Package 'dataRetrieval'

Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey and U.S. Environmental Protection Agency water quality and hydrology data from web services. Data are discovered from National Water Information System <https://waterservices.usgs.gov/> and <https://waterdata.usgs.gov/nwis>. Water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.
Authors: Laura DeCicco [aut, cre] , Robert Hirsch [aut] , David Lorenz [aut], Jordan Read [ctb], Jordan Walker [ctb], Lindsay Platt [ctb], David Watkins [aut] , David Blodgett [aut] , Mike Johnson [aut] , Aliesha Krall [ctb] , Lee Stanish [ctb]
Maintainer: Laura DeCicco <[email protected]>
License: CC0
Version: 2.7.17.9000
Built: 2024-11-05 17:16:08 UTC
Source: https://github.com/doi-usgs/dataretrieval

Help Index

add a water year column

Description

Add a column to the dataRetrieval data frame with the water year. WQP queries will return a water year column for the start and end dates of the data.

Usage

addWaterYear(rawData)

Arguments

rawData

the daily- or unit-values datset retrieved from NWISweb. Must have at least one of the following columns to add the new water year columns: 'dateTime', 'Date', 'ActivityStartDate', or 'ActivityEndDate'. The date column(s) can be character, POSIXct, Date. They cannot be numeric.

Value

data.frame with an additional integer column with "WY" appended to the date column name. For WQP, there will be 2 columns: 'ActivityStartDateWY' and 'ActivityEndDateWY'.

Examples

nwisData <- readNWISdv("04085427", "00060", "2022-01-01", "2022-06-30")
nwisData <- addWaterYear(nwisData)

wqpData <- readWQPqw("USGS-01594440", "01075", "", "")
wqpData <- addWaterYear(wqpData)

Extract WY from a date

Description

Determine the correct water year based on a calendar date.

Usage

calcWaterYear(dateVec)

Arguments

dateVec

vector of dates as character ("YYYY-DD-MM"), Date, or POSIXct. Numeric does not work.

Details

This function calculates a water year based on the USGS definition that a water year starts on October 1 of the year before, and ends on September 30. For example, water year 2015 started on 2014-10-01 and ended on 2015-09-30.

Value

numeric vector indicating the water year

Examples

x <- seq(as.Date("2010-01-01"), as.Date("2010-12-31"), by = "month")
calcWaterYear(x)

y <- c("2010-01-01", "1994-02", "1980", "2009-11-01", NA)
calcWaterYear(y)

Date Check for Water Quality Portal

Description

Checks date format for inputs to the Water Quality Portal. Used in readWQPqw and readWQPdata.

Usage

checkWQPdates(values)

Arguments

values

named list with arguments to send to the Water Quality Portal

Value

values named list with corrected arguments to send to the Water Quality Portal

Examples

values <- list(
  startDateLo = "01-01-2002",
  characteristicName = "Phosphorous",
  endDate = as.Date("2014-01-01")
)
values <- checkWQPdates(values)

Construct NWIS url for data retrieval

Description

Imports data from NWIS web service.

Usage

constructNWISURL(
  siteNumbers,
  parameterCd = "00060",
  startDate = "",
  endDate = "",
  service,
  statCd = "00003",
  format = "xml",
  expanded = TRUE,
  ratingType = "base",
  statReportType = "daily",
  statType = "mean"
)

Arguments

siteNumbers

string or vector of strings USGS site number. This is usually an 8 digit number
parameterCd

string or vector of USGS parameter code. This is usually an 5 digit number.
startDate

character starting date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates retrieval for the earliest possible record.
endDate

character ending date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates retrieval for the latest possible record.
service

string USGS service to call. Possible values are "dv" (daily values), "uv" (unit/instantaneous values), "gwlevels" (groundwater),and "rating" (rating curve), "peak", "meas" (discrete streamflow measurements), "stat" (statistics web service BETA).
statCd

string or vector USGS statistic code only used for daily value service. This is usually 5 digits. Daily mean (00003) is the default.
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 possibility 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".
expanded

logical defaults to TRUE. If TRUE, retrieves additional information, only applicable for qw data.
ratingType

can be "base", "corr", or "exsa". Only applies to rating curve data.
statReportType

character Only used for statistics service requests. Time division for statistics: daily, monthly, or annual. Default is daily. Note that daily provides statistics for each calendar day over the specified range of water years, i.e. no more than 366 data points will be returned for each site/parameter. Use readNWISdata or readNWISdv for daily averages. Also note that "annual" returns statistics for the calendar year. Use readNWISdata for water years. Monthly and yearly provide statistics for each month and year within the range individually.
statType

character Only used for statistics service requests. Type(s) of statistics to output for daily values. Default is mean, which is the only option for monthly and yearly report types. See the statistics service documentation at https://waterservices.usgs.gov/docs/statistics/ for a full list of codes.

Value

url string

Examples

site_id <- "01594440"
startDate <- "1985-01-01"
endDate <- ""
pCode <- c("00060", "00010")
url_daily <- constructNWISURL(site_id, pCode,
  startDate, endDate, "dv",
  statCd = c("00003", "00001")
)
url_unit <- constructNWISURL(site_id, pCode, "2012-06-28", "2012-06-30", "iv")

url_qw_single <- constructNWISURL(site_id, "01075", startDate, endDate, "qw")
url_qw <- constructNWISURL(
  site_id, c("01075", "00029", "00453"),
  startDate, endDate, "qw"
)
url_daily_tsv <- constructNWISURL(site_id, pCode, startDate, endDate, "dv",
  statCd = c("00003", "00001"), format = "tsv"
)
url_rating <- constructNWISURL(site_id, service = "rating", ratingType = "base")
url_peak <- constructNWISURL(site_id, service = "peak")
url_meas <- constructNWISURL(site_id, service = "meas")
url_gwl <- constructNWISURL(site_id, service = "gwlevels",
                            startDate = "2024-05-01", endDate = "2024-05-30")

Construct URL for NWIS water use data service

Description

Reconstructs URLs to retrieve data from here: https://waterdata.usgs.gov/nwis/wu

Usage

constructUseURL(years, stateCd, countyCd, categories)

Arguments

years

integer Years for data retrieval. Must be years ending in 0 or 5, or "ALL", which retrieves all available years.
stateCd

could be character (full name, abbreviation, id), or numeric (id)
countyCd

could be numeric (County IDs from countyCdLookup) or character ("ALL")
categories

character Two-letter cateogory abbreviation(s)

Value

url string

Examples

url <- constructUseURL(
  years = c(1990, 1995),
  stateCd = "Ohio",
  countyCd = c(1, 3),
  categories = "ALL"
)

Construct WQP url for data retrieval

Description

Construct WQP url for data retrieval. This function gets the data from here: https://www.waterqualitydata.us

Usage

constructWQPURL(siteNumbers, parameterCd, startDate, endDate, legacy = TRUE)

Arguments

siteNumbers

string or vector of strings USGS site number.
parameterCd

string or vector of USGS parameter code. This is usually an 5 digit number.
startDate

character starting date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates retrieval for the earliest possible record.
endDate

character ending date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates retrieval for the latest possible record.
legacy

Logical. If TRUE, uses legacy WQP services. Default is TRUE. Setting legacy = FALSE uses WQX3.0 WQP services, which are in-development, use with caution.

Value

url string

Examples

site_ids <- c("USGS-02292010", "USGS-02276877")
startDate <- "2020-01-01"
endDate <- ""
pCode <- c("80154", "00613")
url_wqp <- constructWQPURL(
  site_ids,
  pCode,
  startDate, endDate
)
url_wqp
charNames <- c(
  "Temperature",
  "Temperature, sample",
  "Temperature, water",
  "Temperature, water, deg F"
)
obs_url_orig <- constructWQPURL(
  siteNumbers = c(
    "IIDFG-41WSSPAHS",
    "USGS-02352560"
  ),
  parameterCd = charNames,
  startDate, ""
)
obs_url_orig

US County Code Lookup Table

Description

Data originally pulled from https://www2.census.gov/geo/docs/reference/codes/files/national_county.txt on April 1, 2015. On Feb. 11, 2022, the fields were updated with the file found in inst/extdata, which is used internally with NWIS retrievals.

Value

countyCd data frame.

Name Type Description
STUSAB character State abbreviation
STATE character two-digit ANSI code
COUNTY character three-digit county code
COUNTY_NAME character County full name
COUNTY_ID character County id

Examples

head(countyCd)

County code look up

Description

Function to simplify finding county and county code definitions. Used in readNWISdata and readNWISuse.

Usage

countyCdLookup(state, county, outputType = "id")

Arguments

state

could be character (full name, abbreviation, id), or numeric (id)
county

could be character (name, with or without "County") or numeric (id)
outputType

character can be "fullName", "tableIndex", "id", or "fullEntry".

Examples

id <- countyCdLookup(state = "WI", county = "Dane")
name <- countyCdLookup(state = "OH", county = 13, output = "fullName")
index <- countyCdLookup(state = "Pennsylvania", county = "ALLEGHENY COUNTY", output = "tableIndex")
fromIDs <- countyCdLookup(state = 13, county = 5, output = "fullName")
already_correct <- countyCdLookup(county = "51001")

Create NWIS data citation

Description

Uses attributes from the NWIS functions to create data citations.

Usage

create_NWIS_bib(x)

Arguments

x

Any data returned from an NWIS function, must include "queryTime" and "url" attributes, which should come with the data by default.

Details

See ?bibentry for more information.

Value

bibentry object to use for citing the data.

Examples

nwisData <- readNWISdv("04085427", "00060", "2012-01-01", "2012-06-30")
nwis_citation <- create_NWIS_bib(nwisData)
nwis_citation

print(nwis_citation, style = "Bibtex")
print(nwis_citation, style = "citation")

Create WQP data citation

Description

Uses attributes from the WQP functions to create data citations.

Usage

create_WQP_bib(x)

Arguments

x

Any data returned from an NWIS function, must include "queryTime" and "url" attributes, which should come with the data by default.

Details

See ?bibentry for more information.

Value

bibentry object to use for citing the data.

Examples

WQPData <- readWQPqw("USGS-05288705",
                     parameterCd = "00300")
wqp_citation <- create_WQP_bib(WQPData)
wqp_citation

print(wqp_citation, style = "Bibtex")
print(wqp_citation, style = "citation")

R Client for the Network Linked Data Index

Description

Provides a formal client to the USGS Network Linked Data Index.

Usage

findNLDI(
  comid = NULL,
  nwis = NULL,
  wqp = NULL,
  huc12 = NULL,
  location = NULL,
  origin = NULL,
  nav = NULL,
  find = c("flowlines"),
  distance_km = 100,
  no_sf = FALSE,
  warn = TRUE
)

Arguments

comid

numeric or character. An NHDPlusV2 COMID
nwis

numeric or character. A USGS NWIS surface water siteID
wqp

numeric or character. A water quality point ID
huc12

numeric or character. A WBD HUC12 unit ID
location

numeric vector. Coordinate pair in WGS84 SRS ordered lng/lat (X,Y)
origin

named list. Specifying a feature type and ID (e.g. list("comid" = 101))
nav

character vector. where to navigate from the starting point. Options include along the upper mainsteam (UM), upstream tributary (UT), downstream mainstem (DM) and downstream divergences (DD). You may select one or more of the abbreviations ("UM", "UT", DM", "DD").
find

character vector. Define what resources to find along the navigation path(s) (see get_nldi_sources()$source). Can also include 'basin' or 'flowline', which will return the upstream basin of the starting feature or flowlines along the navigation respectively. The default is "flowlines". If you provide any other resource, AND want flowlines, then flowlines must be explicitly requested.
distance_km

numeric. Define how far to look along the navigation path in kilometers (default = 100)
no_sf

if available, should 'sf' be used for parsing, defaults to 'TRUE' if 'sf' is locally installed
warn

(default TRUE) should warnings be printed

Details

The function is useful for topology and location based feature discovery. A user must specify an origin feature, optional navigation direction(s) along the network, as well as features to identify along the navigated paths. Valid starting options can be given by one of the following arguments: comid, nwis, huc12, wqp, location, and start.

Value

a list of data.frames if sf is not installed, a list of sf objects if it is

Examples

# Find Features / Define origin features

## Find feature by COMID
findNLDI(comid = 101)

## Find feature by NWIS ID
findNLDI(nwis = "11120000")

## Find feature by WQP ID
findNLDI(wqp = "USGS-04024315")

## Find feature by LOCATION
findNLDI(location = c(-115, 40))

## GENERAL ORIGIN: COMID
findNLDI(origin = list("comid" = 101))

## GENERAL ORIGIN: WaDE
findNLDI(origin = list("wade" = "CA_45206"))

# Navigation (flowlines will be returned if find is unspecified)
# UPPER MAINSTEM of USGS-11120000
findNLDI(nwis = "11120000", nav = "UM")

# MULTI-REQUEST
# UPPER MAINSTEM and TRIBUTARY of USGS-11120000
findNLDI(nwis = "11120000", nav = c("UT", "UM"))

# Discover Features(flowlines will not be returned unless included in find)

## Find feature(s) on the upper tributary of USGS-11120000
findNLDI(nwis = "11120000", nav = "UT", find = c("nwis", "wqp"))

## Find upstream basin boundary and  of USGS-11120000
findNLDI(nwis = "11120000", find = "basin")

# Control Distance
## Limit search to 50 km
findNLDI(comid = 101, nav = "DM", find = c("nwis", "wqp", "flowlines"), distance_km = 50)

Get current NLDI offerings

Description

Used to query the current resources available through the NLDI

Usage

get_nldi_sources(url = pkg.env$nldi_base)

Arguments

url

URL for NLDI sources. Default is supplied by package environment.

Value

data.frame

Examples

get_nldi_sources()

getting header information from a WQP query

Description

getting header information from a WQP query

Usage

getQuerySummary(url)

Arguments

url

the query url

Function to return data from web services

Description

This function accepts a url parameter, and returns the raw data. The function enhances GET with more informative error messages. To add a custom user agent, create an environmental variable: CUSTOM_DR_UA

Usage

getWebServiceData(obs_url, ...)

Arguments

obs_url

character containing the url for the retrieval
...

information to pass to header request

Value

raw data from web services

Examples

siteNumber <- "02177000"
startDate <- "2012-09-01"
endDate <- "2012-10-01"
offering <- "00003"
property <- "00060"
obs_url <- constructNWISURL(siteNumber, property, startDate, endDate, "dv")

rawData <- getWebServiceData(obs_url)

Function to return data from the National Ground Water Monitoring Network waterML2 format

Description

This function accepts a url parameter for a WaterML2 getObservation. This function is still under development, but the general functionality is correct.

Usage

importNGWMN(input, asDateTime = FALSE, tz = "UTC")

Arguments

input

character or raw, containing the url for the retrieval or a path to the data file, or raw XML.
asDateTime

logical, if TRUE returns date and time as POSIXct, if FALSE, character
tz

character to set timezone attribute of dateTime. Default is "UTC", and converts the date times to UTC, properly accounting for daylight savings times based on the data's provided time zone offset. Possible values to provide are "America/New_York", "America/Chicago", "America/Denver", "America/Los_Angeles", "America/Anchorage", as well as the following which do not use daylight savings time: "America/Honolulu", "America/Jamaica", "America/Managua", "America/Phoenix", and "America/Metlakatla". See also OlsonNames() for more information on time zones.

Value

mergedDF a data frame source, time, value, uom, uomTitle, comment, gmlID

Examples

obs_url <- paste("https://cida.usgs.gov/ngwmn_cache/sos?request=GetObservation",
  "service=SOS", "version=2.0.0",
  "observedProperty=urn:ogc:def:property:OGC:GroundWaterLevel",
  "responseFormat=text/xml",
  "featureOfInterest=VW_GWDP_GEOSERVER.USGS.403836085374401",
  sep = "&"
)

#data_returned <- importNGWMN(obs_url)

Function to return data from the NWIS RDB 1.0 format

Description

This function accepts a url parameter that already contains the desired NWIS site, parameter code, statistic, startdate and enddate. It is not recommended to use the RDB format for importing multi-site data.

Usage

importRDB1(obs_url, asDateTime = TRUE, convertType = TRUE, tz = "UTC")

Arguments

obs_url

character containing the url for the retrieval or a file path to the data file.
asDateTime

logical, if TRUE returns date and time as POSIXct, if FALSE, Date
convertType

logical, defaults to TRUE. If TRUE, the function will convert the data to dates, datetimes, numerics based on a standard algorithm. If false, everything is returned as a character
tz

character to set timezone attribute of datetime. Default converts the datetimes to UTC (properly accounting for daylight savings times based on the data's provided tz_cd column). Recommended US values include "UTC", "America/New_York", "America/Chicago", "America/Denver", "America/Los_Angeles", "America/Anchorage", "America/Honolulu", "America/Jamaica", "America/Managua", "America/Phoenix", and "America/Metlakatla". For a complete list, see https://en.wikipedia.org/wiki/List_of_tz_database_time_zones

Value

A data frame with the following columns:

Name Type Description
agency_cd character The NWIS code for the agency reporting the data
site_no character The USGS site number
datetime POSIXct The date and time of the value converted to UTC (if asDateTime = TRUE),
character or raw character string (if asDateTime = FALSE)
tz_cd character The time zone code for datetime
code character Any codes that qualify the corresponding value
value numeric The numeric value for the parameter
tz_cd_reported The originally reported time zone

Note that code and value are repeated for the parameters requested. The names are of the form XD_P_S, where X is literal, D is an option description of the parameter, P is the parameter code, and S is the statistic code (if applicable). If a date/time (dt) column contained incomplete date and times, a new column of dates and time was inserted. This could happen when older data was reported as dates, and newer data was reported as a date/time.

There are also several useful attributes attached to the data frame:

Name Type Description
url character The url used to generate the data
queryTime POSIXct The time the data was returned
comment character Header comments from the RDB file

Examples

site_id <- "02177000"
startDate <- "2012-09-01"
endDate <- "2012-10-01"
offering <- "00003"
property <- "00060"

obs_url <- constructNWISURL(site_id, property,
  startDate, endDate, "dv",
  format = "tsv"
)

data <- importRDB1(obs_url)


urlMultiPcodes <- constructNWISURL("04085427", c("00060", "00010"),
  startDate, endDate, "dv",
  statCd = c("00003", "00001"), "tsv"
)

multiData <- importRDB1(urlMultiPcodes)

unitDataURL <- constructNWISURL(site_id, property,
  "2020-10-30", "2020-11-01", "uv",
  format = "tsv"
) # includes timezone switch

unitData <- importRDB1(unitDataURL, asDateTime = TRUE)

iceSite <- "04024000"
start <- "2015-11-09"
end <- "2015-11-24"
urlIce <- constructNWISURL(iceSite, "00060", start, end, "uv", format = "tsv")

ice <- importRDB1(urlIce, asDateTime = TRUE)
iceNoConvert <- importRDB1(urlIce, convertType = FALSE)

# User file:
filePath <- system.file("extdata", package = "dataRetrieval")
fileName <- "RDB1Example.txt"
fullPath <- file.path(filePath, fileName)
importUserRDB <- importRDB1(fullPath)

Function to return data from the NWISWeb WaterML1.1 service

Description

This function accepts a url parameter that already contains the desired NWIS site, parameter code, statistic, startdate and enddate.

Usage

importWaterML1(obs_url, asDateTime = FALSE, tz = "UTC")

Arguments

obs_url

character or raw, containing the url for the retrieval or a file path to the data file, or raw XML.
asDateTime

logical, if TRUE returns date and time as POSIXct, if FALSE, Date
tz

character to set timezone attribute of datetime. Default converts the datetimes to UTC (properly accounting for daylight savings times based on the data's provided tz_cd column). Recommended US values include "UTC", "America/New_York", "America/Chicago", "America/Denver", "America/Los_Angeles", "America/Anchorage", "America/Honolulu", "America/Jamaica", "America/Managua", "America/Phoenix", and "America/Metlakatla". For a complete list, see https://en.wikipedia.org/wiki/List_of_tz_database_time_zones

Value

A data frame with the following columns:

Name Type Description
agency_cd character The NWIS code for the agency reporting the data
site_no character The USGS site number
POSIXct The date and time of the value converted to UTC (if asDateTime = TRUE),
character or raw character string (if asDateTime = FALSE)
tz_cd character The time zone code for
code character Any codes that qualify the corresponding value
value numeric The numeric value for the parameter

Note that code and value are repeated for the parameters requested. The names are of the form X_D_P_S, where X is literal, D is an option description of the parameter, P is the parameter code, and S is the statistic code (if applicable).

There are also several useful attributes attached to the data frame:

Name Type Description
url character The url used to generate the data
siteInfo data.frame A data frame containing information on the requested sites
variableInfo data.frame A data frame containing information on the requested parameters
statisticInfo data.frame A data frame containing information on the requested statistics on the data
queryTime POSIXct The time the data was returned

See Also

renameNWISColumns

Examples

site_id <- "02177000"
startDate <- "2012-09-01"
endDate <- "2012-10-01"
offering <- "00003"
property <- "00060"
obs_url <- constructNWISURL(site_id, property, startDate, endDate, "dv")

data <- importWaterML1(obs_url, asDateTime = TRUE)


unitDataURL <- constructNWISURL(
  site_id, property,
  "2013-11-03", "2013-11-03", "uv"
)
unitData <- importWaterML1(unitDataURL, TRUE)

# Two sites, two pcodes, one site has two data descriptors:
siteNumber <- c("01480015", "04085427")
obs_url <- constructNWISURL(
  siteNumber, c("00060", "00010"),
  startDate, endDate, "dv"
)
data <- importWaterML1(obs_url)
data$dateTime <- as.Date(data$dateTime)
data <- renameNWISColumns(data)
names(attributes(data))
attr(data, "url")
attr(data, "disclaimer")

inactiveSite <- "05212700"
inactiveSite <- constructNWISURL(inactiveSite, "00060", 
                                 "2014-01-01", "2014-01-10", "dv")
inactiveSite <- importWaterML1(inactiveSite)

inactiveAndAcitive <- c("07334200", "05212700")
inactiveAndAcitive <- constructNWISURL(inactiveAndAcitive, 
                         "00060", "2014-01-01", "2014-01-10", "dv")
inactiveAndAcitive <- importWaterML1(inactiveAndAcitive)

# Timezone change with specified local timezone:
tzURL <- constructNWISURL("04027000", c("00300", "63680"), 
                          "2011-11-05", "2011-11-07", "uv")
tzIssue <- importWaterML1(tzURL,
  asDateTime = TRUE, tz = "America/Chicago"
)

# raw XML
url <- constructNWISURL(
  service = "dv", siteNumber = "02319300", parameterCd = "00060",
  startDate = "2014-01-01", endDate = "2014-01-01"
)
raw <- httr::content(httr::GET(url), as = "raw")
rawParsed <- importWaterML1(raw)

filePath <- system.file("extdata", package = "dataRetrieval")
fileName <- "WaterML1Example.xml"
fullPath <- file.path(filePath, fileName)
importFile <- importWaterML1(fullPath, TRUE)

Parse the WaterML2 timeseries portion of a waterML2 file

Description

Returns data frame columns of all information with each time series measurement; Anything defined as a default, is returned as an attribute of that data frame.

Usage

importWaterML2(input, asDateTime = FALSE, tz = "UTC")

Arguments

input

XML with only the wml2:MeasurementTimeseries node and children
asDateTime

logical, if TRUE returns date and time as POSIXct, if FALSE, character
tz

character to set timezone attribute of datetime. Default is an empty quote, which converts the datetimes to UTC (properly accounting for daylight savings times based on the data's provided time zone offset). Possible values are "America/New_York", "America/Chicago", "America/Denver", "America/Los_Angeles", "America/Anchorage", "America/Honolulu", "America/Jamaica", "America/Managua", "America/Phoenix", and "America/Metlakatla"

Examples

baseURL <- "https://waterservices.usgs.gov/nwis/dv/?format=waterml,2.0"
URL <- paste(baseURL, "sites=01646500",
  "startDT=2014-09-01",
  "endDT=2014-09-08",
  "statCd=00003",
  "parameterCd=00060",
  sep = "&"
)

timesereies <- importWaterML2(URL, asDateTime = TRUE, tz = "UTC")

Basic Water Quality Portal Data parser

Description

Imports data from the Water Quality Portal based on a specified url.

Usage

importWQP(obs_url, tz = "UTC", csv = TRUE, convertType = TRUE)

Arguments

obs_url

character URL to Water Quality Portal#' @keywords data import USGS web service
tz

character to set timezone attribute of datetime. Default is UTC (properly accounting for daylight savings times based on the data's provided tz_cd column). Possible values include "America/New_York","America/Chicago", "America/Denver","America/Los_Angeles", "America/Anchorage","America/Honolulu","America/Jamaica","America/Managua", "America/Phoenix", and "America/Metlakatla"
csv

logical. Is the data coming back with a csv or tsv format. Default is FALSE. Currently, the summary service does not support tsv, for other services tsv is the safer choice.
convertType

logical, defaults to TRUE. If TRUE, the function will convert the data to dates, datetimes, numerics based on a standard algorithm. If false, everything is returned as a character.

Value

retval dataframe raw data returned from the Water Quality Portal. Additionally, a POSIXct dateTime column is supplied for start and end times, and converted to UTC. See https://www.waterqualitydata.us/portal_userguide/ for more information.

See Also

readWQPdata, readWQPqw, whatWQPsites

Examples

# These examples require an internet connection to run

## Examples take longer than 5 seconds:

rawSampleURL <- constructWQPURL("USGS-01594440", "01075", "", "")

rawSample <- importWQP(rawSampleURL)


STORETex <- constructWQPURL("WIDNR_WQX-10032762", "Specific conductance", "", "")

STORETdata <- importWQP(STORETex)

STORETdata_char <- importWQP(STORETex, convertType = FALSE)

Is this a dataRetrieval user

Description

Reveals if this is a user or not

Usage

is_dataRetrieval_user()

Examples

is_dataRetrieval_user()

List of USGS parameter codes

Description

Complete list of USGS parameter codes as of Oct. 24, 2024.

Value

parameterData data frame with information about USGS parameters.

Name Type Description
parameter_cd character 5-digit USGS parameter code
parameter_group_nm character USGS parameter group name
parameter_nm character USGS parameter name
casrn character Chemical Abstracts Service (CAS) Registry Number
srsname character Substance Registry Services Name
parameter_units character Parameter units

Examples

head(parameterCdFile[, 1:2])

Convert WQP columns to correct types

Description

Takes the character results and converts to numeric and dates.

Usage

parse_WQP(retval, tz = "UTC")

Arguments

retval

Data frame from WQP
tz

character to set timezone attribute of datetime. Default is UTC (properly accounting for daylight savings times based on the associated "TimeZone" column). Possible values include "America/New_York","America/Chicago", "America/Denver","America/Los_Angeles", "America/Anchorage","America/Honolulu","America/Jamaica","America/Managua", "America/Phoenix", and "America/Metlakatla"

Value

data frame retval with converted columns

Examples

# These examples require an internet connection to run
rawSampleURL <- constructWQPURL("USGS-01594440", "01075", "", "")

## Examples take longer than 5 seconds:



rawSample <- importWQP(rawSampleURL, convertType = FALSE)
convertedSample <- parse_WQP(rawSample)

Parameter code to characteristic name

Description

This function is useful to fine what characteristic name, result sample fraction, unit code, and other parameters are mapped with USGS parameter codes. This information is useful for converting workflows from a more traditional NWIS water quality retrieval to a Water Quality Portal retrieval.

Usage

pcode_to_name(parameterCd = "all")

Arguments

parameterCd

character that contains the code for a character vector of 5-digit parameter codes. Default is "all" which will return a complete list of parameter codes that have been mapped to a characteristic name.

Value

a data frame with columns "parm_cd", "description", "characteristicname", "measureunitcode", "resultsamplefraction", "resulttemperaturebasis", "resultstatisticalbasis", "resulttimebasis", "resultweightbasis", "resultparticlesizebasis", "last_rev_dt"

Examples

pcodes <- c("00070", "00075", "00430", "52642")


all <- pcode_to_name()
some <- pcode_to_name(pcodes)

Import data from the National Groundwater Monitoring Network.

Description

Only water level data and site locations and names are currently available through the web service.

Usage

readNGWMNdata(service, ..., asDateTime = TRUE, tz = "UTC")

Arguments

service

char Service for the request - "observation" and "featureOfInterest" are implemented.
...

Other parameters to supply, namely siteNumbers or bbox
asDateTime

logical if TRUE, will convert times to POSIXct format. Currently defaults to FALSE since time zone information is not included.
tz

character to set timezone attribute of dateTime. Default is "UTC", and converts the date times to UTC, properly accounting for daylight savings times based on the data's provided time zone offset. Possible values to provide are "America/New_York", "America/Chicago", "America/Denver", "America/Los_Angeles", "America/Anchorage", as well as the following which do not use daylight savings time: "America/Honolulu", "America/Jamaica", "America/Managua", "America/Phoenix", and "America/Metlakatla". See also OlsonNames() for more information on time zones.

Examples

# one site
site <- "USGS.430427089284901"
#oneSite <- readNGWMNdata(siteNumbers = site, service = "observation")

# multiple sites
sites <- c("USGS.272838082142201", "USGS.404159100494601", "USGS.401216080362703")
# Very slow:
# multiSiteData <- readNGWMNdata(siteNumbers = sites, service = "observation")
# attributes(multiSiteData)

# non-USGS site
# accepts colon or period between agency and ID
site <- "MBMG:702934"
# data <- readNGWMNdata(siteNumbers = site, service = "featureOfInterest")

# bounding box
# bboxSites <- readNGWMNdata(service = "featureOfInterest", bbox = c(30, -102, 31, 99))
# retrieve  sites.  Set asDateTime to false since one site has an invalid date
# Very slow:
# bboxData <- readNGWMNdata(service = "observation", siteNumbers = bboxSites$site[1:3],
#                           asDateTime = FALSE)

Retrieve groundwater levels from the National Ground Water Monitoring Network.

Description

Retrieve groundwater levels from the National Ground Water Monitoring Network.

Usage

readNGWMNlevels(siteNumbers, asDateTime = TRUE, tz = "UTC")

Arguments

siteNumbers

character Vector of feature IDs formatted with agency code and site number separated by a period or semicolon, e.g. USGS.404159100494601.
asDateTime

logical Should dates and times be converted to date/time objects, or returned as character? Defaults to TRUE. Must be set to FALSE if a site contains non-standard dates.
tz

character to set timezone attribute of dateTime. Default is "UTC", and converts the date times to UTC, properly accounting for daylight savings times based on the data's provided time zone offset. Possible values to provide are "America/New_York", "America/Chicago", "America/Denver", "America/Los_Angeles", "America/Anchorage", as well as the following which do not use daylight savings time: "America/Honolulu", "America/Jamaica", "America/Managua", "America/Phoenix", and "America/Metlakatla". See also OlsonNames() for more information on time zones.

Examples

# one site
site <- "USGS.430427089284901"
# oneSite <- readNGWMNlevels(siteNumbers = site)

# multiple sites
sites <- c("USGS:272838082142201", "USGS:404159100494601", "USGS:401216080362703")
# multiSiteData <- readNGWMNlevels(sites)

# non-USGS site
site <- "MBMG.103306"
# data <- readNGWMNlevels(siteNumbers = site, asDateTime = FALSE)

# site with no data returns empty data frame
noDataSite <- "UTGS.401544112060301"
# noDataSite <- readNGWMNlevels(siteNumbers = noDataSite)

Retrieve site data from the National Ground Water Monitoring Network.

Description

Retrieve site data from the National Ground Water Monitoring Network.

Usage

readNGWMNsites(siteNumbers)

Arguments

siteNumbers

character Vector of feature IDs formatted with agency code and site number separated by a period or semicolon, e.g. USGS.404159100494601.

Value

A data frame the following columns: #'

Name Type Description
site char Site FID
description char Site description
dec_lat_va, dec_lon_va numeric Site latitude and longitude

Examples

# one site
site <- "USGS.430427089284901"
#oneSite <- readNGWMNsites(siteNumbers = site)

# non-USGS site
site <- "MBMG.103306"
#siteInfo <- readNGWMNsites(siteNumbers = site)

General Data Import from NWIS

Description

Returns data from the NWIS web service. Arguments to the function should be based on https://waterservices.usgs.gov service calls. See examples below for ideas of constructing queries.

Usage

readNWISdata(..., asDateTime = TRUE, convertType = TRUE, tz = "UTC")

Arguments

...

see https://waterservices.usgs.gov/docs/site-service/ for a complete list of options. A list of arguments can also be supplied. One important argument to include is "service". Possible values are "iv" (for instantaneous), "dv" (for daily values), "gwlevels" (for groundwater levels), "site" (for site service), "measurement", and "stat" (for statistics service). Note: "measurement" calls go to: https://nwis.waterdata.usgs.gov/usa/nwis for data requests, and use different call requests schemes. The statistics service has a limited selection of arguments (see https://waterservices.usgs.gov/docs/site-service/).
asDateTime

logical, if TRUE returns date and time as POSIXct, if FALSE, Date
convertType

logical, defaults to TRUE. If TRUE, the function will convert the data to dates, datetimes, numerics based on a standard algorithm. If false, everything is returned as a character
tz

character to set timezone attribute of dateTime. Default is "UTC", and converts the date times to UTC, properly accounting for daylight savings times based on the data's provided tz_cd column. Possible values to provide are "America/New_York", "America/Chicago", "America/Denver", "America/Los_Angeles", "America/Anchorage", as well as the following which do not use daylight savings time: "America/Honolulu", "America/Jamaica", "America/Managua", "America/Phoenix", and "America/Metlakatla". See also OlsonNames() for more information on time zones.

Details

This function requires users to create their own arguments based on the NWIS web services. It is a more complicated function to use compared to other NWIS functions such as readNWISdv, readNWISuv, readNWISgwl, etc. However, this function adds a lot of flexibility to the possible queries. This function will also behave exactly as NWIS when it comes to date queries. NWIS by default will only return the latest value for the daily and instantaneous services. So if you do not provide a starting date, you will only get back the latest value. If you want the full period of record, you can use "startDate = '1900-01-01'". Other options for dates are periods, such as "period = 'P7D'" which translates to a period of 7 days. For period, use only a positive ISO-8601 duration format, which should not be expressed in periods of less than a day, or in increments of months M or years Y. period returns data for a site generally from now to a time in the past. Note that when period is used all data up to the most recent value are returned.

Value

A data frame with the following columns:

Name Type Description
agency character The NWIS code for the agency reporting the data
site character The USGS site number
dateTime POSIXct The date and time (if applicable) of the measurement, converted to UTC for unit value data. R only allows one time zone attribute per column. For unit data spanning a time zone change, converting the data to UTC solves this problem. For daily data, the time zone attribute is the time zone of the first returned measurement.
tz_cd character The time zone code for dateTime column
code character Any codes that qualify the corresponding value
value numeric The numeric value for the parameter

Note that code and value are repeated for the parameters requested. The names are of the form X_D_P_S, where X is literal, D is an option description of the parameter, P is the parameter code, and S is the statistic code (if applicable).

There are also several useful attributes attached to the data frame:

Name Type Description
url character The url used to generate the data
siteInfo data.frame A data frame containing information on the requested sites
variableInfo data.frame A data frame containing information on the requested parameters
statisticInfo data.frame A data frame containing information on the requested statistics on the data
queryTime POSIXct The time the data was returned

See Also

renameNWISColumns, importWaterML1, importRDB1

Examples

# Examples not run for time considerations

dataTemp <- readNWISdata(stateCd = "OH", parameterCd = "00010", service = "dv")
instFlow <- readNWISdata(
  sites = "05114000", service = "iv",
  parameterCd = "00060",
  startDate = "2014-05-01T00:00Z", endDate = "2014-05-01T12:00Z"
)

instFlowCDT <- readNWISdata(
  sites = "05114000", service = "iv",
  parameterCd = "00060",
  startDate = "2014-05-01T00:00", endDate = "2014-05-01T12:00",
  tz = "America/Chicago"
)

multiSite <- readNWISdata(
  sites = c("04025500", "040263491"),
  service = "iv", parameterCd = "00060"
)

bBoxEx <- readNWISdata(bBox = c(-83, 36.5, -81, 38.5), parameterCd = "00010")

startDate <- as.Date("2013-10-01")
endDate <- as.Date("2014-09-30")
waterYear <- readNWISdata(
  bBox = c(-83, 36.5, -82.5, 36.75),
  parameterCd = "00010",
  service = "dv",
  startDate = startDate,
  endDate = endDate
)

siteInfo <- readNWISdata(
  stateCd = "WI", parameterCd = "00010",
  hasDataTypeCd = "iv", service = "site"
)
temp <- readNWISdata(
  bBox = c(-83, 36.5, -82.5, 36.75), parameterCd = "00010", service = "site",
  seriesCatalogOutput = TRUE
)
GWL <- readNWISdata(site_no = c("392725077582401", 
                                "375907091432201"),
                    parameterCd = "62610",
                    service = "gwlevels")
                    
levels <- readNWISdata(stateCd = "WI", 
                       service = "gwlevels",
                       startDate = "2024-05-01",
                       endDate = "2024-05-30") 
                    
meas <- readNWISdata(
  state_cd = "WI", service = "measurements",
  format = "rdb_expanded"
)

waterYearStat <- readNWISdata(
  site = c("01646500"),
  service = "stat",
  statReportType = "annual",
  statYearType = "water",
  missingData = "on"
)
monthlyStat <- readNWISdata(
  site = c("01646500"),
  service = "stat",
  statReportType = "monthly"
)

dailyStat <- readNWISdata(
  site = c("01646500"),
  service = "stat",
  statReportType = "daily",
  statType = c("p25", "p50", "p75", "min", "max"),
  parameterCd = "00060"
)

arg.list <- list(
  site = "03111548",
  statReportType = "daily",
  statType = c("p25", "p50", "p75", "min", "max"),
  parameterCd = "00060"
)
allDailyStats_2 <- readNWISdata(arg.list, service = "stat")

# use county names to get data
dailyStaffordVA <- readNWISdata(
  stateCd = "Virginia",
  countyCd = "Stafford",
  parameterCd = "00060",
  startDate = "2015-01-01",
  endDate = "2015-01-30"
)
va_counties <- c("51001", "51003", "51005", "51007", "51009", "51011", "51013", "51015")
va_counties_data <- readNWISdata(
  startDate = "2015-01-01", endDate = "2015-12-31",
  parameterCd = "00060", countycode = va_counties
)

site_id <- "01594440"
rating_curve <- readNWISdata(service = "rating", site_no = site_id, file_type = "base")
all_sites_base <- readNWISdata(service = "rating", file_type = "base")
all_sites_core <- readNWISdata(service = "rating", file_type = "corr")
all_sites_exsa <- readNWISdata(service = "rating", file_type = "exsa")
all_sites_24hrs <- readNWISdata(service = "rating", file_type = "exsa", period = 24)

peak_data <- readNWISdata(
  service = "peak",
  site_no = c("01594440", "040851325"),
  range_selection = "data_range"
)

peak_data <- readNWISdata(
  service = "peak",
  state_cd = "PA"
)

peak_data <- readNWISdata(
  service = "peak",
  huc2_cd = "20"
)

Daily Value USGS NWIS Data Retrieval

Description

Imports data from NWIS daily web service. This function gets the data from here: https://waterservices.usgs.gov/docs/dv-service/daily-values-service-details/ Inputs to this function are just USGS site ids, USGS parameter codes, USGS statistic codes, and start and end date. For a more complex query, use readNWISdata, with an argument service = "dv". Data coming the daily web services are aggregates of the instantaneous (sensor) web services. Not all statistical codes are available for all data. Use the function whatNWISdata to discover what data is available for a USGS site. The column data_type_cd with the values "dv" returned from whatNWISdata) are available from this service.

Usage

readNWISdv(
  siteNumbers,
  parameterCd,
  startDate = "",
  endDate = "",
  statCd = "00003"
)

Arguments

siteNumbers

character USGS site number. This is usually an 8 digit number. Multiple sites can be requested with a character vector.
parameterCd

character of USGS parameter code(s). This is usually an 5 digit number.
startDate

character starting date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates retrieval for the earliest possible record. Date arguments are always specified in local time.
endDate

character ending date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates retrieval for the latest possible record. Date arguments are always specified in local time.
statCd

character USGS statistic code. This is usually 5 digits. Daily mean (00003) is the default.

Details

More information on the web service can be found here: https://waterservices.usgs.gov/test-tools, choosing the "Daily Value Service".

Value

A data frame with the following columns:

Name Type Description
agency character The NWIS code for the agency reporting the data
site character The USGS site number
Date Date The date of the value
code character Any codes that qualify the corresponding value
value numeric The numeric value for the parameter

Note that code and value are repeated for the parameters requested. The names are of the form X_D_P_S, where X is literal, D is an option description of the parameter, P is the parameter code, and S is the statistic code (if applicable).

There are also several useful attributes attached to the data frame:

Name Type Description
url character The url used to generate the data
siteInfo data.frame A data frame containing information on the requested sites
variableInfo data.frame A data frame containing information on the requested parameters
statisticInfo data.frame A data frame containing information on the requested statistics on the data
queryTime POSIXct The time the data was returned

See Also

renameNWISColumns, importWaterML1

Examples

site_id <- "04085427"
startDate <- "2012-01-01"
endDate <- "2012-06-30"
pCode <- "00060"

rawDailyQ <- readNWISdv(site_id, pCode, startDate, endDate)
rawDailyQAndTempMeanMax <- readNWISdv(site_id, c("00010", "00060"),
  startDate, endDate,
  statCd = c("00001", "00003")
)
rawDailyQAndTempMeanMax <- renameNWISColumns(rawDailyQAndTempMeanMax)
rawDailyMultiSites <- readNWISdv(c("01491000", "01645000"), c("00010", "00060"),
  startDate, endDate,
  statCd = c("00001", "00003")
)
# Site with no data:
x <- readNWISdv("10258500", "00060", "2014-09-08", "2014-09-14")
names(attributes(x))
attr(x, "siteInfo")
attr(x, "variableInfo")

site <- "05212700"
notActive <- readNWISdv(site, "00060", "2014-01-01", "2014-01-07")

Groundwater level measurements retrieval from USGS (NWIS)

Description

Imports groundwater level data from NWIS web service. This function gets the data from here: https://waterservices.usgs.gov/docs/groundwater-levels/groundwater-levels-details/ Inputs to this function are just USGS site ids, USGS parameter codes, and start and end date. For a more complex query, use readNWISdata, including an argument service="gwlevels". Not all parameter codes are available for all data. Use the function whatNWISdata to discover what data is available for a USGS site. The column data_type_cd with the values "gw" returned from whatNWISdata) are available from this service.

Usage

readNWISgwl(
  siteNumbers,
  startDate = "",
  endDate = "",
  parameterCd = NA,
  convertType = TRUE,
  tz = "UTC"
)

Arguments

siteNumbers

character USGS site number (or multiple sites). This is usually an 8 digit number
startDate

character starting date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates retrieval for the earliest possible record.
endDate

character ending date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates retrieval for the latest possible record.
parameterCd

character USGS parameter code. This is usually an 5 digit number. Default is "".
convertType

logical, defaults to TRUE. If TRUE, the function will convert the data to dates, datetimes, numerics based on a standard algorithm. If false, everything is returned as a character
tz

character to set timezone attribute of dateTime. Default is "UTC", and converts the date times to UTC, properly accounting for daylight savings times based on the data's provided tz_cd column. Possible values to provide are "America/New_York", "America/Chicago", "America/Denver", "America/Los_Angeles", "America/Anchorage", as well as the following which do not use daylight savings time: "America/Honolulu", "America/Jamaica", "America/Managua", "America/Phoenix", and "America/Metlakatla". See also OlsonNames() for more information on time zones.

Details

More information on the web service can be found here: https://waterservices.usgs.gov/test-tools, choosing the "Groundwater Levels Value Service".

Mixed date/times come back from the service depending on the year that the data was collected. See https://waterdata.usgs.gov/usa/nwis/gw for details about groundwater. By default the returned dates are converted to date objects, unless convertType is specified as FALSE. Sites with non-standard date formats (i.e. lacking a day) can be affected (see examples). See https://waterservices.usgs.gov/docs/groundwater-levels/ for more information.

Value

A data frame with the following columns:

Name Type Description
agency_cd character The NWIS code for the agency reporting the data
site_no character The USGS site number
site_tp_cd character Site type code
lev_dt Date Date level measured
lev_tm character Time level measured
lev_tz_cd character Time datum
lev_va numeric Water level value in feet below land surface
sl_lev_va numeric Water level value in feet above specific vertical datum
lev_status_cd character The status of the site at the time the water level was measured
lev_agency_cd character The agency code of the person measuring the water level

There are also several useful attributes attached to the data frame:

Name Type Description
url character The url used to generate the data
queryTime POSIXct The time the data was returned
comment character Header comments from the RDB file
siteInfo data.frame A data frame containing information on the requested sites

See Also

constructNWISURL, importRDB1

Examples

site_id <- "434400121275801"

data <- readNWISgwl(site_id)
sites <- c("434400121275801", "375907091432201")
data2 <- readNWISgwl(sites, "", "")
data3 <- readNWISgwl("420125073193001", "", "")
# handling of data where date has no day
data4 <- readNWISgwl("425957088141001", startDate = "1980-01-01")

data5 <- readNWISgwl("263819081585801", parameterCd = "72019")

Surface-water measurement data retrieval from USGS (NWIS)

Description

Reads surface-water measurement data from NWISweb. Data is retrieved from https://waterdata.usgs.gov/nwis. See https://waterdata.usgs.gov/usa/nwis/sw for details about surface water.

Usage

readNWISmeas(
  siteNumbers,
  startDate = "",
  endDate = "",
  tz = "UTC",
  expanded = FALSE,
  convertType = TRUE
)

Arguments

siteNumbers

character USGS site number (or multiple sites). This is usually an 8 digit number
startDate

character starting date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates retrieval for the earliest possible record.
endDate

character ending date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates retrieval for the latest possible record.
tz

character to set timezone attribute of dateTime. Default is "UTC", and converts the date times to UTC, properly accounting for daylight savings times based on the data's provided tz_cd column. Possible values to provide are "America/New_York", "America/Chicago", "America/Denver", "America/Los_Angeles", "America/Anchorage", as well as the following which do not use daylight savings time: "America/Honolulu", "America/Jamaica", "America/Managua", "America/Phoenix", and "America/Metlakatla". See also OlsonNames() for more information on time zones.
expanded

logical. Whether or not (TRUE or FALSE) to call the expanded data.
convertType

logical, defaults to TRUE. If TRUE, the function will convert the data to dates, datetimes, numerics based on a standard algorithm. If false, everything is returned as a character

Value

A data frame with at least the following columns:

Name Type Description
agency_cd character The NWIS code for the agency reporting the data
site_no character The USGS site number
measurement_dt POSIXct The date and time (in POSIXct) of the measurement. Unless specified with the tz parameter, this is converted to UTC. If the measurement_dt column is an incomplete, a measurement_dt_date and measurement_dt_time column are added to the returned data frame.
tz_cd character The time zone code for the measurement_dt column

See https://waterdata.usgs.gov/usa/nwis/sw for details about surface water, and https://waterdata.usgs.gov/nwis/help?output_formats_help for help on the columns and codes.

There are also several useful attributes attached to the data frame:

Name Type Description
url character The url used to generate the data
queryTime POSIXct The time the data was returned
comment character Header comments from the RDB file
siteInfo data.frame A data frame containing information on the requested sites
tz_cd_reported The originally reported time zone

See Also

constructNWISURL, importRDB1

Examples

site_ids <- c("01594440", "040851325")

data <- readNWISmeas(site_ids)
Meas05316840 <- readNWISmeas("05316840")
Meas05316840.ex <- readNWISmeas("05316840", expanded = TRUE)
Meas07227500.ex <- readNWISmeas("07227500", expanded = TRUE)
Meas07227500.exRaw <- readNWISmeas("07227500", expanded = TRUE, convertType = FALSE)

USGS Parameter Data Retrieval

Description

Imports data from NWIS about meaured parameter based on user-supplied parameter code or codes. This function gets the data from here: https://nwis.waterdata.usgs.gov/nwis/pmcodes

Usage

readNWISpCode(parameterCd)

Arguments

parameterCd

character of USGS parameter codes (or multiple parameter codes). These are 5 digit number codes, more information can be found here: https://help.waterdata.usgs.gov/. To get a complete list of all current parameter codes in the USGS, use "all" as the input.

Value

parameterData data frame with the following information:

Name Type Description
parameter_cd character 5-digit USGS parameter code
parameter_group_nm character USGS parameter group name
parameter_nm character USGS parameter name
casrn character Chemical Abstracts Service (CAS) Registry Number
srsname character Substance Registry Services Name
parameter_units character Parameter units

See Also

importRDB1

Examples

paramINFO <- readNWISpCode(c("01075", "00060", "00931"))
paramINFO <- readNWISpCode(c("01075", "00060", "00931", NA))

all_codes <- readNWISpCode("all")

one_extra <- readNWISpCode(c("01075", "12345"))

Peak flow data from USGS (NWIS)

Description

Reads peak flow from NWISweb. Data is retrieved from https://waterdata.usgs.gov/nwis. In some cases, the specific date of the peak data is not know. This function will default to converting complete dates to a "Date" object, and converting incomplete dates to "NA". If those incomplete dates are needed, set the 'asDateTime' argument to FALSE. No dates will be converted to R Date objects.

Usage

readNWISpeak(
  siteNumbers,
  startDate = "",
  endDate = "",
  asDateTime = TRUE,
  convertType = TRUE
)

Arguments

siteNumbers

character USGS site number(or multiple sites). This is usually an 8 digit number.
startDate

character starting date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates retrieval for the earliest possible record.
endDate

character ending date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates retrieval for the latest possible record.
asDateTime

logical default to TRUE. When TRUE, the peak_dt column is converted to a Date object, and incomplete dates are removed. When FALSE, no columns are removed, but no dates are converted.
convertType

logical, defaults to TRUE. If TRUE, the function will convert the data to dates, datetimes, numerics based on a standard algorithm. If false, everything is returned as a character

Value

A data frame with the following columns:

Name Type Description
agency_cd character The NWIS code for the agency reporting the data
site_no character The USGS site number
peak_dt Date Date of peak streamflow
peak_tm character Time of peak streamflow as character
peak_va numeric Annual peak streamflow value in cfs
peak_cd character Peak Discharge-Qualification codes (see comment for more information)
gage_ht numeric Gage height for the associated peak streamflow in feet
gage_ht_cd character Gage height qualification codes
year_last_pk numeric Peak streamflow reported is the highest since this year
ag_dt Date Date of maximum gage-height for water year (if not concurrent with peak)
ag_tm character Time of maximum gage-height for water year (if not concurrent with peak)
ag_gage_ht numeric maximum Gage height for water year in feet (if not concurrent with peak)
ag_gage_ht_cd character maximum Gage height code

There are also several useful attributes attached to the data frame:

Name Type Description
url character The url used to generate the data
queryTime POSIXct The time the data was returned
comment character Header comments from the RDB file
siteInfo data.frame A data frame containing information on the requested sites

See Also

constructNWISURL, importRDB1

Examples

site_ids <- c("01594440", "040851325")

data <- readNWISpeak(site_ids)
data2 <- readNWISpeak(site_ids, asDateTime = FALSE)
stations <- c("06011000")
peakdata <- readNWISpeak(stations, convertType = FALSE)

Rating table for an active USGS streamgage retrieval

Description

Reads current rating table for an active USGS streamgage from NWISweb. Data is retrieved from https://waterdata.usgs.gov/nwis.

Usage

readNWISrating(siteNumber, type = "base", convertType = TRUE)

Arguments

siteNumber

character USGS site number. This is usually an 8 digit number
type

character can be "base", "corr", or "exsa"
convertType

logical, defaults to TRUE. If TRUE, the function will convert the data to dates, datetimes, numerics based on a standard algorithm. If false, everything is returned as a character

Value

A data frame. If type is "base, " then the columns are INDEP, typically the gage height, in feet; DEP, typically the streamflow, in cubic feet per second; and STOR, where "*" indicates that the pair are a fixed point of the rating curve. If type is "exsa, " then an additional column, SHIFT, is included that indicates the current shift in the rating for that value of INDEP. If type is "corr, " then the columns are INDEP, typically the gage height, in feet; CORR, the correction for that value; and CORRINDEP, the corrected value for CORR.
If type is "base, " then the data frame has an attribute called "RATING" that describes the rating curve is included.

There are also several useful attributes attached to the data frame:

Name Type Description
url character The url used to generate the data
queryTime POSIXct The time the data was returned
comment character Header comments from the RDB file
siteInfo data.frame A data frame containing information on the requested sites
RATING character Rating information

Note

Not all active USGS streamgages have traditional rating curves that relate flow to stage.

See Also

constructNWISURL, importRDB1

Examples

site_id <- "01594440"

data <- readNWISrating(site_id, "base")
attr(data, "RATING")

USGS Site File Data Retrieval

Description

Imports data from USGS site file site. This function gets data from here: https://waterservices.usgs.gov/

Usage

readNWISsite(siteNumbers)

Arguments

siteNumbers

character USGS site number (or multiple sites). This is usually an 8 digit number

Value

A data frame with at least the following columns:

Name Type Description
agency_cd character The NWIS code for the agency reporting the data
site_no character The USGS site number
station_nm character Site name
site_tp_cd character Site type
lat_va numeric DMS latitude
long_va numeric DMS longitude
dec_lat_va numeric Decimal latitude
dec_long_va numeric Decimal longitude
coord_meth_cd character Latitude-longitude method
coord_acy_cd character Latitude-longitude accuracy
coord_datum_cd character Latitude-longitude datum
dec_coord_datum_cd character Decimal Latitude-longitude datum
district_cd character District code
state_cd character State code
county_cd character County code
country_cd character Country code
land_net_ds character Land net location description
map_nm character Name of location map
map_scale_fc character Scale of location map
alt_va numeric Altitude of Gage/land surface
alt_meth_cd character Method altitude determined
alt_acy_va numeric Altitude accuracy
alt_datum_cd character Altitude datum
huc_cd character Hydrologic unit code
basin_cd character Drainage basin code
topo_cd character Topographic setting code
instruments_cd character Flags for instruments at site
construction_dt character Date of first construction
inventory_dt character Date site established or inventoried
drain_area_va numeric Drainage area
contrib_drain_area_va numeric Contributing drainage area
tz_cd character Time Zone abbreviation
local_time_fg character Site honors Daylight Savings Time
reliability_cd character Data reliability code
gw_file_cd character Data-other GW files
nat_aqfr_cd character National aquifer code
aqfr_cd character Local aquifer code
aqfr_type_cd character Local aquifer type code
well_depth_va numeric Well depth
hole_depth_va numeric Hole depth
depth_src_cd character Source of depth data
project_no character Project number

There are also several useful attributes attached to the data frame:

Name Type Description
url character The url used to generate the data
queryTime POSIXct The time the data was returned
comment character Header comments from the RDB file

Examples

siteINFO <- readNWISsite("05114000")
siteINFOMulti <- readNWISsite(c("05114000", "09423350"))

Site statistics retrieval from USGS (NWIS)

Description

Retrieves site statistics from the USGS Statistics Web Service beta. See https://waterservices.usgs.gov/docs/statistics/ for more information.

Usage

readNWISstat(
  siteNumbers,
  parameterCd,
  startDate = "",
  endDate = "",
  convertType = TRUE,
  statReportType = "daily",
  statType = "mean"
)

Arguments

siteNumbers

character USGS site number (or multiple sites). This is usually an 8 digit number.
parameterCd

character USGS parameter code. This is usually a 5 digit number.
startDate

character starting date for data retrieval in the form YYYY, YYYY-MM, or YYYY-MM-DD. Dates cannot be more specific than the statReportType, i.e. startDate for monthly statReportTypes cannot include days, and annual statReportTypes cannot include days or months. Months and days are optional for the daily statReportType. Default is "" which indicates retrieval for the earliest possible record. For daily data, this indicates the start of the period the statistics will be computed over.
endDate

character ending date for data retrieval in the form YYYY, YYYY-MM, or YYYY-MM-DD. Default is "" which indicates retrieval for the latest possible record. For daily data, this indicates the end of the period the statistics will be computed over. The same restrictions as startDate apply.
convertType

logical, defaults to TRUE. If TRUE, the function will convert the data to numerics based on a standard algorithm. Years, months, and days (if appliccable) are also returned as numerics in separate columns. If convertType is false, everything is returned as a character.
statReportType

character time division for statistics: daily, monthly, or annual. Default is daily. Note that daily provides statistics for each calendar day over the specified range of water years, i.e. no more than 366 data points will be returned for each site/parameter. Use readNWISdata or readNWISdv for daily averages. Also note that 'annual' returns statistics for the calendar year. Use readNWISdata for water years. Monthly and yearly provide statistics for each month and year within the range indivually.
statType

character type(s) of statistics to output for daily values. Default is mean, which is the only option for monthly and yearly report types. See the statistics service documentation at https://waterservices.usgs.gov/docs/statistics/ for a full list of codes.

Value

A data frame with the following columns:

Name Type Description
agency_cd character The NWIS code for the agency reporting the data
site_no character The USGS site number
parameter_cd character The USGS parameter code
Other columns will be present depending on statReportType and statType

See Also

constructNWISURL, importRDB1

Examples

x1 <- readNWISstat(
  siteNumbers = c("02319394"),
  parameterCd = c("00060"),
  statReportType = "annual"
)

# all the annual mean discharge data for two sites
x2 <- readNWISstat(
  siteNumbers = c("02319394", "02171500"),
  parameterCd = c("00010", "00060"),
  statReportType = "annual"
)

# Request p25, p75, and mean values for temperature and discharge for the 2000s
# Note that p25 and p75 were not available for temperature, and return NAs
x <- readNWISstat(
  siteNumbers = c("02171500"),
  parameterCd = c("00010", "00060"),
  statReportType = "daily",
  statType = c("mean", "median"),
  startDate = "2000", endDate = "2010"
)

Water use data retrieval from USGS (NWIS)

Description

Retrieves water use data from USGS Water Use Data for the Nation. See https://waterdata.usgs.gov/nwis/wu for more information. All available use categories for the supplied arguments are retrieved.

Usage

readNWISuse(
  stateCd,
  countyCd,
  years = "ALL",
  categories = "ALL",
  convertType = TRUE,
  transform = FALSE
)

Arguments

stateCd

could be character (full name, abbreviation, id), or numeric (id). Only one is accepted per query.
countyCd

could be character (name, with or without "County", or "ALL"), numeric (id), or NULL, which will return state or national data depending on the stateCd argument. "ALL" may also be supplied, which will return data for every county in a state. Can be a vector of counties in the same state.
years

integer Years for data retrieval. Must be years ending in 0 or 5. Default is all available years.
categories

character categories of water use. Defaults to "ALL". Specific categories must be supplied as two- letter abbreviations as seen in the URL when using the NWIS water use web interface. Note that there are different codes for national and state level data.
convertType

logical defaults to TRUE. If TRUE, the function will convert the data to numerics based on a standard algorithm. Years, months, and days (if appliccable) are also returned as numerics in separate columns. If convertType is false, everything is returned as a character.
transform

logical only intended for use with national data. Defaults to FALSE, with data being returned as presented by the web service. If TRUE, data will be transformed and returned with column names, which will reformat national data to be similar to state data.

Value

A data frame with at least the year of record, and all available statistics for the given geographic parameters. County and state fields will be included as appropriate.

Examples

# All data for a county
allegheny <- readNWISuse(stateCd = "Pennsylvania", countyCd = "Allegheny")

# Data for an entire state for certain years
ohio <- readNWISuse(years = c(2000, 2005, 2010), stateCd = "OH", countyCd = NULL)

# Data for an entire state, county by county
pr <- readNWISuse(years = c(2000, 2005, 2010), stateCd = "PR", countyCd = "ALL")

# All national-scale data, transforming data frame to named columns from named rows
national <- readNWISuse(stateCd = NULL, countyCd = NULL, transform = TRUE)

# Washington, DC data
dc <- readNWISuse(stateCd = "DC", countyCd = NULL)

# data for multiple counties, with different input formatting
paData <- readNWISuse(stateCd = "42", countyCd = c("Allegheny County", "BUTLER", 1, "031"))

# retrieving two specific categories for an entire state
ks <- readNWISuse(stateCd = "KS", countyCd = NULL, categories = c("IT", "LI"))

Instantaneous value data retrieval from USGS (NWIS)

Description

Imports data from NWIS web service. This function gets the data from here: https://waterservices.usgs.gov/docs/instantaneous-values/instantaneous-values-details/ Inputs to this function are just USGS site ids, USGS parameter codes, and start and end date. For a more complex query, use readNWISdata, including an arguement service="uv". Not all parameter codes are available for all data. Use the function whatNWISdata to discover what data is available for a USGS site. The column data_type_cd with the values "uv" returned from whatNWISdata) are available from this service.

Usage

readNWISuv(siteNumbers, parameterCd, startDate = "", endDate = "", tz = "UTC")

Arguments

siteNumbers

character USGS site number (or multiple sites). This is usually an 8 digit number
parameterCd

character USGS parameter code. This is usually an 5 digit number.
startDate

character starting date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates retrieval for the earliest possible record. Simple date arguments are specified in local time. See more information here: https://waterservices.usgs.gov/docs/instantaneous-values/.
endDate

character ending date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates retrieval for the latest possible record. Simple date arguments are specified in local time. See more information here: https://waterservices.usgs.gov/docs/instantaneous-values/.
tz

character to set timezone attribute of dateTime. Default is "UTC", and converts the date times to UTC, properly accounting for daylight savings times based on the data's provided tz_cd column. Possible values to provide are "America/New_York", "America/Chicago", "America/Denver", "America/Los_Angeles", "America/Anchorage", as well as the following which do not use daylight savings time: "America/Honolulu", "America/Jamaica", "America/Managua", "America/Phoenix", and "America/Metlakatla". See also OlsonNames() for more information on time zones.

Details

More information on the web service can be found here: https://waterservices.usgs.gov/test-tools, choosing the "Instantaneous Value Service".

Value

A data frame with the following columns:

Name Type Description
agency_cd character The NWIS code for the agency reporting the data
site_no character The USGS site number
dateTime POSIXct The date and time of the value converted to UTC
tz_cd character The time zone code for dateTime
code character Any codes that qualify the corresponding value
value numeric The numeric value for the parameter

Note that code and value are repeated for the parameters requested. The names are of the form: X_D_P_S, where X is literal, D is an option description of the parameter, P is the parameter code, and S is the statistic code (if applicable).

There are also several useful attributes attached to the data frame:

Name Type Description
url character The url used to generate the data
siteInfo data.frame A data frame containing information on the requested sites
variableInfo data.frame A data frame containing information on the requested parameters
statisticInfo data.frame A data frame containing information on the requested statistics on the data
queryTime POSIXct The time the data was returned

See Also

renameNWISColumns, importWaterML1

Examples

site_id <- "05114000"
parameterCd <- "00060"
startDate <- "2014-10-10"
endDate <- "2014-10-10"


rawData <- readNWISuv(site_id, parameterCd, startDate, endDate)

rawData_today <- readNWISuv(site_id, parameterCd, Sys.Date(), Sys.Date())

timeZoneChange <- readNWISuv(
  c("04024430", "04024000"), parameterCd,
  "2013-11-03", "2013-11-03"
)

centralTime <- readNWISuv(site_id, parameterCd,
  "2014-10-10T12:00", "2014-10-10T23:59",
  tz = "America/Chicago"
)

# Adding 'Z' to the time indicates to the web service to call the data with UTC time:
GMTdata <- readNWISuv(
  site_id, parameterCd,
  "2014-10-10T00:00Z", "2014-10-10T23:59Z"
)

General Data Import from Water Quality Portal

Description

Imports data from Water Quality Portal web service. This function gets the data from here: https://www.waterqualitydata.us.

Usage

readWQPdata(
  ...,
  service = "Result",
  querySummary = FALSE,
  tz = "UTC",
  ignore_attributes = FALSE,
  convertType = TRUE
)

Arguments

...

see https://www.waterqualitydata.us/webservices_documentation for a complete list of options. A list of arguments can also be supplied. For more information see the above description for this help file. If no "service" argument is supplied, it will default to "ResultWQX3". One way to figure out how to construct a WQP query is to go to the "Advanced" form in the Water Quality Portal. Use the form to discover what parameters are available. Once the query is set in the form, scroll down to the "Query URL". You will see the parameters after "https://www.waterqualitydata.us/#". For example, if you chose "Nutrient" in the Characteristic Group dropdown, you will see characteristicType=Nutrient in the Query URL. The corresponding argument for dataRetrieval is characteristicType = "Nutrient". dataRetrieval users do not need to include mimeType, and providers is optional (these arguments are picked automatically).
service

character. See Details for more information.
querySummary

logical to only return the number of records and unique sites that will be returned from this query. Choosing TRUE is deprecated, readWQPsummary is recommended instead.
tz

character to set timezone attribute of dateTime. Default is "UTC", and converts the date times to UTC, properly accounting for daylight savings times based on the data's provided tz_cd column. Possible values to provide are "America/New_York","America/Chicago", "America/Denver","America/Los_Angeles", "America/Anchorage", as well as the following which do not use daylight savings time: "America/Honolulu", "America/Jamaica","America/Managua","America/Phoenix", and "America/Metlakatla". See also OlsonNames() for more information on time zones.
ignore_attributes

logical to choose to ignore fetching site and status attributes. Default is FALSE.
convertType

logical, defaults to TRUE. If TRUE, the function will convert the data to dates, datetimes, numerics based on a standard algorithm. If false, everything is returned as a character.

Details

This function uses ... as a query input, which can be very flexible, but also has a steeper learning curve. For a quick overview, scroll down to the Examples in this help file to see many query options.

There are currently 10 legacy options for data provided by the Water Quality Portal:

Legacy:

WQP Radio Button service argument Base URL
Sample Results Result /data/Result/search
Site Data Only Station /data/Station/search
Sampling Activity Activity /data/Activity/search
Sampling Activity Metrics ActivityMetric /data/ActivityMetric/search
Site Summary (not advertised on WQP) SiteSummary /data/summary/monitoringLocation/search
Project Data Project /data/Project/search
Project Monitoring Location Weighting Data ProjectMonitoringLocationWeighting /data/ProjectMonitoringLocationWeighting/search
Result Detection Quantitation Limit Data ResultDetectionQuantitationLimit /data/ResultDetectionQuantitationLimit/search
Biological Habitat Metrics BiologicalMetric /data/BiologicalMetric/search
Organization Data Organization /data/Organization/search

There are 4 WQX3 options. These are still in-development, and should be used with caution.

WQP Radio Button service argument Base URL dataProfile
Monitoring Locations StationWQX3 /wqx3/Station/search
Full Physical Chemical ResultWQX3 /wqx3/Result/search fullPhysChem
Narrow ResultWQX3 /wqx3/Result/search narrow
Basic Physical Chemical ResultWQX3 /wqx3/Result/search basicPhysChem
Sampling Activity ActivityWQX3 /wqx3/Activity/search

Value

A data frame, the specific columns will depend on the "service" and/or "dataProfile".

There are also several useful attributes attached to the data frame:

Name Type Description
url character The url used to generate the data
siteInfo data.frame A data frame containing information on the requested sites
headerInfo data.frame A data frame returned from the WQP status service
queryTime POSIXct The time the data was returned

Examples

nameToUse <- "pH"
pHData <- readWQPdata(siteid = "USGS-04024315", 
                      characteristicName = nameToUse)
ncol(pHData)
attr(pHData, "siteInfo")
attr(pHData, "queryTime")

# More examples:
# querying by county
DeWitt <- readWQPdata(
  statecode = "Illinois",
  countycode = "DeWitt",
  characteristicName = "Nitrogen"
)

# Data profile: "Sampling Activity"
activity <- readWQPdata(
  siteid = "USGS-04024315",
  service = "Activity"
)

Dane_activity <- readWQPdata(
  statecode = "Wisconsin",
  countycode = "Dane",
  startDateLo = "2023-01-01",
  startDateHi = "2023-12-31",
  service = "Activity"
)

########################################################
# Additional examples:

pHData_legacy <- readWQPdata(siteid = "USGS-04024315", 
                      characteristicName = nameToUse,
                      service = "Result",
                      dataProfile = "narrowResult")
 
# Data profiles: "Organization Data" 
org_data <- readWQPdata(
  statecode = "WI",
  countycode = "Dane",
  service = "Organization"
)

# Data profiles: "Project Data"  
project_data <- readWQPdata(
  statecode = "WI",
  countycode = "Dane",
  service = "Project"
)

# Data profiles: "Project Monitoring Location Weighting Data"
proj_mlwd <- readWQPdata(
  statecode = "WI",
  countycode = "Dane",
  service = "ProjectMonitoringLocationWeighting"
)

# Data profiles: "Sample Results (physical/chemical metadata)" 
samp_data <- readWQPdata(
  siteid = "USGS-04024315",
  dataProfile = "resultPhysChem",
  service = "Result"
)

# Data profiles: "Sample Results (biological metadata)"
samp_bio <- readWQPdata(
  siteid = "USGS-04024315",
  dataProfile = "biological",
  service = "Result"
)

# Data profiles: "Sample Results (narrow)" 
samp_narrow <- readWQPdata(
  siteid = "USGS-04024315",
  service = "Result",
  dataProfile = "narrowResult"
)

# Data profiles: "Sampling Activity"  
samp_activity <- readWQPdata(
  siteid = "USGS-04024315",
  dataProfile = "activityAll",
  service = "Activity"
)

# Data profile: "Sampling Activity Metrics"
act_metrics <- readWQPdata(
  statecode = "WI",
  countycode = "Dane",
  service = "ActivityMetric"
)

# Data profile: "Result Detection Quantitation Limit Data"  
dl_data <- readWQPdata(
  siteid = "USGS-04024315",
  service = "ResultDetectionQuantitationLimit"
)

# other options:
Phosphorus <- readWQPdata(
  statecode = "WI", countycode = "Dane", 
  characteristicName = "Phosphorus",
  startDateLo = "2023-01-01",
  ignore_attributes = TRUE,
  convertType = FALSE
)

Raw Data Import for Water Quality Portal

Description

Imports data from the Water Quality Portal. This function gets the data from here: https://www.waterqualitydata.us. There are four required input arguments: siteNumbers, parameterCd, startDate, and endDate. parameterCd can either be a USGS 5-digit code, or a characteristic name. The sites can be either USGS, or other Water Quality Portal offered sites. It is required to use the 'full' site name, such as 'USGS-01234567'.

Usage

readWQPqw(
  siteNumbers,
  parameterCd,
  startDate = "",
  endDate = "",
  tz = "UTC",
  legacy = TRUE,
  querySummary = FALSE,
  ignore_attributes = FALSE,
  convertType = TRUE
)

Arguments

siteNumbers

character site number. This needs to include the full agency code prefix.
parameterCd

vector of USGS 5-digit parameter code or characteristicNames. Leaving this blank will return all of the measured values during the specified time period.
startDate

character starting date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates retrieval for the earliest possible record. Date arguments are always specified in local time.
endDate

character ending date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates retrieval for the latest possible record. Date arguments are always specified in local time.
tz

character to set timezone attribute of dateTime. Default is "UTC", and converts the date times to UTC, properly accounting for daylight savings times based on the data provided tz_cd column. Possible values to provide are "America/New_York","America/Chicago", "America/Denver","America/Los_Angeles", "America/Anchorage", as well as the following which do not use daylight savings time: "America/Honolulu", "America/Jamaica","America/Managua","America/Phoenix", and "America/Metlakatla". See also OlsonNames() for more information on time zones.
legacy

Logical. If TRUE, uses legacy WQP services. Default is TRUE. Setting legacy = FALSE uses WQX3.0 WQP services, which are in-development, use with caution.
querySummary

logical to look at number of records and unique sites that will be returned from this query.
ignore_attributes

logical to choose to ignore fetching site and parameter attributes. Default is FALSE.
convertType

logical, defaults to TRUE. If TRUE, the function will convert the data to dates, datetimes, numerics based on a standard algorithm. If false, everything is returned as a character.

Value

A data frame derived from the default data profile.

There are also several useful attributes attached to the data frame:

Name Type Description
url character The url used to generate the data
siteInfo data.frame A data frame containing information on the requested sites
variableInfo data.frame A data frame containing information on the requested parameters
queryTime POSIXct The time the data was returned

See Also

readWQPdata, whatWQPsites, and importWQP

Examples

rawPcode <- readWQPqw("USGS-01594440", "01075", "", "")

attr(rawPcode, "siteInfo")
attr(rawPcode, "queryTime")


rawCharacteristicName <- readWQPqw("WIDNR_WQX-10032762", "Specific conductance", "", "")
rawPHsites <- readWQPqw(c("USGS-05406450", "USGS-05427949", "WIDNR_WQX-133040"), "pH", "", "")
nwisEx <- readWQPqw("USGS-04024000", c("34247", "30234", "32104", "34220"), "", "2022-12-20")

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

Summary of Data Available from Water Quality Portal

Description

Returns a list of sites with year-by-year information on what data is available. The function gets the data from: https://www.waterqualitydata.us. Arguments to the function should be based on https://www.waterqualitydata.us/webservices_documentation. The information returned from this function describes the available data at the WQP sites, and some metadata on the sites themselves.

Usage

readWQPsummary(...)

Arguments

...

see https://www.waterqualitydata.us/webservices_documentation for a complete list of options. A list of arguments can also be supplied. One way to figure out how to construct a WQP query is to go to the "Advanced" form in the Water Quality Portal: https://www.waterqualitydata.us/#mimeType=csv&providers=NWIS&providers=STORET Use the form to discover what parameters are available. Once the query is set in the form, scroll down to the "Query URL". You will see the parameters after "https://www.waterqualitydata.us/#". For example, if you chose "Nutrient" in the Characteristic Group dropdown, you will see characteristicType=Nutrient in the Query URL. The corresponding argument for dataRetrieval is characteristicType = "Nutrient". dataRetrieval users do not need to include mimeType, and providers is optional (these arguments are picked automatically).

Value

A data frame from the data returned from the Water Quality Portal

See Also

whatWQPsites whatWQPdata

Examples

# Summary of a single site for the last 5 years:
site_5 <- readWQPsummary(
  siteid = "USGS-07144100",
  summaryYears = 5
)

# Summary of a single site for the full period of record:
site_all <- readWQPsummary(
  siteid = "USGS-07144100",
  summaryYears = "all"
)

# Summary of the data available from streams in a single county:
dane_county_data <- readWQPsummary(
  countycode = "US:55:025",
  summaryYears = 5,
  siteType = "Stream"
)

# Summary of the data all available from lakes in a single county:
lake_sites <- readWQPsummary(
  siteType = "Lake, Reservoir, Impoundment",
  countycode = "US:55:025"
)

# Summary of the data available for the last 5 years in New Jersey:
state1 <- readWQPsummary(
  statecode = "NJ",
  summaryYears = 5,
  siteType = "Stream"
)

renameColumns

Description

Rename columns coming back from NWIS data retrievals. Daily and unit value columns have names derived from their data descriptor, parameter, and statistic codes. This function reads information from the header and the arguments in the call to to rename those columns.

Usage

renameNWISColumns(
  rawData,
  p00010 = "Wtemp",
  p00045 = "Precip",
  p00060 = "Flow",
  p00065 = "GH",
  p00095 = "SpecCond",
  p00300 = "DO",
  p00400 = "pH",
  p62611 = "GWL",
  p63680 = "Turb",
  p72019 = "WLBLS",
  ...
)

Arguments

rawData

the daily- or unit-values datset retrieved from NWISweb.
p00010

the base name for parameter code 00010.
p00045

the base name for parameter code 00045.
p00060

the base name for parameter code 00060.
p00065

the base name for parameter code 00065.
p00095

the base name for parameter code 00095.
p00300

the base name for parameter code 00300.
p00400

the base name for parameter code 00400.
p62611

the base name for parameter code 62611.
p63680

the base name for parameter code 63680.
p72019

the base name for parameter code 72019.
...

named arguments for the base name for any other parameter code. The form of the name must be like pXXXXX, where XXXXX is the parameter code.

Value

A dataset like data with selected columns renamed.

Note

The following statistics codes are converted by renameNWISColumns.

00000

Instantaneous Value, suffix: Inst

00001

Maximum value, suffix: Max

00002

Minimum value, suffix: Min

00003

Mean value, no suffix

00006

Sum of values, suffix: Sum

00007

Modal value, suffix: Mode

00008

Median value, suffix: Median

00012

Equivalent mean value, suffix: EqMean

00021

Tidal high-high value, suffix: HiHiTide

00022

Tidal low-high value, suffix: LoHiTide

00023

Tidal high-low value, suffix: HiLoTide

00024

Tidal low-low value, suffix: LoLoTide

See Also

readNWISdv, readNWISuv

Examples

siteWithTwo <- "01480015"
startDate <- "2012-09-01"
endDate <- "2012-10-01"

twoResults <- readNWISdv(siteWithTwo, "00060", startDate, endDate)
names(twoResults)
renamedCols <- renameNWISColumns(twoResults)
names(renamedCols)
# Custom names:
newNames <- renameNWISColumns(twoResults, p00060 = "Discharge")
names(newNames)

Set data endpoint

Description

access Indicate which dataRetrieval access code you want to use options: c('public','internal')

Usage

setAccess(access = "public")

Arguments

access

code for data access. Options are: "public","internal","cooperator", or "USGS".

  • "internal" represents Access=3 ...for a single water science center

  • "USGS" represents Access=2 ...for all water science centers

  • "cooperator" represents Access=1

  • "public" represents Access=0, public access

Author(s)

Luke Winslow, Jordan S Read

Examples

setAccess("internal")

setAccess("public")

US State Code Lookup Table

Description

Data originally pulled from https://www2.census.gov/geo/docs/reference/state.txt on April 1, 2015. On Feb. 11, 2022, the fields were updated with the file found in inst/extdata, which is used internally with NWIS retrievals.

Value

stateCd data frame.

Name Type Description
STATE character FIPS State Code
STUSAB character Official United States Postal Service (USPS) Code
STATE_NAME character State Name
STATENS character Geographic Names Information System Identifier (GNISID)

Examples

head(stateCd)

State code look up

Description

Function to simplify finding state and state code definitions. Used in readNWISdata and readWQPdata.

Usage

stateCdLookup(input, outputType = "postal")

Arguments

input

could be character (full name, abbreviation, id), or numeric (id)
outputType

character can be "postal", "fullName", "tableIndex", or "id".

Examples

fullName <- stateCdLookup("wi", "fullName")
abbriev <- stateCdLookup("Wisconsin", "postal")
id <- stateCdLookup("WI", "id")
name <- stateCdLookup(55, "fullName")
index <- stateCdLookup("WI", "tableIndex")
stateCd[index, ]
stateCdLookup(c("West Virginia", "Wisconsin", 200, 55, "MN"))

USGS data availability

Description

Imports a table of available parameters, period of record, and count. See https://waterservices.usgs.gov/docs/site-service/ for more information.

Usage

whatNWISdata(..., convertType = TRUE)

Arguments

...

see https://waterservices.usgs.gov/docs/site-service/ for a complete list of options. A list of arguments can also be supplied.
convertType

logical, defaults to TRUE. If TRUE, the function will convert the data to dates, datetimes, numerics based on a standard algorithm. If false, everything is returned as a character

Details

This function requires users to create their own arguments based on the NWIS web services. It is a more complicated function to use compared to other NWIS functions such as readNWISdv, readNWISuv, etc. However, this function adds a lot of flexibility to the possible queries. If the "service" argument is included, the results will be filtered to the proper data_type_cd. This is a great function to use before a large data set, by filtering down the number of sites that have useful data.

Value

A data frame with the following columns:

Name Type Description
agency_cd character The NWIS code for the agency reporting the data
site_no character The USGS site number
station_nm character Site name
site_tp_cd character Site type
dec_lat_va numeric Decimal latitude
dec_long_va numeric Decimal longitude
coord_acy_cd character Latitude-longitude accuracy
dec_coord_datum_cd character Decimal Latitude-longitude datum
alt_va character Altitude of Gage or land surface
alt_acy_va character Altitude accuracy
alt_datum_cd character Altitude datum
huc_cd character Hydrologic unit code
data_type_cd character Data type
parm_cd character Parameter code
stat_cd character Statistical code
dd_nu character Internal database key
loc_web_ds character Additional measurement description
medium_grp_cd character Medium group code
parm_grp_cd character Parameter group code
srs_id character SRS ID
access_cd character Access code
begin_date Date Begin date
end_date Date End date
count_nu integer Record count
parameter_group_nm character Parameter group name
parameter_nm character Parameter name
casrn character Chemical Abstracts Service (CAS) Registry Number
srsname character Substance Registry Services
parameter_units character Parameter units

There are also several useful attributes attached to the data frame:

Name Type Description
url character The url used to generate the data
comment character Header comments from the RDB file
queryTime POSIXct The time the data was returned

Examples

availableData <- whatNWISdata(siteNumber = "05114000")

# To find just unit value ('instantaneous') data:
uvData <- whatNWISdata(siteNumber = "05114000",
                       service = "uv")
uvDataMulti <- whatNWISdata(siteNumber = c("05114000", "09423350"),
                            service = c("uv", "dv"))
flowAndTemp <- whatNWISdata(
  stateCd = "WI", service = "dv",
  parameterCd = c("00060", "00010"),
  statCd = "00003"
)
sites <- whatNWISdata(stateCd = "WI",
                      parameterCd = "00060",
                      siteType = "ST", 
                      service = "site")
                      
sites <- whatNWISdata(stateCd = "WI",
                      service = "gwlevels")

Site Data Import from NWIS

Description

Returns a list of sites from the NWIS web service. This function gets the data from: https://waterservices.usgs.gov/docs/site-service/. Mapper format is used

Usage

whatNWISsites(...)

Arguments

...

see https://waterservices.usgs.gov/docs/site-service/ for a complete list of options. A list (or lists) can also be supplied.

Value

A data frame with at least the following columns:

Name Type Description
agency_cd character The NWIS code for the agency reporting the data
site_no character The USGS site number
station_nm character Station name
site_tp_cd character Site type code
dec_lat_va numeric Decimal latitude
dec_long_va numeric Decimal longitude
queryTime POSIXct Query time

There are also several useful attributes attached to the data frame:

Name Type Description
url character The url used to generate the data
queryTime POSIXct The time the data was returned

Examples

siteListPhos <- whatNWISsites(stateCd = "OH", parameterCd = "00665")
oneSite <- whatNWISsites(sites = "05114000")

Data Available from Water Quality Portal

Description

Returns a list of sites from the Water Quality Portal web service. This function gets the data from: https://www.waterqualitydata.us. Arguments to the function should be based on https://www.waterqualitydata.us/webservices_documentation. The information returned from whatWQPdata describes the available data at the WQP sites, and some metadata on the sites themselves. For example, a row is returned for each individual site that fulfills this query. In that we can learn how many sampling activities and results are available for the query. It does not break those results down by any finer grain. For example, if you ask for "Nutrients" (characteristicGroup), you will not learn what specific nutrients are available at that site. For that kind of data discovery see readWQPsummary.

Usage

whatWQPdata(..., saveFile = tempfile(), convertType = TRUE)

Arguments

...

see https://www.waterqualitydata.us/webservices_documentation for a complete list of options. A list of arguments can also be supplied. One way to figure out how to construct a WQP query is to go to the "Advanced" form in the Water Quality Portal: https://www.waterqualitydata.us/#mimeType=csv&providers=NWIS&providers=STORET Use the form to discover what parameters are available. Once the query is set in the form, scroll down to the "Query URL". You will see the parameters after "https://www.waterqualitydata.us/#". For example, if you chose "Nutrient" in the Characteristic Group dropdown, you will see characteristicType=Nutrient in the Query URL. The corresponding argument for dataRetrieval is characteristicType = "Nutrient". dataRetrieval users do not need to include mimeType, and providers is optional (these arguments are picked automatically).
saveFile

path to save the incoming geojson output.
convertType

logical, defaults to TRUE. If TRUE, the function will convert the data to dates, datetimes, numerics based on a standard algorithm. If false, everything is returned as a character.

Value

A data frame based on the Water Quality Portal results.

See Also

whatWQPsites readWQPsummary readWQPdata

Examples

site1 <- whatWQPdata(siteid = "USGS-01594440")

type <- "Stream"
sites <- whatWQPdata(countycode = "US:55:025", siteType = type)

lakeSites <- whatWQPdata(siteType = "Lake, Reservoir, Impoundment",
                         countycode = "US:55:025")
lakeSites_chars <- whatWQPdata(
  siteType = "Lake, Reservoir, Impoundment",
  countycode = "US:55:025", convertType = FALSE)


bbox <- c(-86.9736, 34.4883, -86.6135, 34.6562)
what_bb <- whatWQPdata(bBox = bbox)

Site Data Import from Water Quality Portal

Description

Returns a list of sites from the Water Quality Portal web service. This function gets the data from: https://www.waterqualitydata.us. Arguments to the function should be based on https://www.waterqualitydata.us/webservices_documentation. The return from this function returns the basic metadata on WQP sites. It is generally faster than the whatWQPdata function, but does not return information on what data was collected at the site.

Usage

whatWQPsamples(..., convertType = TRUE, legacy = TRUE)

whatWQPmetrics(..., convertType = TRUE)

whatWQPsites(..., legacy = TRUE)

Arguments

...

see https://www.waterqualitydata.us/webservices_documentation for a complete list of options. A list of arguments can also be supplied. One way to figure out how to construct a WQP query is to go to the "Advanced" form in the Water Quality Portal: https://www.waterqualitydata.us/#mimeType=csv&providers=NWIS&providers=STORET Use the form to discover what parameters are available. Once the query is set in the form, scroll down to the "Query URL". You will see the parameters after "https://www.waterqualitydata.us/#". For example, if you chose "Nutrient" in the Characteristic Group dropdown, you will see characteristicType=Nutrient in the Query URL. The corresponding argument for dataRetrieval is characteristicType = "Nutrient". dataRetrieval users do not need to include mimeType, and providers is optional (these arguments are picked automatically).
convertType

logical, defaults to TRUE. If TRUE, the function will convert the data to dates, datetimes, numerics based on a standard algorithm. If false, everything is returned as a character.
legacy

Logical. If TRUE, uses legacy WQP services. Default is TRUE. Setting legacy = FALSE uses WQX3.0 WQP services, which are in-development, use with caution.

Details

The readWQPsummary function has

Value

data frame

See Also

whatWQPdata readWQPsummary

whatNWISdata

Examples

site1 <- whatWQPsamples(siteid = "USGS-01594440")

type <- "Stream"

sites <- whatWQPsamples(countycode = "US:55:025", siteType = type)

lakeSites_samples <- whatWQPsamples(siteType = "Lake, Reservoir, Impoundment",
                                    countycode = "US:55:025")



type <- "Stream"

sites <- whatWQPmetrics(countycode = "US:55:025", siteType = type)
lakeSites_metrics <- whatWQPmetrics(siteType = "Lake, Reservoir, Impoundment",
                                    countycode = "US:55:025")




site1 <- whatWQPsites(siteid = "USGS-01594440")

type <- "Stream"
sites <- whatWQPsites(
  countycode = "US:55:025",
  characteristicName = "Phosphorus",
  siteType = type
)

Get WQP service metadata

Description

The information from this request is only available for a limited time after the original query from the WQP. In the readWQPdata and readWQPqw functions, the results from this function will be attached as an attribute to the data.

Usage

wqp_check_status(wqp_request_id)

Arguments

wqp_request_id

A character returned from the header of a WQP request.

Value

a list generated from the WQP describing what data was returned.

Examples

rawPcode <- readWQPqw("USGS-01594440", "01075", ignore_attributes = TRUE)
headerInfo <- attr(rawPcode, "headerInfo")
wqp_request_id <- headerInfo$`wqp-request-id`
count_info <- wqp_check_status(wqp_request_id)
count_info[["dataProviders"]]

Pad string with leading zeros

Description

Function to pad a string with leading zeros. Useful for parameter codes and USGS site IDs.

Usage

zeroPad(x, padTo)

Arguments

x

character
padTo

number Final desired length of the character

Value

x character returned with leading zeros

Examples

pCode <- "10"
correctPCode <- zeroPad(pCode, 5)
pCodes <- c("100", "1000", "0", "12345", "1565465465465465")
correctPCodes <- zeroPad(pCodes, 5)
pCodeNA <- c(1, 2, NA)
padPCodeNA <- zeroPad(pCodeNA, 4)