readWQPdata: General Data Import from Water Quality Portal

View source: R/readWQPdata.R

readWQPdataR Documentation

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
)



dataRetrieval documentation built on Oct. 31, 2024, 9:07 a.m.