General Data Import from Water Quality Portal — readWQPdata • dataRetrieval

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

Usage

readWQPdata(
  ...,
  service = "ResultWQX3",
  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.

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

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 and 4 modern WQX options for data provided by the Water Quality Portal:

WQX:

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

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

Examples

# \donttest{
nameToUse <- "pH"
pHData <- readWQPdata(siteid = "USGS-04024315", 
                      characteristicName = nameToUse)
ncol(pHData)
#> [1] 182
attr(pHData, "url")
#> [1] "https://www.waterqualitydata.us/wqx3/Result/search?siteid=USGS-04024315&characteristicName=pH&mimeType=csv&dataProfile=fullPhysChem"
attr(pHData, "siteInfo")
#> # A tibble: 1 × 56
#>   Org_Identifier Org_FormalName   ProviderName Location_Identifier Location_Name
#>   <chr>          <chr>            <chr>        <chr>               <chr>        
#> 1 USGS           U.S. Geological… USGS         USGS-04024315       LITTLE BALSA…
#> # ℹ 51 more variables: Location_Type <chr>, Location_Description <chr>,
#> #   Location_State <chr>, Location_CountryName <chr>,
#> #   Location_CountyName <chr>, Location_CountryCode <chr>,
#> #   Location_StatePostalCode <chr>, Location_CountyCode <chr>,
#> #   Location_HUCEightDigitCode <chr>, Location_HUCTwelveDigitCode <chr>,
#> #   Location_TribalLandIndicator <chr>, Location_TribalLand <chr>,
#> #   Location_Latitude <dbl>, Location_Longitude <dbl>, …
attr(pHData, "headerInfo")[["dataProviders"]]
#>   name completeOrCancelled failed sourceRowCount outputRowCount
#> 1 usgs                TRUE  FALSE             33             32
#> 2  epa                TRUE  FALSE              1              0
#>   millisecondsToFirstResponse secondsToCompletion
#> 1                           2                   0
#> 2                         131                   0
attr(pHData, "queryTime")
#> [1] "2024-06-15 12:45:29 GMT"

# dataProfile = Basic Physical Chemical
pHData_basic <- readWQPdata(siteid = "USGS-04024315", 
                      characteristicName = nameToUse,
                      dataProfile = "basicPhysChem")
attr(pHData_basic, "url") 
#> [1] "https://www.waterqualitydata.us/wqx3/Result/search?siteid=USGS-04024315&characteristicName=pH&dataProfile=basicPhysChem&mimeType=csv"
ncol(pHData_basic)
#> [1] 100

# dataProfile = Narrow
pHData_narrow <- readWQPdata(siteid = "USGS-04024315", 
                      characteristicName = nameToUse,
                      dataProfile = "narrow")
attr(pHData_narrow, "url") 
#> [1] "https://www.waterqualitydata.us/wqx3/Result/search?siteid=USGS-04024315&characteristicName=pH&dataProfile=narrow&mimeType=csv"
ncol(pHData_narrow)
#> [1] 65

# vs legacy:
pHData_legacy <- readWQPdata(siteid = "USGS-04024315", 
                      characteristicName = nameToUse,
                      service = "Result",
                      dataProfile = "narrowResult")
#> NEWS: Legacy data profiles will be retired. Please begin converting
#> workflows to the WQX 3.0 profiles. Also, data from legacy profiles do not
#> include USGS data newer than March 11, 2024. More details:
#> https://doi-usgs.github.io/dataRetrieval/articles/Status.html
attr(pHData_legacy, "url")
#> [1] "https://www.waterqualitydata.us/data/Result/search?siteid=USGS-04024315&characteristicName=pH&dataProfile=narrowResult&mimeType=csv"

# Data profiles: "Site Data Only"
site_data <- readWQPdata(
  statecode = "WI",
  countycode = "Dane",
  service = "StationWQX3"
)

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

# Legacy examples:

# Data profiles: "Organization Data" (legacy)
org_data <- readWQPdata(
  statecode = "WI",
  countycode = "Dane",
  service = "Organization"
)
#> NEWS: Legacy profile requested, and no equivalent/similar WQX 3.0
#> profile currently exists. Legacy profiles do not include USGS data newer
#> than March 11, 2024. 
#> More details: 
#> https://doi-usgs.github.io/dataRetrieval/articles/Status.html

# Data profiles: "Project Data"  (legacy)
project_data <- readWQPdata(
  statecode = "WI",
  countycode = "Dane",
  service = "Project"
)
#> NEWS: Legacy profile requested, and no equivalent/similar WQX 3.0
#> profile currently exists. Legacy profiles do not include USGS data newer
#> than March 11, 2024. 
#> More details: 
#> https://doi-usgs.github.io/dataRetrieval/articles/Status.html

# Data profiles: "Project Monitoring Location Weighting Data"  (legacy)
proj_mlwd <- readWQPdata(
  statecode = "WI",
  countycode = "Dane",
  service = "ProjectMonitoringLocationWeighting"
)
#> NEWS: Legacy profile requested, and no equivalent/similar WQX 3.0
#> profile currently exists. Legacy profiles do not include USGS data newer
#> than March 11, 2024. 
#> More details: 
#> https://doi-usgs.github.io/dataRetrieval/articles/Status.html
#> New names:
#> • `ResourceSubjectText` -> `ResourceSubjectText...13`
#> • `ResourceSubjectText` -> `ResourceSubjectText...15`

# Data profiles: "Sample Results (physical/chemical metadata)"  (legacy)
samp_data <- readWQPdata(
  siteid = "USGS-04024315",
  dataProfile = "resultPhysChem",
  service = "Result"
)
#> NEWS: Legacy data profiles will be retired. Please begin converting
#> workflows to the WQX 3.0 profiles. Also, data from legacy profiles do not
#> include USGS data newer than March 11, 2024. More details:
#> https://doi-usgs.github.io/dataRetrieval/articles/Status.html

# Data profiles: "Sample Results (biological metadata)"  (legacy)
samp_bio <- readWQPdata(
  siteid = "USGS-04024315",
  dataProfile = "biological",
  service = "Result"
)
#> NEWS: Legacy data profiles will be retired. Please begin converting
#> workflows to the WQX 3.0 profiles. Also, data from legacy profiles do not
#> include USGS data newer than March 11, 2024. More details:
#> https://doi-usgs.github.io/dataRetrieval/articles/Status.html

# Data profiles: "Sample Results (narrow)" (legacy)
samp_narrow <- readWQPdata(
  siteid = "USGS-04024315",
  service = "Result",
  dataProfile = "narrowResult"
)
#> NEWS: Legacy data profiles will be retired. Please begin converting
#> workflows to the WQX 3.0 profiles. Also, data from legacy profiles do not
#> include USGS data newer than March 11, 2024. More details:
#> https://doi-usgs.github.io/dataRetrieval/articles/Status.html

# Data profiles: "Sampling Activity"  (legacy)
samp_activity <- readWQPdata(
  siteid = "USGS-04024315",
  dataProfile = "activityAll",
  service = "Activity"
)
#> NEWS: Legacy profile requested, and no equivalent/similar WQX 3.0
#> profile currently exists. Legacy profiles do not include USGS data newer
#> than March 11, 2024. 
#> More details: 
#> https://doi-usgs.github.io/dataRetrieval/articles/Status.html

# Data profile: "Sampling Activity Metrics"  (legacy)
act_metrics <- readWQPdata(
  statecode = "WI",
  countycode = "Dane",
  service = "ActivityMetric"
)
#> NEWS: Legacy profile requested, and no equivalent/similar WQX 3.0
#> profile currently exists. Legacy profiles do not include USGS data newer
#> than March 11, 2024. 
#> More details: 
#> https://doi-usgs.github.io/dataRetrieval/articles/Status.html

# Data profile: "Result Detection Quantitation Limit Data"  (legacy)
dl_data <- readWQPdata(
  siteid = "USGS-04024315",
  service = "ResultDetectionQuantitationLimit"
)
#> NEWS: Legacy profile requested, and no equivalent/similar WQX 3.0
#> profile currently exists. Legacy profiles do not include USGS data newer
#> than March 11, 2024. 
#> More details: 
#> https://doi-usgs.github.io/dataRetrieval/articles/Status.html

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