diff --git a/DESCRIPTION b/DESCRIPTION
index 9785dc0aaeb0c19044c429ed14a822483c34d6bc..d02adb0a7f84b8a9822724e1c9fdf6800d81b26d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: dataRetrieval
Type: Package
Title: Retrieval functions for hydrologic data
-Version: 1.3.1
-Date: 2014-07-01
+Version: 1.3.2
+Date: 2014-08-04
Author: Robert M. Hirsch, Laura De Cicco
Maintainer: Laura De Cicco <ldecicco@usgs.gov>
Description: Collection of functions to help retrieve USGS data from either web
diff --git a/NAMESPACE b/NAMESPACE
index 8fd30ff5db340e868a1767a2ec21b17f8f5b8b00..7db39b0446d485d8c85d3fc366a0688ec9ba4ae2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -15,10 +15,8 @@ export(getDataFromFile)
export(getGeneralWQPData)
export(getMetaData)
export(getParameterInfo)
-export(getQWData)
export(getQWDataFromFile)
export(getRDB1Data)
-export(getRawQWData)
export(getSTORETSampleData)
export(getSampleData)
export(getSampleDataFromFile)
@@ -38,9 +36,10 @@ export(populateSiteINFO)
export(processQWData)
export(removeDuplicates)
export(renameColumns)
-export(retrieveNWISData)
+export(retrieveNWISdvData)
export(retrieveNWISqwData)
-export(retrieveUnitNWISData)
+export(retrieveNWISunitData)
+export(retrieveWQPqwData)
import(RCurl)
import(XML)
import(reshape2)
diff --git a/NEWS b/NEWS
index 20ef1f46e5e43500c03b4247a8621209b93ef533..0c14291543e686b98068355715149c5b7b2c0a74 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,11 @@
+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
+
+
dataRetrieval 1.2.2
===========
diff --git a/R/constructNWISURL.r b/R/constructNWISURL.r
index 2aaf71a40aa615a5149538863b84acef890ada8a..88083fdd77f0a8cf7fa013a72b60cf8cd225eb49 100644
--- a/R/constructNWISURL.r
+++ b/R/constructNWISURL.r
@@ -27,7 +27,7 @@
#' url_unit <- constructNWISURL(siteNumber,pCode,"2012-06-28","2012-06-30",'iv')
#' url_qw_single <- constructNWISURL(siteNumber,"01075",startDate,endDate,'qw')
#' url_qw <- constructNWISURL(siteNumber,c('01075','00029','00453'),startDate,endDate,'qw')
-#' url_wqp <- constructNWISURL(siteNumber,c('01075','00029','00453'),startDate,endDate,'wqp')
+#' url_wqp <- constructNWISURL(paste("USGS",siteNumber,sep="-"),c('01075','00029','00453'),startDate,endDate,'wqp')
#' url_daily_tsv <- constructNWISURL(siteNumber,pCode,startDate,endDate,'dv',statCd=c("00003","00001"),format="tsv")
constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,statCd="00003", format="xml",expanded=FALSE,interactive=TRUE){
@@ -87,6 +87,14 @@ constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,st
wqp = {
siteNumber <- formatCheckSiteNumber(siteNumber, interactive=interactive)
+ #Check for pcode:
+ if(all(nchar(parameterCd) == 5)){
+ suppressWarnings(pCodeLogic <- all(!is.na(as.numeric(parameterCd))))
+ } else {
+ pCodeLogic <- FALSE
+ parameterCd <- URLencode(parameterCd)
+ }
+
if(length(parameterCd)>1){
parameterCd <- paste(parameterCd, collapse=";")
}
@@ -98,10 +106,10 @@ constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,st
endDate <- format(as.Date(endDate), format="%m-%d-%Y")
}
- baseURL <- "http://www.waterqualitydata.us/Result/search?siteid=USGS-"
+ baseURL <- "http://www.waterqualitydata.us/Result/search?siteid="
url <- paste(baseURL,
siteNumber,
- "&pCode=",
+ ifelse(pCodeLogic,"&pCode=","&characteristicName="),
parameterCd,
"&startDateLo=",
startDate,
diff --git a/R/getDVData.r b/R/getDVData.r
index d98ee3b176440d1a65d697cd718421e9dd216e82..a35374be178a609e1812c6692bc1b52294d6e161 100644
--- a/R/getDVData.r
+++ b/R/getDVData.r
@@ -18,14 +18,14 @@
#' @keywords data import USGS WRTDS
#' @export
#' @return Daily dataframe
-#' @seealso \code{\link{retrieveNWISData}}, \code{\link{populateDaily}}
+#' @seealso \code{\link{retrieveNWISdvData}}, \code{\link{populateDaily}}
#' @examples
#' # These examples require an internet connection to run
#' Daily <- getDVData('01594440','00060', '1985-01-01', '1985-03-31')
#' DailyCFS <- getDVData('01594440','00060', '1985-01-01', '1985-03-31',convert=FALSE)
#' DailySuspSediment <- getDVData('01594440','80154', '1985-01-01', '1985-03-31')
getDVData <- function (siteNumber,ParameterCd,StartDate,EndDate,interactive=TRUE,convert=TRUE,format="tsv"){
- data <- retrieveNWISData(siteNumber,ParameterCd,StartDate,EndDate,interactive=interactive,format=format)
+ data <- retrieveNWISdvData(siteNumber,ParameterCd,StartDate,EndDate,interactive=interactive,format=format)
# need to setup conversion factor because the NWIS data are in cfs but we store in cms
names(data) <- c('agency', 'site', 'dateTime', 'value', 'code') # do a merge instead?
diff --git a/R/getQWData.r b/R/getQWData.r
deleted file mode 100644
index 28903c4bdd66f26ea5690dab94983af96a20fcf2..0000000000000000000000000000000000000000
--- a/R/getQWData.r
+++ /dev/null
@@ -1,25 +0,0 @@
-#' Data Import for USGS NWIS Water Quality Data
-#'
-#' Imports and processes data from NWIS web service. This function gets the data from here: \url{http://www.waterqualitydata.us}
-#' A list of parameter codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes/}
-#' A list of statistic codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
-#'
-#' @param siteNumber string USGS site number. This is usually an 8 digit number
-#' @param ParameterCd string USGS parameter code. This is usually an 5 digit number. Multiple parameter codes can be inputted with a ';' separator. Leaving this blank will return all of the measured values during the specified time period.
-#' @param StartDate string starting date for data retrieval in the form YYYY-MM-DD.
-#' @param EndDate string ending date for data retrieval in the form YYYY-MM-DD.
-#' @param interactive logical Option for interactive mode. If true, there is user interaction for error handling and data checks.
-#' @keywords data import USGS web service
-#' @return retval dataframe with first column dateTime, and at least one qualifier and value columns
-#' (subsequent qualifier/value columns could follow depending on requested parameter codes)
-#' @export
-#' @examples
-#' # These examples require an internet connection to run
-#' rawProcessedSample <- getQWData('01594440','01075', '1985-01-01', '1985-03-31')
-#' rawProcessedSampleAll <- getQWData('05114000','', '1985-01-01', '1985-03-31')
-#' rawProcessedSampleSelect <- getQWData('05114000','00915;00931', '1985-01-01', '1985-04-30')
-getQWData <- function(siteNumber,ParameterCd,StartDate,EndDate,interactive=TRUE){
- rawSample <- getRawQWData(siteNumber,ParameterCd,StartDate,EndDate,interactive)
- retval <- processQWData(rawSample)
- return(retval)
-}
diff --git a/R/getRawQWData.r b/R/getRawQWData.r
index ff4eb5859fbd2bc1593878288d0e24a3bfa0bc2b..393f558812c32cdebf8976568b1c1203245ef5d3 100644
--- a/R/getRawQWData.r
+++ b/R/getRawQWData.r
@@ -16,20 +16,25 @@
#' @import RCurl
#' @examples
#' # These examples require an internet connection to run
-#' rawSample <- getRawQWData('01594440','01075', '1985-01-01', '1985-03-31')
-#' rawSampleAll <- getRawQWData('05114000','', '1985-01-01', '1985-03-31')
-#' rawSampleSelect <- getRawQWData('05114000',c('00915','00931'), '1985-01-01', '1985-04-30')
-getRawQWData <- function(siteNumber,ParameterCd,StartDate,EndDate,interactive=TRUE){
+#' rawSample <- retrieveWQPqwData('USGS-01594440','01075', '1985-01-01', '1985-03-31')
+#' rawSampleAll <- retrieveWQPqwData('USGS-05114000','', '1985-01-01', '1985-03-31')
+#' rawSampleSelect <- retrieveWQPqwData('USGS-05114000',c('00915','00931'), '1985-01-01', '1985-04-30')
+#' rawStoret <- retrieveWQPqwData('WIDNR_WQX-10032762','Specific conductance', '', '')
+retrieveWQPqwData <- function(siteNumber,ParameterCd,StartDate,EndDate,interactive=TRUE){
url <- constructNWISURL(siteNumber,ParameterCd,StartDate,EndDate,"wqp",interactive=interactive)
-# require(RCurl)
+
h <- basicHeaderGatherer()
doc <- getURI(url, headerfunction = h$update)
numToBeReturned <- as.numeric(h$value()["Total-Result-Count"])
- suppressWarnings(retval <- read.delim(url, header = TRUE, quote="\"", dec=".", sep='\t', colClasses=c('character'), fill = TRUE))
- actualNumReturned <- nrow(retval)
-
- if(actualNumReturned != numToBeReturned) warning(numToBeReturned, " sample results were expected, ", actualNumReturned, " were returned")
-
- return(retval)
+ if (!is.na(numToBeReturned) | numToBeReturned != 0){
+ suppressWarnings(retval <- read.delim(url, header = TRUE, quote="\"", dec=".", sep='\t', colClasses=c('character'), fill = TRUE))
+ actualNumReturned <- nrow(retval)
+
+ if(actualNumReturned != numToBeReturned) warning(numToBeReturned, " sample results were expected, ", actualNumReturned, " were returned")
+
+ return(retval)
+ } else {
+ warning("No data to retrieve")
+ }
}
diff --git a/R/getSTORETSampleData.R b/R/getSTORETSampleData.R
index 0029d140391939a768e0cc7296636fdb2df764de..ceab291367220853aed8d11bbddd6b8a6db18269 100644
--- a/R/getSTORETSampleData.R
+++ b/R/getSTORETSampleData.R
@@ -1,10 +1,8 @@
#' Import Sample Data for WRTDS
#'
-#' Imports data from NWIS web service. This function gets the data from here: \url{http://qwwebservices.usgs.gov/}
-#' A list of parameter codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes/}
-#' A list of statistic codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
-#' For raw data, use getQWData. This function will retrieve the raw data, and compress it (summing constituents). See
-#' chapter 7 of the EGRET user guide for more details.
+#' Imports data from the Water Quality Portal. This function gets the data from: \url{http://www.waterqualitydata.us}
+#' For raw data, use getWQPData. This function will retrieve the raw data, and compress it (summing constituents). See
+#' chapter 7 of the EGRET user guide for more details, then converts it to the Sample dataframe structure.
#'
#' @param siteNumber string site number. If USGS, it should be in the form :'USGS-XXXXXXXXX...'
#' @param characteristicName string
diff --git a/R/getWQPData.r b/R/getWQPData.r
index 582ebeea9f525d278f33e992c7833482beac09ae..80a836e5160252d884705bff7254c2c28a6307a4 100644
--- a/R/getWQPData.r
+++ b/R/getWQPData.r
@@ -1,8 +1,8 @@
#' Data Import from Water Quality Portal
#'
-#' Imports data from Water Quality Portal web service. This function gets the data from here: \url{http://www.waterqualitydata.us}. This function is more general than getQWData
+#' Imports data from Water Quality Portal web service. This function gets the data from: \url{http://www.waterqualitydata.us}. This function is more general than getQWData
#' because it allows for other agencies rather than the USGS. Therefore, the 5-digit parameter code cannot be used.
-#' Instead, this function uses characteristicName. A complete list can be found here \url{http://www.waterqualitydata.us/Codes/Characteristicname}
+#' Instead, this function uses characteristicName. A complete list can be found here
#'
#' @param siteNumber string site number. If USGS, it should be in the form :'USGS-XXXXXXXXX...'
#' @param characteristicName string
@@ -16,77 +16,30 @@
#' @import RCurl
#' @examples
#' # These examples require an internet connection to run
-#' getWQPData('USGS-01594440','Chloride', '', '')
-#' getWQPData('WIDNR_WQX-10032762','Specific conductance', '', '')
+#' Chloride <- getWQPData('USGS-01594440','Chloride', '', '')
+#' SC <- getWQPData('WIDNR_WQX-10032762','Specific conductance', '', '')
+#' NWIS_Cl <- getWQPData('USGS-04024000','30234', '', '')
+#' MultipleQW <- getWQPData('USGS-04024000',c('30234','90095'), '', '')
getWQPData <- function(siteNumber,characteristicName,StartDate,EndDate,interactive=TRUE){
-
-# require(RCurl)
-
- StartDate <- formatCheckDate(StartDate, "StartDate", interactive=interactive)
- EndDate <- formatCheckDate(EndDate, "EndDate", interactive=interactive)
- dateReturn <- checkStartEndDate(StartDate, EndDate, interactive=interactive)
- StartDate <- dateReturn[1]
- EndDate <- dateReturn[2]
-
- if (nzchar(StartDate)){
- StartDate <- format(as.Date(StartDate), format="%m-%d-%Y")
- }
- if (nzchar(EndDate)){
- EndDate <- format(as.Date(EndDate), format="%m-%d-%Y")
+ retval <- retrieveWQPqwData(siteNumber=siteNumber,
+ ParameterCd=characteristicName,
+ StartDate=StartDate,
+ EndDate=EndDate,
+ interactive=interactive)
+ #Check for pcode:
+ if(all(nchar(characteristicName) == 5)){
+ suppressWarnings(pCodeLogic <- all(!is.na(as.numeric(characteristicName))))
+ } else {
+ pCodeLogic <- FALSE
}
-
- characteristicName <- URLencode(characteristicName)
-
- baseURL <- "http://www.waterqualitydata.us/Result/search?siteid="
- url <- paste(baseURL,
- siteNumber,
- "&characteristicName=",
- characteristicName, # to get multi-parameters, use a semicolen
- "&startDateLo=",
- StartDate,
- "&startDateHi=",
- EndDate,
- "&countrycode=US&mimeType=tsv",sep = "")
- h <- basicHeaderGatherer()
- doc <- getURI(url, headerfunction = h$update)
- numToBeReturned <- as.numeric(h$value()["Total-Result-Count"])
-
- suppressWarnings(retval <- read.delim(url, header = TRUE, quote="\"", dec=".", sep='\t', colClasses=c('character'), fill = TRUE))
-
- qualifier <- ifelse((retval$ResultDetectionConditionText == "Not Detected" |
- retval$ResultDetectionConditionText == "Detected Not Quantified" |
- retval$ResultMeasureValue < retval$DetectionQuantitationLimitMeasure.MeasureValue),"<","")
-
- correctedData<-ifelse((nchar(qualifier)==0),retval$ResultMeasureValue,retval$DetectionQuantitationLimitMeasure.MeasureValue)
- test <- data.frame(retval$CharacteristicName)
-
- # test$dateTime <- as.POSIXct(strptime(paste(retval$ActivityStartDate,retval$ActivityStartTime.Time,sep=" "), "%Y-%m-%d %H:%M:%S"))
- test$dateTime <- as.Date(retval$ActivityStartDate, "%Y-%m-%d")
-
- originalLength <- nrow(test)
-
- if (!is.na(numToBeReturned)){
- if(originalLength != numToBeReturned) warning(numToBeReturned, " sample results were expected, ", originalLength, " were returned")
-
- test$qualifier <- qualifier
- test$value <- as.numeric(correctedData)
-
- test <- test[!is.na(test$dateTime),]
- newLength <- nrow(test)
- if (originalLength != newLength){
- numberRemoved <- originalLength - newLength
- warningMessage <- paste(numberRemoved, " rows removed because no date was specified", sep="")
- warning(warningMessage)
- }
-
- colnames(test)<- c("CharacteristicName","dateTime","qualifier","value")
- data <- reshape(test, idvar="dateTime", timevar = "CharacteristicName", direction="wide")
- data$dateTime <- format(data$dateTime, "%Y-%m-%d")
- data$dateTime <- as.Date(data$dateTime)
- return(data)
+
+ if(nrow(retval) > 0){
+ data <- processQWData(retval,pCodeLogic)
} else {
- warning("No data retrieved")
+ data <- NULL
}
+ return(data)
+
}
diff --git a/R/getWQPSites.R b/R/getWQPSites.R
index 190df9a2941ce9b1c3853aa0630d866db0cb1c37..73c9e7d75a79796a1593f5511441b1ff9d0b32dc 100644
--- a/R/getWQPSites.R
+++ b/R/getWQPSites.R
@@ -1,8 +1,7 @@
-#' Site DAta Import from Water Quality Portal
+#' Site Data Import from Water Quality Portal
#'
-#' Imports site data from Water Quality Portal web service. This function gets the data from here: \url{http://www.waterqualitydata.us}. This function is more general than getQWData
-#' because it allows for other agencies rather than the USGS. Therefore, the 5-digit parameter code cannot be used.
-#' Instead, this function uses characteristicName. A complete list can be found here \url{http://www.waterqualitydata.us/Codes/Characteristicname}
+#' Returns a list of sites from the Water Quality Portal web service. This function gets the data from: \url{http://www.waterqualitydata.us}.
+#' Arguments to the function should be based on \url{www.waterqualitydata.us/webservices_documentation.jsp}
#'
#' @param \dots see \url{www.waterqualitydata.us/webservices_documentation.jsp} for a complete list of options
#' @keywords data import WQP web service
diff --git a/R/getWaterML1Data.r b/R/getWaterML1Data.r
index 774f65b10701bf2e22c27377b4b1ddd89c3151be..0957c42fae272ef2b8c7092029a14b36ea9b48ed 100644
--- a/R/getWaterML1Data.r
+++ b/R/getWaterML1Data.r
@@ -17,6 +17,8 @@
#' data <- getWaterML1Data(obs_url)
#' urlMulti <- constructNWISURL("04085427",c("00060","00010"),startDate,endDate,'dv',statCd=c("00003","00001"))
#' multiData <- getWaterML1Data(urlMulti)
+#' goundwaterExampleURL <- "http://waterservices.usgs.gov/nwis/gwlevels/?format=waterml&sites=431049071324301&startDT=2013-10-01&endDT=2014-06-30"
+#' groundWater <- getWaterML1Data(goundwaterExampleURL)
getWaterML1Data <- function(obs_url){
# This is more elegent, but requires yet another package dependency RCurl...which I now require for wqp
@@ -80,12 +82,20 @@ getWaterML1Data <- function(obs_url){
assign(valueName,value)
assign(qualName,qualifier)
- df <- data.frame(dateTime,
- tzAbbriev,
- get(valueName),
- get(qualName)
- )
- names(df) <- c("dateTime","tz_cd",valueName,qualName)
+ if(length(get(qualName))!=0){
+ df <- data.frame(dateTime,
+ tzAbbriev,
+ get(valueName),
+ get(qualName)
+ )
+ names(df) <- c("dateTime","tz_cd",valueName,qualName)
+ } else {
+ df <- data.frame(dateTime,
+ tzAbbriev,
+ get(valueName)
+ )
+ names(df) <- c("dateTime","tz_cd",valueName)
+ }
if (1 == i & valuesIndex[1] == j){
mergedDF <- df
diff --git a/R/populateDaily.r b/R/populateDaily.r
index 9a3d4fff015081f450dc8726a9c67048649434f6..2ec2d3ed66d39e59db1361729859076842e20ff2 100644
--- a/R/populateDaily.r
+++ b/R/populateDaily.r
@@ -51,14 +51,9 @@ populateDaily <- function(rawData,qConvert,interactive=TRUE){ # rawData is a da
qshift<- 0.001*mean(localDaily$Q, na.rm=TRUE)
if (interactive){
- negNums <- length(which(localDaily$Q<0))
- zeroNums <- length(which(localDaily$Q == 0))
-
- if (negNums > 0) {
- cat("There were", as.character(negNums), "negative flow days \n")
- cat("Negative values are not supported in the EGRET package\n")
- }
+ zeroNums <- length(which(localDaily$Q == 0))
+
if (zeroNums > 0){
cat("There were", as.character(zeroNums), "zero flow days \n")
}
@@ -70,6 +65,11 @@ populateDaily <- function(rawData,qConvert,interactive=TRUE){ # rawData is a da
qshift<-0.0
}
+ negNums <- length(which(localDaily$Q<0))
+ if (negNums > 0) {
+ cat("There were", as.character(negNums), "negative flow days \n")
+ cat("Negative values are not supported in the EGRET package\n")
+ }
localDaily$Q<-localDaily$Q+qshift
@@ -94,7 +94,20 @@ populateDaily <- function(rawData,qConvert,interactive=TRUE){ # rawData is a da
#these next two lines show the user where the gaps in the data are if there are any
n<-nrow(localDaily)
- for(i in 2:n) {if((localDaily$Julian[i]-localDaily$Julian[i-1])>1) cat("\n discharge data jumps from",as.character(localDaily$Date[i-1]),"to",as.character(localDaily$Date[i]))}
+ for(i in 2:n) {
+ if((localDaily$Julian[i]-localDaily$Julian[i-1])>1) cat("\n discharge data jumps from",as.character(localDaily$Date[i-1]),"to",as.character(localDaily$Date[i]))
+ }
+
+ numNAs <- sum(is.na(localDaily$Q))
+ if(numNAs > 0){
+ cat(numNAs, "discharge measurements are not reported (NA's). \nMany of the EGRET functions will not work with missing discharge measurements.")
+ if (localDaily$Julian[max(which(is.na(localDaily$Q)),na.rm = TRUE)]-
+ localDaily$Julian[min(which(is.na(localDaily$Q)),na.rm = TRUE)]+1 == numNAs){
+ cat("\nNA gap is from",as.character(localDaily$Date[min(which(is.na(localDaily$Q)),na.rm = TRUE)]),"to",
+ as.character(localDaily$Date[max(which(is.na(localDaily$Q)),na.rm = TRUE)]))
+ }
+ }
+
}
return (localDaily)
diff --git a/R/processQWData.r b/R/processQWData.r
index 1bf93416818372b9f8aa61e4f041d9be9d96fee1..2779b108d6647559f381bab592affd327e030d01 100644
--- a/R/processQWData.r
+++ b/R/processQWData.r
@@ -4,16 +4,17 @@
#' conditions to determine if a value is left censored or not. Censored values are given the qualifier
#' "<". The dataframe is also converted from a long to wide format.
#'
-#' @param data dataframe from
+#' @param data dataframe from Water Quality Portal
+#' @param pCode logical if TRUE, assume data came from a pCode search, if FALSE, characteristic name.
#' @keywords data import USGS web service
#' @return data dataframe with first column dateTime, and at least one qualifier and value columns
#' (subsequent qualifier/value columns could follow depending on the number of parameter codes)
#' @export
#' @examples
#' # These examples require an internet connection to run
-#' rawSample <- getRawQWData('01594440','01075', '1985-01-01', '1985-03-31')
+#' rawSample <- retrieveWQPqwData('USGS-01594440','01075', '1985-01-01', '1985-03-31')
#' rawSampleSelect <- processQWData(rawSample)
-processQWData <- function(data){
+processQWData <- function(data,pCode=TRUE){
qualifier <- ifelse((data$ResultDetectionConditionText == "Not Detected" |
data$ResultDetectionConditionText == "Detected Not Quantified" |
@@ -37,8 +38,15 @@ processQWData <- function(data){
warning(warningMessage)
}
- colnames(test)<- c("USGSPCode","dateTime","qualifier","value")
- data <- suppressWarnings(reshape(test, idvar="dateTime", timevar = "USGSPCode", direction="wide"))
+ if (pCode){
+ colnames(test)<- c("USGSPCode","dateTime","qualifier","value")
+ newTimeVar <- "USGSPCode"
+ } else {
+ colnames(test)<- c("CharacteristicName","dateTime","qualifier","value")
+ newTimeVar <- "CharacteristicName"
+ }
+
+ data <- suppressWarnings(reshape(test, idvar="dateTime", timevar = newTimeVar, direction="wide"))
data$dateTime <- format(data$dateTime, "%Y-%m-%d")
data$dateTime <- as.Date(data$dateTime)
return(data)
diff --git a/R/renameColumns.R b/R/renameColumns.R
index fe4bb30e384b4d268871c94763a13425d0c3c5c5..e8414376e334b6af02b1235ee7a3e03e77c67ba7 100644
--- a/R/renameColumns.R
+++ b/R/renameColumns.R
@@ -9,10 +9,10 @@
#' @examples
#' # This example requires an internet connection to run
#' siteNumber <- '05114000'
-#' rawData <- retrieveNWISData(siteNumber,c("00010","00060","00300"),"2001-01-01","2002-01-01",StatCd=c("00001","00003"))
+#' rawData <- retrieveNWISdvData(siteNumber,c("00010","00060","00300"),"2001-01-01","2002-01-01",StatCd=c("00001","00003"))
#' rawData <- renameColumns(rawData)
#' today <- as.character(Sys.Date())
-#' rawData2 <- retrieveUnitNWISData(siteNumber,c("00010","00060"),today,today)
+#' rawData2 <- retrieveNWISunitData(siteNumber,c("00010","00060"),today,today)
#' rawData2 <- renameColumns(rawData2)
renameColumns <- function(rawData){
diff --git a/R/retrieveNWISData.r b/R/retrieveNWISData.r
index 5835f762dc488f8512d04663e5e5b92c779fd324..b003fd98fb385c6a14c3095a577b60027f14738a 100644
--- a/R/retrieveNWISData.r
+++ b/R/retrieveNWISData.r
@@ -22,11 +22,11 @@
#' startDate <- '2012-01-01'
#' endDate <- '2012-06-30'
#' pCode <- '00060'
-#' rawDailyQ <- retrieveNWISData(siteNumber,pCode, startDate, endDate)
-#' rawDailyTemperature <- retrieveNWISData(siteNumber,'00010', startDate, endDate, StatCd='00001')
-#' rawDailyTemperatureTSV <- retrieveNWISData(siteNumber,'00010', startDate, endDate, StatCd='00001',format='tsv')
-#' rawDailyQAndTempMeanMax <- retrieveNWISData(siteNumber,c('00010','00060'), startDate, endDate, StatCd=c('00001','00003'))
-retrieveNWISData <- function (siteNumber,ParameterCd,StartDate,EndDate,StatCd="00003",format="tsv",interactive=TRUE){
+#' rawDailyQ <- retrieveNWISdvData(siteNumber,pCode, startDate, endDate)
+#' rawDailyTemperature <- retrieveNWISdvData(siteNumber,'00010', startDate, endDate, StatCd='00001')
+#' rawDailyTemperatureTSV <- retrieveNWISdvData(siteNumber,'00010', startDate, endDate, StatCd='00001',format='tsv')
+#' rawDailyQAndTempMeanMax <- retrieveNWISdvData(siteNumber,c('00010','00060'), startDate, endDate, StatCd=c('00001','00003'))
+retrieveNWISdvData <- function (siteNumber,ParameterCd,StartDate,EndDate,StatCd="00003",format="tsv",interactive=TRUE){
url <- constructNWISURL(siteNumber,ParameterCd,StartDate,EndDate,"dv",statCd=StatCd,format=format,interactive=interactive)
diff --git a/R/retrieveUnitNWISData.r b/R/retrieveUnitNWISData.r
index aa9102675ee7b55ae26c4b33d960e676c71e3a72..1e2d5bd6fe1e7d10b9f53b9fa17001a2728f6333 100644
--- a/R/retrieveUnitNWISData.r
+++ b/R/retrieveUnitNWISData.r
@@ -21,9 +21,9 @@
#' StartDate <- as.character(Sys.Date())
#' EndDate <- as.character(Sys.Date())
#' # These examples require an internet connection to run
-#' rawData <- retrieveUnitNWISData(siteNumber,ParameterCd,StartDate,EndDate)
-#' rawData2 <- retrieveUnitNWISData(siteNumber,ParameterCd,StartDate,EndDate,"tsv")
-retrieveUnitNWISData <- function (siteNumber,ParameterCd,StartDate,EndDate,format="xml",interactive=TRUE){
+#' rawData <- retrieveNWISunitData(siteNumber,ParameterCd,StartDate,EndDate)
+#' rawData2 <- retrieveNWISunitData(siteNumber,ParameterCd,StartDate,EndDate,"tsv")
+retrieveNWISunitData <- function (siteNumber,ParameterCd,StartDate,EndDate,format="xml",interactive=TRUE){
url <- constructNWISURL(siteNumber,ParameterCd,StartDate,EndDate,"uv",format=format,interactive=interactive)
if (format == "xml") {
diff --git a/man/constructNWISURL.Rd b/man/constructNWISURL.Rd
index 0bc40a932b05a06b2ad1c82e1b9c95fa099ac4c7..e74348de283bed3ec9f1ee9963543a2254a4b1c5 100644
--- a/man/constructNWISURL.Rd
+++ b/man/constructNWISURL.Rd
@@ -45,7 +45,7 @@ url_daily <- constructNWISURL(siteNumber,pCode,startDate,endDate,'dv',statCd=c("
url_unit <- constructNWISURL(siteNumber,pCode,"2012-06-28","2012-06-30",'iv')
url_qw_single <- constructNWISURL(siteNumber,"01075",startDate,endDate,'qw')
url_qw <- constructNWISURL(siteNumber,c('01075','00029','00453'),startDate,endDate,'qw')
-url_wqp <- constructNWISURL(siteNumber,c('01075','00029','00453'),startDate,endDate,'wqp')
+url_wqp <- constructNWISURL(paste("USGS",siteNumber,sep="-"),c('01075','00029','00453'),startDate,endDate,'wqp')
url_daily_tsv <- constructNWISURL(siteNumber,pCode,startDate,endDate,'dv',statCd=c("00003","00001"),format="tsv")
}
\keyword{USGS}
diff --git a/man/getDVData.Rd b/man/getDVData.Rd
index 64b881747ac7d629e10488fe2dd4db48316a4db5..be9af2d0fbb161528468db6f608811ae76c5795e 100644
--- a/man/getDVData.Rd
+++ b/man/getDVData.Rd
@@ -40,7 +40,7 @@ DailyCFS <- getDVData('01594440','00060', '1985-01-01', '1985-03-31',convert=FAL
DailySuspSediment <- getDVData('01594440','80154', '1985-01-01', '1985-03-31')
}
\seealso{
-\code{\link{retrieveNWISData}}, \code{\link{populateDaily}}
+\code{\link{retrieveNWISdvData}}, \code{\link{populateDaily}}
}
\keyword{USGS}
\keyword{WRTDS}
diff --git a/man/getQWData.Rd b/man/getQWData.Rd
deleted file mode 100644
index 5a2c876c2717411b7e06ab296dffdc3e1b4aeb28..0000000000000000000000000000000000000000
--- a/man/getQWData.Rd
+++ /dev/null
@@ -1,39 +0,0 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
-\name{getQWData}
-\alias{getQWData}
-\title{Data Import for USGS NWIS Water Quality Data}
-\usage{
-getQWData(siteNumber, ParameterCd, StartDate, EndDate, interactive = TRUE)
-}
-\arguments{
-\item{siteNumber}{string USGS site number. This is usually an 8 digit number}
-
-\item{ParameterCd}{string USGS parameter code. This is usually an 5 digit number. Multiple parameter codes can be inputted with a ';' separator. Leaving this blank will return all of the measured values during the specified time period.}
-
-\item{StartDate}{string starting date for data retrieval in the form YYYY-MM-DD.}
-
-\item{EndDate}{string ending date for data retrieval in the form YYYY-MM-DD.}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-retval dataframe with first column dateTime, and at least one qualifier and value columns
-(subsequent qualifier/value columns could follow depending on requested parameter codes)
-}
-\description{
-Imports and processes data from NWIS web service. This function gets the data from here: \url{http://www.waterqualitydata.us}
-A list of parameter codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes/}
-A list of statistic codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
-}
-\examples{
-# These examples require an internet connection to run
-rawProcessedSample <- getQWData('01594440','01075', '1985-01-01', '1985-03-31')
-rawProcessedSampleAll <- getQWData('05114000','', '1985-01-01', '1985-03-31')
-rawProcessedSampleSelect <- getQWData('05114000','00915;00931', '1985-01-01', '1985-04-30')
-}
-\keyword{USGS}
-\keyword{data}
-\keyword{import}
-\keyword{service}
-\keyword{web}
-
diff --git a/man/getSTORETSampleData.Rd b/man/getSTORETSampleData.Rd
index ffd7fca433d95bfaf7a65e9fa699b3146c8c0583..0029feac94ac2e9740d17130799ac703a0edcf04 100644
--- a/man/getSTORETSampleData.Rd
+++ b/man/getSTORETSampleData.Rd
@@ -21,11 +21,9 @@ getSTORETSampleData(siteNumber, characteristicName, StartDate, EndDate,
Sample dataframe
}
\description{
-Imports data from NWIS web service. This function gets the data from here: \url{http://qwwebservices.usgs.gov/}
-A list of parameter codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes/}
-A list of statistic codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
-For raw data, use getQWData. This function will retrieve the raw data, and compress it (summing constituents). See
-chapter 7 of the EGRET user guide for more details.
+Imports data from the Water Quality Portal. This function gets the data from: \url{http://www.waterqualitydata.us}
+For raw data, use getWQPData. This function will retrieve the raw data, and compress it (summing constituents). See
+chapter 7 of the EGRET user guide for more details, then converts it to the Sample dataframe structure.
}
\examples{
# These examples require an internet connection to run
diff --git a/man/getWQPData.Rd b/man/getWQPData.Rd
index 425540f4ac547b4d06f0e40a634ac5313cf53be0..29efdc5fa33ff9a7098e2c9634b27fd4f92ba24e 100644
--- a/man/getWQPData.Rd
+++ b/man/getWQPData.Rd
@@ -22,14 +22,16 @@ retval dataframe with first column dateTime, and at least one qualifier and valu
(subsequent qualifier/value columns could follow depending on requested parameter codes)
}
\description{
-Imports data from Water Quality Portal web service. This function gets the data from here: \url{http://www.waterqualitydata.us}. This function is more general than getQWData
+Imports data from Water Quality Portal web service. This function gets the data from: \url{http://www.waterqualitydata.us}. This function is more general than getQWData
because it allows for other agencies rather than the USGS. Therefore, the 5-digit parameter code cannot be used.
-Instead, this function uses characteristicName. A complete list can be found here \url{http://www.waterqualitydata.us/Codes/Characteristicname}
+Instead, this function uses characteristicName. A complete list can be found here
}
\examples{
# These examples require an internet connection to run
-getWQPData('USGS-01594440','Chloride', '', '')
-getWQPData('WIDNR_WQX-10032762','Specific conductance', '', '')
+Chloride <- getWQPData('USGS-01594440','Chloride', '', '')
+SC <- getWQPData('WIDNR_WQX-10032762','Specific conductance', '', '')
+NWIS_Cl <- getWQPData('USGS-04024000','30234', '', '')
+MultipleQW <- getWQPData('USGS-04024000',c('30234','90095'), '', '')
}
\keyword{WQP}
\keyword{data}
diff --git a/man/getWQPSites.Rd b/man/getWQPSites.Rd
index 8949272c182ccc1be70c8b5c42ce149aef1f9c56..357c1f731bac22c2f15e9fe32909edef2c6430fb 100644
--- a/man/getWQPSites.Rd
+++ b/man/getWQPSites.Rd
@@ -1,7 +1,7 @@
% Generated by roxygen2 (4.0.1): do not edit by hand
\name{getWQPSites}
\alias{getWQPSites}
-\title{Site DAta Import from Water Quality Portal}
+\title{Site Data Import from Water Quality Portal}
\usage{
getWQPSites(...)
}
@@ -13,9 +13,8 @@ retval dataframe with first column dateTime, and at least one qualifier and valu
(subsequent qualifier/value columns could follow depending on requested parameter codes)
}
\description{
-Imports site data from Water Quality Portal web service. This function gets the data from here: \url{http://www.waterqualitydata.us}. This function is more general than getQWData
-because it allows for other agencies rather than the USGS. Therefore, the 5-digit parameter code cannot be used.
-Instead, this function uses characteristicName. A complete list can be found here \url{http://www.waterqualitydata.us/Codes/Characteristicname}
+Returns a list of sites from the Water Quality Portal web service. This function gets the data from: \url{http://www.waterqualitydata.us}.
+Arguments to the function should be based on \url{www.waterqualitydata.us/webservices_documentation.jsp}
}
\examples{
setInternet2(use=NA)
diff --git a/man/getWaterML1Data.Rd b/man/getWaterML1Data.Rd
index 6735e0f697d431d63dbc41ae34bbb4e7b864dd24..b845b95aab3ae93e62c3d5ef0afa7c7044912937 100644
--- a/man/getWaterML1Data.Rd
+++ b/man/getWaterML1Data.Rd
@@ -25,5 +25,7 @@ obs_url <- constructNWISURL(sites,property,startDate,endDate,'dv')
data <- getWaterML1Data(obs_url)
urlMulti <- constructNWISURL("04085427",c("00060","00010"),startDate,endDate,'dv',statCd=c("00003","00001"))
multiData <- getWaterML1Data(urlMulti)
+goundwaterExampleURL <- "http://waterservices.usgs.gov/nwis/gwlevels/?format=waterml&sites=431049071324301&startDT=2013-10-01&endDT=2014-06-30"
+groundWater <- getWaterML1Data(goundwaterExampleURL)
}
diff --git a/man/processQWData.Rd b/man/processQWData.Rd
index c6f00a870becbc95122aeee4b6e3d15868280d3d..a1df95dda27c70d59ae87530326f4bf7dc176919 100644
--- a/man/processQWData.Rd
+++ b/man/processQWData.Rd
@@ -3,10 +3,12 @@
\alias{processQWData}
\title{Processing of USGS NWIS Water Quality Data}
\usage{
-processQWData(data)
+processQWData(data, pCode = TRUE)
}
\arguments{
-\item{data}{dataframe from}
+\item{data}{dataframe from Water Quality Portal}
+
+\item{pCode}{logical if TRUE, assume data came from a pCode search, if FALSE, characteristic name.}
}
\value{
data dataframe with first column dateTime, and at least one qualifier and value columns
@@ -19,7 +21,7 @@ conditions to determine if a value is left censored or not. Censored values are
}
\examples{
# These examples require an internet connection to run
-rawSample <- getRawQWData('01594440','01075', '1985-01-01', '1985-03-31')
+rawSample <- retrieveWQPqwData('USGS-01594440','01075', '1985-01-01', '1985-03-31')
rawSampleSelect <- processQWData(rawSample)
}
\keyword{USGS}
diff --git a/man/renameColumns.Rd b/man/renameColumns.Rd
index 6a67074a6c714a3c4b6afd72ad3384792689e62f..0a07040c9e83f2f39f5beae4c84e0d831111a427 100644
--- a/man/renameColumns.Rd
+++ b/man/renameColumns.Rd
@@ -17,10 +17,10 @@ Rename columns coming back from NWIS data retrievals
\examples{
# This example requires an internet connection to run
siteNumber <- '05114000'
-rawData <- retrieveNWISData(siteNumber,c("00010","00060","00300"),"2001-01-01","2002-01-01",StatCd=c("00001","00003"))
+rawData <- retrieveNWISdvData(siteNumber,c("00010","00060","00300"),"2001-01-01","2002-01-01",StatCd=c("00001","00003"))
rawData <- renameColumns(rawData)
today <- as.character(Sys.Date())
-rawData2 <- retrieveUnitNWISData(siteNumber,c("00010","00060"),today,today)
+rawData2 <- retrieveNWISunitData(siteNumber,c("00010","00060"),today,today)
rawData2 <- renameColumns(rawData2)
}
\keyword{USGS}
diff --git a/man/retrieveNWISData.Rd b/man/retrieveNWISdvData.Rd
similarity index 78%
rename from man/retrieveNWISData.Rd
rename to man/retrieveNWISdvData.Rd
index 92c25247e99f7300dc9e55338150129165a3f128..1665a85779a11b310a2d748f0f8f3554fda06e11 100644
--- a/man/retrieveNWISData.Rd
+++ b/man/retrieveNWISdvData.Rd
@@ -1,9 +1,9 @@
% Generated by roxygen2 (4.0.1): do not edit by hand
-\name{retrieveNWISData}
-\alias{retrieveNWISData}
+\name{retrieveNWISdvData}
+\alias{retrieveNWISdvData}
\title{Raw Data Import for USGS NWIS Data}
\usage{
-retrieveNWISData(siteNumber, ParameterCd, StartDate, EndDate,
+retrieveNWISdvData(siteNumber, ParameterCd, StartDate, EndDate,
StatCd = "00003", format = "tsv", interactive = TRUE)
}
\arguments{
@@ -37,10 +37,10 @@ siteNumber <- '04085427'
startDate <- '2012-01-01'
endDate <- '2012-06-30'
pCode <- '00060'
-rawDailyQ <- retrieveNWISData(siteNumber,pCode, startDate, endDate)
-rawDailyTemperature <- retrieveNWISData(siteNumber,'00010', startDate, endDate, StatCd='00001')
-rawDailyTemperatureTSV <- retrieveNWISData(siteNumber,'00010', startDate, endDate, StatCd='00001',format='tsv')
-rawDailyQAndTempMeanMax <- retrieveNWISData(siteNumber,c('00010','00060'), startDate, endDate, StatCd=c('00001','00003'))
+rawDailyQ <- retrieveNWISdvData(siteNumber,pCode, startDate, endDate)
+rawDailyTemperature <- retrieveNWISdvData(siteNumber,'00010', startDate, endDate, StatCd='00001')
+rawDailyTemperatureTSV <- retrieveNWISdvData(siteNumber,'00010', startDate, endDate, StatCd='00001',format='tsv')
+rawDailyQAndTempMeanMax <- retrieveNWISdvData(siteNumber,c('00010','00060'), startDate, endDate, StatCd=c('00001','00003'))
}
\keyword{USGS}
\keyword{data}
diff --git a/man/retrieveUnitNWISData.Rd b/man/retrieveNWISunitData.Rd
similarity index 88%
rename from man/retrieveUnitNWISData.Rd
rename to man/retrieveNWISunitData.Rd
index 05b8d4ea11332916f8c023e1eb217fdb1ef07ae4..c630e9179c45c3b5f4a1a1159f2642e79ab68157 100644
--- a/man/retrieveUnitNWISData.Rd
+++ b/man/retrieveNWISunitData.Rd
@@ -1,9 +1,9 @@
% Generated by roxygen2 (4.0.1): do not edit by hand
-\name{retrieveUnitNWISData}
-\alias{retrieveUnitNWISData}
+\name{retrieveNWISunitData}
+\alias{retrieveNWISunitData}
\title{Raw Data Import for Instantaneous USGS NWIS Data}
\usage{
-retrieveUnitNWISData(siteNumber, ParameterCd, StartDate, EndDate,
+retrieveNWISunitData(siteNumber, ParameterCd, StartDate, EndDate,
format = "xml", interactive = TRUE)
}
\arguments{
@@ -35,8 +35,8 @@ ParameterCd <- '00060'
StartDate <- as.character(Sys.Date())
EndDate <- as.character(Sys.Date())
# These examples require an internet connection to run
-rawData <- retrieveUnitNWISData(siteNumber,ParameterCd,StartDate,EndDate)
-rawData2 <- retrieveUnitNWISData(siteNumber,ParameterCd,StartDate,EndDate,"tsv")
+rawData <- retrieveNWISunitData(siteNumber,ParameterCd,StartDate,EndDate)
+rawData2 <- retrieveNWISunitData(siteNumber,ParameterCd,StartDate,EndDate,"tsv")
}
\keyword{USGS}
\keyword{data}
diff --git a/man/getRawQWData.Rd b/man/retrieveWQPqwData.Rd
similarity index 73%
rename from man/getRawQWData.Rd
rename to man/retrieveWQPqwData.Rd
index b4cec31bf6538e8f87660742a4629d9b33867969..d679f2fdf5b9fa9cb76371fb05446f106e815cce 100644
--- a/man/getRawQWData.Rd
+++ b/man/retrieveWQPqwData.Rd
@@ -1,9 +1,10 @@
% Generated by roxygen2 (4.0.1): do not edit by hand
-\name{getRawQWData}
-\alias{getRawQWData}
+\name{retrieveWQPqwData}
+\alias{retrieveWQPqwData}
\title{Raw Data Import for USGS NWIS Water Quality Data}
\usage{
-getRawQWData(siteNumber, ParameterCd, StartDate, EndDate, interactive = TRUE)
+retrieveWQPqwData(siteNumber, ParameterCd, StartDate, EndDate,
+ interactive = TRUE)
}
\arguments{
\item{siteNumber}{string USGS site number. This is usually an 8 digit number}
@@ -27,9 +28,10 @@ A list of statistic codes can be found here: \url{http://nwis.waterdata.usgs.gov
}
\examples{
# These examples require an internet connection to run
-rawSample <- getRawQWData('01594440','01075', '1985-01-01', '1985-03-31')
-rawSampleAll <- getRawQWData('05114000','', '1985-01-01', '1985-03-31')
-rawSampleSelect <- getRawQWData('05114000',c('00915','00931'), '1985-01-01', '1985-04-30')
+rawSample <- retrieveWQPqwData('USGS-01594440','01075', '1985-01-01', '1985-03-31')
+rawSampleAll <- retrieveWQPqwData('USGS-05114000','', '1985-01-01', '1985-03-31')
+rawSampleSelect <- retrieveWQPqwData('USGS-05114000',c('00915','00931'), '1985-01-01', '1985-04-30')
+rawStoret <- retrieveWQPqwData('WIDNR_WQX-10032762','Specific conductance', '', '')
}
\keyword{USGS}
\keyword{data}
diff --git a/vignettes/dataRetrieval-concordance.tex b/vignettes/dataRetrieval-concordance.tex
index 19e8199efeefbbfcf32e9b38669b8ab97e04c80f..4c9c14712f612496a3609dbe58d84413073e4f60 100644
--- a/vignettes/dataRetrieval-concordance.tex
+++ b/vignettes/dataRetrieval-concordance.tex
@@ -1,9 +1,9 @@
\Sconcordance{concordance:dataRetrieval.tex:dataRetrieval.Rnw:%
-1 126 1 49 0 1 7 15 1 1 9 51 1 3 0 36 1 2 0 11 1 24 0 %
-24 1 3 0 23 1 3 0 6 1 7 0 18 1 3 0 25 1 1 0 17 1 9 0 %
-6 1 7 0 21 1 8 0 16 1 2 0 11 1 23 0 21 1 9 0 20 1 3 0 %
-6 1 17 0 27 1 6 0 11 1 9 0 15 1 4 0 19 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 %
-95 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}
+1 126 1 49 0 1 7 15 1 1 14 55 1 3 0 36 1 2 0 11 1 24 %
+0 24 1 3 0 23 1 3 0 6 1 7 0 18 1 3 0 25 1 1 0 17 1 9 %
+0 6 1 7 0 21 1 8 0 16 1 2 0 11 1 23 0 21 1 9 0 20 1 3 %
+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 %
+18 0 8 1 4 0 55 1}
diff --git a/vignettes/dataRetrieval.Rnw b/vignettes/dataRetrieval.Rnw
index 571507536f12d486d77dfc11c214fc24be10bc66..74cc2821d9ac9ee3e397c5cdb976ddf039190a08 100644
--- a/vignettes/dataRetrieval.Rnw
+++ b/vignettes/dataRetrieval.Rnw
@@ -52,7 +52,7 @@
{\thesubsubsection}{0.5em}{}
\titlecontents{section}
-[2.3em] % adjust left margin
+[2em] % adjust left margin
{\sffamily} % font formatting
{\contentslabel{2.3em}} % section label and offset
{\hspace*{-2.3em}}
@@ -73,14 +73,14 @@
{\titlerule*[0.25pc]{.}\contentspage}
\titlecontents{table}
-[-2.3em] % adjust left margin
+[0em] % adjust left margin
{\sffamily} % font formatting
{\textbf{Table}\hspace*{2em} \contentslabel {2em}} % section label and offset
{\hspace*{4em}}
{\titlerule*[0.25pc]{.}\contentspage}
\titlecontents{figure}
-[-2.3em] % adjust left margin
+[0em] % adjust left margin
{\sffamily} % font formatting
{\textbf{Figure}\hspace*{2em} \contentslabel {2em}} % section label and offset
{\hspace*{4em}}
@@ -152,15 +152,24 @@ knit_hooks$set(inline = function(x) {
if (is.numeric(x)) round(x, 3)})
knit_hooks$set(crop = hook_pdfcrop)
-bold.colHeaders <- function(x) paste("\\multicolumn{1}{c}{\\textbf{\\textsf{", x, "}}}", sep = "")
+bold.colHeaders <- function(x) {
+ x <- gsub("\\^(\\d)","$\\^\\1$",x)
+ x <- gsub("\\%","\\\\%",x)
+ x <- gsub("\\_"," ",x)
+ returnX <- paste("\\multicolumn{1}{c}{\\textbf{\\textsf{", x, "}}}", sep = "")
+}
addSpace <- function(x) ifelse(x != "1", "[5pt]","")
@
+\noindent{\huge\textsf{\textbf{The dataRetrieval R package}}}
+\noindent\textsf{By Laura De Cicco and Robert Hirsch}
-\maketitle
+\noindent\textsf{\today}
-\newpage
+% \maketitle
+%
+% \newpage
\tableofcontents
\listoffigures
@@ -188,7 +197,7 @@ ChoptankInfo <- getSiteFileData(siteNumber)
parameterCd <- "00060"
#Raw daily data:
-rawDailyData <- retrieveNWISData(siteNumber,parameterCd,
+rawDailyData <- retrieveNWISdvData(siteNumber,parameterCd,
"1980-01-01","2010-01-01")
# Data compiled for EGRET analysis
Daily <- getDVData(siteNumber,parameterCd,
@@ -378,7 +387,7 @@ Parameter information is obtained from \url{http://nwis.waterdata.usgs.gov/nwis/
\subsection{Daily Values}
\label{sec:usgsDaily}
%------------------------------------------------------------
-To obtain daily records of USGS data, use the \texttt{retrieveNWISData} function. The arguments for this function are siteNumber, parameterCd, startDate, endDate, statCd, and a logical (TRUE/FALSE) interactive. There are 2 default arguments: statCd (defaults to \texttt{"}00003\texttt{"}), and interactive (defaults to TRUE). If you want to use the default values, you do not need to list them in the function call. By setting the \texttt{"}interactive\texttt{"} option to FALSE, the operation of the function will advance automatically. It might make more sense to run large batch collections with the interactive option set to FALSE.
+To obtain daily records of USGS data, use the \texttt{retrieveNWISdvData} function. The arguments for this function are siteNumber, parameterCd, startDate, endDate, statCd, and a logical (TRUE/FALSE) interactive. There are 2 default arguments: statCd (defaults to \texttt{"}00003\texttt{"}), and interactive (defaults to TRUE). If you want to use the default values, you do not need to list them in the function call. By setting the \texttt{"}interactive\texttt{"} option to FALSE, the operation of the function will advance automatically. It might make more sense to run large batch collections with the interactive option set to FALSE.
The dates (start and end) must be in the format \texttt{"}YYYY-MM-DD\texttt{"} (note: the user must include the quotes). Setting the start date to \texttt{"}\texttt{"} (no space) will prompt the program to ask for the earliest date, and setting the end date to \texttt{"}\texttt{"} (no space) will prompt for the latest available date.
@@ -389,7 +398,7 @@ parameterCd <- "00060" # Discharge (ft3/s)
startDate <- "" # Will request earliest date
endDate <- "" # Will request latest date
-discharge <- retrieveNWISData(siteNumber,
+discharge <- retrieveNWISdvData(siteNumber,
parameterCd, startDate, endDate)
names(discharge)
@
@@ -405,7 +414,7 @@ statCd <- c("00001","00003") # Mean and maximum
startDate <- "2012-01-01"
endDate <- "2012-05-01"
-temperatureAndFlow <- retrieveNWISData(siteNumber, parameterCd,
+temperatureAndFlow <- retrieveNWISdvData(siteNumber, parameterCd,
startDate, endDate, StatCd=statCd)
@
@@ -451,14 +460,14 @@ There are occasions where NWIS values are not reported as numbers, instead there
\subsection{Unit Values}
\label{sec:usgsRT}
%------------------------------------------------------------
-Any data collected at regular time intervals (such as 15-minute or hourly) are known as \enquote{unit values}. Many of these are delivered on a real time basis and very recent data (even less than an hour old in many cases) are available through the function \texttt{retrieveUnitNWISData}. Some of these unit values are available for many years, and some are only available for a recent time period such as 120 days. Here is an example of a retrieval of such data.
+Any data collected at regular time intervals (such as 15-minute or hourly) are known as \enquote{unit values}. Many of these are delivered on a real time basis and very recent data (even less than an hour old in many cases) are available through the function \texttt{retrieveNWISunitData}. Some of these unit values are available for many years, and some are only available for a recent time period such as 120 days. Here is an example of a retrieval of such data.
<<label=getNWISUnit, echo=TRUE>>=
parameterCd <- "00060" # Discharge (ft3/s)
startDate <- "2012-05-12"
endDate <- "2012-05-13"
-dischargeToday <- retrieveUnitNWISData(siteNumber, parameterCd,
+dischargeToday <- retrieveNWISunitData(siteNumber, parameterCd,
startDate, endDate)
@
@@ -479,7 +488,7 @@ Note that time now becomes important, so the variable datetime is a POSIXct, and
\subsection{Water Quality Values}
\label{sec:usgsWQP}
%------------------------------------------------------------
-To get USGS water quality data from water samples collected at the streamgage or other monitoring site (as distinct from unit values collected through some type of automatic monitor) we can use the function \texttt{retrieveNWISqwData}, with the input arguments: siteNumber, parameterCd, startDate, endDate, and interactive (similar to \texttt{retrieveUnitNWISData} and \texttt{retrieveNWISData}).
+To get USGS water quality data from water samples collected at the streamgage or other monitoring site (as distinct from unit values collected through some type of automatic monitor) we can use the function \texttt{retrieveNWISqwData}, with the input arguments: siteNumber, parameterCd, startDate, endDate, and interactive (similar to \texttt{retrieveNWISunitData} and \texttt{retrieveNWISdvData}).
<<label=getQW, echo=TRUE>>=
@@ -516,11 +525,13 @@ There are additional water quality data sets available from the Water Quality Da
<<label=getQWData, echo=TRUE>>=
-# specificCond <- getWQPData('WIDNR_WQX-10032762',
-# 'Specific conductance','','')
-# head(specificCond)
+specificCond <- getWQPData('WIDNR_WQX-10032762',
+ 'Specific conductance','','')
+head(specificCond)
@
+There are
+
\FloatBarrier
%------------------------------------------------------------
\subsection{URL Construction}
@@ -611,7 +622,7 @@ Notice that the \enquote{Day of the year} column can span from 1 to 366. The 366
\subsection{Sample Data}
\label{Samplesubsection}
%------------------------------------------------------------
-The \texttt{getSampleData} function retrieves USGS sample data from NWIS. The arguments for this function are also siteNumber, ParameterCd, StartDate, EndDate, interactive. These are the same inputs as \texttt{getRawQWData} or \texttt{getQWData} as described in the previous section.
+The \texttt{getSampleData} function retrieves USGS sample data from NWIS. The arguments for this function are also siteNumber, ParameterCd, StartDate, EndDate, interactive. These are the same inputs as \texttt{retrieveWQPqwData} or \texttt{getWQPData} as described in the previous section.
<<secondExample>>=
parameterCd <- "00618"
@@ -708,7 +719,7 @@ print(xTab,
@
-The dataRetrieval package will \enquote{add up} all the values in a given row to form the total for that sample when using the Sample dataframe. Thus, you only want to enter data that should be added together. If you want a dataframe with multiple constituents that are not summed, do not use getSampleData, getSTORETSampleData, or getSampleDataFromFile. The raw data functions: \texttt{getWQPData}, \texttt{retrieveNWISqwData}, \texttt{getRawQWData}, \texttt{getQWData} will not sum constituents, but leave them in their individual columns.
+The dataRetrieval package will \enquote{add up} all the values in a given row to form the total for that sample when using the Sample dataframe. Thus, you only want to enter data that should be added together. If you want a dataframe with multiple constituents that are not summed, do not use getSampleData, getSTORETSampleData, or getSampleDataFromFile. The raw data functions: \texttt{getWQPData}, \texttt{retrieveNWISqwData}, \texttt{retrieveWQPqwData}, \texttt{getWQPData} will not sum constituents, but leave them in their individual columns.
For example, we might know the value for dp on 5/30/2005, but we don't want to put it in the table because under the rules of this data set, we are not supposed to add it in to the values in 2005.
@@ -879,18 +890,17 @@ Tables \ref{tab:dataRetrievalFunctions1} and \ref{tab:dataRetrievalMisc} summari
\multicolumn{1}{c}{\textbf{\textsf{Function Name}}} &
\multicolumn{1}{c}{\textbf{\textsf{Description}}} \\ [0pt]
\hline
- Daily & \texttt{retrieveNWISData} & Raw USGS daily data \\
+ Daily & \texttt{retrieveNWISdvData} & Raw USGS daily data \\
[5pt]Daily\tnote{1} & \texttt{getDVData} & USGS daily values \\
[5pt]Daily\tnote{1} & \texttt{getDailyDataFromFile} & User generated daily data \\
[5pt]Sample & \texttt{retrieveNWISqwData} & Raw USGS water quality data \\
- [5pt]Sample & \texttt{getRawQWData} & Raw Water Quality Data Portal data \\
+ [5pt]Sample & \texttt{retrieveWQPqwData} & Raw Water Quality Data Portal data \\
[5pt]Sample & \texttt{getQWDataFromFile} & Raw user generated water quality data \\
- [5pt]Sample & \texttt{getQWData} & USGS Water Quality Portal data \\
[5pt]Sample & \texttt{getWQPData} & General Water Quality Portal\\
[5pt]Sample\tnote{1} & \texttt{getSampleData} & USGS water quality data\\
[5pt]Sample\tnote{1} & \texttt{getSTORETSampleData} & STORET Water Quality Data Portal data \\
[5pt]Sample\tnote{1} & \texttt{getSampleDataFromFile} & User generated sample data \\
- [5pt]Unit & \texttt{retrieveUnitNWISData} & Raw USGS instantaneous data \\
+ [5pt]Unit & \texttt{retrieveNWISunitData} & Raw USGS instantaneous data \\
[5pt]Information\tnote{1} & \texttt{getMetaData} & USGS station and parameter code information \\
[5pt]Information & \texttt{getParameterInfo} & USGS parameter code information \\
[5pt]Information & \texttt{getSiteFileData} & USGS station information \\
diff --git a/vignettes/dataRetrieval.lof b/vignettes/dataRetrieval.lof
index 582b0ff3d40294bd7c1e46f08f8794fb108430d3..f201798eacc0cebbef04b60d9acfa41b477c3a5c 100644
--- a/vignettes/dataRetrieval.lof
+++ b/vignettes/dataRetrieval.lof
@@ -1,7 +1,7 @@
\select@language {american}
-\contentsline {figure}{\numberline {1}{\ignorespaces Temperature and discharge plot of Choptank River in 2012}}{12}{figure.caption.4}
-\contentsline {figure}{\numberline {2}{\ignorespaces Nitrate plot of Choptank River}}{15}{figure.caption.5}
-\contentsline {figure}{\numberline {3}{\ignorespaces Default multiPlotDataOverview}}{27}{figure.caption.10}
-\contentsline {figure}{\numberline {4}{\ignorespaces A simple R help file\relax }}{31}{figure.caption.14}
-\contentsline {figure}{\numberline {5}{\ignorespaces A simple table produced in Microsoft Excel\relax }}{34}{figure.caption.15}
+\contentsline {figure}{\numberline {1}{\ignorespaces Temperature and discharge plot of Choptank River in 2012}}{11}{figure.caption.4}
+\contentsline {figure}{\numberline {2}{\ignorespaces Nitrate plot of Choptank River}}{14}{figure.caption.5}
+\contentsline {figure}{\numberline {3}{\ignorespaces Default multiPlotDataOverview}}{26}{figure.caption.10}
+\contentsline {figure}{\numberline {4}{\ignorespaces A simple R help file\relax }}{30}{figure.caption.14}
+\contentsline {figure}{\numberline {5}{\ignorespaces A simple table produced in Microsoft Excel\relax }}{33}{figure.caption.15}
\contentsfinish
diff --git a/vignettes/dataRetrieval.log b/vignettes/dataRetrieval.log
index 543b8cc6256af806c9032f4dce7aa35e4f451a5e..f053973c87381856b42db677c3a5d80e70ba3e23 100644
--- a/vignettes/dataRetrieval.log
+++ b/vignettes/dataRetrieval.log
@@ -1,18 +1,18 @@
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+This is pdfTeX, Version 3.1415926-2.5-1.40.14 (MiKTeX 2.9) (preloaded format=pdflatex 2014.8.2) 3 AUG 2014 14:57
entering extended mode
**dataRetrieval.tex
-(D:\LADData\RCode\dataRetrieval\vignettes\dataRetrieval.tex
+(C:\RCodes\dataRetrieval\vignettes\dataRetrieval.tex
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[][]\OT1/pcr/m/n/10.95 url_uv[] []<-[] []\OT1/pcr/b/n/10.95 constructNWISURL[][
]\OT1/pcr/m/n/10.95 (siteNumber,[][]"00060"[][],startDate,endDate,[][]\TS1/pcr/
m/n/10.95 '\OT1/pcr/m/n/10.95 uv\TS1/pcr/m/n/10.95 '[][]\OT1/pcr/m/n/10.95 )[][
@@ -823,22 +841,26 @@ m/n/10.95 '\OT1/pcr/m/n/10.95 uv\TS1/pcr/m/n/10.95 '[][]\OT1/pcr/m/n/10.95 )[][
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[] \OT1/pcr/m/n/10.95 First day of the discharge record is 2000-01-01 and last
day is 2013-01-01[]
[]
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[] \OT1/pcr/m/n/10.95 The first sample is from 2000-01-04 and the last sample i
s from 2012-12-18[]
[]
@@ -898,69 +917,75 @@ s from 2012-12-18[]
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+[] \OT1/pcr/m/n/10.95 Sample1 <- localSample[!duplicated(localSample[c("DecYea
+r","ConcHigh")]),][]
+ []
+
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[]\OT1/pcr/m/n/10.95 Suspended sediment concentration (SSC) 1980-10-01 1991-09-
30 3651 mg/l[]
[]
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diff --git a/vignettes/dataRetrieval.lot b/vignettes/dataRetrieval.lot
index cc647ff2674014ecbf2d5a37029198b27cfb40d1..164c696eb71c96951282ed9ca0ab2b9248da1276 100644
--- a/vignettes/dataRetrieval.lot
+++ b/vignettes/dataRetrieval.lot
@@ -1,10 +1,10 @@
\select@language {american}
-\contentsline {table}{\numberline {1}{\ignorespaces Common USGS Parameter Codes\relax }}{6}{table.caption.1}
-\contentsline {table}{\numberline {2}{\ignorespaces Commonly used USGS Stat Codes\relax }}{7}{table.caption.2}
-\contentsline {table}{\numberline {3}{\ignorespaces Daily mean data availabile at the Choptank River near Greensboro, MD. [Some columns deleted for space considerations]\relax }}{8}{table.caption.3}
+\contentsline {table}{\numberline {1}{\ignorespaces Common USGS Parameter Codes\relax }}{5}{table.caption.1}
+\contentsline {table}{\numberline {2}{\ignorespaces Commonly used USGS Stat Codes\relax }}{6}{table.caption.2}
+\contentsline {table}{\numberline {3}{\ignorespaces Daily mean data availabile at the Choptank River near Greensboro, MD. [Some columns deleted for space considerations]\relax }}{7}{table.caption.3}
\contentsline {table}{\numberline {4}{\ignorespaces Daily dataframe\relax }}{18}{table.caption.6}
-\contentsline {table}{\numberline {5}{\ignorespaces Sample dataframe\relax }}{20}{table.caption.8}
-\contentsline {table}{\numberline {6}{\ignorespaces Example data\relax }}{21}{table.caption.9}
-\contentsline {table}{\numberline {7}{\ignorespaces dataRetrieval functions\relax }}{29}{table.caption.12}
-\contentsline {table}{\numberline {8}{\ignorespaces dataRetrieval miscellaneous functions\relax }}{29}{table.caption.13}
+\contentsline {table}{\numberline {5}{\ignorespaces Sample dataframe\relax }}{19}{table.caption.8}
+\contentsline {table}{\numberline {6}{\ignorespaces Example data\relax }}{20}{table.caption.9}
+\contentsline {table}{\numberline {7}{\ignorespaces dataRetrieval functions\relax }}{28}{table.caption.12}
+\contentsline {table}{\numberline {8}{\ignorespaces dataRetrieval miscellaneous functions\relax }}{28}{table.caption.13}
\contentsfinish
diff --git a/vignettes/dataRetrieval.pdf b/vignettes/dataRetrieval.pdf
index b655d7a645a9e5981325ec96fcf5d92a31e69238..ac5e5885a40977f288bbb088b839b505230a37f2 100644
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diff --git a/vignettes/dataRetrieval.tex b/vignettes/dataRetrieval.tex
index 161ba002a2f5b5a53224043b0761a770471d41ad..ce9715cc12d0c519d1431dd0ef3b1c7954e5ac68 100644
--- a/vignettes/dataRetrieval.tex
+++ b/vignettes/dataRetrieval.tex
@@ -101,7 +101,7 @@
{\thesubsubsection}{0.5em}{}
\titlecontents{section}
-[2.3em] % adjust left margin
+[2em] % adjust left margin
{\sffamily} % font formatting
{\contentslabel{2.3em}} % section label and offset
{\hspace*{-2.3em}}
@@ -122,14 +122,14 @@
{\titlerule*[0.25pc]{.}\contentspage}
\titlecontents{table}
-[-2.3em] % adjust left margin
+[0em] % adjust left margin
{\sffamily} % font formatting
{\textbf{Table}\hspace*{2em} \contentslabel {2em}} % section label and offset
{\hspace*{4em}}
{\titlerule*[0.25pc]{.}\contentspage}
\titlecontents{figure}
-[-2.3em] % adjust left margin
+[0em] % adjust left margin
{\sffamily} % font formatting
{\textbf{Figure}\hspace*{2em} \contentslabel {2em}} % section label and offset
{\hspace*{4em}}
@@ -191,11 +191,15 @@
+\noindent{\huge\textsf{\textbf{The dataRetrieval R package}}}
+\noindent\textsf{By Laura De Cicco and Robert Hirsch}
-\maketitle
+\noindent\textsf{\today}
-\newpage
+% \maketitle
+%
+% \newpage
\tableofcontents
\listoffigures
@@ -225,7 +229,7 @@ A quick workflow for major dataRetrieval functions:
\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00060"}
\hlcom{#Raw daily data:}
-\hlstd{rawDailyData} \hlkwb{<-} \hlkwd{retrieveNWISData}\hlstd{(siteNumber,parameterCd,}
+\hlstd{rawDailyData} \hlkwb{<-} \hlkwd{retrieveNWISdvData}\hlstd{(siteNumber,parameterCd,}
\hlstr{"1980-01-01"}\hlstd{,}\hlstr{"2010-01-01"}\hlstd{)}
\hlcom{# Data compiled for EGRET analysis}
\hlstd{Daily} \hlkwb{<-} \hlkwd{getDVData}\hlstd{(siteNumber,parameterCd,}
@@ -262,8 +266,8 @@ Once the site-ID is known, the next required input for USGS data retrievals is t
Not every station will measure all parameters. A short list of commonly measured parameters is shown in Table \ref{tab:params}.
-% latex table generated in R 3.1.0 by xtable 1.7-3 package
-% Tue Jul 15 09:39:32 2014
+% latex table generated in R 3.1.1 by xtable 1.7-3 package
+% Sun Aug 03 14:57:17 2014
\begin{table}[ht]
\caption{Common USGS Parameter Codes}
\label{tab:params}
@@ -325,8 +329,8 @@ 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 3.1.0 by xtable 1.7-3 package
-% Tue Jul 15 09:39:33 2014
+% latex table generated in R 3.1.1 by xtable 1.7-3 package
+% Sun Aug 03 14:57:19 2014
\begin{table}[ht]
\caption{Commonly used USGS Stat Codes}
\label{tab:stat}
@@ -406,8 +410,8 @@ To discover what data is available for a particular USGS site, including measure
\end{knitrout}
-% latex table generated in R 3.1.0 by xtable 1.7-3 package
-% Tue Jul 15 09:39:34 2014
+% latex table generated in R 3.1.1 by xtable 1.7-3 package
+% Sun Aug 03 14:57:20 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}
@@ -419,7 +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 & 2014-07-14 & 24302 & ft$^3$/s \\
+ [5pt] & Stream flow, mean. daily & 1948-01-01 & 2014-08-02 & 24321 & ft$^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 \\
@@ -475,7 +479,7 @@ Parameter information is obtained from \url{http://nwis.waterdata.usgs.gov/nwis/
\subsection{Daily Values}
\label{sec:usgsDaily}
%------------------------------------------------------------
-To obtain daily records of USGS data, use the \texttt{retrieveNWISData} function. The arguments for this function are siteNumber, parameterCd, startDate, endDate, statCd, and a logical (TRUE/FALSE) interactive. There are 2 default arguments: statCd (defaults to \texttt{"}00003\texttt{"}), and interactive (defaults to TRUE). If you want to use the default values, you do not need to list them in the function call. By setting the \texttt{"}interactive\texttt{"} option to FALSE, the operation of the function will advance automatically. It might make more sense to run large batch collections with the interactive option set to FALSE.
+To obtain daily records of USGS data, use the \texttt{retrieveNWISdvData} function. The arguments for this function are siteNumber, parameterCd, startDate, endDate, statCd, and a logical (TRUE/FALSE) interactive. There are 2 default arguments: statCd (defaults to \texttt{"}00003\texttt{"}), and interactive (defaults to TRUE). If you want to use the default values, you do not need to list them in the function call. By setting the \texttt{"}interactive\texttt{"} option to FALSE, the operation of the function will advance automatically. It might make more sense to run large batch collections with the interactive option set to FALSE.
The dates (start and end) must be in the format \texttt{"}YYYY-MM-DD\texttt{"} (note: the user must include the quotes). Setting the start date to \texttt{"}\texttt{"} (no space) will prompt the program to ask for the earliest date, and setting the end date to \texttt{"}\texttt{"} (no space) will prompt for the latest available date.
@@ -487,7 +491,7 @@ The dates (start and end) must be in the format \texttt{"}YYYY-MM-DD\texttt{"} (
\hlstd{startDate} \hlkwb{<-} \hlstr{""} \hlcom{# Will request earliest date}
\hlstd{endDate} \hlkwb{<-} \hlstr{""} \hlcom{# Will request latest date}
-\hlstd{discharge} \hlkwb{<-} \hlkwd{retrieveNWISData}\hlstd{(siteNumber,}
+\hlstd{discharge} \hlkwb{<-} \hlkwd{retrieveNWISdvData}\hlstd{(siteNumber,}
\hlstd{parameterCd, startDate, endDate)}
\hlkwd{names}\hlstd{(discharge)}
\end{alltt}
@@ -511,7 +515,7 @@ Another example that doesn't use the defaults would be a request for mean and ma
\hlstd{startDate} \hlkwb{<-} \hlstr{"2012-01-01"}
\hlstd{endDate} \hlkwb{<-} \hlstr{"2012-05-01"}
-\hlstd{temperatureAndFlow} \hlkwb{<-} \hlkwd{retrieveNWISData}\hlstd{(siteNumber, parameterCd,}
+\hlstd{temperatureAndFlow} \hlkwb{<-} \hlkwd{retrieveNWISdvData}\hlstd{(siteNumber, parameterCd,}
\hlstd{startDate, endDate,} \hlkwc{StatCd}\hlstd{=statCd)}
\end{alltt}
\end{kframe}
@@ -590,7 +594,7 @@ There are occasions where NWIS values are not reported as numbers, instead there
\subsection{Unit Values}
\label{sec:usgsRT}
%------------------------------------------------------------
-Any data collected at regular time intervals (such as 15-minute or hourly) are known as \enquote{unit values}. Many of these are delivered on a real time basis and very recent data (even less than an hour old in many cases) are available through the function \texttt{retrieveUnitNWISData}. Some of these unit values are available for many years, and some are only available for a recent time period such as 120 days. Here is an example of a retrieval of such data.
+Any data collected at regular time intervals (such as 15-minute or hourly) are known as \enquote{unit values}. Many of these are delivered on a real time basis and very recent data (even less than an hour old in many cases) are available through the function \texttt{retrieveNWISunitData}. Some of these unit values are available for many years, and some are only available for a recent time period such as 120 days. Here is an example of a retrieval of such data.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
@@ -598,7 +602,7 @@ Any data collected at regular time intervals (such as 15-minute or hourly) are k
\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00060"} \hlcom{# Discharge (ft3/s)}
\hlstd{startDate} \hlkwb{<-} \hlstr{"2012-05-12"}
\hlstd{endDate} \hlkwb{<-} \hlstr{"2012-05-13"}
-\hlstd{dischargeToday} \hlkwb{<-} \hlkwd{retrieveUnitNWISData}\hlstd{(siteNumber, parameterCd,}
+\hlstd{dischargeToday} \hlkwb{<-} \hlkwd{retrieveNWISunitData}\hlstd{(siteNumber, parameterCd,}
\hlstd{startDate, endDate)}
\end{alltt}
\end{kframe}
@@ -638,7 +642,7 @@ Note that time now becomes important, so the variable datetime is a POSIXct, and
\subsection{Water Quality Values}
\label{sec:usgsWQP}
%------------------------------------------------------------
-To get USGS water quality data from water samples collected at the streamgage or other monitoring site (as distinct from unit values collected through some type of automatic monitor) we can use the function \texttt{retrieveNWISqwData}, with the input arguments: siteNumber, parameterCd, startDate, endDate, and interactive (similar to \texttt{retrieveUnitNWISData} and \texttt{retrieveNWISData}).
+To get USGS water quality data from water samples collected at the streamgage or other monitoring site (as distinct from unit values collected through some type of automatic monitor) we can use the function \texttt{retrieveNWISqwData}, with the input arguments: siteNumber, parameterCd, startDate, endDate, and interactive (similar to \texttt{retrieveNWISunitData} and \texttt{retrieveNWISdvData}).
\begin{knitrout}
@@ -692,13 +696,24 @@ There are additional water quality data sets available from the Water Quality Da
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlcom{# specificCond <- getWQPData('WIDNR_WQX-10032762',}
-\hlcom{# 'Specific conductance','','')}
-\hlcom{# head(specificCond)}
+\hlstd{specificCond} \hlkwb{<-} \hlkwd{getWQPData}\hlstd{(}\hlstr{'WIDNR_WQX-10032762'}\hlstd{,}
+ \hlstr{'Specific conductance'}\hlstd{,}\hlstr{''}\hlstd{,}\hlstr{''}\hlstd{)}
+\hlkwd{head}\hlstd{(specificCond)}
\end{alltt}
+\begin{verbatim}
+ dateTime qualifier. value.
+1 2011-02-14 1360
+2 2011-02-17 1930
+3 2011-03-03 1240
+4 2011-03-10 1480
+5 2011-03-29 1130
+6 2011-04-07 1200
+\end{verbatim}
\end{kframe}
\end{knitrout}
+There are
+
\FloatBarrier
%------------------------------------------------------------
\subsection{URL Construction}
@@ -773,8 +788,8 @@ There are 4750 data points, and 4750 days.
-% latex table generated in R 3.1.0 by xtable 1.7-3 package
-% Tue Jul 15 09:39:42 2014
+% latex table generated in R 3.1.1 by xtable 1.7-3 package
+% Sun Aug 03 14:57:39 2014
\begin{table}[ht]
\caption{Daily dataframe}
\label{tab:DailyDF1}
@@ -812,7 +827,7 @@ Notice that the \enquote{Day of the year} column can span from 1 to 366. The 366
\subsection{Sample Data}
\label{Samplesubsection}
%------------------------------------------------------------
-The \texttt{getSampleData} function retrieves USGS sample data from NWIS. The arguments for this function are also siteNumber, ParameterCd, StartDate, EndDate, interactive. These are the same inputs as \texttt{getRawQWData} or \texttt{getQWData} as described in the previous section.
+The \texttt{getSampleData} function retrieves USGS sample data from NWIS. The arguments for this function are also siteNumber, ParameterCd, StartDate, EndDate, interactive. These are the same inputs as \texttt{retrieveWQPqwData} or \texttt{getWQPData} as described in the previous section.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
@@ -894,8 +909,8 @@ To illustrate how the dataRetrieval package handles a more complex censoring pro
-% latex table generated in R 3.1.0 by xtable 1.7-3 package
-% Tue Jul 15 09:39:43 2014
+% latex table generated in R 3.1.1 by xtable 1.7-3 package
+% Sun Aug 03 14:57:40 2014
\begin{table}[ht]
\caption{Example data}
\label{tab:exampleComplexQW}
@@ -916,7 +931,7 @@ To illustrate how the dataRetrieval package handles a more complex censoring pro
\end{table}
-The dataRetrieval package will \enquote{add up} all the values in a given row to form the total for that sample when using the Sample dataframe. Thus, you only want to enter data that should be added together. If you want a dataframe with multiple constituents that are not summed, do not use getSampleData, getSTORETSampleData, or getSampleDataFromFile. The raw data functions: \texttt{getWQPData}, \texttt{retrieveNWISqwData}, \texttt{getRawQWData}, \texttt{getQWData} will not sum constituents, but leave them in their individual columns.
+The dataRetrieval package will \enquote{add up} all the values in a given row to form the total for that sample when using the Sample dataframe. Thus, you only want to enter data that should be added together. If you want a dataframe with multiple constituents that are not summed, do not use getSampleData, getSTORETSampleData, or getSampleDataFromFile. The raw data functions: \texttt{getWQPData}, \texttt{retrieveNWISqwData}, \texttt{retrieveWQPqwData}, \texttt{getWQPData} will not sum constituents, but leave them in their individual columns.
For example, we might know the value for dp on 5/30/2005, but we don't want to put it in the table because under the rules of this data set, we are not supposed to add it in to the values in 2005.
@@ -1162,18 +1177,17 @@ Tables \ref{tab:dataRetrievalFunctions1} and \ref{tab:dataRetrievalMisc} summari
\multicolumn{1}{c}{\textbf{\textsf{Function Name}}} &
\multicolumn{1}{c}{\textbf{\textsf{Description}}} \\ [0pt]
\hline
- Daily & \texttt{retrieveNWISData} & Raw USGS daily data \\
+ Daily & \texttt{retrieveNWISdvData} & Raw USGS daily data \\
[5pt]Daily\tnote{1} & \texttt{getDVData} & USGS daily values \\
[5pt]Daily\tnote{1} & \texttt{getDailyDataFromFile} & User generated daily data \\
[5pt]Sample & \texttt{retrieveNWISqwData} & Raw USGS water quality data \\
- [5pt]Sample & \texttt{getRawQWData} & Raw Water Quality Data Portal data \\
+ [5pt]Sample & \texttt{retrieveWQPqwData} & Raw Water Quality Data Portal data \\
[5pt]Sample & \texttt{getQWDataFromFile} & Raw user generated water quality data \\
- [5pt]Sample & \texttt{getQWData} & USGS Water Quality Portal data \\
[5pt]Sample & \texttt{getWQPData} & General Water Quality Portal\\
[5pt]Sample\tnote{1} & \texttt{getSampleData} & USGS water quality data\\
[5pt]Sample\tnote{1} & \texttt{getSTORETSampleData} & STORET Water Quality Data Portal data \\
[5pt]Sample\tnote{1} & \texttt{getSampleDataFromFile} & User generated sample data \\
- [5pt]Unit & \texttt{retrieveUnitNWISData} & Raw USGS instantaneous data \\
+ [5pt]Unit & \texttt{retrieveNWISunitData} & Raw USGS instantaneous data \\
[5pt]Information\tnote{1} & \texttt{getMetaData} & USGS station and parameter code information \\
[5pt]Information & \texttt{getParameterInfo} & USGS parameter code information \\
[5pt]Information & \texttt{getSiteFileData} & USGS station information \\
@@ -1249,11 +1263,10 @@ 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}
@@ -1337,7 +1350,7 @@ 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 2014-07-14 24302 ft3/s
+2 2014-08-02 24321 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/dataRetrieval.toc b/vignettes/dataRetrieval.toc
index 7109b28de4d8a7d2e2565bfdb7812c404d83f893..98ce2415db047ab7c18fdacd93bd460a53f01e81 100644
--- a/vignettes/dataRetrieval.toc
+++ b/vignettes/dataRetrieval.toc
@@ -1,28 +1,28 @@
\select@language {american}
-\contentsline {section}{\numberline {1}Introduction to dataRetrieval}{4}{section.1}
-\contentsline {section}{\numberline {2}General USGS Web Retrievals}{5}{section.2}
-\contentsline {subsection}{\numberline {2.1}Site Information}{7}{subsection.2.1}
-\contentsline {subsubsection}{\numberline {2.1.1}getSiteFileData}{7}{subsubsection.2.1.1}
-\contentsline {subsubsection}{\numberline {2.1.2}getDataAvailability}{8}{subsubsection.2.1.2}
-\contentsline {subsection}{\numberline {2.2}Parameter Information}{9}{subsection.2.2}
-\contentsline {subsection}{\numberline {2.3}Daily Values}{9}{subsection.2.3}
-\contentsline {subsection}{\numberline {2.4}Unit Values}{13}{subsection.2.4}
-\contentsline {subsection}{\numberline {2.5}Water Quality Values}{14}{subsection.2.5}
-\contentsline {subsection}{\numberline {2.6}STORET Water Quality Retrievals}{16}{subsection.2.6}
-\contentsline {subsection}{\numberline {2.7}URL Construction}{16}{subsection.2.7}
-\contentsline {section}{\numberline {3}Data Retrievals Structured For Use In The EGRET Package}{17}{section.3}
-\contentsline {subsection}{\numberline {3.1}INFO Data}{17}{subsection.3.1}
+\contentsline {section}{\numberline {1}Introduction to dataRetrieval}{3}{section.1}
+\contentsline {section}{\numberline {2}General USGS Web Retrievals}{4}{section.2}
+\contentsline {subsection}{\numberline {2.1}Site Information}{6}{subsection.2.1}
+\contentsline {subsubsection}{\numberline {2.1.1}getSiteFileData}{6}{subsubsection.2.1.1}
+\contentsline {subsubsection}{\numberline {2.1.2}getDataAvailability}{7}{subsubsection.2.1.2}
+\contentsline {subsection}{\numberline {2.2}Parameter Information}{8}{subsection.2.2}
+\contentsline {subsection}{\numberline {2.3}Daily Values}{8}{subsection.2.3}
+\contentsline {subsection}{\numberline {2.4}Unit Values}{12}{subsection.2.4}
+\contentsline {subsection}{\numberline {2.5}Water Quality Values}{13}{subsection.2.5}
+\contentsline {subsection}{\numberline {2.6}STORET Water Quality Retrievals}{15}{subsection.2.6}
+\contentsline {subsection}{\numberline {2.7}URL Construction}{15}{subsection.2.7}
+\contentsline {section}{\numberline {3}Data Retrievals Structured For Use In The EGRET Package}{16}{section.3}
+\contentsline {subsection}{\numberline {3.1}INFO Data}{16}{subsection.3.1}
\contentsline {subsection}{\numberline {3.2}Daily Data}{17}{subsection.3.2}
-\contentsline {subsection}{\numberline {3.3}Sample Data}{19}{subsection.3.3}
-\contentsline {subsection}{\numberline {3.4}Censored Values: Summation Explanation}{20}{subsection.3.4}
-\contentsline {subsection}{\numberline {3.5}User-Generated Data Files}{22}{subsection.3.5}
-\contentsline {subsubsection}{\numberline {3.5.1}getDailyDataFromFile}{22}{subsubsection.3.5.1}
-\contentsline {subsubsection}{\numberline {3.5.2}getSampleDataFromFile}{24}{subsubsection.3.5.2}
-\contentsline {subsection}{\numberline {3.6}Merge Report}{25}{subsection.3.6}
-\contentsline {subsection}{\numberline {3.7}EGRET Plots}{26}{subsection.3.7}
-\contentsline {section}{\numberline {4}Summary}{28}{section.4}
-\contentsline {section}{\numberline {5}Getting Started in R}{30}{section.5}
-\contentsline {subsection}{\numberline {5.1}New to R?}{30}{subsection.5.1}
-\contentsline {subsection}{\numberline {5.2}R User: Installing dataRetrieval}{32}{subsection.5.2}
-\contentsline {section}{\numberline {6}Creating tables in Microsoft from R}{32}{section.6}
+\contentsline {subsection}{\numberline {3.3}Sample Data}{18}{subsection.3.3}
+\contentsline {subsection}{\numberline {3.4}Censored Values: Summation Explanation}{19}{subsection.3.4}
+\contentsline {subsection}{\numberline {3.5}User-Generated Data Files}{21}{subsection.3.5}
+\contentsline {subsubsection}{\numberline {3.5.1}getDailyDataFromFile}{21}{subsubsection.3.5.1}
+\contentsline {subsubsection}{\numberline {3.5.2}getSampleDataFromFile}{23}{subsubsection.3.5.2}
+\contentsline {subsection}{\numberline {3.6}Merge Report}{24}{subsection.3.6}
+\contentsline {subsection}{\numberline {3.7}EGRET Plots}{25}{subsection.3.7}
+\contentsline {section}{\numberline {4}Summary}{27}{section.4}
+\contentsline {section}{\numberline {5}Getting Started in R}{29}{section.5}
+\contentsline {subsection}{\numberline {5.1}New to R?}{29}{subsection.5.1}
+\contentsline {subsection}{\numberline {5.2}R User: Installing dataRetrieval}{31}{subsection.5.2}
+\contentsline {section}{\numberline {6}Creating tables in Microsoft from R}{31}{section.6}
\contentsfinish
diff --git a/vignettes/figure/egretEx.pdf b/vignettes/figure/egretEx.pdf
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