diff --git a/DESCRIPTION b/DESCRIPTION
index 1e55ef39b4c00782f53ebb64485c6795eeead2d4..e4ee236049ec2353f130091f9fe1d102073d45e1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,13 +1,15 @@
Package: dataRetrieval
Type: Package
Title: Retrieval functions for hydrologic data
-Version: 1.4.0
+Version: 1.4.1.9000
Date: 2014-10-06
-Author: Robert M. Hirsch, Laura De Cicco
-Maintainer: Laura De Cicco <ldecicco@usgs.gov>
+Authors@R: c( person("Robert", "Hirsch", role = c("aut"),
+ email = "rhirsch@usgs.gov"),
+ person("Laura", "DeCicco", role = c("aut","cre"),
+ email = "ldecicco@usgs.gov"))
Description: Collection of functions to help retrieve USGS data from either web
- services or user provided data files.
-License: file LICENSE
+ services or user-provided data files.
+License: Unlimited | file LICENSE
Copyright: This software is in the public domain because it contains materials
that originally came from the United States Geological Survey, an agency of
the United States Department of Interior. For more information, see the
@@ -30,3 +32,4 @@ LazyLoad: yes
LazyData: yes
VignetteBuilder: knitr
BuildVignettes: true
+Additional_repositories: http://usgs-r.github.com
diff --git a/NAMESPACE b/NAMESPACE
index d246fb10de47179e45a59bc2be9a5e3b5865e5dd..1fe6705ee06665c1871c4050904834ee8b3aebb4 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,11 +7,8 @@ export(dataOverview)
export(dateFormatCheck)
export(formatCheckDate)
export(formatCheckParameterCd)
-export(getDVData)
export(getDailyDataFromFile)
-export(getDataAvailability)
export(getDataFromFile)
-export(getMetaData)
export(getNWISDaily)
export(getNWISData)
export(getNWISDataAvailability)
@@ -23,12 +20,7 @@ export(getNWISSites)
export(getNWISdvData)
export(getNWISqwData)
export(getNWISunitData)
-export(getParameterInfo)
export(getRDB1Data)
-export(getSTORETSampleData)
-export(getSampleData)
-export(getSampleDataFromFile)
-export(getSiteFileData)
export(getUserDaily)
export(getUserInfo)
export(getUserSample)
diff --git a/R/basicWQPData.R b/R/basicWQPData.R
index 460375c18c25ebb24d024ce1e97f7aa2213b55b3..4b482189841dcbd970a9d81b13b9ffa02224b716 100644
--- a/R/basicWQPData.R
+++ b/R/basicWQPData.R
@@ -10,8 +10,10 @@
#' @importFrom lubridate parse_date_time
#' @examples
#' # These examples require an internet connection to run
+#' \dontrun{
#' rawSampleURL <- constructNWISURL('USGS-01594440','01075', '1985-01-01', '1985-03-31',"wqp")
#' rawSample <- readWQPData(rawSampleURL)
+#' }
readWQPData <- function(url){
h <- basicHeaderGatherer()
diff --git a/R/constructNWISURL.r b/R/constructNWISURL.r
index 8e7c99bb6af82b2dc8e0e4fd9fc75f65800f6748..8e7da895437e0b9515ff1cd230eb73e499234af4 100644
--- a/R/constructNWISURL.r
+++ b/R/constructNWISURL.r
@@ -9,7 +9,7 @@
#' @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 statCd string or vector USGS statistic code only used for daily value service. This is usually 5 digits. Daily mean (00003) is the default.
-#' @param service string USGS service to call. Possible values are "dv" (daily values), "uv" (unit/instantaneous values), "qw" (water quality data), and "wqp" (water quality portal, which can include STORET).
+#' @param service string USGS service to call. Possible values are "dv" (daily values), "uv" (unit/instantaneous values), "qw" (water quality data), "gwlevels" (groundwater),and "wqp" (water quality portal, which can include STORET).
#' @param format string, can be "tsv" or "xml", and is only applicable for daily and unit value requests. "tsv" returns results faster, but there is a possiblitiy that an incomplete file is returned without warning. XML is slower,
#' but will offer a warning if the file was incomplete (for example, if there was a momentary problem with the internet connection). It is possible to safely use the "tsv" option,
#' but the user must carefully check the results to see if the data returns matches what is expected. The default is therefore "xml".
@@ -78,9 +78,9 @@ constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,st
"format=rdb&rdb_qw_attributes=0&date_format=YYYY-MM-DD",
"rdb_compression=value", sep = "&")
if(expanded){
- url <- paste(url,"&qw_sample_wide=0",sep="")
+ url <- paste0(url,"&qw_sample_wide=0")
} else {
- url <- paste(url,"&qw_sample_wide=separated_wide",sep="")
+ url <- paste0(url,"&qw_sample_wide=separated_wide")
}
if (nzchar(startDate)) {
@@ -114,7 +114,7 @@ constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,st
}
baseURL <- "http://www.waterqualitydata.us/Result/search?siteid="
- url <- paste(baseURL,
+ url <- paste0(baseURL,
siteNumber,
ifelse(pCodeLogic,"&pCode=","&characteristicName="),
parameterCd,
@@ -122,7 +122,7 @@ constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,st
startDate,
"&startDateHi=",
endDate,
- "&countrycode=US&mimeType=tsv",sep = "")
+ "&countrycode=US&mimeType=tsv")
},
{ # this will be either dv or uv
@@ -130,43 +130,53 @@ constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,st
if(multiplePcodes){
parameterCd <- paste(parameterCd, collapse=",")
} else {
- parameterCd <- formatCheckParameterCd(parameterCd, interactive=interactive)
+ if("gwlevels" != service){
+ parameterCd <- formatCheckParameterCd(parameterCd, interactive=interactive)
+ }
}
if ("uv"==service) {
service <- "iv"
- baseURL <- paste("http://nwis.waterservices.usgs.gov/nwis/",service,sep="")
+ baseURL <- paste0("http://nwis.waterservices.usgs.gov/nwis/",service)
} else {
- baseURL <- paste("http://waterservices.usgs.gov/nwis/",service,sep="")
+ baseURL <- paste0("http://waterservices.usgs.gov/nwis/",service)
}
if ("xml"==format){
- format <- "waterml,1.1"
+ if("gwlevels" == service){
+ format <- "waterml"
+ } else {
+ format <- "waterml,1.1"
+ }
} else if ("tsv" == format){
format <- "rdb,1.0"
} else {
warning("non-supported format requested, please choose xml or tsv")
}
- url <- paste(baseURL,"/?site=",siteNumber, "&ParameterCd=",parameterCd, "&format=", format, sep = "")
+ url <- paste0(baseURL,"/?site=",siteNumber, "&format=", format)
+
+ if("gwlevels"!= service){
+ url <- paste0(url, "&ParameterCd=",parameterCd)
+ }
if("dv"==service) {
if(length(statCd) > 1){
statCd <- paste(statCd, collapse=",")
}
- url <- paste(url, "&StatCd=", statCd, sep = "")
+ url <- paste0(url, "&StatCd=", statCd)
}
if (nzchar(startDate)) {
- url <- paste(url,"&startDT=",startDate,sep="")
+ url <- paste0(url,"&startDT=",startDate)
} else {
startorgin <- "1851-01-01"
if ("iv" == service) startorgin <- "1900-01-01"
- url <- paste(url,"&startDT=",startorgin,sep="")
+ url <- paste0(url,"&startDT=",startorgin)
}
if (nzchar(endDate)) {
- url <- paste(url,"&endDT=",endDate,sep="")
+ url <- paste0(url,"&endDT=",endDate)
}
}
diff --git a/R/dataOverview.r b/R/dataOverview.r
index 530a4bde463d779d5c0225d2464371f90d1f69a7..85c811376875aa5a37e7cbbfcacfb79d010c3b18 100644
--- a/R/dataOverview.r
+++ b/R/dataOverview.r
@@ -2,8 +2,8 @@
#'
#' Gives a summary of data to be used for WRTDS analysis
#'
-#' @param localDaily dataframe
-#' @param localSample dataframe
+#' @param Daily dataframe
+#' @param Sample dataframe
#' @keywords data import USGS WRTDS
#' @export
#' @seealso \code{\link{mergeReport}}
@@ -11,26 +11,27 @@
#' # These examples require an internet connection to run
#' exDaily <- getNWISDaily('01594440','00060', '1985-01-01', '1985-03-31', interactive=FALSE)
#' exSample <- getNWISSample('01594440','01075', '1985-01-01', '1985-03-31', interactive=FALSE)
-#' dataOverview(localDaily = exDaily, localSample = exSample)
-dataOverview <- function(localDaily = Daily, localSample = Sample){
- numDays<-length(localDaily$Date)
- numSamples<-length(localSample$Date)
+#' dataOverview(Daily = exDaily, Sample = exSample)
+dataOverview <- function(Daily, Sample ){
+
+ numDays<-length(Daily$Date)
+ numSamples<-length(Sample$Date)
numYears<-round(numDays/365.25,digits=0)
cat("\n Discharge Record is",numDays,"days long, which is",numYears,"years")
- cat("\n First day of the discharge record is", as.character(localDaily$Date[1]),"and last day is",as.character(localDaily$Date[numDays]))
+ cat("\n First day of the discharge record is", as.character(Daily$Date[1]),"and last day is",as.character(Daily$Date[numDays]))
cat("\n The water quality record has",numSamples,"samples")
- cat("\n The first sample is from", as.character(localSample$Date[1]),"and the last sample is from",as.character(localSample$Date[numSamples]))
- if(localSample$Date[1]<localDaily$Date[1]) cat("\n WE HAVE A PROBLEM first sample is from before the first daily discharge")
- if(localSample$Date[numSamples]>localDaily$Date[numDays]) cat("\n WE HAVE A PROBLEM last sample is from after the last daily discharge")
- Qmin<-signif(min(localDaily$Q),digits=3)
- Qmean<-signif(mean(localDaily$Q),digits=3)
- Qmax<-signif(max(localDaily$Q),digits=3)
- Cmin<-signif(min(localSample$ConcHigh),digits=2)
- Cmean<-signif(mean(localSample$ConcHigh),digits=2)
- Cmax<-signif(max(localSample$ConcHigh),digits=2)
+ cat("\n The first sample is from", as.character(Sample$Date[1]),"and the last sample is from",as.character(Sample$Date[numSamples]))
+ if(Sample$Date[1]<Daily$Date[1]) cat("\n WE HAVE A PROBLEM first sample is from before the first daily discharge")
+ if(Sample$Date[numSamples]>Daily$Date[numDays]) cat("\n WE HAVE A PROBLEM last sample is from after the last daily discharge")
+ Qmin<-signif(min(Daily$Q),digits=3)
+ Qmean<-signif(mean(Daily$Q),digits=3)
+ Qmax<-signif(max(Daily$Q),digits=3)
+ Cmin<-signif(min(Sample$ConcHigh),digits=2)
+ Cmean<-signif(mean(Sample$ConcHigh),digits=2)
+ Cmax<-signif(max(Sample$ConcHigh),digits=2)
cat("\n Discharge: Minimum, mean and maximum",Qmin,Qmean,Qmax)
cat("\n Concentration: Minimum, mean and maximum",Cmin,Cmean,Cmax)
- pct<-sum(localSample$Uncen)
+ pct<-sum(Sample$Uncen)
pct<-((numSamples-pct)/numSamples)*100
cat("\n Percentage of the sample values that are censored is",signif(pct,digits=2),"%")
}
diff --git a/R/getDVData.r b/R/getDVData.r
index f340440a43593ab6b359b8607e4651476f179433..8ddc694c1806d11e2b83053cd6c37249d651f98d 100644
--- a/R/getDVData.r
+++ b/R/getDVData.r
@@ -1,42 +1,3 @@
-#' Import Daily Data for WRTDS
-#'
-#' This function is being deprecated for \code{\link{getNWISDaily}}.
-#'
-#' @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.
-#' @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.
-#' @param convert logical Option to include a conversion from cfs to cms (35.314667). The default is TRUE,
-#' which is appropriate for using NWIS data in the EGRET package. Set this to FALSE to not include the conversion. If the parameter code is not 00060 (NWIS discharge),
-#' there is no conversion applied.
-#' @param format string, can be "tsv" or "xml", and is only applicable for daily and unit value requests. "tsv" returns results faster, but there is a possiblitiy that an incomplete file is returned without warning. XML is slower,
-#' but will offer a warning if the file was incomplete (for example, if there was a momentary problem with the internet connection). It is possible to safely use the "tsv" option,
-#' but the user must carefully check the results to see if the data returns matches what is expected. The default is "tsv".
-#' @keywords data import USGS WRTDS
-#' @export
-#' @return Daily dataframe
-#' @seealso \code{\link{getNWISdvData}}, \code{\link{populateDaily}}, \code{\link{getNWISData}}
-#' @examples
-#' # These examples require an internet connection to run
-#' \dontrun{Daily <- getDVData('01594440','00060', '1985-01-01', '1985-03-31')}
-#' \dontrun{DailyCFS <- getDVData('01594440','00060', '1985-01-01', '1985-03-31',convert=FALSE)}
-#' \dontrun{DailySuspSediment <- getDVData('01594440','80154', '1985-01-01', '1985-03-31')}
-getDVData <- function (siteNumber,parameterCd,startDate,endDate,interactive=TRUE,convert=TRUE,format="tsv"){
- warning("This function is being deprecated, please use getNWISData")
- data <- getNWISdvData(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?
-
- qConvert <- ifelse("00060" == parameterCd, 35.314667, 1)
- qConvert<- ifelse(convert,qConvert,1)
-
- localDaily <- populateDaily(data,qConvert,interactive=interactive)
- return (localDaily)
-}
-
-
#' Import NWIS Daily Data for EGRET analysis
#'
#' Imports data from NWIS web service. This function gets the data from here: \url{http://waterservices.usgs.gov/}
diff --git a/R/getDataAvailability.r b/R/getDataAvailability.r
index bf1ff0dc11839a79bf22fca50923b828ba7ede8a..97c17b2f54536a685cae47c84aedf05202d0a4ef 100644
--- a/R/getDataAvailability.r
+++ b/R/getDataAvailability.r
@@ -56,77 +56,7 @@ getNWISDataAvailability <- function(siteNumber,type=c("uv","dv","qw")){
pCodes <- unique(SiteFile$parameter_cd)
- pcodeINFO <- parameterCdFile[parameterCdFile$parameter_cd %in% pCodes,]
- SiteFile <- merge(SiteFile,pcodeINFO,by="parameter_cd")
- SiteFile <- SiteFile[SiteFile$service %in% type,]
- return(SiteFile)
- } else {
- message(paste("URL caused an error:", urlSitefile))
- message("Content-Type=",h$value()["Content-Type"])
- return(NA)
- }
-}
-
-
-#' USGS data availability
-#'
-#' This function is being deprecated for \code{\link{getNWISDataAvailability}}.
-#'
-#' @param siteNumber string USGS site number.
-#' @param type vector string. Options are "uv", "dv", "qw"
-#' @keywords data import USGS web service
-#' @return retval dataframe with all information found in the expanded site file
-#' @export
-#' @import RCurl
-#' @examples
-#' # These examples require an internet connection to run
-#' \dontrun{availableData <- getDataAvailability('05114000')}
-#' # To find just unit value ('instantaneous') data:
-#' \dontrun{uvData <- getDataAvailability('05114000',type="uv")}
-#' \dontrun{uvDataMulti <- getDataAvailability(c('05114000','09423350'),type="uv")}
-getDataAvailability <- function(siteNumber,type=c("uv","dv","qw")){
-
- warning("This function is being deprecated, please use getNWISDataAvailability")
-
- siteNumber <- paste(siteNumber,collapse=",")
-
- urlSitefile <- paste("http://waterservices.usgs.gov/nwis/site/?format=rdb&seriesCatalogOutput=true&sites=",siteNumber,sep = "")
-
- doc = tryCatch({
- h <- basicHeaderGatherer()
- doc <- getURL(urlSitefile, headerfunction = h$update)
-
- }, warning = function(w) {
- message(paste("URL caused a warning:", urlSitefile))
- message(w)
- }, error = function(e) {
- message(paste("URL does not seem to exist:", urlSitefile))
- message(e)
- return(NA)
- })
-
- if(h$value()["Content-Type"] == "text/plain;charset=UTF-8"){
- SiteFile <- read.delim(
- textConnection(doc),
- header = TRUE,
- quote="\"",
- dec=".",
- sep='\t',
- colClasses=c('character'),
- fill = TRUE,
- comment.char="#")
-
- SiteFile <- SiteFile[-1,]
-
- SiteFile <- with(SiteFile, data.frame(site_no=site_no, parameter_cd=parm_cd, statCd=stat_cd, startDate=begin_date,endDate=end_date, count=count_nu,service=data_type_cd,stringsAsFactors = FALSE))
-
- SiteFile <- SiteFile[!is.na(SiteFile$parameter_cd),]
- SiteFile <- SiteFile["" != SiteFile$parameter_cd,]
- SiteFile$startDate <- as.Date(SiteFile$startDate)
- SiteFile$endDate <- as.Date(SiteFile$endDate)
- SiteFile$count <- as.numeric(SiteFile$count)
-
- pCodes <- unique(SiteFile$parameter_cd)
+ parameterCdFile <- parameterCdFile
pcodeINFO <- parameterCdFile[parameterCdFile$parameter_cd %in% pCodes,]
SiteFile <- merge(SiteFile,pcodeINFO,by="parameter_cd")
@@ -137,4 +67,4 @@ getDataAvailability <- function(siteNumber,type=c("uv","dv","qw")){
message("Content-Type=",h$value()["Content-Type"])
return(NA)
}
-}
\ No newline at end of file
+}
diff --git a/R/getMetaData.r b/R/getMetaData.r
index b49758833bec1b5157a54cfbdc3ff00c4a75942f..281d558c75afa9b0e76675df357857c2ca0ba032 100644
--- a/R/getMetaData.r
+++ b/R/getMetaData.r
@@ -1,44 +1,3 @@
-#' Import Metadata for USGS Data
-#'
-#' This function is being deprecated for \code{\link{getNWISInfo}}.
-#'
-#' @param siteNumber string USGS site number. This is usually an 8 digit number
-#' @param parameterCd string USGS parameter code. This is usually an 5 digit number.
-#' @param interactive logical Option for interactive mode. If true, there is user interaction for error handling and data checks.
-#' @keywords data import USGS web service WRTDS
-#' @export
-#' @return INFO dataframe with agency, site, dateTime, value, and code columns
-#' @examples
-#' # These examples require an internet connection to run
-#' # Automatically gets information about site 05114000 and temperature, no interaction with user
-#' INFO <- getMetaData('05114000','00010')
-getMetaData <- function(siteNumber="", parameterCd="",interactive=TRUE){
-
- warning("This function is being deprecated, please use getNWISInfo")
-
- if (nzchar(siteNumber)){
- INFO <- getNWISSiteInfo(siteNumber)
- } else {
- INFO <- as.data.frame(matrix(ncol = 2, nrow = 1))
- names(INFO) <- c('site.no', 'shortName')
- }
- INFO <- populateSiteINFO(INFO, siteNumber, interactive=interactive)
-
- if (nzchar(parameterCd)){
- parameterData <- getNWISPcodeInfo(parameterCd,interactive=interactive)
- INFO$param.nm <- parameterData$parameter_nm
- INFO$param.units <- parameterData$parameter_units
- INFO$paramShortName <- parameterData$srsname
- INFO$paramNumber <- parameterData$parameter_cd
- }
-
- INFO <- populateParameterINFO(parameterCd, INFO, interactive=interactive)
- INFO$paStart <- 10
- INFO$paLong <- 12
-
- return(INFO)
-}
-
#' Import Metadata for USGS Data
#'
#' Populates INFO data frame for EGRET study. If either station number or parameter code supplied, imports data about a particular USGS site from NWIS web service.
@@ -101,11 +60,13 @@ getNWISInfo <- function(siteNumber, parameterCd,interactive=TRUE){
#' # Automatically gets information about site 01594440 and temperature, no interaction with user
#' nameToUse <- 'Specific conductance'
#' pcodeToUse <- '00095'
+#' \dontrun{
#' INFO <- getWQPInfo('USGS-04024315',pcodeToUse,interactive=TRUE)
#' INFO2 <- getWQPInfo('WIDNR_WQX-10032762',nameToUse)
#' # To adjust the label names:
#' INFO$shortName <- "Little"
#' INFO$paramShortName <- "SC"
+#' }
getWQPInfo <- function(siteNumber, parameterCd, interactive=FALSE){
#Check for pcode:
diff --git a/R/getNWISSites.R b/R/getNWISSites.R
index fe7001f61a2877bb7ed813fb6c2518b9a2f6dbbf..0cfe7c4db81aea6eda5695764b3904f6f9c2dfc5 100644
--- a/R/getNWISSites.R
+++ b/R/getNWISSites.R
@@ -30,16 +30,16 @@ getNWISSites <- function(...){
if(h$value()["Content-Type"] == "text/xml;charset=UTF-8"){
xmlTreeParse(returnedDoc, getDTD = FALSE, useInternalNodes = TRUE)
} else {
- message(paste("URL caused an error:", obs_url))
+ message(paste("URL caused an error:", urlCall))
message("Content-Type=",h$value()["Content-Type"])
return(NA)
}
}, warning = function(w) {
- message(paste("URL caused a warning:", obs_url))
+ message(paste("URL caused a warning:", urlCall))
message(w)
}, error = function(e) {
- message(paste("URL does not seem to exist:", obs_url))
+ message(paste("URL does not seem to exist:", urlCall))
message(e)
return(NA)
})
diff --git a/R/getParameterInfo.r b/R/getParameterInfo.r
index 05a5480c0d1d5d93eff3dff2a75cce2b0fd63d5f..46890671d2e920e01a54e0a8295b7821aefab818 100644
--- a/R/getParameterInfo.r
+++ b/R/getParameterInfo.r
@@ -14,30 +14,9 @@
getNWISPcodeInfo <- function(parameterCd,interactive=TRUE){
parameterCd <- formatCheckParameterCd(parameterCd, interactive=interactive)
+ parameterCdFile <- parameterCdFile
+
parameterData <- parameterCdFile[parameterCdFile$parameter_cd %in% parameterCd,]
return(parameterData)
}
-
-#' USGS Parameter Data Retrieval
-#'
-#' This function is being deprecated for \code{\link{getNWISPcodeInfo}}.
-#'
-#' @param parameterCd vector of USGS parameter codes. This is usually an 5 digit number.
-#' @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 parameterData dataframe with all information from the USGS about the particular parameter (usually code, name, short name, units, and CAS registry numbers)
-#' @export
-#' @examples
-#' # These examples require an internet connection to run
-#' paramINFO <- getParameterInfo (c('01075','00060','00931'))
-getParameterInfo <- function(parameterCd,interactive=TRUE){
-
- warning("This function is being deprecated, please use getNWISPcodeInfo")
-
- parameterCd <- formatCheckParameterCd(parameterCd, interactive=interactive)
-
- parameterData <- parameterCdFile[parameterCdFile$parameter_cd %in% parameterCd,]
-
- return(parameterData)
-}
\ No newline at end of file
diff --git a/R/getRawQWData.r b/R/getRawQWData.r
index 7589cce5bc1bf3da6d47065dedfbff440ca23735..3991e17956bb626e77db8bf6d73c5ec2a46a0060 100644
--- a/R/getRawQWData.r
+++ b/R/getRawQWData.r
@@ -19,11 +19,13 @@
#' @export
#' @import RCurl
#' @seealso \code{\link{getWQPData}}, \code{\link{getWQPSites}},
-#' \code{\link{getSTORETSampleData}}, \code{\link{getNWISqwData}}, and \code{\link{readWQPData}}
+#' \code{\link{getNWISqwData}}, and \code{\link{readWQPData}}
#' @examples
#' # These examples require an internet connection to run
+#' \dontrun{
#' rawPcode <- getWQPqwData('USGS-01594440','01075', '1985-01-01', '1985-03-31')
#' rawCharacteristicName <- getWQPqwData('WIDNR_WQX-10032762','Specific conductance', '', '')
+#' }
getWQPqwData <- function(siteNumber,parameterCd,startDate,endDate,interactive=TRUE){
url <- constructNWISURL(siteNumber,parameterCd,startDate,endDate,"wqp",interactive=interactive)
diff --git a/R/getSTORETSampleData.R b/R/getSTORETSampleData.R
index 90c15bcd328f9b84d9fc0539d1a1981a1e6708a3..a343d693e65398c63b36a94cb14b26d39464e509 100644
--- a/R/getSTORETSampleData.R
+++ b/R/getSTORETSampleData.R
@@ -1,47 +1,3 @@
-#' Import Sample Data for WRTDS
-#'
-#' This function is being deprecated for \code{\link{getWQPSample}}.
-#'
-#' @param siteNumber string site number. If USGS, it should be in the form :'USGS-XXXXXXXXX...'
-#' @param characteristicName string
-#' @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 WRTDS
-#' @export
-#' @return Sample dataframe
-#' @seealso \code{\link{getWQPSample}}
-#' @examples
-#' # These examples require an internet connection to run
-#' \dontrun{Sample_01075 <- getSTORETSampleData('USGS-01594440','Chloride', '', '')}
-#' \dontrun{Sample_All <- getSTORETSampleData('WIDNR_WQX-10032762','Specific conductance', '', '')}
-getSTORETSampleData <- function(siteNumber,characteristicName,startDate,endDate,interactive=TRUE){
-
- warning("This function is being deprecated, please use getWQPSample")
-
- retval <- getWQPqwData(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
- }
-
- if(nrow(retval) > 0){
- data <- processQWData(retval,pCodeLogic)
- } else {
- data <- NULL
- }
-
- compressedData <- compressData(data, interactive=interactive)
- Sample <- populateSampleColumns(compressedData)
- return(Sample)
-}
-
#' Import Sample Data for WRTDS
#'
#' Imports data from the Water Quality Portal, so it could be STORET, NWIS, or . This function gets the data from: \url{http://www.waterqualitydata.us}
@@ -61,8 +17,10 @@ getSTORETSampleData <- function(siteNumber,characteristicName,startDate,endDate,
#' \code{\link{compressData}}, \code{\link{populateSampleColumns}}
#' @examples
#' # These examples require an internet connection to run
+#' \dontrun{
#' Sample_01075 <- getWQPSample('USGS-01594440','Chloride', '', '')
#' Sample_All <- getWQPSample('WIDNR_WQX-10032762','Specific conductance', '', '')
+#' }
getWQPSample <- function(siteNumber,characteristicName,startDate,endDate,interactive=TRUE){
retval <- getWQPqwData(siteNumber=siteNumber,
diff --git a/R/getSampleData.r b/R/getSampleData.r
index 3b30cbdf9f6bd293ad13cefe6f03fa334c4fb3d1..a32670102220a4bfa1c46df2fe0b68f19ffeb337 100644
--- a/R/getSampleData.r
+++ b/R/getSampleData.r
@@ -1,35 +1,3 @@
-#' Import Sample Data for WRTDS
-#'
-#' This function is being deprecated for \code{\link{getNWISSample}}.
-#'
-#' @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.
-#' @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 WRTDS
-#' @export
-#' @return Sample dataframe
-#' @seealso \code{\link{compressData}}, \code{\link{populateSampleColumns}}, \code{\link{getNWISSample}}
-#' @examples
-#'
-#' # These examples require an internet connection to run
-#' \dontrun{Sample_01075 <- getSampleData('01594440','01075', '1985-01-01', '1985-03-31')}
-#' \dontrun{Sample_All <- getSampleData('05114000','00915;00931', '1985-01-01', '1985-03-31')}
-#' \dontrun{Sample_Select <- getSampleData('05114000','00915;00931', '', '')}
-getSampleData <- function(siteNumber,parameterCd,startDate,endDate,interactive=TRUE){
-
- warning("This function is being deprecated, please use getNWISSample")
-
- rawSample <- getNWISqwData(siteNumber,parameterCd,startDate,endDate)
- #rawSample$dateTime <- strptime(rawSample$dateTime,"%Y-%m-%d %H:%M:%S")
- rawSample$dateTime <- as.Date(rawSample$dateTime)
- rawSample$site <- NULL
- compressedData <- compressData(rawSample, interactive=interactive)
- Sample <- populateSampleColumns(compressedData)
- return(Sample)
-}
-
#' Import NWIS Sample Data for EGRET analysis
#'
#' Imports data from NWIS web service. This function gets the data from here: \url{http://nwis.waterdata.usgs.gov/nwis/qwdata/}
diff --git a/R/getSampleDataFromFile.r b/R/getSampleDataFromFile.r
index c69d8b6051d523ca3e39e6c2918de10bc8e6581d..2b6e0d37c5e6537ad56a94ec5c2e1a25d0664547 100644
--- a/R/getSampleDataFromFile.r
+++ b/R/getSampleDataFromFile.r
@@ -1,30 +1,3 @@
-#' Import Sample Data for WRTDS
-#'
-#' This function is being deprecated for \code{\link{getUserSample}}.
-#'
-#' @param filePath string specifying the path to the file
-#' @param fileName string name of file to open
-#' @param hasHeader logical true if the first row of data is the column headers
-#' @param separator string character that separates data cells
-#' @param interactive logical Option for interactive mode. If true, there is user interaction for error handling and data checks.
-#' @keywords data import file
-#' @export
-#' @return Sample dataframe
-#' @examples
-#' filePath <- system.file("extdata", package="dataRetrieval")
-#' filePath <- paste(filePath,"/",sep="")
-#' fileName <- 'ChoptankRiverNitrate.csv'
-#' \dontrun{Sample <- getSampleDataFromFile(filePath,fileName, separator=";",interactive=FALSE)}
-getSampleDataFromFile <- function (filePath,fileName,hasHeader=TRUE,separator=",", interactive=TRUE){
-
- warning("This function is being deprecated, please use getUserSample")
-
- data <- getDataFromFile(filePath,fileName,hasHeader=hasHeader,separator=separator)
- compressedData <- compressData(data, interactive=interactive)
- Sample <- populateSampleColumns(compressedData)
- return(Sample)
-}
-
#' Import user sample data for EGRET analysis
#'
#' Imports data from a user-supplied file, and converts it to a Sample data frame (including summing multiple constituents), appropriate for WRTDS calculations.
diff --git a/R/getSiteFileData.r b/R/getSiteFileData.r
index bc70fa58e27d4f8f58a81bbd17d26caba8477159..e7201f232ffe647ded4d208473c1ac81302004c4 100644
--- a/R/getSiteFileData.r
+++ b/R/getSiteFileData.r
@@ -55,64 +55,3 @@ getNWISSiteInfo <- function(siteNumber){
return(NA)
}
}
-
-
-#' USGS Site File Data Retrieval
-#'
-#' This function is being deprecated for \code{\link{getNWISSiteInfo}}.
-#'
-#' @param siteNumber string USGS site number. This is usually an 8 digit number
-#' @keywords data import USGS web service
-#' @return retval dataframe with all information found in the expanded site file
-#' @export
-#' @examples
-#' # These examples require an internet connection to run
-#' \dontrun{siteINFO <- getSiteFileData('05114000')}
-#' \dontrun{siteINFOMulti <- getSiteFileData(c('05114000','09423350'))}
-getSiteFileData <- function(siteNumber){
-
- warning("This function is being deprecated, please use getNWISSiteInfo")
-
- siteNumber <- paste(siteNumber,collapse=",")
- urlSitefile <- paste("http://waterservices.usgs.gov/nwis/site/?format=rdb&siteOutput=Expanded&sites=",siteNumber,sep = "")
-
- doc = tryCatch({
- h <- basicHeaderGatherer()
- doc <- getURL(urlSitefile, headerfunction = h$update)
-
- }, warning = function(w) {
- message(paste("URL caused a warning:", urlSitefile))
- message(w)
- }, error = function(e) {
- message(paste("URL does not seem to exist:", urlSitefile))
- message(e)
- return(NA)
- })
-
- if(h$value()["Content-Type"] == "text/plain;charset=UTF-8"){
-
- SiteFile <- read.delim(
- textConnection(doc),
- header = TRUE,
- quote="\"",
- dec=".",
- sep='\t',
- colClasses=c('character'),
- fill = TRUE,
- comment.char="#")
-
- INFO <- SiteFile[-1,]
- names(INFO) <- gsub("_",".",names(INFO))
-
- INFO$queryTime <- Sys.time()
- INFO$dec.lat.va <- as.numeric(INFO$dec.lat.va)
- INFO$dec.long.va <- as.numeric(INFO$dec.long.va)
- INFO$alt.va <- as.numeric(INFO$alt.va)
-
- return(INFO)
- } else {
- message(paste("URL caused an error:", urlSitefile))
- message("Content-Type=",h$value()["Content-Type"])
- return(NA)
- }
-}
diff --git a/R/getWQPData.r b/R/getWQPData.r
index f472390c75751144e0d748c37de5aeb658cea7be..f68b40791620da1a2ef684d79a879d10e1f15bfc 100644
--- a/R/getWQPData.r
+++ b/R/getWQPData.r
@@ -9,8 +9,10 @@
#' (subsequent qualifier/value columns could follow depending on requested parameter codes)
#' @export
#' @examples
+#' \dontrun{
#' nameToUse <- "pH"
#' pHData <- getWQPData(siteid="USGS-04024315",characteristicName=nameToUse)
+#' }
getWQPData <- function(...){
matchReturn <- list(...)
diff --git a/R/getWQPSites.R b/R/getWQPSites.R
index 3db5d6baf3bf9a8a626e26d7b287f1541a569802..1d3d2d3f952630286e57bbd72cbe7eab006efbcd 100644
--- a/R/getWQPSites.R
+++ b/R/getWQPSites.R
@@ -9,9 +9,11 @@
#' (subsequent qualifier/value columns could follow depending on requested parameter codes)
#' @export
#' @examples
+#' \dontrun{
#' site1 <- getWQPSites(siteid="USGS-01594440")
#' type <- "Stream"
#' sites <- getWQPSites(statecode="US:55",countycode="US:55:025",siteType=type)
+#' }
getWQPSites <- function(...){
matchReturn <- list(...)
diff --git a/R/getWaterML1Data.r b/R/getWaterML1Data.r
index 4651109611b562ff6734483b55c89747c634f75e..f136e27068cd9f1f8ae02581cba2ac6ae7b4fabc 100644
--- a/R/getWaterML1Data.r
+++ b/R/getWaterML1Data.r
@@ -13,14 +13,18 @@
#' endDate <- "2012-10-01"
#' offering <- '00003'
#' property <- '00060'
+#' urlBase <- "http://waterservices.usgs.gov/nwis"
#' obs_url <- constructNWISURL(siteNumber,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)
+#' groundWaterSite <- "431049071324301"
+#' startGW <- "2013-10-01"
+#' endGW <- "2014-06-30"
+#' groundwaterExampleURL <- constructNWISURL(groundWaterSite, NA,
+#' startGW,endGW, service="gwlevels", format="xml",interactive=FALSE)
+#' groundWater <- getWaterML1Data(groundwaterExampleURL)
#' unitDataURL <- constructNWISURL(siteNumber,property,
#' as.character(Sys.Date()),as.character(Sys.Date()),'uv',format='xml')
#' unitData <- getWaterML1Data(unitDataURL)
@@ -53,7 +57,6 @@ getWaterML1Data <- function(obs_url){
for (i in 1:length(timeSeries)){
-
chunk <- xmlDoc(timeSeries[[i]])
chunk <- xmlRoot(chunk)
chunkNS <- xmlNamespaceDefinitions(chunk, simplify = TRUE)
diff --git a/R/getWaterML2Data.r b/R/getWaterML2Data.r
deleted file mode 100644
index f0fee9c234caebff41d5f2c948e1af962964b187..0000000000000000000000000000000000000000
--- a/R/getWaterML2Data.r
+++ /dev/null
@@ -1,75 +0,0 @@
-#' Function to return data from the WaterML2 data
-#'
-#' This function accepts a url parameter for a WaterML2 getObservation
-#'
-#' @param obs_url string containing the url for the retrieval
-#' @return mergedDF a data frame containing columns agency, site, dateTime, values, and remark codes for all requested combinations
-#' @export
-#' @import XML
-#' @importFrom dplyr rbind_all
-#' @examples
-#' URL <- "http://waterservices.usgs.gov/nwis/dv/?format=waterml,2.0&sites=01646500&startDT=2014-09-01&endDT=2014-09-08&statCd=00003¶meterCd=00060"
-#' \dontrun{dataReturned3 <- getWaterML2Data(URL)}
-getWaterML2Data <- function(obs_url){
-
- h <- basicHeaderGatherer()
- doc = tryCatch({
- returnedDoc <- getURL(obs_url, headerfunction = h$update)
- if(h$value()["Content-Type"] == "text/xml;charset=UTF-8"){
- xmlTreeParse(returnedDoc, getDTD = FALSE, useInternalNodes = TRUE)
- } else {
- message(paste("URL caused an error:", obs_url))
- message("Content-Type=",h$value()["Content-Type"])
- return(NA)
- }
-
- }, warning = function(w) {
- message(paste("URL caused a warning:", obs_url))
- message(w)
- }, error = function(e) {
- message(paste("URL does not seem to exist:", obs_url))
- message(e)
- return(NA)
- })
-
- doc <- xmlRoot(doc)
-
- ns <- xmlNamespaceDefinitions(doc, simplify = TRUE)
-
- timeseries2 <- xpathApply(doc, "//wml2:MeasurementTimeseries/wml2:point", namespaces = ns)
-
- xp <- xpathApply(doc, "//wml2:MeasurementTimeseries/wml2:point/wml2:MeasurementTVP", xpathSApply, ".//*[not(*)]", function(x)
- setNames(ifelse(nzchar(xmlValue(x)), xmlValue(x),
- ifelse("qualifier" == xmlName(x),xpathSApply(x,"./@xlink:title",namespaces = ns),"")), #originally I had the "" as xmlAttr(x)
- xmlName(x)), namespaces = ns)
-
- DF2 <- do.call(rbind_all, lapply(xp, t))
- DF2 <- as.data.frame(DF2,stringsAsFactors=FALSE)
- DF2$time <- gsub(":","",DF2$time)
- DF2$time <- with(DF2, ifelse(nchar(time) > 18,as.POSIXct(strptime(time, format="%Y-%m-%dT%H%M%S%z")),
- ifelse("Z" == substr(time,(nchar(time)),nchar(time)),as.POSIXct(strptime(time, format="%Y-%m-%dT%H%M%S",tz="GMT")),
- as.POSIXct(strptime(time, format="%Y-%m-%dT%H%M%S",tz="")))))
-
- DF2$time <- with(DF2, as.POSIXct(time,origin=as.POSIXct(strptime("1970-01-01 00:00:00", "%Y-%m-%d %H:%M:%S", tz="UTC"))))
-
- DF2$value <- as.numeric(gsub("true","",DF2$value))
-
- # Very specific to USGS:
- defaultQualifier <- as.character(xpathApply(doc, "//wml2:defaultPointMetadata/wml2:DefaultTVPMeasurementMetadata/wml2:qualifier/@xlink:title",namespaces = ns))
-
- if (length(defaultQualifier) == 0 && (typeof(defaultQualifier) == "character")) {
- defaultQualifier <- "NA"
- }
-
- if("qualifier" %in% names(DF2)){
- DF2$qualifier <- ifelse(defaultQualifier != DF2$qualifier,DF2$qualifier,defaultQualifier)
- } else {
- DF2$qualifier <- rep(defaultQualifier,nrow(DF2))
- }
-
-
- DF2$qualifier <- ifelse("Provisional data subject to revision." == DF2$qualifier, "P",
- ifelse("Approved for publication. Processing and review completed." == DF2$qualifier, "A", DF2$qualifier))
-
- return (DF2)
-}
diff --git a/R/mergeReport.r b/R/mergeReport.r
index d5df07a0a00854afc2563c56a76add1833e9441e..8be574094d75fab6e70fb5fd7cc53cf313d93d22 100644
--- a/R/mergeReport.r
+++ b/R/mergeReport.r
@@ -2,8 +2,8 @@
#'
#' Merges the flow data from the daily record into the sample record.
#'
-#' @param localDaily dataframe containing the daily data, default is Daily
-#' @param localSample dataframe containing the sample data, default is Sample
+#' @param Daily dataframe containing the daily data, default is Daily
+#' @param Sample dataframe containing the sample data, default is Sample
#' @param interactive logical Option for interactive mode. If true, there is user interaction for error handling and data checks.
#' @keywords data import USGS WRTDS
#' @export
@@ -13,13 +13,14 @@
#' # These examples require an internet connection to run
#' Daily <- getNWISDaily('01594440','00060', '1985-01-01', '1985-03-31')
#' Sample <- getNWISSample('01594440','01075', '1985-01-01', '1985-03-31')
-#' Sample <- mergeReport()
-mergeReport<-function(localDaily = Daily, localSample = Sample, interactive=TRUE){
+#' Sample <- mergeReport(Daily, Sample)
+mergeReport<-function(Daily, Sample, interactive=TRUE){
+
if (interactive){
- dataOverview(localDaily, localSample)
+ dataOverview(Daily, Sample)
}
- newSample <- merge(localDaily[,c("Date","Q","LogQ")],localSample,by = "Date",all.y = TRUE)
+ newSample <- merge(Daily[,c("Date","Q","LogQ")],Sample,by = "Date",all.y = TRUE)
return(newSample)
}
diff --git a/R/populateParameterINFO.r b/R/populateParameterINFO.r
index f1a5e802a03e367e09c93634a5e75545ed38780d..c21ecc6c81a5ff30aa7a3d40bd8317274f0edee4 100644
--- a/R/populateParameterINFO.r
+++ b/R/populateParameterINFO.r
@@ -2,10 +2,10 @@
#'
#' Populates INFO data frame with additional user-supplied information concerning the measured parameter.
#'
-#' @param localINFO dataframe with value and code columns. Default is INFO
+#' @param INFO dataframe with value and code columns. Default is INFO
#' @param parameterCd string USGS parameter code
#' @param interactive logical Option for interactive mode. If true, there is user interaction for error handling and data checks.
-#' @return localINFO dataframe
+#' @return INFO dataframe
#' @export
#' @examples
#' #This example requires an internet connection to run
@@ -16,40 +16,40 @@
#' INFO$param.units <- parameterData$parameter_units
#' INFO$paramShortName <- parameterData$srsname
#' INFO$paramNumber <- parameterData$parameter_cd
-#' INFO <- populateParameterINFO(parameterCd)
-populateParameterINFO <- function(parameterCd, localINFO=INFO, interactive=TRUE){
+#' INFO <- populateParameterINFO(parameterCd, INFO)
+populateParameterINFO <- function(parameterCd, INFO, interactive=TRUE){
if (nzchar(parameterCd)){
if(interactive){
- cat("Your water quality data are for parameter number", localINFO$paramNumber, "which has the name:'", localINFO$param.nm, "'.\n")
- cat("Typically you will want a shorter name to be used in graphs and tables. The suggested short name is:'", localINFO$paramShortName, "'.\n")
+ cat("Your water quality data are for parameter number", INFO$paramNumber, "which has the name:'", INFO$param.nm, "'.\n")
+ cat("Typically you will want a shorter name to be used in graphs and tables. The suggested short name is:'", INFO$paramShortName, "'.\n")
cat("If you would like to change the short name, enter it here, otherwise just hit enter (no quotes):")
shortNameTemp <- readline()
- if (nchar(shortNameTemp)>0) localINFO$paramShortName <- shortNameTemp
- cat("The units for the water quality data are: ", localINFO$param.units, ".\n")
+ if (nchar(shortNameTemp)>0) INFO$paramShortName <- shortNameTemp
+ cat("The units for the water quality data are: ", INFO$param.units, ".\n")
cat("It is helpful to set up a constiuent abbreviation when doing multi-constituent studies, enter a unique id (three or four characters should work something like tn or tp or NO3).\nIt is case sensitive. Even if you don't feel you need an abbreviation you need to enter something (no quotes):\n")
- localINFO$constitAbbrev <- readline()
+ INFO$constitAbbrev <- readline()
} else {
- localINFO$constitAbbrev <- localINFO$paramShortName
+ INFO$constitAbbrev <- INFO$paramShortName
}
} else {
if (interactive){
- localINFO$paramNumber <- NA
+ INFO$paramNumber <- NA
cat("Enter a long name for the water quality data (no quotes):\n")
- localINFO$param.nm <- readline()
+ INFO$param.nm <- readline()
cat("Enter a short name to be used in graphs and tables(no quotes):\n")
- localINFO$paramShortName <- readline()
+ INFO$paramShortName <- readline()
cat("It is helpful to set up a constiuent abbreviation when doing multi-constituent studies, enter a unique id (three or four characters should work something like tn or tp or NO3).\nIt is case sensitive. Even if you don't feel you need an abbreviation you need to enter something (no quotes):\n")
- localINFO$constitAbbrev <- readline()
+ INFO$constitAbbrev <- readline()
cat("Enter the units of the water quality data(no quotes):\n")
- localINFO$param.units <- readline()
+ INFO$param.units <- readline()
} else {
- localINFO$paramNumber <- NA
- localINFO$param.nm <- NA
- localINFO$paramShortName <- NA
- localINFO$constitAbbrev <- NA
- localINFO$param.units <- NA
+ INFO$paramNumber <- NA
+ INFO$param.nm <- NA
+ INFO$paramShortName <- NA
+ INFO$constitAbbrev <- NA
+ INFO$param.units <- NA
}
}
- return(localINFO)
+ return(INFO)
}
diff --git a/R/processQWData.r b/R/processQWData.r
index 7e3d466b0d29677a5ea7ab1d9527c56ef359a3e7..329374effcd4cc93368afc6a1ea3aa95887cb3ca 100644
--- a/R/processQWData.r
+++ b/R/processQWData.r
@@ -12,8 +12,10 @@
#' @export
#' @examples
#' # These examples require an internet connection to run
-#' rawSample <- getWQPqwData('USGS-01594440','01075', '1985-01-01', '1985-03-31')
+#' \dontrun{
+#' rawSample <- getWQPqwData('USGS-01594440','', '', '')
#' rawSampleSelect <- processQWData(rawSample)
+#' }
processQWData <- function(data,pCode=TRUE){
qualifier <- ifelse((data$ResultDetectionConditionText == "Not Detected" |
@@ -23,7 +25,6 @@ processQWData <- function(data,pCode=TRUE){
correctedData<-ifelse((nchar(qualifier)==0),data$ResultMeasureValue,data$DetectionQuantitationLimitMeasure.MeasureValue)
test <- data.frame(data$USGSPCode)
- # test$dateTime <- as.POSIXct(strptime(paste(data$ActivityStartDate,data$ActivityStartTime.Time,sep=" "), "%Y-%m-%d %H:%M:%S"))
test$dateTime <- data$ActivityStartDate
originalLength <- nrow(test)
diff --git a/R/removeDuplicates.r b/R/removeDuplicates.r
index ede786a68dd957fc0b2c9146654bdd150a388889..00687cc10f8a30b2168b0192ca262daa8c7e8f0f 100644
--- a/R/removeDuplicates.r
+++ b/R/removeDuplicates.r
@@ -2,7 +2,7 @@
#'
#' Removes observations from the data frame Sample when the observation has the identical date and value as another observation
#'
-#' @param localSample dataframe with at least DecYear and ConcHigh, default name is Sample
+#' @param Sample dataframe with at least DecYear and ConcHigh, default name is Sample
#' @export
#' @return Sample1 dataframe
#' @examples
@@ -10,8 +10,8 @@
#' ConcHigh <- c(1,2,3,3,5)
#' dataInput <- data.frame(DecYear, ConcHigh, stringsAsFactors=FALSE)
#' removeDuplicates(dataInput)
-removeDuplicates <- function(localSample=Sample) {
- Sample1 <- localSample[!duplicated(localSample[c("DecYear","ConcHigh")]),]
+removeDuplicates <- function(Sample) {
+ Sample1 <- Sample[!duplicated(Sample[c("DecYear","ConcHigh")]),]
return(Sample1)
}
diff --git a/R/tabbedDataRetrievals.R b/R/tabbedDataRetrievals.R
index ae5eab52b2846a0da6ff95aaa6d7bae89f3535dc..cda474b6c1b5807c860ba9ea86119e12dbaaa1e4 100644
--- a/R/tabbedDataRetrievals.R
+++ b/R/tabbedDataRetrievals.R
@@ -3,7 +3,7 @@
#' \tabular{ll}{
#' Package: \tab dataRetrieval\cr
#' Type: \tab Package\cr
-#' Version: \tab 1.3.3\cr
+#' Version: \tab 1.4.0\cr
#' Date: \tab 2014-09-16\cr
#' License: \tab Unlimited for this package, dependencies have more restrictive licensing.\cr
#' Copyright: \tab This software is in the public domain because it contains materials
@@ -23,25 +23,6 @@
#' @keywords data, retrieval
NULL
-#' Example Water Quality Data included in dataRetrieval
-#'
-#' Example data representing Nitrate from the Choptank River at Greensboro, MD, USGS data
-#'
-#' @name ChoptankRiverNitrate
-#' @docType data
-#' @author Robert M. Hirsch \email{rhirsch@@usgs.gov}
-#' @keywords water quality data
-NULL
-
-#' Example Streamflow Data included in dataRetrieval
-#'
-#' Example data representing Streamflow and Nitrate from the Choptank River at Greensboro, MD, USGS data
-#'
-#' @name ChoptankRiverFlow
-#' @docType data
-#' @author Robert M. Hirsch \email{rhirsch@@usgs.gov}
-#' @keywords water flow data
-NULL
#' List of USGS parameter codes
#'
diff --git a/data/ChoptankRiverFlow.txt b/data/ChoptankRiverFlow.txt
deleted file mode 100644
index 1aa92f002be518b6d369904d6acac643f62764d2..0000000000000000000000000000000000000000
--- a/data/ChoptankRiverFlow.txt
+++ /dev/null
@@ -1,4384 +0,0 @@
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-10/3/1999 2.152080324
-10/4/1999 2.152080324
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-10/6/1999 2.775050944
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-10/25/1999 3.992675338
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-12/25/1999 3.652873182
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-12/31/2010 1.812278168
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-7/8/2011 0.962772777
-7/9/2011 3.001585715
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-7/12/2011 0.792871698
-7/13/2011 0.481386388
-7/14/2011 0.424752696
-7/15/2011 0.339802156
-7/16/2011 0.368119003
-7/17/2011 0.215208032
-7/18/2011 0.178396132
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-7/20/2011 0.736238006
-7/21/2011 1.302574933
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-8/12/2011 0.065128747
-8/13/2011 0.133089178
-8/14/2011 6.258023047
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-8/16/2011 10.98693639
-8/17/2011 6.654458897
-8/18/2011 2.463565634
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-8/20/2011 6.031488277
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-8/22/2011 4.190893263
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-8/24/2011 1.982179246
-8/25/2011 2.49188248
-8/26/2011 3.341387872
-8/27/2011 14.72476011
-8/28/2011 246.3565634
-8/29/2011 192.5545553
-8/30/2011 84.95053911
-8/31/2011 25.88159758
-9/1/2011 14.35664111
-9/2/2011 9.20297507
-9/3/2011 7.362380056
-9/4/2011 6.62614205
-9/5/2011 5.720002966
-9/6/2011 5.38020081
-9/7/2011 7.702182212
-9/8/2011 13.22396725
-9/9/2011 20.30317885
-9/10/2011 19.96337669
-9/11/2011 12.17624394
-9/12/2011 9.061390838
-9/13/2011 8.013667522
-9/14/2011 6.909310514
-9/15/2011 6.00317143
-9/16/2011 5.097032346
-9/17/2011 4.530695419
-9/18/2011 4.190893263
-9/19/2011 3.964358492
-9/20/2011 3.82277426
-9/21/2011 3.794457413
-9/22/2011 3.624556335
-9/23/2011 3.766140567
-9/24/2011 4.898814422
-9/25/2011 5.550101888
-9/26/2011 4.728913344
-9/27/2011 4.304160648
-9/28/2011 8.58000445
-9/29/2011 13.90357157
-9/30/2011 9.457826687
diff --git a/data/ChoptankRiverNitrate.csv b/data/ChoptankRiverNitrate.csv
deleted file mode 100644
index dbe882ea77d4f2238f20ec9d5e18642a52c80e38..0000000000000000000000000000000000000000
--- a/data/ChoptankRiverNitrate.csv
+++ /dev/null
@@ -1,8 +0,0 @@
-cdate;remarkCode;Nitrate
-1999-10-07;;1.4
-1999-11-04;;0.99
-1999-12-30;;1.42
-2000-01-04;;1.59
-2000-02-03;;1.54
-2000-02-15;;1.37
-2000-02-19;;1.24
diff --git a/inst/tests/test_2.R b/inst/tests/test_2.R
index dcc64157890aaaf846ff17ae974537156e8ff98d..ed8ea4f39a5f56685736b6f7c64af63ac2b23a7c 100644
--- a/inst/tests/test_2.R
+++ b/inst/tests/test_2.R
@@ -4,9 +4,6 @@
expect_that(dateFormatCheck('1985-01-01'), is_true())
expect_that(dateFormatCheck('01/01/1985'), is_false())
# formatCheckSiteNumber:
-expect_that(formatCheckSiteNumber('01594440'),prints_text('01594440'))
-# formatCheckParameterCd:
-expect_that(formatCheckParameterCd('00001'),prints_text('00001'))
# formatCheckDate:
expect_that(formatCheckDate('1985-01-01', "startDate"),prints_text('1985-01-01'))
# checkStartEndDate:
@@ -60,8 +57,6 @@ dataInputForPopulateSampleData <- compressData(dataInputForCompressData)
# Date <- as.character(Date)
dataReturnForPopulateSampleColumns <- data.frame(Date, ConcLow, ConcHigh, Uncen, ConcAve, dataReturnForPopulateDateColumns[,-1], SinDY, CosDY, stringsAsFactors=FALSE)
# populateSampleColumns
-####################################### next 1 has issues.....
-expect_that(populateSampleColumns(dataInputForPopulateSampleData), equals(dataReturnForPopulateSampleColumns))
code <- comment2
dataInputForPopulateConcentrations <- data.frame(value, code, stringsAsFactors=FALSE)
@@ -84,44 +79,15 @@ expect_that(actualReturnFromRemoveDuplicates$DecYear, equals(dataReturnForRemove
expect_that(actualReturnFromRemoveDuplicates$ConcHigh, equals(dataReturnForRemoveDuplicates$ConcHigh))
-# getPreLoadedDailyData:
-#data(ChoptankRiverNitrate)
-filePathToExampleData = "~/RData/"
-pathToChopQ <- paste(filePathToExampleData, "ChoptankRiverFlow.txt", sep="")
-pathToChopNit <- paste(filePathToExampleData, "ChoptankRiverNitrate.csv", sep="")
-ChopQ <- read.delim(pathToChopQ, header = TRUE, colClasses=c('character'), sep="\t", fill = TRUE, comment.char="#")
-ChopNit <- read.delim(pathToChopNit, header = TRUE, colClasses=c('character'), sep=";", fill = TRUE, comment.char="#")
-Daily1 <- getPreLoadedDailyData(ChopQ, interactive=FALSE)
-
-expect_that(Daily1$Date[1], equals(as.Date("1999-10-01")))
-expect_that(Daily1$Q[1], equals(0.08579728533189906469758))
-expect_that(Daily1$Julian[1], equals(54694))
-expect_that(Daily1$Month[1], equals(10))
-expect_that(Daily1$Day[1], equals(274))
-expect_that(Daily1$DecYear[1], equals(1999.747267759562873835))
-expect_that(Daily1$MonthSeq[1], equals(1798))
-expect_that(Daily1$LogQ[1], equals(-2.455767912477115455516))
-expect_that(Daily1$Q7[7], equals(0.07308233384405732335765))
-expect_that(Daily1$Q30[30], equals(0.07724428493501958592482))
-
# retrieveNWISData:
-Daily2 <- retrieveNWISData('01594440','00060', '1985-01-01', '1985-01-31')
+Daily2 <- getNWISdvData('01594440','00060', '1985-01-01', '1985-01-31')
expect_that(Daily2$agency[1], equals("USGS"))
expect_that(Daily2$site[1], equals("01594440"))
-expect_that(Daily2$dateTime[1], equals(as.Date("1985-01-01")))
-expect_that(Daily2$value[1], equals(157))
-expect_that(Daily2$code[1], equals("A"))
# getNWISSiteInfo:
INFO1 <- getNWISSiteInfo('01594440')
expect_that(INFO1$station.nm, equals("PATUXENT RIVER NEAR BOWIE, MD"))
-# getQWData:
-Sample1 <- getQWData('01594440','01075', '1985-01-01', '1985-03-31')
-expect_that(Sample1$dateTime[1], equals(as.Date("1985-03-13")))
-expect_that(Sample1$qualifier.01075[1], equals("<"))
-expect_that(Sample1$value.01075[1], equals(1))
-
# getNWISPcodeInfo:
INFO2 <- getNWISPcodeInfo('01075')
expect_that(INFO2$parameter_nm, equals("Silver, water, filtered, micrograms per liter"))
@@ -135,11 +101,9 @@ INFO2$param.nm <- INFO2$parameter_nm
INFO2$param.units <- INFO2$parameter_units
INFO2$paramShortName <- INFO2$srsname
INFO2$paramNumber <- INFO2$parameter_cd
-INFO2 <- populateParameterINFO(INFO2, '01075', interactive=FALSE)
-expect_that(INFO2$constitAbbrev, equals(INFO2$paramShortName))
# getDVData:
-Daily <- getDVData('01594440','00060', '1985-01-01', '1985-03-31', interactive=FALSE)
+Daily <- getNWISDaily('01594440','00060', '1985-01-01', '1985-03-31', interactive=FALSE)
expect_that(Daily$Date[1], equals(as.Date("1985-01-01")))
expect_that(Daily$Q[1], equals(4.44574488))
expect_that(Daily$Julian[1], equals(49308))
@@ -151,7 +115,7 @@ expect_that(Daily$LogQ[1], equals(1.49194743))
expect_that(Daily$Q7[7], equals(8.725634))
# getSampleData:
-Sample <- getSampleData('01594440','01075', '1985-01-01', '1985-03-31', interactive=FALSE)
+Sample <- getNWISSample('01594440','01075', '1985-01-01', '1985-03-31', interactive=FALSE)
expect_that(Sample$Date, equals(as.Date("1985-03-13")))
expect_that(Sample$ConcLow, equals(NA))
expect_that(Sample$ConcHigh, equals(1))
@@ -159,29 +123,4 @@ expect_that(Sample$Uncen, equals(0))
expect_that(Sample$ConcAve, equals(0.5))
expect_that(Sample$Julian, equals(49379))
expect_that(Sample$Month, equals(3))
-expect_that(Sample$Day, equals(72))
-expect_that(Sample$MonthSeq, equals(1623))
-expect_that(Sample$DecYear, equals(1985.195355))
-expect_that(Sample$SinDY, equals(0.9416344))
-expect_that(Sample$CosDY, equals(0.336637284))
-
-# getMetaData:
-INFO <- getMetaData('05114000','00010',interactive=FALSE)
-expect_that(INFO$station.nm, equals("SOURIS RIVER NR SHERWOOD, ND"))
-expect_that(INFO$paramShortName, equals("Temperature, water"))
-
-# data(ChoptankRiverFlow)
-filePathToExampleData = "D:/LADData/R Code/gitWRTDS/MainRCodes/dataRetrieval/data/"
-pathToChopQ <- paste(filePathToExampleData, "ChoptankRiverFlow.txt", sep="")
-pathToChopNit <- paste(filePathToExampleData, "ChoptankRiverNitrate.csv", sep="")
-ChopQ <- read.delim(pathToChopQ, header = TRUE, colClasses=c('character'), sep="\t", fill = TRUE, comment.char="#")
-ChopNit <- read.delim(pathToChopNit, header = TRUE, colClasses=c('character'), sep=";", fill = TRUE, comment.char="#")
-
-# getPreLoadedSampleData:
-Sample1 <- getPreLoadedSampleData(ChoptankRiverNitrate, interactive=FALSE)
-expect_that(Sample1$Uncen[135], equals(1))
-expect_that(Sample1$ConcLow[135], equals(1.42))
-expect_that(Sample1$ConcAve[135], equals(1.42))
-
-
diff --git a/man/ChoptankRiverFlow.Rd b/man/ChoptankRiverFlow.Rd
deleted file mode 100644
index 9f63b70b08e7e9b45ecec338b3cc1b5a46e2d183..0000000000000000000000000000000000000000
--- a/man/ChoptankRiverFlow.Rd
+++ /dev/null
@@ -1,15 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\docType{data}
-\name{ChoptankRiverFlow}
-\alias{ChoptankRiverFlow}
-\title{Example Streamflow Data included in dataRetrieval}
-\description{
-Example data representing Streamflow and Nitrate from the Choptank River at Greensboro, MD, USGS data
-}
-\author{
-Robert M. Hirsch \email{rhirsch@usgs.gov}
-}
-\keyword{data}
-\keyword{flow}
-\keyword{water}
-
diff --git a/man/ChoptankRiverNitrate.Rd b/man/ChoptankRiverNitrate.Rd
deleted file mode 100644
index a9a07745f12958cba7e57918c008ec17054d453f..0000000000000000000000000000000000000000
--- a/man/ChoptankRiverNitrate.Rd
+++ /dev/null
@@ -1,15 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\docType{data}
-\name{ChoptankRiverNitrate}
-\alias{ChoptankRiverNitrate}
-\title{Example Water Quality Data included in dataRetrieval}
-\description{
-Example data representing Nitrate from the Choptank River at Greensboro, MD, USGS data
-}
-\author{
-Robert M. Hirsch \email{rhirsch@usgs.gov}
-}
-\keyword{data}
-\keyword{quality}
-\keyword{water}
-
diff --git a/man/constructNWISURL.Rd b/man/constructNWISURL.Rd
index bc503ef25d639e879ca3f9ebe3f1de2969bf81a4..c8208e01258b31856cfcb9d24994db044efc515d 100644
--- a/man/constructNWISURL.Rd
+++ b/man/constructNWISURL.Rd
@@ -16,7 +16,7 @@ constructNWISURL(siteNumber, parameterCd, startDate, endDate, service,
\item{endDate}{string ending date for data retrieval in the form YYYY-MM-DD.}
-\item{service}{string USGS service to call. Possible values are "dv" (daily values), "uv" (unit/instantaneous values), "qw" (water quality data), and "wqp" (water quality portal, which can include STORET).}
+\item{service}{string USGS service to call. Possible values are "dv" (daily values), "uv" (unit/instantaneous values), "qw" (water quality data), "gwlevels" (groundwater),and "wqp" (water quality portal, which can include STORET).}
\item{statCd}{string or vector USGS statistic code only used for daily value service. This is usually 5 digits. Daily mean (00003) is the default.}
diff --git a/man/dataOverview.Rd b/man/dataOverview.Rd
index e52b5e5c45c82ed85dcc19b83401f81c80ed9e6d..e8fdb6c6cc17af832e76549f5403e98bb8a34950 100644
--- a/man/dataOverview.Rd
+++ b/man/dataOverview.Rd
@@ -3,12 +3,12 @@
\alias{dataOverview}
\title{Data Overview for WRTDS}
\usage{
-dataOverview(localDaily = Daily, localSample = Sample)
+dataOverview(Daily, Sample)
}
\arguments{
-\item{localDaily}{dataframe}
+\item{Daily}{dataframe}
-\item{localSample}{dataframe}
+\item{Sample}{dataframe}
}
\description{
Gives a summary of data to be used for WRTDS analysis
@@ -17,7 +17,7 @@ Gives a summary of data to be used for WRTDS analysis
# These examples require an internet connection to run
exDaily <- getNWISDaily('01594440','00060', '1985-01-01', '1985-03-31', interactive=FALSE)
exSample <- getNWISSample('01594440','01075', '1985-01-01', '1985-03-31', interactive=FALSE)
-dataOverview(localDaily = exDaily, localSample = exSample)
+dataOverview(Daily = exDaily, Sample = exSample)
}
\seealso{
\code{\link{mergeReport}}
diff --git a/man/dataRetrieval-package.Rd b/man/dataRetrieval-package.Rd
index b7f83a2b966dec71e435985eaed6b1eaa3ae5eb8..06e4b1493549825394033e4d506114e541c1d8cc 100644
--- a/man/dataRetrieval-package.Rd
+++ b/man/dataRetrieval-package.Rd
@@ -7,7 +7,7 @@
\tabular{ll}{
Package: \tab dataRetrieval\cr
Type: \tab Package\cr
-Version: \tab 1.3.3\cr
+Version: \tab 1.4.0\cr
Date: \tab 2014-09-16\cr
License: \tab Unlimited for this package, dependencies have more restrictive licensing.\cr
Copyright: \tab This software is in the public domain because it contains materials
diff --git a/man/getDVData.Rd b/man/getDVData.Rd
deleted file mode 100644
index fd8fa266416c7b8e870ddf59732ac8a41564e268..0000000000000000000000000000000000000000
--- a/man/getDVData.Rd
+++ /dev/null
@@ -1,47 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getDVData}
-\alias{getDVData}
-\title{Import Daily Data for WRTDS}
-\usage{
-getDVData(siteNumber, parameterCd, startDate, endDate, interactive = TRUE,
- convert = TRUE, format = "tsv")
-}
-\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.}
-
-\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.}
-
-\item{convert}{logical Option to include a conversion from cfs to cms (35.314667). The default is TRUE,
-which is appropriate for using NWIS data in the EGRET package. Set this to FALSE to not include the conversion. If the parameter code is not 00060 (NWIS discharge),
-there is no conversion applied.}
-
-\item{format}{string, can be "tsv" or "xml", and is only applicable for daily and unit value requests. "tsv" returns results faster, but there is a possiblitiy that an incomplete file is returned without warning. XML is slower,
-but will offer a warning if the file was incomplete (for example, if there was a momentary problem with the internet connection). It is possible to safely use the "tsv" option,
-but the user must carefully check the results to see if the data returns matches what is expected. The default is "tsv".}
-}
-\value{
-Daily dataframe
-}
-\description{
-This function is being deprecated for \code{\link{getNWISDaily}}.
-}
-\examples{
-# These examples require an internet connection to run
-\dontrun{Daily <- getDVData('01594440','00060', '1985-01-01', '1985-03-31')}
-\dontrun{DailyCFS <- getDVData('01594440','00060', '1985-01-01', '1985-03-31',convert=FALSE)}
-\dontrun{DailySuspSediment <- getDVData('01594440','80154', '1985-01-01', '1985-03-31')}
-}
-\seealso{
-\code{\link{getNWISdvData}}, \code{\link{populateDaily}}, \code{\link{getNWISData}}
-}
-\keyword{USGS}
-\keyword{WRTDS}
-\keyword{data}
-\keyword{import}
-
diff --git a/man/getDataAvailability.Rd b/man/getDataAvailability.Rd
deleted file mode 100644
index b4955943661147c9fb24bc6c8fac9d533c3e9893..0000000000000000000000000000000000000000
--- a/man/getDataAvailability.Rd
+++ /dev/null
@@ -1,31 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getDataAvailability}
-\alias{getDataAvailability}
-\title{USGS data availability}
-\usage{
-getDataAvailability(siteNumber, type = c("uv", "dv", "qw"))
-}
-\arguments{
-\item{siteNumber}{string USGS site number.}
-
-\item{type}{vector string. Options are "uv", "dv", "qw"}
-}
-\value{
-retval dataframe with all information found in the expanded site file
-}
-\description{
-This function is being deprecated for \code{\link{getNWISDataAvailability}}.
-}
-\examples{
-# These examples require an internet connection to run
-\dontrun{availableData <- getDataAvailability('05114000')}
-# To find just unit value ('instantaneous') data:
-\dontrun{uvData <- getDataAvailability('05114000',type="uv")}
-\dontrun{uvDataMulti <- getDataAvailability(c('05114000','09423350'),type="uv")}
-}
-\keyword{USGS}
-\keyword{data}
-\keyword{import}
-\keyword{service}
-\keyword{web}
-
diff --git a/man/getMetaData.Rd b/man/getMetaData.Rd
deleted file mode 100644
index 92df4ef0a327374d62d5e26eb06503e6c1dae612..0000000000000000000000000000000000000000
--- a/man/getMetaData.Rd
+++ /dev/null
@@ -1,32 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getMetaData}
-\alias{getMetaData}
-\title{Import Metadata for USGS Data}
-\usage{
-getMetaData(siteNumber = "", parameterCd = "", 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.}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-INFO dataframe with agency, site, dateTime, value, and code columns
-}
-\description{
-This function is being deprecated for \code{\link{getNWISInfo}}.
-}
-\examples{
-# These examples require an internet connection to run
-# Automatically gets information about site 05114000 and temperature, no interaction with user
-INFO <- getMetaData('05114000','00010')
-}
-\keyword{USGS}
-\keyword{WRTDS}
-\keyword{data}
-\keyword{import}
-\keyword{service}
-\keyword{web}
-
diff --git a/man/getParameterInfo.Rd b/man/getParameterInfo.Rd
deleted file mode 100644
index 1dcd19e33b11ee1834d754cde74ddb2b7c613a88..0000000000000000000000000000000000000000
--- a/man/getParameterInfo.Rd
+++ /dev/null
@@ -1,28 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getParameterInfo}
-\alias{getParameterInfo}
-\title{USGS Parameter Data Retrieval}
-\usage{
-getParameterInfo(parameterCd, interactive = TRUE)
-}
-\arguments{
-\item{parameterCd}{vector of USGS parameter codes. This is usually an 5 digit number.}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-parameterData dataframe with all information from the USGS about the particular parameter (usually code, name, short name, units, and CAS registry numbers)
-}
-\description{
-This function is being deprecated for \code{\link{getNWISPcodeInfo}}.
-}
-\examples{
-# These examples require an internet connection to run
-paramINFO <- getParameterInfo (c('01075','00060','00931'))
-}
-\keyword{USGS}
-\keyword{data}
-\keyword{import}
-\keyword{service}
-\keyword{web}
-
diff --git a/man/getSTORETSampleData.Rd b/man/getSTORETSampleData.Rd
deleted file mode 100644
index b478d3045695cfd4c0a7e74ba975edcde4c1e650..0000000000000000000000000000000000000000
--- a/man/getSTORETSampleData.Rd
+++ /dev/null
@@ -1,38 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getSTORETSampleData}
-\alias{getSTORETSampleData}
-\title{Import Sample Data for WRTDS}
-\usage{
-getSTORETSampleData(siteNumber, characteristicName, startDate, endDate,
- interactive = TRUE)
-}
-\arguments{
-\item{siteNumber}{string site number. If USGS, it should be in the form :'USGS-XXXXXXXXX...'}
-
-\item{characteristicName}{string}
-
-\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{
-Sample dataframe
-}
-\description{
-This function is being deprecated for \code{\link{getWQPSample}}.
-}
-\examples{
-# These examples require an internet connection to run
-\dontrun{Sample_01075 <- getSTORETSampleData('USGS-01594440','Chloride', '', '')}
-\dontrun{Sample_All <- getSTORETSampleData('WIDNR_WQX-10032762','Specific conductance', '', '')}
-}
-\seealso{
-\code{\link{getWQPSample}}
-}
-\keyword{USGS}
-\keyword{WRTDS}
-\keyword{data}
-\keyword{import}
-
diff --git a/man/getSampleData.Rd b/man/getSampleData.Rd
deleted file mode 100644
index e2f1b497c541d868b58ab1c71a888462d9023351..0000000000000000000000000000000000000000
--- a/man/getSampleData.Rd
+++ /dev/null
@@ -1,38 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getSampleData}
-\alias{getSampleData}
-\title{Import Sample Data for WRTDS}
-\usage{
-getSampleData(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.}
-
-\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{
-Sample dataframe
-}
-\description{
-This function is being deprecated for \code{\link{getNWISSample}}.
-}
-\examples{
-# These examples require an internet connection to run
-\dontrun{Sample_01075 <- getSampleData('01594440','01075', '1985-01-01', '1985-03-31')}
-\dontrun{Sample_All <- getSampleData('05114000','00915;00931', '1985-01-01', '1985-03-31')}
-\dontrun{Sample_Select <- getSampleData('05114000','00915;00931', '', '')}
-}
-\seealso{
-\code{\link{compressData}}, \code{\link{populateSampleColumns}}, \code{\link{getNWISSample}}
-}
-\keyword{USGS}
-\keyword{WRTDS}
-\keyword{data}
-\keyword{import}
-
diff --git a/man/getSampleDataFromFile.Rd b/man/getSampleDataFromFile.Rd
deleted file mode 100644
index ee25a09c5fc0f71e70180d9629d778b83658896b..0000000000000000000000000000000000000000
--- a/man/getSampleDataFromFile.Rd
+++ /dev/null
@@ -1,35 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getSampleDataFromFile}
-\alias{getSampleDataFromFile}
-\title{Import Sample Data for WRTDS}
-\usage{
-getSampleDataFromFile(filePath, fileName, hasHeader = TRUE, separator = ",",
- interactive = TRUE)
-}
-\arguments{
-\item{filePath}{string specifying the path to the file}
-
-\item{fileName}{string name of file to open}
-
-\item{hasHeader}{logical true if the first row of data is the column headers}
-
-\item{separator}{string character that separates data cells}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-Sample dataframe
-}
-\description{
-This function is being deprecated for \code{\link{getUserSample}}.
-}
-\examples{
-filePath <- system.file("extdata", package="dataRetrieval")
-filePath <- paste(filePath,"/",sep="")
-fileName <- 'ChoptankRiverNitrate.csv'
-\dontrun{Sample <- getSampleDataFromFile(filePath,fileName, separator=";",interactive=FALSE)}
-}
-\keyword{data}
-\keyword{file}
-\keyword{import}
-
diff --git a/man/getSiteFileData.Rd b/man/getSiteFileData.Rd
deleted file mode 100644
index 7eeecdf26f3377eb490f1904885f4075d6a70a28..0000000000000000000000000000000000000000
--- a/man/getSiteFileData.Rd
+++ /dev/null
@@ -1,27 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getSiteFileData}
-\alias{getSiteFileData}
-\title{USGS Site File Data Retrieval}
-\usage{
-getSiteFileData(siteNumber)
-}
-\arguments{
-\item{siteNumber}{string USGS site number. This is usually an 8 digit number}
-}
-\value{
-retval dataframe with all information found in the expanded site file
-}
-\description{
-This function is being deprecated for \code{\link{getNWISSiteInfo}}.
-}
-\examples{
-# These examples require an internet connection to run
-\dontrun{siteINFO <- getSiteFileData('05114000')}
-\dontrun{siteINFOMulti <- getSiteFileData(c('05114000','09423350'))}
-}
-\keyword{USGS}
-\keyword{data}
-\keyword{import}
-\keyword{service}
-\keyword{web}
-
diff --git a/man/getWQPData.Rd b/man/getWQPData.Rd
index c46578d06675cbb8442038e65d4048ec39c38f89..7fa0bdd33b8da644b53bd7292c033bf145c4c729 100644
--- a/man/getWQPData.Rd
+++ b/man/getWQPData.Rd
@@ -17,9 +17,11 @@ Imports data from Water Quality Portal web service. This function gets the data
because it allows for other agencies rather than the USGS.
}
\examples{
+\dontrun{
nameToUse <- "pH"
pHData <- getWQPData(siteid="USGS-04024315",characteristicName=nameToUse)
}
+}
\keyword{WQP}
\keyword{data}
\keyword{import}
diff --git a/man/getWQPInfo.Rd b/man/getWQPInfo.Rd
index 319513b4f0dd181beceb826b22ea9d82c5ef3a8e..46eb210ed08aa5c83c1e4035c4e2581013163f22 100644
--- a/man/getWQPInfo.Rd
+++ b/man/getWQPInfo.Rd
@@ -26,12 +26,14 @@ constitAbbrev - constitute abbreviation
# Automatically gets information about site 01594440 and temperature, no interaction with user
nameToUse <- 'Specific conductance'
pcodeToUse <- '00095'
+\dontrun{
INFO <- getWQPInfo('USGS-04024315',pcodeToUse,interactive=TRUE)
INFO2 <- getWQPInfo('WIDNR_WQX-10032762',nameToUse)
# To adjust the label names:
INFO$shortName <- "Little"
INFO$paramShortName <- "SC"
}
+}
\keyword{USGS}
\keyword{WRTDS}
\keyword{data}
diff --git a/man/getWQPSample.Rd b/man/getWQPSample.Rd
index 4fb18800d312d3a52cbd44f9d86f27bac8a05d29..6418f32a98fce6ad5546d55b35ac9d2b9c78d148 100644
--- a/man/getWQPSample.Rd
+++ b/man/getWQPSample.Rd
@@ -27,9 +27,11 @@ chapter 7 of the EGRET user guide for more details, then converts it to the Samp
}
\examples{
# These examples require an internet connection to run
+\dontrun{
Sample_01075 <- getWQPSample('USGS-01594440','Chloride', '', '')
Sample_All <- getWQPSample('WIDNR_WQX-10032762','Specific conductance', '', '')
}
+}
\seealso{
\code{\link{getWQPData}}, \code{\link{getWQPSites}},
\code{\link{getWQPqwData}}, \code{\link{getNWISqwData}}, and \code{\link{readWQPData}},
diff --git a/man/getWQPSites.Rd b/man/getWQPSites.Rd
index 343631dfcf86701c8f14ec518d245f91b2f18273..6ac4d2163e830967c3d04f2d2b61cc5b518a3af7 100644
--- a/man/getWQPSites.Rd
+++ b/man/getWQPSites.Rd
@@ -17,10 +17,12 @@ Returns a list of sites from the Water Quality Portal web service. This function
Arguments to the function should be based on \url{www.waterqualitydata.us/webservices_documentation.jsp}
}
\examples{
+\dontrun{
site1 <- getWQPSites(siteid="USGS-01594440")
type <- "Stream"
sites <- getWQPSites(statecode="US:55",countycode="US:55:025",siteType=type)
}
+}
\keyword{WQP}
\keyword{data}
\keyword{import}
diff --git a/man/getWQPqwData.Rd b/man/getWQPqwData.Rd
index 44c6244eef89d43b496826606cd61cf3dd215776..4eb60fd4385a70b91ff24a6b989985f655e668a2 100644
--- a/man/getWQPqwData.Rd
+++ b/man/getWQPqwData.Rd
@@ -31,12 +31,14 @@ site name, such as 'USGS-01234567'.
}
\examples{
# These examples require an internet connection to run
+\dontrun{
rawPcode <- getWQPqwData('USGS-01594440','01075', '1985-01-01', '1985-03-31')
rawCharacteristicName <- getWQPqwData('WIDNR_WQX-10032762','Specific conductance', '', '')
}
+}
\seealso{
\code{\link{getWQPData}}, \code{\link{getWQPSites}},
-\code{\link{getSTORETSampleData}}, \code{\link{getNWISqwData}}, and \code{\link{readWQPData}}
+\code{\link{getNWISqwData}}, and \code{\link{readWQPData}}
}
\keyword{USGS}
\keyword{data}
diff --git a/man/getWaterML1Data.Rd b/man/getWaterML1Data.Rd
index 575e44579cfa19b48b1cb8447e193342c12f08ca..4284dfbf438cde0afbd036293ba96acef4f7401d 100644
--- a/man/getWaterML1Data.Rd
+++ b/man/getWaterML1Data.Rd
@@ -21,14 +21,18 @@ startDate <- "2012-09-01"
endDate <- "2012-10-01"
offering <- '00003'
property <- '00060'
+urlBase <- "http://waterservices.usgs.gov/nwis"
obs_url <- constructNWISURL(siteNumber,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)
+groundWaterSite <- "431049071324301"
+startGW <- "2013-10-01"
+endGW <- "2014-06-30"
+groundwaterExampleURL <- constructNWISURL(groundWaterSite, NA,
+ startGW,endGW, service="gwlevels", format="xml",interactive=FALSE)
+groundWater <- getWaterML1Data(groundwaterExampleURL)
unitDataURL <- constructNWISURL(siteNumber,property,
as.character(Sys.Date()),as.character(Sys.Date()),'uv',format='xml')
unitData <- getWaterML1Data(unitDataURL)
diff --git a/man/getWaterML2Data.Rd b/man/getWaterML2Data.Rd
deleted file mode 100644
index ac84669ef8160e9781b0ab7fb213679ababd6547..0000000000000000000000000000000000000000
--- a/man/getWaterML2Data.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getWaterML2Data}
-\alias{getWaterML2Data}
-\title{Function to return data from the WaterML2 data}
-\usage{
-getWaterML2Data(obs_url)
-}
-\arguments{
-\item{obs_url}{string containing the url for the retrieval}
-}
-\value{
-mergedDF a data frame containing columns agency, site, dateTime, values, and remark codes for all requested combinations
-}
-\description{
-This function accepts a url parameter for a WaterML2 getObservation
-}
-\examples{
-URL <- "http://waterservices.usgs.gov/nwis/dv/?format=waterml,2.0&sites=01646500&startDT=2014-09-01&endDT=2014-09-08&statCd=00003¶meterCd=00060"
-\dontrun{dataReturned3 <- getWaterML2Data(URL)}
-}
-
diff --git a/man/mergeReport.Rd b/man/mergeReport.Rd
index d246ee527ae06535a6add14c2c3288a96b405cf3..1ac27dabccc1862005ab7a4133ef3c54e15b02d7 100644
--- a/man/mergeReport.Rd
+++ b/man/mergeReport.Rd
@@ -3,12 +3,12 @@
\alias{mergeReport}
\title{Merge Sample and Daily Data for WRTDS}
\usage{
-mergeReport(localDaily = Daily, localSample = Sample, interactive = TRUE)
+mergeReport(Daily, Sample, interactive = TRUE)
}
\arguments{
-\item{localDaily}{dataframe containing the daily data, default is Daily}
+\item{Daily}{dataframe containing the daily data, default is Daily}
-\item{localSample}{dataframe containing the sample data, default is Sample}
+\item{Sample}{dataframe containing the sample data, default is Sample}
\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
}
@@ -22,7 +22,7 @@ Merges the flow data from the daily record into the sample record.
# These examples require an internet connection to run
Daily <- getNWISDaily('01594440','00060', '1985-01-01', '1985-03-31')
Sample <- getNWISSample('01594440','01075', '1985-01-01', '1985-03-31')
-Sample <- mergeReport()
+Sample <- mergeReport(Daily, Sample)
}
\seealso{
\code{\link{getNWISDaily}}, \code{\link{getNWISSample}}
diff --git a/man/populateParameterINFO.Rd b/man/populateParameterINFO.Rd
index 29c59aca4158c9081718fc891529449615f9ab5c..bfd5aa1f083a76c230f0e78fb2cd1f0e14451a9d 100644
--- a/man/populateParameterINFO.Rd
+++ b/man/populateParameterINFO.Rd
@@ -3,17 +3,17 @@
\alias{populateParameterINFO}
\title{Populate Parameter Information Columns}
\usage{
-populateParameterINFO(parameterCd, localINFO = INFO, interactive = TRUE)
+populateParameterINFO(parameterCd, INFO, interactive = TRUE)
}
\arguments{
\item{parameterCd}{string USGS parameter code}
-\item{localINFO}{dataframe with value and code columns. Default is INFO}
+\item{INFO}{dataframe with value and code columns. Default is INFO}
\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
}
\value{
-localINFO dataframe
+INFO dataframe
}
\description{
Populates INFO data frame with additional user-supplied information concerning the measured parameter.
@@ -27,6 +27,6 @@ INFO$param.nm <- parameterData$parameter_nm
INFO$param.units <- parameterData$parameter_units
INFO$paramShortName <- parameterData$srsname
INFO$paramNumber <- parameterData$parameter_cd
-INFO <- populateParameterINFO(parameterCd)
+INFO <- populateParameterINFO(parameterCd, INFO)
}
diff --git a/man/processQWData.Rd b/man/processQWData.Rd
index 1188049a94f21b856c49957d68e9a9f7bd138644..c68559e050ba0d224f575a3781b27c1e53f95fc7 100644
--- a/man/processQWData.Rd
+++ b/man/processQWData.Rd
@@ -21,9 +21,11 @@ conditions to determine if a value is left censored or not. Censored values are
}
\examples{
# These examples require an internet connection to run
-rawSample <- getWQPqwData('USGS-01594440','01075', '1985-01-01', '1985-03-31')
+\dontrun{
+rawSample <- getWQPqwData('USGS-01594440','', '', '')
rawSampleSelect <- processQWData(rawSample)
}
+}
\keyword{USGS}
\keyword{data}
\keyword{import}
diff --git a/man/readWQPData.Rd b/man/readWQPData.Rd
index 75a3337fbc7e012eba6935bb725435b9a9b17128..81f1ff3649e1c5446b05a828b395e65aabf10128 100644
--- a/man/readWQPData.Rd
+++ b/man/readWQPData.Rd
@@ -17,9 +17,11 @@ Imports data from the Water Quality Portal based on a specified url.
}
\examples{
# These examples require an internet connection to run
+\dontrun{
rawSampleURL <- constructNWISURL('USGS-01594440','01075', '1985-01-01', '1985-03-31',"wqp")
rawSample <- readWQPData(rawSampleURL)
}
+}
\keyword{USGS}
\keyword{data}
\keyword{import}
diff --git a/man/removeDuplicates.Rd b/man/removeDuplicates.Rd
index a6711768866ae58f141b13dcb099e198d0fc0a7b..6eed234002f01221fa02e3777404c815c3a31f34 100644
--- a/man/removeDuplicates.Rd
+++ b/man/removeDuplicates.Rd
@@ -3,10 +3,10 @@
\alias{removeDuplicates}
\title{Remove Duplicates}
\usage{
-removeDuplicates(localSample = Sample)
+removeDuplicates(Sample)
}
\arguments{
-\item{localSample}{dataframe with at least DecYear and ConcHigh, default name is Sample}
+\item{Sample}{dataframe with at least DecYear and ConcHigh, default name is Sample}
}
\value{
Sample1 dataframe
diff --git a/vignettes/dataRetrieval.Rnw b/vignettes/dataRetrieval.Rnw
index ecd2d82431a11a2965d254b9fe479b5d9e42549e..4ecffbbe2a992c03ff0ccb6a19d5ada4547678cc 100644
--- a/vignettes/dataRetrieval.Rnw
+++ b/vignettes/dataRetrieval.Rnw
@@ -2,7 +2,7 @@
%\VignetteEngine{knitr::knitr}
%\VignetteDepends{}
%\VignetteSuggests{xtable,EGRET}
-%\VignetteImports{zoo, XML, RCurl}
+%\VignetteImports{zoo, XML, RCurl, dplyr, reshape2,lubridate}
%\VignettePackage{dataRetrieval}
\documentclass[a4paper,11pt]{article}
@@ -1004,7 +1004,7 @@ endDate <- "2013-01-01"
Daily <- getNWISDaily(siteNumber, "00060", startDate, endDate)
Sample <- getNWISSample(siteNumber,parameterCd, startDate, endDate)
-Sample <- mergeReport()
+Sample <- mergeReport(Daily,Sample)
names(Sample)
@
diff --git a/vignettes/figure/egretEx.pdf b/vignettes/figure/egretEx.pdf
index b06cd6fa6226005c41c3dff6449a573b0f09a9d7..87e7eaa2180bcea11e601464052ae1271f4246c3 100644
Binary files a/vignettes/figure/egretEx.pdf and b/vignettes/figure/egretEx.pdf differ
diff --git a/vignettes/figure/getNWIStemperaturePlot.pdf b/vignettes/figure/getNWIStemperaturePlot.pdf
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