Merge pull request #50 from ldecicco-USGS/master

UTC

DESCRIPTION

@@ -2,7 +2,7 @@ Package: dataRetrieval
 Type: Package
 Title: Retrieval Functions for USGS and EPA Hydrologic and Water Quality Data
 Version: 2.0.1.9000
-Date: 2014-11-24
+Date: 2014-12-02
 Authors@R: c( person("Robert", "Hirsch", role = c("aut"),
     email = "rhirsch@usgs.gov"),
     person("Laura", "DeCicco", role = c("aut","cre"),

R/constructNWISURL.r

@@ -203,12 +203,13 @@ constructNWISURL <- function(siteNumber,parameterCd="00060",startDate="",endDate
         }
          
     )
-  
-  if(url.exists(url)){
-    return(url)
-  } else {
-    stop("The following url doesn't seem to exist:\n",url)    
-  }  
+# This was waaay to slow:  
+#   if(url.exists(url)){
+#     return(url)
+#   } else {
+#     stop("The following url doesn't seem to exist:\n",url)    
+#   }  
+  return(url)
 }
 
 

R/importRDB1.r

@@ -39,7 +39,6 @@
 #' comment \tab character \tab Header comments from the RDB file \cr
 #' }
 #' @export
-#' @import RCurl
 #' @examples
 #' siteNumber <- "02177000"
 #' startDate <- "2012-09-01"
@@ -81,7 +80,14 @@ importRDB1 <- function(obs_url, asDateTime=FALSE, qw=FALSE, convertType = TRUE,
                           "America/Phoenix","America/Metlakatla"))
   }
   
-  if(url.exists(obs_url)){
+  if(file.exists(obs_url)){
+    
+    doc <- obs_url
+    fileVecChar <- scan(obs_url, what = "", sep = "\n", quiet=TRUE)
+    pndIndx<-regexpr("^#", fileVecChar)
+    hdr <- fileVecChar[pndIndx > 0L]
+    
+  } else {
     
     # 400 bad site id
     # 404 outside date range, wrong pcode
@@ -111,11 +117,6 @@ importRDB1 <- function(obs_url, asDateTime=FALSE, qw=FALSE, convertType = TRUE,
       message(e)
       return(NA)
     })
-  } else {
-    doc <- obs_url
-    fileVecChar <- scan(obs_url, what = "", sep = "\n", quiet=TRUE)
-    pndIndx<-regexpr("^#", fileVecChar)
-    hdr <- fileVecChar[pndIndx > 0L]
   }
   
   tmp <- read.delim(  
@@ -179,6 +180,8 @@ importRDB1 <- function(obs_url, asDateTime=FALSE, qw=FALSE, convertType = TRUE,
         
         if(tz != ""){
           attr(data[,regexpr('d$', dataType) > 0], "tzone") <- tz
+        } else {
+          attr(data[,regexpr('d$', dataType) > 0], "tzone") <- "UTC"
         }
        
       } else if (qw){
@@ -222,6 +225,8 @@ importRDB1 <- function(obs_url, asDateTime=FALSE, qw=FALSE, convertType = TRUE,
         
         if(tz != ""){
           attr(data$startDateTime, "tzone") <- tz
+        } else {
+          attr(data$startDateTime, "tzone") <- "UTC"
         }
         
         if(composite){
@@ -231,6 +236,8 @@ importRDB1 <- function(obs_url, asDateTime=FALSE, qw=FALSE, convertType = TRUE,
           
           if(tz != ""){
             attr(data$endDateTime, "tzone") <- tz
+          } else {
+            attr(data$endDateTime, "tzone") <- "UTC"
           }
         }
         

R/importWaterML1.r

@@ -86,7 +86,9 @@
 #' inactiveAndAcitive <- importWaterML1(inactiveAndAcitive)
 importWaterML1 <- function(obs_url,asDateTime=FALSE, tz=""){
   
-  if(url.exists(obs_url)){
+  if(file.exists(obs_url)){
+    doc <- xmlTreeParse(obs_url, getDTD = FALSE, useInternalNodes = TRUE)
+  } else {
     doc = tryCatch({
       h <- basicHeaderGatherer()
       returnedDoc <- getURI(obs_url, headerfunction = h$update)
@@ -106,8 +108,6 @@ importWaterML1 <- function(obs_url,asDateTime=FALSE, tz=""){
       message(e)
       return(NA)
     }) 
-  } else {
-    doc <- xmlTreeParse(obs_url, getDTD = FALSE, useInternalNodes = TRUE)
   }
   
   if(tz != ""){
@@ -274,19 +274,21 @@ importWaterML1 <- function(obs_url,asDateTime=FALSE, tz=""){
   
                 datetime <- substr(datetime,1,23)
                 datetime <- as.POSIXct(datetime, "%Y-%m-%dT%H:%M:%OS", tz = "UTC")
-                datetime <- datetime + tzHours*60*60
+                datetime <- datetime - tzHours*60*60
                 df$tz_cd <- as.character(zoneAbbrievs[tzOffset]) 
               }
               
               if(!("tz_cd" %in% names(df))){
                 df$tz_cd <- zoneAbbrievs[1]
                 tzHours <- as.numeric(substr(names(zoneAbbrievs[1]),1,3))
-                datetime <- datetime + tzHours*60*60
+                datetime <- datetime - tzHours*60*60
               }
             }
             
             if(tz != ""){
               attr(datetime, "tzone") <- tz
+            } else {
+              attr(datetime, "tzone") <- "UTC"
             }
             
             

R/readNWISdv.r

@@ -15,7 +15,6 @@
 #' agency \tab character \tab The NWIS code for the agency reporting the data\cr
 #' site \tab character \tab The USGS site number \cr
 #' datetime \tab Date \tab The date of the value \cr 
-#' tz_cd \tab character \tab The time zone code for datetime \cr
 #' code \tab character \tab Any codes that qualify the corresponding value\cr
 #' value \tab numeric \tab The numeric value for the parameter \cr
 #' }
@@ -66,6 +65,7 @@ readNWISdv <- function (siteNumber,parameterCd,startDate="",endDate="",statCd="0
   data <- importWaterML1(url, asDateTime=FALSE)
   if(nrow(data)>0){
     data$dateTime <- as.Date(data$dateTime)
+    data$tz_cd <- NULL
   }
   
 

R/readNWISqw.r

@@ -8,7 +8,7 @@
 #' @param pCodes character of USGS parameter code(s).  This is usually an 5 digit number.
 #' @param startDate character starting date for data retrieval in the form YYYY-MM-DD.
 #' @param endDate character ending date for data retrieval in the form YYYY-MM-DD.
-#' @param expanded logical defaults to FALSE. If TRUE, retrieves additional information. Expanded data includes
+#' @param expanded logical defaults to TRUE. If TRUE, retrieves additional information. Expanded data includes
 #' remark_cd (remark code), result_va (result value), val_qual_tx (result value qualifier code), meth_cd (method code),
 #' dqi_cd (data-quality indicator code), rpt_lev_va (reporting level), and rpt_lev_cd (reporting level type).
 #' @param reshape logical. Will reshape the data if TRUE (default)
@@ -53,7 +53,7 @@
 #'           startDate,endDate,expanded=TRUE,reshape=FALSE)
 #'           
 readNWISqw <- function (siteNumber,pCodes,startDate="",endDate="",
-                        expanded=FALSE,reshape=TRUE,tz=""){  
+                        expanded=TRUE,reshape=FALSE,tz=""){  
   
   url <- constructNWISURL(siteNumber,pCodes,startDate,endDate,"qw",expanded=expanded)
   

man/readNWISdv.Rd

@@ -24,7 +24,6 @@ Name \tab Type \tab Description \cr
 agency \tab character \tab The NWIS code for the agency reporting the data\cr
 site \tab character \tab The USGS site number \cr
 datetime \tab Date \tab The date of the value \cr
-tz_cd \tab character \tab The time zone code for datetime \cr
 code \tab character \tab Any codes that qualify the corresponding value\cr
 value \tab numeric \tab The numeric value for the parameter \cr
 }

man/readNWISqw.Rd

@@ -4,7 +4,7 @@
 \title{Raw Data Import for USGS NWIS QW Data}
 \usage{
 readNWISqw(siteNumber, pCodes, startDate = "", endDate = "",
-  expanded = FALSE, reshape = TRUE, tz = "")
+  expanded = TRUE, reshape = FALSE, tz = "")
 }
 \arguments{
 \item{siteNumber}{character of USGS site numbers.  This is usually an 8 digit number}
@@ -15,7 +15,7 @@ readNWISqw(siteNumber, pCodes, startDate = "", endDate = "",
 
 \item{endDate}{character ending date for data retrieval in the form YYYY-MM-DD.}
 
-\item{expanded}{logical defaults to FALSE. If TRUE, retrieves additional information. Expanded data includes
+\item{expanded}{logical defaults to TRUE. If TRUE, retrieves additional information. Expanded data includes
 remark_cd (remark code), result_va (result value), val_qual_tx (result value qualifier code), meth_cd (method code),
 dqi_cd (data-quality indicator code), rpt_lev_va (reporting level), and rpt_lev_cd (reporting level type).}