Initial framework for new WQP summary function.

NAMESPACE

@@ -43,6 +43,7 @@ export(stateCdLookup)
 export(whatNWISdata)
 export(whatNWISsites)
 export(whatWQPdata)
+export(whatWQPdata2)
 export(whatWQPmetrics)
 export(whatWQPsamples)
 export(whatWQPsites)

R/whatWQPdata2.R

+
+#' Data Available from Water Quality Portal
+#'
+#' Returns a list of sites from the Water Quality Portal web service. This
+#' function gets the data from: \url{https://www.waterqualitydata.us}.
+#' Arguments to the function should be based on
+#' \url{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.
+#'
+#' @param \dots see \url{https://www.waterqualitydata.us/webservices_documentation}
+#'  for a complete list of options. A list of arguments can also be supplied. 
+#' @return A data frame with at least the following columns:
+#' \tabular{lll}{ 
+#' Name \tab Type \tab Description \cr
+#'  "Provider" \tab character \tab Providing database.  \cr            
+#'  "MonitoringLocationIdentifier" \tab character \tab	A designator used to 
+#' describe the unique name, number, or code assigned to identify 
+#' the monitoring location.\cr
+#'  "YearSummarized" \tab numeric \tab The year of the summary \cr
+#'  "CharacteristicType" \tab character \tab CharacteristicType  \cr  
+#'  "CharacteristicName" \tab character \tab	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.\cr 
+#'  "ActivityCount" \tab numeric \tab The number of times the location was sampled \cr
+#'  "ResultCount" \tab numeric \tab The number of individual data results. \cr
+#'  "LastResultSubmittedDate" \tab Date \tab Date when data was last submitted. \cr
+#'  "OrganizationIdentifier" \tab character \tab  A designator used to uniquely 
+#' identify a unique business establishment within a context.\cr
+#'  "OrganizationFormalName" \tab character \tab  The legal designator
+#' (i.e. formal name) of an organization.\cr
+#'  "MonitoringLocationName \tab character \tab MonitoringLocationName \cr 
+#'  "MonitoringLocationTypeName" \tab character \tab MonitoringLocationTypeName \cr
+#'  "ResolvedMonitoringLocationTypeName" \tab character \tab  \cr
+#'  "HUCEightDigitCode" \tab character \tab 8-digit HUC id. \cr
+#'  "MonitoringLocationUrl" \tab character \tab URL to monitoring location. \cr
+#'  "CountyName" \tab character \tab County of sampling location. \cr
+#'  "StateName" \tab character \tab State of sampling location. \cr  
+#'  "MonitoringLocationLatitude"  \tab numeric \tab latitude of sampling 
+#'  location. \cr
+#'  "MonitoringLocationLongitude" \tab numeric \tab longitude of sampling 
+#'  location. \cr
+#' }
+#' @export
+#' @examplesIf is_dataRetrieval_user()
+#' \donttest{
+#' dane_county_data <- whatWQPdata2(countycode = "US:55:025",
+#'                         summaryYears = 5,
+#'                         siteType = "Stream")
+#' 
+#' 
+#' lake_sites <- whatWQPdata2(siteType = "Lake, Reservoir, Impoundment",
+#'                          CharacteristicName = "Temperature, water",
+#'                          countycode = "US:55:025")
+#' # Compare with the the results of whatWQPdata:                        
+#' lake_sites2 <- whatWQPdata(siteType = "Lake, Reservoir, Impoundment",
+#'                          CharacteristicName = "Temperature, water",
+#'                          countycode = "US:55:025")
+#'                          
+#' }
+whatWQPdata2 <- function(...){
+  
+  values <- readWQPdots(..., zip = "no")
+  
+  values <- values$values
+
+  if("service" %in% names(values)){
+    values <- values[!(names(values) %in% "service")]
+  }
+  
+  if(!"dataProfile" %in% names(values)){
+    values[["dataProfile"]] <- "periodOfRecord"
+  }
+
+  if("CharacteristicName" %in% names(values)){
+    CharacteristicName <- values[["CharacteristicName"]]
+    values <- values[names(values) != "CharacteristicName"]
+  } else {
+    CharacteristicName <- "all"
+  }
+
+  values <- sapply(values, function(x) URLencode(x, reserved = TRUE))
+  
+  baseURL <- drURL("SiteSummary", arg.list = values)
+  
+  baseURL <- appendDrURL(baseURL, mimeType = "csv")
+  
+  withCallingHandlers({
+    retval <- importWQP(baseURL, zip = FALSE, csv = TRUE)
+  }, warning=function(w) {
+    if (any( grepl( "Number of rows returned not matched in header", w)))
+      invokeRestart("muffleWarning")
+  })
+  
+  if(!("all" %in% CharacteristicName)){
+    retval <- retval[retval$CharacteristicName %in% CharacteristicName,]
+  }
+  
+  attr(retval, "queryTime") <- Sys.time()
+  attr(retval, "url") <- baseURL
+  
+  return(retval)
+}
+
+

man/whatWQPdata2.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/whatWQPdata2.R
+\name{whatWQPdata2}
+\alias{whatWQPdata2}
+\title{Data Available from Water Quality Portal}
+\usage{
+whatWQPdata2(...)
+}
+\arguments{
+\item{\dots}{see \url{https://www.waterqualitydata.us/webservices_documentation}
+for a complete list of options. A list of arguments can also be supplied.}
+}
+\value{
+A data frame with at least the following columns:
+\tabular{lll}{ 
+Name \tab Type \tab Description \cr
+ "Provider" \tab character \tab Providing database.  \cr            
+ "MonitoringLocationIdentifier" \tab character \tab	A designator used to 
+describe the unique name, number, or code assigned to identify 
+the monitoring location.\cr
+ "YearSummarized" \tab numeric \tab The year of the summary \cr
+ "CharacteristicType" \tab character \tab CharacteristicType  \cr  
+ "CharacteristicName" \tab character \tab	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.\cr 
+ "ActivityCount" \tab numeric \tab The number of times the location was sampled \cr
+ "ResultCount" \tab numeric \tab The number of individual data results. \cr
+ "LastResultSubmittedDate" \tab Date \tab Date when data was last submitted. \cr
+ "OrganizationIdentifier" \tab character \tab  A designator used to uniquely 
+identify a unique business establishment within a context.\cr
+ "OrganizationFormalName" \tab character \tab  The legal designator
+(i.e. formal name) of an organization.\cr
+ "MonitoringLocationName \tab character \tab MonitoringLocationName \cr 
+ "MonitoringLocationTypeName" \tab character \tab MonitoringLocationTypeName \cr
+ "ResolvedMonitoringLocationTypeName" \tab character \tab  \cr
+ "HUCEightDigitCode" \tab character \tab 8-digit HUC id. \cr
+ "MonitoringLocationUrl" \tab character \tab URL to monitoring location. \cr
+ "CountyName" \tab character \tab County of sampling location. \cr
+ "StateName" \tab character \tab State of sampling location. \cr  
+ "MonitoringLocationLatitude"  \tab numeric \tab latitude of sampling 
+ location. \cr
+ "MonitoringLocationLongitude" \tab numeric \tab longitude of sampling 
+ location. \cr
+}
+}
+\description{
+Returns a list of sites from the Water Quality Portal web service. This
+function gets the data from: \url{https://www.waterqualitydata.us}.
+Arguments to the function should be based on
+\url{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.
+}
+\examples{
+\dontshow{if (is_dataRetrieval_user()) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\donttest{
+dane_county_data <- whatWQPdata2(countycode = "US:55:025",
+                        summaryYears = 5,
+                        siteType = "Stream")
+
+
+lake_sites <- whatWQPdata2(siteType = "Lake, Reservoir, Impoundment",
+                         CharacteristicName = "Temperature, water",
+                         countycode = "US:55:025")
+# Compare with the the results of whatWQPdata:                        
+lake_sites2 <- whatWQPdata(siteType = "Lake, Reservoir, Impoundment",
+                         CharacteristicName = "Temperature, water",
+                         countycode = "US:55:025")
+                         
+}
+\dontshow{\}) # examplesIf}
+}

tests/testthat/tests_general.R

@@ -418,3 +418,41 @@ test_that("internal functions",{
 })
 
 
+test_that("whatWQPdata2", {
+  testthat::skip_on_cran()
+  
+  dane_county_data <- whatWQPdata2(countycode = "US:55:025",
+                                   summaryYears = 5,
+                                   siteType = "Stream")
+  
+  summary_names <- c("Provider",                          
+                     "MonitoringLocationIdentifier",      
+                     "YearSummarized",                    
+                     "CharacteristicType",                
+                     "CharacteristicName",                
+                     "ActivityCount",                     
+                     "ResultCount",                       
+                     "LastResultSubmittedDate",           
+                     "OrganizationIdentifier",            
+                     "OrganizationFormalName",           
+                     "MonitoringLocationName",           
+                     "MonitoringLocationTypeName",        
+                     "ResolvedMonitoringLocationTypeName",
+                     "HUCEightDigitCode",
+                     "MonitoringLocationUrl",             
+                     "CountyName",            
+                     "StateName",                       
+                     "MonitoringLocationLatitude",        
+                     "MonitoringLocationLongitude" )
+  
+  expect_true(all(summary_names %in% names(dane_county_data)))
+  expect_true(diff(range(dane_county_data$YearSummarized)) <= 5)
+  
+  lake_sites <- whatWQPdata2(siteType = "Lake, Reservoir, Impoundment",
+                             CharacteristicName = "Temperature, water",
+                             countycode = "US:55:025")
+  
+  expect_true(all(summary_names %in% names(lake_sites)))
+  expect_true(diff(range(lake_sites$YearSummarized)) >= 5)
+})
+