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dataRetrieval dataRetrieval

CRAN version

The dataRetrieval package was created to simplify the process of loading hydrologic data into the R environment. It is designed to retrieve the major data types of U.S. Geological Survey (USGS) hydrology data that are available on the Web, as well as data from the Water Quality Portal (WQP), which currently houses water quality data from the Environmental Protection Agency (EPA), U.S. Department of Agriculture (USDA), and USGS. Direct USGS data is obtained from a service called the National Water Information System (NWIS).

For complete tutorial information, see:

https://doi-usgs.github.io/dataRetrieval/

https://waterdata.usgs.gov/blog/dataretrieval/

dataRetrieval Introduction 1

dataRetrieval Introduction 2

⚠️ USGS discrete water-quality data availability and format are changing. Beginning in mid-March 2024 the data obtained from legacy profiles will not include new USGS data or recent updates to existing data. To view the status of changes in data availability and code functionality, visit: https://doi-usgs.github.io/dataRetrieval/articles/Status.html

If you have additional questions about these changes, email CompTools@usgs.gov.

Sample Workflow

USGS

library(dataRetrieval)
# Choptank River near Greensboro, MD
siteNumber <- "01491000"
ChoptankInfo <- readNWISsite(siteNumber)
parameterCd <- "00060"

# Raw daily data:
rawDailyData <- readNWISdv(
  siteNumber, parameterCd,
  "1980-01-01", "2010-01-01"
)

pCode <- readNWISpCode(parameterCd)

Water Quality Portal

specificCond <- readWQPqw(
  siteNumbers = "WIDNR_WQX-10032762",
  parameterCd = "Specific conductance",
  startDate = "2011-05-01",
  endDate = "2011-09-30"
)

Network Linked Data Index

features <- findNLDI(
  nwis = "01491000",
  nav = "UT",
  find = c("basin", "wqp")
)

Installation of dataRetrieval

To install the dataRetrieval package, you must be using R 3.0 or greater and run the following command:

install.packages("dataRetrieval")

To get cutting-edge changes, install from GitHub using the remotes packages:

library(remotes)
install_github("DOI-USGS/dataRetrieval",
               build_vignettes = TRUE, 
               build_opts = c("--no-resave-data",
                              "--no-manual"))

Reporting bugs

Please consider reporting bugs and asking questions on the Issues page: https://github.com/DOI-USGS/dataRetrieval/issues

Citations

Citing the dataRetrieval package

citation(package = "dataRetrieval")
#> To cite dataRetrieval in publications, please use:
#> 
#>   De Cicco, L.A., Hirsch, R.M., Lorenz, D., Watkins, W.D., Johnson, M.,
#>   2024, dataRetrieval: R packages for discovering and retrieving water
#>   data available from Federal hydrologic web services, v.2.7.15,
#>   doi:10.5066/P9X4L3GE
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     author = {Laura DeCicco and Robert Hirsch and David Lorenz and David Watkins and Mike Johnson},
#>     title = {dataRetrieval: R packages for discovering and retrieving water data available from U.S. federal hydrologic web services},
#>     publisher = {U.S. Geological Survey},
#>     address = {Reston, VA},
#>     version = {2.7.15},
#>     institution = {U.S. Geological Survey},
#>     year = {2024},
#>     doi = {10.5066/P9X4L3GE},
#>     url = {https://code.usgs.gov/water/dataRetrieval},
#>   }

Citing NWIS data

U.S. Geological Survey, 2023, National Water Information System data available on the World Wide Web (USGS Water Data for the Nation), accessed [April 26, 2023], at http://waterdata.usgs.gov/nwis/. http://dx.doi.org/10.5066/F7P55KJN

This can be done using the create_NWIS_bib function:

dv <- readNWISdv("09010500", "00060")

NWIScitation <- create_NWIS_bib(dv)

NWIScitation
#> U.S. Geological Survey (2024). _National Water Information System data
#> available on the World Wide Web (USGS Water Data for the Nation)_.
#> doi:10.5066/F7P55KJN <https://doi.org/10.5066/F7P55KJN>, Accessed Feb
#> 20, 2024,
#> <https://waterservices.usgs.gov/nwis/dv/?site=09010500&format=waterml,1.1&ParameterCd=00060&StatCd=00003&startDT=1851-01-01>.
print(NWIScitation, style = "Bibtex")
#> @Manual{,
#>   title = {National Water Information System data available on the World Wide Web (USGS Water Data for the Nation)},
#>   author = {{U.S. Geological Survey}},
#>   doi = {10.5066/F7P55KJN},
#>   note = {Accessed Feb 20, 2024},
#>   year = {2024},
#>   url = {https://waterservices.usgs.gov/nwis/dv/?site=09010500&format=waterml,1.1&ParameterCd=00060&StatCd=00003&startDT=1851-01-01},
#> }

Citing WQP data

Citations for specific datasets should use this format:

National Water Quality Monitoring Council, YYYY, Water Quality Portal, accessed mm, dd, yyyy, hyperlink_for_query, https://doi.org/10.5066/P9QRKUVJ.

This can be done using the create_WQP_bib function:

SC <- readWQPqw(siteNumbers = "USGS-05288705",
                parameterCd = "00300")

WQPcitation <- create_WQP_bib(SC)
WQPcitation
#> National Water Quality Monitoring Council (2024). _ Water Quality
#> Portal_. doi:10.5066/P9QRKUVJ <https://doi.org/10.5066/P9QRKUVJ>,
#> Accessed Feb 20, 2024,
#> <https://www.waterqualitydata.us/data/Result/search?siteid=USGS-05288705&pCode=00300&mimeType=tsv&zip=yes>.
print(WQPcitation, style = "Bibtex")
#> @Manual{,
#>   title = { Water Quality Portal},
#>   author = {{National Water Quality Monitoring Council}},
#>   doi = {10.5066/P9QRKUVJ},
#>   note = {Accessed Feb 20, 2024},
#>   year = {2024},
#>   url = {https://www.waterqualitydata.us/data/Result/search?siteid=USGS-05288705&pCode=00300&mimeType=tsv&zip=yes},
#> }

Citing Water Quality Portal itself

General Water Quality Portal citations should use the following:

Water Quality Portal. Washington (DC): National Water Quality Monitoring Council, United States Geological Survey (USGS), Environmental Protection Agency (EPA); 2021. https://doi.org/10.5066/P9QRKUVJ.

Package Support

The Water Mission Area of the USGS supports the development and maintenance of dataRetrieval, and most likely further into the future. Resources are available primarily for maintenance and responding to user questions. Priorities on the development of new features are determined by the dataRetrieval development team. This software was last released with USGS record: IP-147158.

Disclaimer

This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The software has not received final approval by the U.S. Geological Survey (USGS). No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. The software is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the software.

About

This R package is designed to obtain USGS or EPA water quality sample data, streamflow data, and metadata directly from web services.

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