readWQPdata: General Data Import from Water Quality Portal

In USGS-R/dataRetrieval: Retrieval Functions for USGS and EPA Hydrology and Water Quality Data

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. because it allows for other agencies rather than the USGS.

Usage

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

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 "Result". 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, zip, and providers is optional (these arguments are picked automatically).
querySummary	logical to only return the number of records and unique sites that will be returned from this query.
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 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.
checkHeader	logical, defaults to FALSE. If TRUE, the code will check that the curl header response for number of rows matches the actual number of rows. During transition to WQX 3.0 profiles, it's unclear if the counts will be correct.

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 "services" provided by the Water Quality Portal:

Name	Base URL
Result (default)	"https://www.waterqualitydata.us/data/Result/search"
Station	"https://www.waterqualitydata.us/data/Station/search"
Activity	"https://www.waterqualitydata.us/data/Activity/search"
ActivityMetric	"https://www.waterqualitydata.us/data/ActivityMetric/search"
SiteSummary	"https://www.waterqualitydata.us/data/summary/monitoringLocation/search"
Project	"https://www.waterqualitydata.us/data/Project/search"
ProjectMonitoringLocationWeighting	"https://www.waterqualitydata.us/data/ProjectMonitoringLocationWeighting/search"
ResultDetectionQuantitationLimit	"https://www.waterqualitydata.us/data/ResultDetectionQuantitationLimit/search"
BiologicalMetric	"https://www.waterqualitydata.us/data/BiologicalMetric/search"
Organization	"https://www.waterqualitydata.us/data/Organization/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
variableInfo	data.frame	A data frame containing information on the requested parameters
queryTime	POSIXct	The time the data was returned

Examples

nameToUse <- "pH"
pHData <- readWQPdata(siteid = "USGS-04024315", characteristicName = nameToUse)
pHData_summary <- readWQPdata(
  bBox = c(-90.10, 42.67, -88.64, 43.35),
  characteristicName = nameToUse, querySummary = TRUE
)
startDate <- as.Date("2013-01-01")
secchi.names <- c(
  "Depth, Secchi disk depth",
  "Depth, Secchi disk depth (choice list)",
  "Secchi Reading Condition (choice list)",
  "Water transparency, Secchi disc"
)
args <- list(
  "startDateLo" = startDate,
  "startDateHi" = "2013-12-31",
  statecode = "WI",
  characteristicName = secchi.names
)

wqp.data <- readWQPdata(args)

args_2 <- list(
  "startDateLo" = startDate,
  "startDateHi" = "2013-12-31",
  statecode = "WI",
  characteristicName = secchi.names,
  querySummary = TRUE
)

wqp.summary <- readWQPdata(args_2)

arg_3 <- list(
  "startDateLo" = startDate,
  "startDateHi" = "2013-12-31"
)
arg_4 <- list(
  statecode = "WI",
  characteristicName = secchi.names
)
wqp.summary <- readWQPdata(arg_3, arg_4, querySummary = TRUE)
wqp.summary_WI <- readWQPdata(arg_3,
  statecode = "WI",
  characteristicName = secchi.names,
  querySummary = TRUE
)

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

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

# Data profiles: "Site Data Only"
site_data <- readWQPdata(
  statecode = "WI",
  countycode = "Dane",
  service = "Station"
)

# 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"
)

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

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

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

# 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"
)

Phosphorus <- readWQPdata(
  statecode = "WI", countycode = "Dane", 
  characteristicName = "Phosphorus",
  startDateLo = "2020-01-01",
  convertType = FALSE
)

USGS-R/dataRetrieval documentation built on April 23, 2024, 4:44 a.m.