1.3702 1.54 1.54 1 1.54
+3 2000-02-15 10.845 2.3837 1.37 1.37 1 1.37
+4 2000-02-19 15.518 2.7420 1.24 1.24 1 1.24
+5 2000-03-23 56.917 4.0416 0.52 0.52 1 0.52
+6 2000-06-05 1.812 0.5946 1.11 1.11 1 1.11
+ Julian Month Day DecYear MonthSeq SinDY CosDY
+1 54789 1 4 2000 1801 0.05576 0.9984
+2 54819 2 34 2000 1802 0.54031 0.8415
+3 54831 2 46 2000 1802 0.70101 0.7132
+4 54835 2 50 2000 1802 0.74829 0.6634
+5 54868 3 83 2000 1803 0.98742 0.1581
+6 54942 6 157 2000 1806 0.44325 -0.8964
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -1263,10 +1263,11 @@ To see the raw code for a particular code, type the name of the function, withou
\hlstd{removeDuplicates}
\end{alltt}
\begin{verbatim}
-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{verbatim}
@@ -1350,7 +1351,7 @@ 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 2014-08-02 24321 ft3/s
+2 2014-08-12 24331 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/figure/egretEx.pdf b/vignettes/figure/egretEx.pdf
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diff --git a/vignettes/figure/getQWtemperaturePlot.pdf b/vignettes/figure/getQWtemperaturePlot.pdf
index b9f4ed9ed16bf6eaf7904973414c08394f37f5e7..27d6cf946d2b0340c1d7bf9b198fb1a9c2ba7a1c 100644
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