Latest build changed the formatting a little. I'm not sure why.

DESCRIPTION

@@ -13,47 +13,6 @@ Copyright: This software is in the public domain because it contains materials
     the United States Department of Interior. For more information, see the
     official USGS copyright policy at
     http://www.usgs.gov/visual-id/credit_usgs.html#copyright
-Collate:
-    'tabbedDataRetrievals.R'
-    'retrieveNWISData.r'
-    'getQWData.r'
-    'getSiteFileData.r'
-    'getDataFromFile.r'
-    'getParameterInfo.r'
-    'checkStartEndDate.r'
-    'dateFormatCheck.r'
-    'formatCheckDate.r'
-    'formatCheckParameterCd.r'
-    'formatCheckSiteNumber.r'
-    'getQWDataFromFile.r'
-    'populateDaily.r'
-    'compressData.r'
-    'populateSampleColumns.r'
-    'populateDateColumns.r'
-    'populateConcentrations.r'
-    'populateSiteINFO.r'
-    'populateParameterINFO.r'
-    'removeDuplicates.r'
-    'getDVData.r'
-    'getDailyDataFromFile.r'
-    'getSampleData.r'
-    'getSampleDataFromFile.r'
-    'getMetaData.r'
-    'mergeReport.r'
-    'dataOverview.r'
-    'getWQPData.r'
-    'retrieveUnitNWISData.r'
-    'getRawQWData.r'
-    'retrieveNWISqwData.r'
-    'processQWData.r'
-    'constructNWISURL.r'
-    'getDataAvailability.r'
-    'getWaterML1Data.r'
-    'padVariable.r'
-    'getRDB1Data.r'
-    'getSTORETSampleData.R'
-    'getWaterML2Data.r'
-    'renameColumns.R'
 Depends:
     R (>= 3.0)
 Imports:

man/ChoptankRiverFlow.Rd

@@ -3,14 +3,13 @@
 \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
+Example data representing Streamflow and Nitrate from the
+Choptank River at Greensboro, MD, USGS data
 }
 \author{
-  Robert M. Hirsch \email{rhirsch@usgs.gov}
+Robert M. Hirsch \email{rhirsch@usgs.gov}
 }
 \keyword{data}
-\keyword{datasets}
 \keyword{flow}
 \keyword{water}
 

man/ChoptankRiverNitrate.Rd

@@ -3,16 +3,15 @@
 \alias{ChoptankRiverNitrate}
 \title{Example Water Quality Data included in dataRetrieval}
 \description{
-  Example data representing Nitrate from the Choptank River
-  at Greensboro, MD, USGS data
-  \if{html}{\figure{Chop1.png}{Example Data}}
-  \if{latex}{\figure{Chop1.png}}
+Example data representing Nitrate from the Choptank River
+at Greensboro, MD, USGS data
+\if{html}{\figure{Chop1.png}{Example Data}}
+\if{latex}{\figure{Chop1.png}}
 }
 \author{
-  Robert M. Hirsch \email{rhirsch@usgs.gov}
+Robert M. Hirsch \email{rhirsch@usgs.gov}
 }
 \keyword{data}
-\keyword{datasets}
 \keyword{quality}
 \keyword{water}
 

man/checkStartEndDate.Rd

@@ -2,7 +2,7 @@
 \alias{checkStartEndDate}
 \title{checkStartEndDate}
 \usage{
-  checkStartEndDate(StartDate, EndDate, interactive = TRUE)
+checkStartEndDate(StartDate, EndDate, interactive = TRUE)
 }
 \arguments{
   \item{StartDate}{string}
@@ -14,12 +14,12 @@
   data checks.}
 }
 \value{
-  vector where first value is StartDate, second is EndDate
+vector where first value is StartDate, second is EndDate
 }
 \description{
-  Checks that the start date is before the end date.  If
-  not, it will give the user the opportunity to correct,
-  otherwise will create a warning.
+Checks that the start date is before the end date.  If not,
+it will give the user the opportunity to correct, otherwise
+will create a warning.
 }
 \examples{
 startDate <- '1985-01-01'

man/compressData.Rd

@@ -2,7 +2,7 @@
 \alias{compressData}
 \title{Compress sample data frame}
 \usage{
-  compressData(data, interactive = TRUE)
+compressData(data, interactive = TRUE)
 }
 \arguments{
   \item{data}{dataframe contains at least dateTime, value,
@@ -13,17 +13,17 @@
   data checks.}
 }
 \value{
-  dataframe returnDataFrame data frame containing dateTime,
-  ConcHigh, ConcLow, Uncen, ConcAve
+dataframe returnDataFrame data frame containing dateTime,
+ConcHigh, ConcLow, Uncen, ConcAve
 }
 \description{
-  Using raw data that has at least dateTime, value, code,
-  populates the measured data portion of the Sample data
-  frame used in WRTDS ConcLow = Lower bound for an observed
-  concentration ConcHigh = Upper bound for an observed
-  concentration ConcAve = Average of ConcLow and ConcHigh.
-  If ConcLow is NA, then ConcAve = ConcHigh/2 Uncen = 1 if
-  uncensored, 0 if censored
+Using raw data that has at least dateTime, value, code,
+populates the measured data portion of the Sample data
+frame used in WRTDS ConcLow = Lower bound for an observed
+concentration ConcHigh = Upper bound for an observed
+concentration ConcAve = Average of ConcLow and ConcHigh.
+If ConcLow is NA, then ConcAve = ConcHigh/2 Uncen = 1 if
+uncensored, 0 if censored
 }
 \examples{
 dateTime <- c('1985-01-01', '1985-01-02', '1985-01-03')

man/constructNWISURL.Rd

@@ -2,9 +2,8 @@
 \alias{constructNWISURL}
 \title{Construct NWIS url for data retrieval}
 \usage{
-  constructNWISURL(siteNumber, parameterCd, startDate,
-    endDate, service, statCd = "00003", format = "xml",
-    interactive = TRUE)
+constructNWISURL(siteNumber, parameterCd, startDate, endDate, service,
+  statCd = "00003", format = "xml", interactive = TRUE)
 }
 \arguments{
   \item{siteNumber}{string or vector of strings USGS site
@@ -44,16 +43,16 @@
   data checks.}
 }
 \value{
-  url string
+url string
 }
 \description{
-  Imports data from NWIS web service. This function gets
-  the data from here:
-  \url{http://nwis.waterdata.usgs.gov/nwis/qwdata} 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}
+Imports data from NWIS web service. This function gets the
+data from here:
+\url{http://nwis.waterdata.usgs.gov/nwis/qwdata} 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{
 siteNumber <- '01594440'

man/dataOverview.Rd

@@ -2,7 +2,7 @@
 \alias{dataOverview}
 \title{Data Overview for WRTDS}
 \usage{
-  dataOverview(localDaily = Daily, localSample = Sample)
+dataOverview(localDaily = Daily, localSample = Sample)
 }
 \arguments{
   \item{localDaily}{dataframe}
@@ -10,7 +10,7 @@
   \item{localSample}{dataframe}
 }
 \description{
-  Gives a summary of data to be used for WRTDS analysis
+Gives a summary of data to be used for WRTDS analysis
 }
 \examples{
 # These examples require an internet connection to run
@@ -19,7 +19,7 @@ exSample <- getSampleData('01594440','01075', '1985-01-01', '1985-03-31', intera
 dataOverview(localDaily = exDaily, localSample = exSample)
 }
 \seealso{
-  \code{\link{mergeReport}}
+\code{\link{mergeReport}}
 }
 \keyword{USGS}
 \keyword{WRTDS}

man/dataRetrieval-package.Rd

@@ -3,33 +3,33 @@
 \alias{dataRetrieval-package}
 \title{Retrieval functions for USGS data}
 \description{
-  \tabular{ll}{ Package: \tab dataRetrieval\cr Type: \tab
-  Package\cr Version: \tab 1.2.1\cr Date: \tab
-  2012-12-31\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 that originally came from
-  the United States Geological Survey, an agency of the
-  United States Department of Interior. For more
-  information, see the official USGS copyright policy at
-  http://www.usgs.gov/visual-id/credit_usgs.html#copyright\cr
-  LazyLoad: \tab yes\cr }
+\tabular{ll}{ Package: \tab dataRetrieval\cr Type: \tab
+Package\cr Version: \tab 1.2.1\cr Date: \tab 2012-12-31\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 that originally came from the United States
+Geological Survey, an agency of the United States
+Department of Interior. For more information, see the
+official USGS copyright policy at
+http://www.usgs.gov/visual-id/credit_usgs.html#copyright\cr
+LazyLoad: \tab yes\cr }
 }
 \details{
-  Collection of functions to help retrieve USGS data from
-  either web services or user provided data files.
+Collection of functions to help retrieve USGS data from
+either web services or user provided data files.
 }
 \author{
-  Robert M. Hirsch \email{rhirsch@usgs.gov}, Laura De Cicco
-  \email{ldecicco@usgs.gov}
+Robert M. Hirsch \email{rhirsch@usgs.gov}, Laura De Cicco
+\email{ldecicco@usgs.gov}
 }
 \references{
-  Hirsch, R. M., Moyer, D. L. and Archfield, S. A. (2010),
-  Weighted Regressions on Time, Discharge, and Season
-  (WRTDS), with an Application to Chesapeake Bay River
-  Inputs. JAWRA Journal of the American Water Resources
-  Association, 46: 857-880. doi:
-  10.1111/j.1752-1688.2010.00482.x
+Hirsch, R. M., Moyer, D. L. and Archfield, S. A. (2010),
+Weighted Regressions on Time, Discharge, and Season
+(WRTDS), with an Application to Chesapeake Bay River
+Inputs. JAWRA Journal of the American Water Resources
+Association, 46: 857-880. doi:
+10.1111/j.1752-1688.2010.00482.x
 }
 \keyword{data,}
 \keyword{retrieval}

man/dateFormatCheck.Rd

@@ -2,17 +2,17 @@
 \alias{dateFormatCheck}
 \title{dateFormatCheck}
 \usage{
-  dateFormatCheck(date)
+dateFormatCheck(date)
 }
 \arguments{
   \item{date}{string}
 }
 \value{
-  condition logical if TRUE,
+condition logical if TRUE,
 }
 \description{
-  Checks to see if format is YYYY-MM-DD. Also performs a
-  few other date checks.
+Checks to see if format is YYYY-MM-DD. Also performs a few
+other date checks.
 }
 \examples{
 date <- '1985-01-01'

man/formatCheckDate.Rd

@@ -2,7 +2,7 @@
 \alias{formatCheckDate}
 \title{formatCheckDate}
 \usage{
-  formatCheckDate(Date, dateString, interactive = TRUE)
+formatCheckDate(Date, dateString, interactive = TRUE)
 }
 \arguments{
   \item{Date}{string}
@@ -15,12 +15,12 @@
   data checks.}
 }
 \value{
-  condition logical if TRUE,
+condition logical if TRUE,
 }
 \description{
-  Response to the date format checker.  If the date is not
-  formated correctly, it will give the user the opportunity
-  to correct, otherwise will create a warning.
+Response to the date format checker.  If the date is not
+formated correctly, it will give the user the opportunity
+to correct, otherwise will create a warning.
 }
 \examples{
 Date <- '1985-01-01'

man/formatCheckParameterCd.Rd

@@ -2,7 +2,7 @@
 \alias{formatCheckParameterCd}
 \title{formatCheckParameterCd}
 \usage{
-  formatCheckParameterCd(ParameterCd, interactive = TRUE)
+formatCheckParameterCd(ParameterCd, interactive = TRUE)
 }
 \arguments{
   \item{ParameterCd}{string to check}
@@ -12,12 +12,12 @@
   data checks.}
 }
 \value{
-  ParameterCd string
+ParameterCd string
 }
 \description{
-  Checks that the parameter code is 5 digits. If it is
-  less, it will pad the string with zeros. If more, ask the
-  user to re-enter.
+Checks that the parameter code is 5 digits. If it is less,
+it will pad the string with zeros. If more, ask the user to
+re-enter.
 }
 \examples{
 pCode <- '01234'

man/formatCheckSiteNumber.Rd

@@ -2,7 +2,7 @@
 \alias{formatCheckSiteNumber}
 \title{formatCheckSiteNumber}
 \usage{
-  formatCheckSiteNumber(siteNumber, interactive = TRUE)
+formatCheckSiteNumber(siteNumber, interactive = TRUE)
 }
 \arguments{
   \item{siteNumber}{string to check}
@@ -12,15 +12,17 @@
   data checks.}
 }
 \value{
-  siteNumber string
+siteNumber string
 }
 \description{
-  Checks that the site code is 8 digits. If it is not 8
-  digits, it confirms with the user.
+Checks that the site code is at least 8 digits. If not, it
+confirms with the user.
 }
 \examples{
 site<- '01234567'
 formatCheckSiteNumber(site)
+site_incorrect <- '1234567'
+formatCheckSiteNumber(site_incorrect)
 }
 \keyword{WRTDS}
 \keyword{flow}

man/getDVData.Rd

@@ -2,8 +2,8 @@
 \alias{getDVData}
 \title{Import Daily Data for WRTDS}
 \usage{
-  getDVData(siteNumber, ParameterCd, StartDate, EndDate,
-    interactive = TRUE, convert = TRUE, format = "tsv")
+getDVData(siteNumber, ParameterCd, StartDate, EndDate, interactive = TRUE,
+  convert = TRUE, format = "tsv")
 }
 \arguments{
   \item{siteNumber}{string USGS site number.  This is
@@ -41,15 +41,15 @@
   expected. The default is "tsv".}
 }
 \value{
-  Daily dataframe
+Daily dataframe
 }
 \description{
-  Imports data from NWIS web service. This function gets
-  the data from here: \url{http://waterservices.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}
+Imports data from NWIS web service. This function gets the
+data from here: \url{http://waterservices.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}
 }
 \examples{
 # These examples require an internet connection to run
@@ -58,8 +58,7 @@ 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{retrieveNWISData}}, \code{\link{populateDaily}}
 }
 \keyword{USGS}
 \keyword{WRTDS}

man/getDailyDataFromFile.Rd

@@ -2,9 +2,8 @@
 \alias{getDailyDataFromFile}
 \title{Import Daily Data for WRTDS}
 \usage{
-  getDailyDataFromFile(filePath, fileName,
-    hasHeader = TRUE, separator = ",", qUnit = 1,
-    interactive = TRUE)
+getDailyDataFromFile(filePath, fileName, hasHeader = TRUE, separator = ",",
+  qUnit = 1, interactive = TRUE)
 }
 \arguments{
   \item{filePath}{string specifying the path to the file}
@@ -26,12 +25,11 @@
   data checks.}
 }
 \value{
-  Daily dataframe
+Daily dataframe
 }
 \description{
-  Imports data from a user-supplied file, and converts it
-  to a Daily data frame, appropriate for WRTDS
-  calculations.
+Imports data from a user-supplied file, and converts it to
+a Daily data frame, appropriate for WRTDS calculations.
 }
 \examples{
 # Examples of how to use getDailyDataFromFile:

man/getDataAvailability.Rd

@@ -2,7 +2,7 @@
 \alias{getDataAvailability}
 \title{USGS data availability}
 \usage{
-  getDataAvailability(siteNumber, interactive = TRUE)
+getDataAvailability(siteNumber, interactive = TRUE)
 }
 \arguments{
   \item{siteNumber}{string USGS site number.  This is
@@ -12,14 +12,14 @@
   If true, a progress indicator is printed to the console.}
 }
 \value{
-  retval dataframe with all information found in the
-  expanded site file
+retval dataframe with all information found in the expanded
+site file
 }
 \description{
-  Imports a table of available parameters, period of
-  record, and count. There is also an option to load the
-  long parameter names and additional information on the
-  parameters with longNames=TRUE.
+Imports a table of available parameters, period of record,
+and count. There is also an option to load the long
+parameter names and additional information on the
+parameters with longNames=TRUE.
 }
 \examples{
 # These examples require an internet connection to run

man/getDataFromFile.Rd

@@ -2,8 +2,7 @@
 \alias{getDataFromFile}
 \title{Basic Data Import for Water Flow Data}
 \usage{
-  getDataFromFile(filePath, fileName, hasHeader = TRUE,
-    separator = ",")
+getDataFromFile(filePath, fileName, hasHeader = TRUE, separator = ",")
 }
 \arguments{
   \item{filePath}{string specifying the path to the file}
@@ -17,14 +16,14 @@
   cells}
 }
 \value{
-  retval dataframe with dateTime, value, and code columns
+retval dataframe with dateTime, value, and code columns
 }
 \description{
-  Imports data from user-supplied data file. Specifically
-  used to import water flow data for use in the WRTDS
-  package. For WRTDS usage, the first column is expected to
-  be dates, the second column measured values. The third
-  column is optional, it contains any remark codes.
+Imports data from user-supplied data file. Specifically
+used to import water flow data for use in the WRTDS
+package. For WRTDS usage, the first column is expected to
+be dates, the second column measured values. The third
+column is optional, it contains any remark codes.
 }
 \examples{
 # Examples of how to use getDataFromFile:

man/getMetaData.Rd

@@ -2,8 +2,7 @@
 \alias{getMetaData}
 \title{Import Metadata for USGS Data}
 \usage{
-  getMetaData(siteNumber = "", parameterCd = "",
-    interactive = TRUE)
+getMetaData(siteNumber = "", parameterCd = "", interactive = TRUE)
 }
 \arguments{
   \item{siteNumber}{string USGS site number.  This is
@@ -17,22 +16,22 @@
   data checks.}
 }
 \value{
-  INFO dataframe with agency, site, dateTime, value, and
-  code columns
+INFO dataframe with agency, site, dateTime, value, and code
+columns
 }
 \description{
-  Populates INFO data frame for WRTDS study.  If either
-  station number or parameter code supplied, imports data
-  about a particular USGS site from NWIS web service. This
-  function gets the data from here:
-  \url{http://waterservices.usgs.gov/} A list of parameter
-  codes can be found here:
-  \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes/} If
-  either station number or parameter code is not supplied,
-  the user will be asked to input data. Additionally, the
-  user will be asked for: staAbbrev - station abbreviation,
-  will be used in naming output files and for structuring
-  batch jobs constitAbbrev - constitute abbreviation
+Populates INFO data frame for WRTDS study.  If either
+station number or parameter code supplied, imports data
+about a particular USGS site from NWIS web service. This
+function gets the data from here:
+\url{http://waterservices.usgs.gov/} A list of parameter
+codes can be found here:
+\url{http://nwis.waterdata.usgs.gov/nwis/pmcodes/} If
+either station number or parameter code is not supplied,
+the user will be asked to input data. Additionally, the
+user will be asked for: staAbbrev - station abbreviation,
+will be used in naming output files and for structuring
+batch jobs constitAbbrev - constitute abbreviation
 }
 \examples{
 # These examples require an internet connection to run

man/getParameterInfo.Rd

@@ -2,7 +2,7 @@
 \alias{getParameterInfo}
 \title{USGS Parameter Data Retrieval}
 \usage{
-  getParameterInfo(parameterCd, interactive = TRUE)
+getParameterInfo(parameterCd, interactive = TRUE)
 }
 \arguments{
   \item{parameterCd}{vector of USGS parameter codes.  This
@@ -13,15 +13,15 @@
   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)
+parameterData dataframe with all information from the USGS
+about the particular parameter (usually code, name, short
+name, units, and CAS registry numbers)
 }
 \description{
-  Imports data from NWIS about meaured parameter based on
-  user-supplied parameter code. This function gets the data
-  from here:
-  \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes}
+Imports data from NWIS about meaured parameter based on
+user-supplied parameter code. This function gets the data
+from here:
+\url{http://nwis.waterdata.usgs.gov/nwis/pmcodes}
 }
 \examples{
 # These examples require an internet connection to run

man/getQWData.Rd

@@ -2,8 +2,7 @@
 \alias{getQWData}
 \title{Data Import for USGS NWIS Water Quality Data}
 \usage{
-  getQWData(siteNumber, ParameterCd, StartDate, EndDate,
-    interactive = TRUE)
+getQWData(siteNumber, ParameterCd, StartDate, EndDate, interactive = TRUE)
 }
 \arguments{
   \item{siteNumber}{string USGS site number.  This is
@@ -26,19 +25,19 @@
   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)
+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}
+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

man/getQWDataFromFile.Rd

@@ -2,8 +2,7 @@
 \alias{getQWDataFromFile}
 \title{Basic Data Import}
 \usage{
-  getQWDataFromFile(filePath, fileName, hasHeader = TRUE,
-    separator = ",")
+getQWDataFromFile(filePath, fileName, hasHeader = TRUE, separator = ",")
 }
 \arguments{
   \item{filePath}{string specifying the path to the file}
@@ -17,16 +16,16 @@
   cells}
 }
 \value{
-  retval dataframe
+retval dataframe
 }
 \description{
-  Imports data from user-supplied data file. Specifically
-  used to import water quality data for use in the WRTDS
-  package. For WRTDS usage, the first column is expected to
-  be dates, the second column remarks (specifically < if
-  censored data), and the third column is measured values.
-  There can be additional columns of data, for each column
-  of data, there should be a remark column preceeding.
+Imports data from user-supplied data file. Specifically
+used to import water quality data for use in the WRTDS
+package. For WRTDS usage, the first column is expected to
+be dates, the second column remarks (specifically < if
+censored data), and the third column is measured values.
+There can be additional columns of data, for each column of
+data, there should be a remark column preceeding.
 }
 \examples{
 # Examples of how to use getQWDataFromFile: