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/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/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/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.log b/vignettes/dataRetrieval.log
index bfdd710bbf7a8d624264c341f44edb1c31ab07c8..105be2591df3c3c3f049d5333ab8169dc829f64f 100644
--- a/vignettes/dataRetrieval.log
+++ b/vignettes/dataRetrieval.log
@@ -1,4 +1,4 @@
-This is pdfTeX, Version 3.1415926-2.5-1.40.14 (MiKTeX 2.9) (preloaded format=pdflatex 2014.8.7) 8 AUG 2014 15:39
+This is pdfTeX, Version 3.1415926-2.5-1.40.14 (MiKTeX 2.9) (preloaded format=pdflatex 2014.8.7) 13 AUG 2014 13:08
entering extended mode
**dataRetrieval.tex
(D:\LADData\RCode\dataRetrieval\vignettes\dataRetrieval.tex
@@ -1022,7 +1022,7 @@ les (x86)/MiKTeX 2.9/fonts/type1/urw/courier/ucrb8a.pfb><C:/Program Files (x86)
rw/helvetic/uhvr8a.pfb><C:/Program Files (x86)/MiKTeX 2.9/fonts/type1/urw/times
/utmr8a.pfb><C:/Program Files (x86)/MiKTeX 2.9/fonts/type1/urw/times/utmri8a.pf
b>
-Output written on dataRetrieval.pdf (33 pages, 335873 bytes).
+Output written on dataRetrieval.pdf (33 pages, 335831 bytes).
PDF statistics:
484 PDF objects out of 1000 (max. 8388607)
84 named destinations out of 1000 (max. 500000)
diff --git a/vignettes/dataRetrieval.pdf b/vignettes/dataRetrieval.pdf
index f62020ecfa6e09995d9db1351c3b6d48346e33b7..ab32ac0ac6810c3430e3bd671e6b9ad7b6106028 100644
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diff --git a/vignettes/dataRetrieval.synctex.gz b/vignettes/dataRetrieval.synctex.gz
index 0efeab0b128c449044f46dcc6562e90a11ae750f..f2742fffb97ddfdbbbc4a0d8fbf026ef220bb2ae 100644
Binary files a/vignettes/dataRetrieval.synctex.gz and b/vignettes/dataRetrieval.synctex.gz differ
diff --git a/vignettes/dataRetrieval.tex b/vignettes/dataRetrieval.tex
index 8b083b15c8674991b1e26c71ced91d24735c6d89..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
-% Fri Aug 08 15:39:28 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
-% Fri Aug 08 15:39:30 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
-% Fri Aug 08 15:39:30 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 & 2014-08-07 & 24326 & 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
-% Fri Aug 08 15:39:49 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
-% Fri Aug 08 15:39:50 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}
@@ -1122,12 +1122,12 @@ There are 4750 data points, and 4750 days.
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 0.06005 0.9982
-2 54819 2 34 2000 1802 0.54392 0.8391
-3 54831 2 46 2000 1802 0.70407 0.7101
-4 54835 2 50 2000 1802 0.75113 0.6602
-5 54868 3 83 2000 1803 0.98809 0.1539
-6 54942 6 157 2000 1806 0.43940 -0.8983
+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}
@@ -1351,7 +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 2014-08-07 24326 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
index 87cadec1ad3a1be69335e470820ad297f6615779..b19a3ca6a90f6f2c1038bf101bb85066cf226e3c 100644
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diff --git a/vignettes/figure/getNWIStemperaturePlot.pdf b/vignettes/figure/getNWIStemperaturePlot.pdf
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diff --git a/vignettes/figure/getQWtemperaturePlot.pdf b/vignettes/figure/getQWtemperaturePlot.pdf
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