Fixed examples and eval of match.call.

DESCRIPTION

 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>

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="&")
   

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="&")
   

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="&")
   

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)
   

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}

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}

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)
 }
 

vignettes/dataRetrieval.log

-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)

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