Merge pull request #151 from ldecicco-USGS/master

readr for importRDB1

DESCRIPTION

 Package: dataRetrieval
 Type: Package
 Title: Retrieval Functions for USGS and EPA Hydrologic and Water Quality Data
-Version: 2.4.0
-Date: 2015-10-14
+Version: 2.4.1
+Date: 2015-11-25
 Authors@R: c( person("Robert", "Hirsch", role = c("aut"),
     email = "rhirsch@usgs.gov"),
     person("Laura", "DeCicco", role = c("aut","cre"),

NAMESPACE

@@ -45,5 +45,6 @@ importFrom(plyr,rbind.fill.matrix)
 importFrom(readr,col_character)
 importFrom(readr,cols)
 importFrom(readr,read_delim)
+importFrom(readr,read_lines)
 importFrom(reshape2,dcast)
 importFrom(reshape2,melt)

NEWS

+dataRetrieval 2.4.0
+==========
+* Package readr now used for tab delimited parsing
+* readr functions used to determine column types. Mostly, this produces the same results. 
+* In the case where there is text in a numeric column (specified by the RDB header), these now remain characters (previously was converted to numeric)
+* Columns that come back from web services as integers remain integers (previously was converted to numeric)
+* Added reported time zone code information. dateTime columns by default get converted to UTC, but the original time zone code (tz_cd for instance) is appended to the data frame.
+
 dataRetrieval 2.3.0
 ===========
 * Converted all Water Quality Portal queries to sorted=no to greatly improve retrieval times

R/importRDB1.r

@@ -7,7 +7,6 @@
 #'
 #' @param obs_url character containing the url for the retrieval or a file path to the data file.
 #' @param asDateTime logical, if \code{TRUE} returns date and time as POSIXct, if \code{FALSE}, Date
-#' @param qw logical, if \code{TRUE} parses as water quality data (where dates/times are in start and end times)
 #' @param tz character to set timezone attribute of datetime. Default is an empty quote, which converts the 
 #' datetimes to UTC (properly accounting for daylight savings times based on the data's provided tz_cd column).
 #' Possible values to provide are "America/New_York","America/Chicago", "America/Denver","America/Los_Angeles",
@@ -46,6 +45,8 @@
 #' @import utils
 #' @import stats
 #' @importFrom dplyr left_join
+#' @importFrom readr read_lines
+#' @importFrom readr read_delim
 #' @examples
 #' siteNumber <- "02177000"
 #' startDate <- "2012-09-01"
@@ -67,10 +68,10 @@
 #' qwURL <- constructNWISURL(c('04024430','04024000'),
 #'           c('34247','30234','32104','34220'),
 #'          "2010-11-03","","qw",format="rdb") 
-#' qwData <- importRDB1(qwURL, qw=TRUE, tz="America/Chicago")
+#' qwData <- importRDB1(qwURL, asDateTime=TRUE, tz="America/Chicago")
 #' iceSite <- '04024000'
-#' start <- "2014-11-09"
-#' end <- "2014-11-28"
+#' start <- "2015-11-09"
+#' end <- "2015-11-24"
 #' urlIce <- constructNWISURL(iceSite,"00060",start, end,"uv",format="tsv")
 #' ice <- importRDB1(urlIce, asDateTime=TRUE)
 #' iceNoConvert <- importRDB1(urlIce, convertType=FALSE)
@@ -81,25 +82,24 @@
 #' fullPath <- file.path(filePath, fileName)
 #' importUserRDB <- importRDB1(fullPath)
 #' 
-importRDB1 <- function(obs_url, asDateTime=FALSE, qw=FALSE, convertType = TRUE, tz=""){
+importRDB1 <- function(obs_url, asDateTime=TRUE, convertType = TRUE, tz=""){
   
   if(tz != ""){
     tz <- match.arg(tz, c("America/New_York","America/Chicago",
                           "America/Denver","America/Los_Angeles",
                           "America/Anchorage","America/Honolulu",
                           "America/Jamaica","America/Managua",
-                          "America/Phoenix","America/Metlakatla"))
+                          "America/Phoenix","America/Metlakatla","UTC"))
   }
   
 
   if(file.exists(obs_url)){
     doc <- obs_url
   } else {
-    rawData <- getWebServiceData(obs_url)
-    doc <- textConnection(rawData)
-    if("warn" %in% names(attr(rawData,"header"))){
+    doc <- getWebServiceData(obs_url)
+    if("warn" %in% names(attr(doc,"header"))){
       data <- data.frame()
-      attr(data, "header") <- attr(rawData,"header")
+      attr(data, "header") <- attr(doc,"header")
       attr(data, "url") <- obs_url
       attr(data, "queryTime") <- Sys.time()
       
@@ -107,175 +107,118 @@ importRDB1 <- function(obs_url, asDateTime=FALSE, qw=FALSE, convertType = TRUE,
     }
   }
   
-  tmp <- read.delim(  
-    doc, 
-    header = TRUE, 
-    quote="\"", 
-    dec=".", 
-    sep='\t',
-    colClasses=c('character'),
-    fill = TRUE, 
-    comment.char="#")
-  
-  fileVecChar <- scan(obs_url, what = "", sep = "\n", quiet=TRUE)
-  pndIndx<-regexpr("^#", fileVecChar)
-  hdr <- fileVecChar[pndIndx > 0L]
+  readr.total <- read_lines(doc)
+  total.rows <- length(readr.total)
+  readr.meta <- readr.total[grep("^#", readr.total)]
+  meta.rows <- length(readr.meta)
+  header.names <- strsplit(readr.total[meta.rows+1],"\t")[[1]]
+
+  if(convertType){
+    readr.data <- suppressWarnings(read_delim(doc, skip = (meta.rows+2),delim="\t",col_names = FALSE))
+  } else {
+    readr.data <- suppressWarnings(read_delim(doc, skip = (meta.rows+2),delim="\t",col_names = FALSE, col_types = cols(.default = "c")))
+  }
   
-  dataType <- tmp[1,]
-  data <- tmp[-1,]
+  names(readr.data) <- header.names
+  comment(readr.data) <- readr.meta
+  readr.data <- as.data.frame(readr.data)
   
-  if(convertType){
-    
-    #This will break if the 2nd (or greater) site has more columns than the first
-    #Therefore, using RDB is not recommended for multi-site queries.
-    #This correction will work if each site has the same number of columns
-    multiSiteCorrections <- -which(as.logical(apply(data[,1:2], 1, FUN=function(x) all(x %in% as.character(dataType[,1:2])))))
-    
-    if(length(multiSiteCorrections) > 0){
-      data <- data[multiSiteCorrections,]
-      
-      findRowsWithHeaderInfo <- as.integer(apply(data[,1:2], 1, FUN = function(x) if(x[1] == names(data)[1] & x[2] == names(data)[2]) 1 else 0))
-      findRowsWithHeaderInfo <- which(findRowsWithHeaderInfo == 0)
-      data <- data[findRowsWithHeaderInfo,]
-    }
-    
-    offsetLibrary <- data.frame(offset=c(5, 4, 6, 5, 7, 6, 8, 7, 9, 8, 10, 10),
-                                tz_cd=c("EST","EDT","CST","CDT","MST","MDT","PST","PDT","AKST","AKDT","HAST","HST"),
-                                stringsAsFactors = FALSE)
+  if (asDateTime & convertType){
 
-    # The suppressed warning occurs when there is text (such as ice) in the numeric column:
-    data[,grep('n$', dataType)] <- suppressWarnings(sapply(data[,grep('n$', dataType)], function(x) as.numeric(x)))
+    header.suffix <- sapply(strsplit(header.names,"_"), function(x)x[length(x)])
+    header.base <- substr(header.names,1,nchar(header.names)-3)
     
-    numberColumns <- grep("_va",names(data))    
-    data[,numberColumns] <- sapply(data[,numberColumns],as.numeric)
-    
-    intColumns <- grep("_nu",names(data))
-    
-    if("current_rating_nu" %in% names(data)){
-      intColumns <- intColumns[!("current_rating_nu" %in% names(data)[intColumns])]
-      data$current_rating_nu <- gsub(" ", "", data$current_rating_nu)
-    }
-    data[,intColumns] <- sapply(data[,intColumns],as.integer)
-    
-    if(length(grep('d$', dataType)) > 0){
-      if (asDateTime & !qw){
-        
-        if("tz_cd" %in% names(data)){
-          offset <- left_join(data[,"tz_cd",drop=FALSE],offsetLibrary, by="tz_cd")
-          offset <- offset$offset
-          offset[is.na(offset)] <- median(offset, na.rm=TRUE)
-        } else {
-          offset <- 0
-        }
-        # offset[is.na(offset)] <- 0
-        rawDateTimes <- data[,regexpr('d$', dataType) > 0]
-        data[,regexpr('d$', dataType) > 0] <- as.POSIXct(data[,regexpr('d$', dataType) > 0], "%Y-%m-%d %H:%M", tz = "UTC")
-
-        
-        if(any(is.na(data[,regexpr('d$', dataType) > 0]))){
-          base.name <- names(data)[regexpr('d$', dataType) > 0]
-          base.name <- gsub("_dt","",base.name)
-          data[,paste(base.name,"date","reported",sep = "_")] <- as.Date(substr(rawDateTimes,1,10))
-          data[,paste(base.name,"tm","reported",sep = "_")] <- substr(rawDateTimes,12,nchar(rawDateTimes))
-        }
-
-        data[,regexpr('d$', dataType) > 0] <- data[,regexpr('d$', dataType) > 0] + offset*60*60
-        data[,regexpr('d$', dataType) > 0] <- as.POSIXct(data[,regexpr('d$', dataType) > 0])
-                
-        data$tz_cd_reported <- data$tz_cd
+    for(i in unique(header.base[header.suffix %in% c("dt","tm")])){
+      
+      if(all(c(paste0(i,"_dt"),paste0(i,"_tm")) %in% header.names)){
+        varname <- paste0(i,"_dateTime")
         
-        if(tz != ""){
-          attr(data[,regexpr('d$', dataType) > 0], "tzone") <- tz
-          data$tz_cd <- rep(tz, nrow(data))
-        } else {
-          attr(data[,regexpr('d$', dataType) > 0], "tzone") <- "UTC"
-          data$tz_cd[!is.na(data[,regexpr('d$', dataType) > 0])] <- "UTC"
-        }   
-       
-      } else if (qw){
+        varval <- as.POSIXct(paste(readr.data[,paste0(i,"_dt")],readr.data[,paste0(i,"_tm")]), "%Y-%m-%d %H:%M", tz = "UTC")
+        readr.data[,varname] <- varval
         
-        if("sample_start_time_datum_cd" %in% names(data)){
-          timeZoneStartOffset <- left_join(data[,"sample_start_time_datum_cd",drop=FALSE],offsetLibrary, 
-                                           by=c("sample_start_time_datum_cd"="tz_cd"))
-          timeZoneStartOffset <- timeZoneStartOffset$offset
-          timeZoneStartOffset[is.na(timeZoneStartOffset)] <- 0
-        } else {
-          timeZoneStartOffset <- 0
-        }
+        tz.name <- paste0(i,"_time_datum_cd")
         
-        composite <- "sample_end_time_datum_cd" %in% names(data)
-        if(composite){
-          timeZoneEndOffset <- left_join(data[,"sample_end_time_datum_cd",drop=FALSE],offsetLibrary, 
-                                           by=c("sample_end_time_datum_cd"="tz_cd"))
-          timeZoneEndOffset <- timeZoneEndOffset$offset
-          timeZoneEndOffset[is.na(timeZoneEndOffset)] <- 0
-        } else {
-          if(any(data$sample_end_dt != "") & any(data$sample_end_dm != "")){
-            if(which(data$sample_end_dt != "") == which(data$sample_end_dm != "")){
-              composite <- TRUE
-            }
-          }
-          timeZoneEndOffset <- 0
+        if(tz.name %in% header.names){
+          readr.data <- convertTZ(readr.data,tz.name,varname,tz)
         }
         
-        if("sample_dt" %in% names(data)){
-          if(any(data$sample_dt != "")){
-            suppressWarnings(data$sample_dt <- as.Date(parse_date_time(data$sample_dt, c("Ymd", "mdY"))))
-          }
-        }
+        tz.name <- paste0(i,"_tz_cd")
         
-        if("sample_end_dt" %in% names(data)){
-          if(any(data$sample_end_dt != "")){
-            suppressWarnings(data$sample_end_dt <- as.Date(parse_date_time(data$sample_end_dt, c("Ymd", "mdY"))))
-          }        
-        }
-        
-        data$startDateTime <- with(data, as.POSIXct(paste(sample_dt, sample_tm),format="%Y-%m-%d %H:%M", tz = "UTC"))
-        data$startDateTime <- data$startDateTime + timeZoneStartOffset*60*60
-        data$startDateTime <- as.POSIXct(data$startDateTime)
-        
-        if(tz != ""){
-          attr(data$startDateTime, "tzone") <- tz
-          data$tz_cd <- rep(tz, nrow(data))
-        } else {
-          attr(data$startDateTime, "tzone") <- "UTC"
-          data$tz_cd[!is.na(data$startDateTime)] <- "UTC"
-        }        
-        
-        if(composite){
-          data$endDateTime <- with(data, as.POSIXct(paste(sample_end_dt, sample_end_tm),format="%Y-%m-%d %H:%M", tz = "UTC"))
-          data$endDateTime <- data$endDateTime + timeZoneEndOffset*60*60
-          data$endDateTime <- as.POSIXct(data$endDateTime)
-          
-          if(tz != ""){
-            attr(data$endDateTime, "tzone") <- tz
-          } else {
-            attr(data$endDateTime, "tzone") <- "UTC"
-          }
-        }
-        
-      } else {
-        for (i in grep('d$', dataType)){
-          if (all(data[,i] != "")){
-            data[,i] <- as.character(data[,i])
-          }
+        if(tz.name %in% header.names){
+          readr.data <- convertTZ(readr.data,tz.name,varname,tz)
         }
       }
     }
+    
+    if("tz_cd" %in% header.names){
+      date.time.cols <- which(sapply(readr.data, function(x) inherits(x, "POSIXct")))
+      readr.data <- convertTZ(readr.data,"tz_cd",date.time.cols,tz)
+    }
+    
+    if("sample_start_time_datum_cd" %in% header.names){
+      readr.data <- convertTZ(readr.data,"sample_start_time_datum_cd","sample_dateTime",tz)
+      
+      if(!("sample_end_time_datum_cd" %in% header.names) & "sample_end_dateTime" %in% names(readr.data)){
+        readr.data <- convertTZ(readr.data,"sample_start_time_datum_cd_reported","sample_end_dateTime",tz)
+        readr.data$sample_start_time_datum_cd_reported<- readr.data$sample_start_time_datum_cd_reported_reported 
+        readr.data$sample_start_time_datum_cd_reported_reported <- NULL 
+      }
+    }
+    
+  }
+  
+  names(readr.data)[names(readr.data) == "sample_dateTime"] <- "startDateTime"
+  names(readr.data)[names(readr.data) == "sample_end_dateTime"] <- "endDateTime"
   
-    row.names(data) <- NULL
+  if("site_no" %in% header.names){
+    if(class(readr.data$site_no) != "character"){
+      readr.data$site_no <- as.character(readr.data$site_no)
+    }
   }
   
-  names(data) <- make.names(names(data))
+  row.names(readr.data) <- NULL
+
+  names(readr.data) <- make.names(names(readr.data))
   
-  comment(data) <- hdr
-  attr(data, "url") <- obs_url
-  attr(data, "queryTime") <- Sys.time()
+  attr(readr.data, "url") <- obs_url
+  attr(readr.data, "queryTime") <- Sys.time()
   if(!file.exists(obs_url)){
-    attr(data, "header") <- attr(rawData, "header")
+    attr(readr.data, "header") <- attr(doc, "header")
   }
   
-  return(data)
+  return(readr.data)
   
+}
 
+convertTZ <- function(df, tz.name, date.time.cols, tz){
+  
+  offsetLibrary <- data.frame(offset=c(5, 4, 6, 5, 7, 6, 8, 7, 9, 8, 10, 10, 0, 0),
+                              code=c("EST","EDT","CST","CDT","MST","MDT","PST","PDT","AKST","AKDT","HAST","HST","", NA),
+                              stringsAsFactors = FALSE)
+  
+  offset <- left_join(df[,tz.name,drop=FALSE],offsetLibrary, by=setNames("code",tz.name))
+  offset <- offset$offset
+  df[,paste0(tz.name,"_reported")] <- df[,tz.name,drop=FALSE]
+  
+  df[,date.time.cols] <- df[,date.time.cols] + offset*60*60
+  df[,date.time.cols] <- as.POSIXct(df[,date.time.cols])
+  
+  if(tz != ""){
+    attr(df[,date.time.cols], "tzone") <- tz
+    df[,tz.name] <- tz
+  } else {
+    attr(df[,date.time.cols], "tzone") <- "UTC"
+    df[!is.na(df[,date.time.cols]),tz.name] <- "UTC"
+  }
+  
+  reported.col <- which(names(df) %in% paste0(tz.name,"_reported"))
+  orig.col <- which(names(df) %in% tz.name)
+  
+  new.order <- 1:ncol(df)
+  new.order[orig.col] <- reported.col
+  new.order[reported.col] <- orig.col
+  
+  df <- df[,new.order]
+  
+  return(df)
 }

R/importWQP.R

@@ -55,22 +55,24 @@ importWQP <- function(obs_url, zip=FALSE, tz=""){
     httpHEAD(obs_url, headerfunction = h$update)
     
     headerInfo <- h$value()
-    numToBeReturned <- as.numeric(headerInfo["Total-Result-Count"])
     
-    if(headerInfo['Total-Result-Count'] == "0"){
-      warning("No data returned")
-      return(data.frame())
-    }
-    
-    if(is.na(numToBeReturned) | numToBeReturned == 0){
-      for(i in grep("Warning",names(headerInfo))){
-        warning(headerInfo[i])
-      }
-      return(data.frame())
-    }
     
     if(headerInfo['status'] == "200"){
       
+      numToBeReturned <- as.numeric(headerInfo["Total-Result-Count"])
+      
+      if(headerInfo['Total-Result-Count'] == "0"){
+        warning("No data returned")
+        return(data.frame())
+      }
+      
+      if(is.na(numToBeReturned) | numToBeReturned == 0){
+        for(i in grep("Warning",names(headerInfo))){
+          warning(headerInfo[i])
+        }
+        return(data.frame())
+      }
+      
       if(zip){
         temp <- tempfile()
         options(timeout = 120)

R/readNWISdata.r

@@ -165,8 +165,7 @@ readNWISdata <- function(service="dv", ...){
   
   if(format == "rdb"){
     possibleError <- tryCatch({
-      retval <- importRDB1(urlCall, asDateTime = (service == "qwdata"), 
-                           qw = (service == "qwdata"), tz = tz)
+      retval <- importRDB1(urlCall, asDateTime = (service == "qwdata"), tz = tz)
     }, error = function(e) {
       stop(e, "with url:", urlCall)
     })
@@ -203,7 +202,6 @@ readNWISdata <- function(service="dv", ...){
         retval$tz_cd <- rep(tz, nrow(retval))
       }
     }
-    
   }
   
   return(retval)

R/readNWISpCode.r

@@ -26,7 +26,7 @@ readNWISpCode <- function(parameterCd){
  
   if(any(parameterCd == "all")){
     fullURL <- "http://nwis.waterdata.usgs.gov/nwis/pmcodes/pmcodes?radio_pm_search=param_group&pm_group=All+--+include+all+parameter+groups&format=rdb&show=parameter_group_nm&show=parameter_nm&show=casrn&show=srsname&show=parameter_units"
-    fullPcodeDownload <- importRDB1(fullURL)
+    fullPcodeDownload <- importRDB1(fullURL, asDateTime = FALSE)
     return(fullPcodeDownload)
     
   } else {

R/readNWISqw.r

@@ -131,8 +131,13 @@ readNWISqw <- function (siteNumbers,parameterCd,startDate="",endDate="",
                             endDate,"qw",expanded=expanded)    
   }
 
-  data <- importRDB1(url,asDateTime=TRUE, qw=TRUE, tz = tz)
-  originalHeader <- comment(data)
+  data <- importRDB1(url,asDateTime=TRUE, tz = tz)
+  
+  url <- attr(data, "url")
+  comment <- attr(data, "comment")
+  queryTime <- attr(data, "queryTime")
+  header <- attr(data, "header")
+
   parameterCd <- unique(data$parm_cd)
   
   if(reshape){
@@ -141,7 +146,8 @@ readNWISqw <- function (siteNumbers,parameterCd,startDate="",endDate="",
                          "sample_end_dt","sample_end_tm","sample_start_time_datum_cd","tm_datum_rlbty_cd",
                          "parm_cd","startDateTime","endDateTime","coll_ent_cd", "medium_cd","project_cd",
                          "aqfr_cd","tu_id","body_part_id", "hyd_cond_cd", "samp_type_cd",
-                         "hyd_event_cd","sample_lab_cm_tx","tz_cd","startDateTime","endDateTime")
+                         "hyd_event_cd","sample_lab_cm_tx","tz_cd","startDateTime","endDateTime",
+                         "sample_start_time_datum_cd_reported","sample_end_time_datum_cd_reported")
       measureCols <- names(data)[!(names(data) %in% columnsToMelt)]
       columnsToMelt <- names(data)[(names(data) %in% columnsToMelt)]
       dataWithPcodes <- data[data$parm_cd != "",]
@@ -156,7 +162,7 @@ readNWISqw <- function (siteNumbers,parameterCd,startDate="",endDate="",
       pCodesReturned <- unique(dataWithPcodes$parm_cd)
       groupByPCode <- as.vector(sapply(pCodesReturned, function(x) grep(x, names(wideDF)) ))
       data <- wideDF[,c(which(names(wideDF) %in% columnsToMelt),groupByPCode)]
-      comment(data) <- originalHeader
+
     } else {
       warning("Reshape can only be used with expanded data. Reshape request will be ignored.")
     }
@@ -172,8 +178,12 @@ readNWISqw <- function (siteNumbers,parameterCd,startDate="",endDate="",
   attr(data, "siteInfo") <- siteInfo
   attr(data, "variableInfo") <- varInfo
   attr(data, "statisticInfo") <- NULL
+  
   attr(data, "url") <- url
-  attr(data, "queryTime") <- Sys.time()
+  attr(data, "comment") <- comment
+  attr(data, "queryTime") <- queryTime
+  attr(data, "header") <- header
+  
   return (data)
 
 }

R/readNWISunit.r

@@ -123,13 +123,14 @@ readNWISuv <- function (siteNumbers,parameterCd,startDate="",endDate="", tz=""){
 #' siteNumbers <- c('01594440','040851325')
 #' \dontrun{
 #' data <- readNWISpeak(siteNumbers)
+#' data2 <- readNWISpeak(siteNumbers, asDateTime=FALSE)
 #' }
 readNWISpeak <- function (siteNumbers,startDate="",endDate="", asDateTime=TRUE){  
   
   # Doesn't seem to be a peak xml service
   url <- constructNWISURL(siteNumbers,NA,startDate,endDate,"peak")
   
-  data <- importRDB1(url, asDateTime=FALSE)
+  data <- importRDB1(url, asDateTime=asDateTime)
   
   if(nrow(data) > 0){
     if(asDateTime){
@@ -204,6 +205,11 @@ readNWISrating <- function (siteNumber,type="base"){
     
   data <- importRDB1(url, asDateTime=FALSE)
   
+  if("current_rating_nu" %in% names(data)){
+    intColumns <- intColumns[!("current_rating_nu" %in% names(data)[intColumns])]
+    data$current_rating_nu <- gsub(" ", "", data$current_rating_nu)
+  }
+  
   if(nrow(data) > 0){
     if(type == "base") {
       Rat <- grep("//RATING ", comment(data), value=TRUE, fixed=TRUE)
@@ -267,6 +273,7 @@ readNWISrating <- function (siteNumber,type="base"){
 #' siteNumbers <- c('01594440','040851325')
 #' \dontrun{
 #' data <- readNWISmeas(siteNumbers)
+#' Meas05316840 <- readNWISmeas("05316840")
 #' }
 readNWISmeas <- function (siteNumbers,startDate="",endDate="", tz=""){  
   
@@ -280,9 +287,31 @@ readNWISmeas <- function (siteNumbers,startDate="",endDate="", tz=""){
       data$diff_from_rating_pc <- as.numeric(data$diff_from_rating_pc)
     }
     
+    url <- attr(data, "url")
+    comment <- attr(data, "comment")
+    queryTime <- attr(data, "queryTime")
+    header <- attr(data, "header")
+    
+    data$measurement_dateTime <- data$measurement_dt
+    data$measurement_dt <- as.Date(data$measurement_dateTime)
+    data$measurement_tm <- strftime(data$measurement_dateTime, "%H:%M")
+    data$measurement_tm[is.na(data$tz_cd_reported)] <- ""
+    indexDT <- which("measurement_dt" == names(data))
+    indexTZ <- which("tz_cd" == names(data))
+    indexTM <- which("measurement_tm" == names(data))
+    indexTZrep <- which("tz_cd_reported" == names(data))
+    newOrder <- c(1:indexDT,indexTM,indexTZrep,c((indexDT+1):ncol(data))[!(c((indexDT+1):ncol(data)) %in% c(indexTZrep,indexTM))])
+
+    data <- data[,newOrder]
+
     siteInfo <- readNWISsite(siteNumbers)
     siteInfo <- left_join(unique(data[,c("agency_cd","site_no")]),siteInfo, by=c("agency_cd","site_no"))
     
+    attr(data, "url") <- url
+    attr(data, "comment") <- comment
+    attr(data, "queryTime") <- queryTime
+    attr(data, "header") <- header
+    
     attr(data, "siteInfo") <- siteInfo
     attr(data, "variableInfo") <- NULL
     attr(data, "statisticInfo") <- NULL    
@@ -342,7 +371,7 @@ readNWISmeas <- function (siteNumbers,startDate="",endDate="", tz=""){
 readNWISgwl <- function (siteNumbers,startDate="",endDate=""){  
   
   url <- constructNWISURL(siteNumbers,NA,startDate,endDate,"gwlevels",format="tsv")
-  data <- importRDB1(url,asDateTime=FALSE)
+  data <- importRDB1(url,asDateTime=TRUE)
 
   if(nrow(data) > 0){
     data$lev_dt <- as.Date(data$lev_dt)

R/renameColumns.R

@@ -45,6 +45,10 @@
 #' url2 <- constructNWISURL(siteWithTwo, "00060",startDate,endDate,'dv')
 #' twoResults <- importWaterML1(url2,TRUE)
 #' twoResults <- renameNWISColumns(twoResults)
+#' url2RDB <- constructNWISURL(siteWithTwo,"00060",
+#'          startDate,endDate,"dv",format="tsv")
+#' rdbResults <- importRDB1(url2RDB)
+#' rdbResults <- renameNWISColumns(rdbResults) 
 #' }
 renameNWISColumns <- function(rawData, p00010="Wtemp", p00045="Precip",
                           p00060="Flow", p00065="GH", p00095="SpecCond", p00300="DO",
@@ -78,7 +82,7 @@ renameNWISColumns <- function(rawData, p00010="Wtemp", p00045="Precip",
   Conv$s00023<- "HiLoTide"
   Conv$s00024<- "LoLoTide"
 
-  dataColumns <- grep("X_", Cnames)
+  dataColumns <- c(grep("X_", Cnames),grep("X\\d{2}", Cnames))
   
   for (i in dataColumns){
     chunks <- strsplit(Cnames[i], "_")[[1]]

man/importRDB1.Rd

@@ -4,16 +4,13 @@
 \alias{importRDB1}
 \title{Function to return data from the NWIS RDB 1.0 format}
 \usage{
-importRDB1(obs_url, asDateTime = FALSE, qw = FALSE, convertType = TRUE,
-  tz = "")
+importRDB1(obs_url, asDateTime = TRUE, convertType = TRUE, tz = "")
 }
 \arguments{
 \item{obs_url}{character containing the url for the retrieval or a file path to the data file.}
 
 \item{asDateTime}{logical, if \code{TRUE} returns date and time as POSIXct, if \code{FALSE}, Date}
 
-\item{qw}{logical, if \code{TRUE} parses as water quality data (where dates/times are in start and end times)}
-
 \item{convertType}{logical, defaults to \code{TRUE}. If \code{TRUE}, the function will convert the data to dates, datetimes,
 numerics based on a standard algorithm. If false, everything is returned as a character}
 
@@ -77,10 +74,10 @@ unitData <- importRDB1(unitDataURL, asDateTime=TRUE)
 qwURL <- constructNWISURL(c('04024430','04024000'),
           c('34247','30234','32104','34220'),
          "2010-11-03","","qw",format="rdb") 
-qwData <- importRDB1(qwURL, qw=TRUE, tz="America/Chicago")
+qwData <- importRDB1(qwURL, asDateTime=TRUE, tz="America/Chicago")
 iceSite <- '04024000'
-start <- "2014-11-09"
-end <- "2014-11-28"
+start <- "2015-11-09"
+end <- "2015-11-24"
 urlIce <- constructNWISURL(iceSite,"00060",start, end,"uv",format="tsv")
 ice <- importRDB1(urlIce, asDateTime=TRUE)
 iceNoConvert <- importRDB1(urlIce, convertType=FALSE)

man/readNWISmeas.Rd

@@ -54,6 +54,7 @@ See \url{http://waterdata.usgs.gov/usa/nwis/sw} for details about surface water.
 siteNumbers <- c('01594440','040851325')
 \dontrun{
 data <- readNWISmeas(siteNumbers)
+Meas05316840 <- readNWISmeas("05316840")
 }
 }
 \seealso{

man/readNWISpeak.Rd

@@ -57,6 +57,7 @@ to R Date objects.
 siteNumbers <- c('01594440','040851325')
 \dontrun{
 data <- readNWISpeak(siteNumbers)
+data2 <- readNWISpeak(siteNumbers, asDateTime=FALSE)
 }
 }
 \seealso{

man/renameNWISColumns.Rd

@@ -68,6 +68,10 @@ endDate <- "2012-10-01"
 url2 <- constructNWISURL(siteWithTwo, "00060",startDate,endDate,'dv')
 twoResults <- importWaterML1(url2,TRUE)
 twoResults <- renameNWISColumns(twoResults)
+url2RDB <- constructNWISURL(siteWithTwo,"00060",
+         startDate,endDate,"dv",format="tsv")
+rdbResults <- importRDB1(url2RDB)
+rdbResults <- renameNWISColumns(rdbResults) 
 }
 }
 \seealso{

tests/testthat/tests_imports.R

@@ -12,7 +12,7 @@ test_that("External importRDB1 tests", {
   obs_url <- constructNWISURL(siteNumber,property,
             startDate,endDate,"dv",format="tsv")
   data <- importRDB1(obs_url)
-  expect_is(data$datetime, 'character') 
+  expect_is(data$datetime, 'Date') 
   
   urlMultiPcodes <- constructNWISURL("04085427",c("00060","00010"),
           startDate,endDate,"dv",statCd=c("00003","00001"),"tsv")
@@ -32,7 +32,7 @@ test_that("External importRDB1 tests", {
   qwURL <- constructNWISURL(c('04024430','04024000'),
            c('34247','30234','32104','34220'),
           "2010-11-03","","qw",format="rdb") 
-  qwData <- importRDB1(qwURL, qw=TRUE, tz="America/Chicago")
+  qwData <- importRDB1(qwURL, tz="America/Chicago")
   expect_is(qwData$sample_dt, 'Date')
   expect_is(qwData$startDateTime, 'POSIXct')
   
@@ -56,7 +56,7 @@ test_that("CRAN-friendly importRDB test", {
   importUserRDB <- importRDB1(fullPath)
   
   # default is to turn dates to characters
-  expect_is(importUserRDB$datetime, 'character')
+  expect_is(importUserRDB$datetime, 'Date')
   
 })