readWQPdata: 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)

Arguments

…

see https://www.waterqualitydata.us/webservices_documentation for a complete list of options. A list of arguments can also be supplied.

querySummary

logical to ONLY return the number of records and unique sites that will be returned from this query. This argument is not supported via the combined list from the … argument

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.

Value

A data frame with at least the following columns:

Name	Type	Description
OrganizationIdentifier	character	A designator used to uniquely identify a unique business establishment within a context.
OrganizationFormalName	character	The legal designator (i.e. formal name) of an organization.
ActivityIdentifier	character	Designator that uniquely identifies an activity within an organization.
ActivityTypeCode	character	The text describing the type of activity.
ActivityMediaName	character	Name or code indicating the environmental medium where the sample was taken.
ActivityMediaSubdivisionName	character	Name or code indicating the environmental matrix as a subdivision of the sample media.
ActivityStartDate	character	The calendar date on which the field activity is started.
ActivityStartTime.Time	character	The time of day that is reported when the field activity began, based on a 24-hour timescale.
ActivityStartTime.TimeZoneCode	character	The time zone for which the time of day is reported. Any of the longitudinal divisions of the earth's surface in which a standard time is kept.
ActivityEndDate	character	The calendar date when the field activity is completed.
ActivityEndTime.Time	character	The time of day that is reported when the field activity ended, based on a 24-hour timescale.
ActivityEndTime.TimeZoneCode	character	The time zone for which the time of day is reported. Any of the longitudinal divisions of the earth's surface in which a standard time is kept.
ActivityDepthHeightMeasure.MeasureValue	character	A measurement of the vertical location (measured from a reference point) at which an activity occurred. Measure value is given in the units stored in ActivityDepthHeightMeasure.MeasureUnitCode.
ActivityDepthHeightMeasure.MeasureUnitCode	character	The code that represents the unit for measuring the item.
ActivityDepthAltitudeReferencePointText	character	The reference used to indicate the datum or reference used to establish the depth/altitude of an activity.
ActivityTopDepthHeightMeasure.MeasureValue	character	A measurement of the upper vertical location of a vertical location range (measured from a reference point) at which an activity occurred. Measure value is given in the units stored in ActivityTopDepthHeightMeasure.MeasureUnitCode.
ActivityTopDepthHeightMeasure.MeasureUnitCode	character	The code that represents the unit for measuring the item.
ActivityBottomDepthHeightMeasure.MeasureValue	character	A measurement of the lower vertical location of a vertical location range (measured from a reference point) at which an activity occurred. Measure value is given in the units stored in ActivityBottomDepthHeightMeasure.MeasureUnitCode.
ActivityBottomDepthHeightMeasure.MeasureUnitCode	character	The code that represents the unit for measuring the item.
ProjectIdentifier	character	A designator used to uniquely identify a data collection project within a context of an organization.
ActivityConductingOrganizationText	character	A name of the Organization conducting an activity.
MonitoringLocationIdentifier	character	A designator used to describe the unique name, number, or code assigned to identify the monitoring location.
ActivityCommentText	character	General comments concerning the activity.
SampleAquifer *	character	A code that designates the aquifer associated with groundwater samples.
HydrologicCondition *	character	Hydrologic condition is the hydrologic condition that is represented by the sample collected (i.e. ? normal, falling, rising, peak stage).
HydrologicEvent *	character	A hydrologic event that is represented by the sample collected (i.e. - storm, drought, snowmelt).
SampleCollectionMethod.MethodIdentifier	character	The identification number or code assigned by the method publisher.
SampleCollectionMethod.MethodIdentifierContext	character	Identifies the source or data system that created or defined the identifier.
SampleCollectionMethod.MethodName	character	The title that appears on the method from the method publisher.
SampleCollectionEquipmentName	character	The name for the equipment used in collecting the sample.
ResultDetectionConditionText	character	The textual descriptor of a result.
CharacteristicName	character	The object, property, or substance which is evaluated or enumerated by either a direct field measurement, a direct field observation, or by laboratory analysis of material collected in the field.
ResultSampleFractionText	character	The text name of the portion of the sample associated with results obtained from a physically-partitioned sample.
ResultMeasureValue	numeric	The reportable measure of the result for the chemical, microbiological or other characteristic being analyzed. Measure value is given in the units stored in ResultMeasure.MeasureUnitCode.
MeasureQualifierCode	character	A code used to identify any qualifying issues that affect the results.
ResultMeasure.MeasureUnitCode	character	The code that represents the unit for measuring the item.
ResultStatusIdentifier	character	Indicates the acceptability of the result with respect to QA/QC criteria.
StatisticalBaseCode	character	The code for the method used to calculate derived results.
ResultValueTypeName	character	A name that qualifies the process which was used in the determination of the result value (e.g., actual, estimated, calculated).
ResultWeightBasisText	character	The name that represents the form of the sample or portion of the sample which is associated with the result value (e.g., wet weight, dry weight, ash-free dry weight).
ResultTimeBasisText	character	The period of time (in days) over which a measurement was made. For example, BOD can be measured as 5 day or 20 day BOD.
ResultTemperatureBasisText	character	The name that represents the controlled temperature at which the sample was maintained during analysis, e.g. 25 deg BOD analysis.
ResultParticleSizeBasisText	character	User defined free text describing the particle size class for which the associated result is defined.
PrecisionValue	character	A measure of mutual agreement among individual measurements of the same property usually under prescribed similar conditions.
ResultCommentText	character	Free text with general comments concerning the result.
USGSPCode *	character	5-digit number used in the US Geological Survey computerized data system, National Water Information System (NWIS), to uniquely identify a specific constituent.
ResultDepthHeightMeasure.MeasureValue +	character	A measurement of the vertical location (measured from a reference point) at which a result occurred.
ResultDepthHeightMeasure.MeasureUnitCode +	character	The code that represents the unit for measuring the item.
ResultDepthAltitudeReferencePointText +	character	The reference used to indicate the datum or reference used to establish the depth/altitude of a result.
SubjectTaxonomicName	character	The name of the organism from which a tissue sample was taken.
SampleTissueAnatomyName *	character	The name of the anatomy from which a tissue sample was taken.
ResultAnalyticalMethod.MethodIdentifier	character	The identification number or code assigned by the method publisher.
ResultAnalyticalMethod.MethodIdentifierContext	character	Identifies the source or data system that created or defined the identifier.
ResultAnalyticalMethod.MethodName	character	The title that appears on the method from the method publisher.
MethodDescriptionText *	character	A brief summary that provides general information about the method.
LaboratoryName	character	The name of Lab responsible for the result.
AnalysisStartDate	character	The calendar date on which the analysis began.
ResultLaboratoryCommentText	character	Remarks which further describe the laboratory procedures which produced the result.
DetectionQuantitationLimitTypeName	character	Text describing the type of detection or quantitation level used in the analysis of a characteristic.
DetectionQuantitationLimitMeasure.MeasureValue	numeric	Constituent concentration that, when processed through the complete method, produces a signal that is statistically different from a blank. Measure value is given in the units stored in DetectionQuantitationLimitMeasure.MeasureUnitCode.
DetectionQuantitationLimitMeasure.MeasureUnitCode	character	The code that represents the unit for measuring the item.
PreparationStartDate	character	The calendar date when the preparation/extraction of the sample for analysis began.
ActivityStartDateTime	POSIXct	Activity start date and time converted to POSIXct UTC.
ActivityEndDateTime	POSIXct	Activity end date and time converted to POSIXct UTC.

* = elements only in NWIS + = elements only in STORET

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

Run this code

# NOT RUN {
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")
# }

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