Adding dataProfile examples

6982ace4 · Laura A DeCicco · aef0beac · 6982ace4 · 6982ace4 · 6982ace4
Commit 6982ace4 authored Feb 10, 2022 by Laura A DeCicco
--- a/R/readWQPdata.R
+++ b/R/readWQPdata.R
@@ -133,6 +133,54 @@
 #'                                 countycode="Lexington", 
 #'                                 parameterCd = "00010") 
 #'                                 
+#' # 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",
+#'                          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",
+#'                            dataProfile = "narrowResult",
+#'                            service = "Result")
+#'                            
+#' # 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")
 #' }
 readWQPdata <- function(..., querySummary=FALSE, tz="UTC", 
                        ignore_attributes = FALSE){
@@ -177,33 +225,36 @@ readWQPdata <- function(..., querySummary=FALSE, tz="UTC",
        siteInfo <- cbind(siteInfoCommon, siteInfo)        
      }
      
-      retvalVariableInfo <- retval[,c("CharacteristicName","USGSPCode",
-                                      "ResultMeasure.MeasureUnitCode","ResultSampleFractionText")]
-      retvalVariableInfo <- unique(retvalVariableInfo)
-      
-      variableInfo <- data.frame(characteristicName=retval$CharacteristicName,
-                                 parameterCd=retval$USGSPCode,
-                                 param_units=retval$ResultMeasure.MeasureUnitCode,
-                                 valueType=retval$ResultSampleFractionText,
-                                 stringsAsFactors=FALSE)
+      attr(retval, "siteInfo") <- siteInfo
      
-      if(!anyNA(variableInfo$parameterCd)){
-        pcodes <- unique(variableInfo$parameterCd[!is.na(variableInfo$parameterCd)])
-        pcodes <- pcodes["" != pcodes]
-        paramINFO <- readNWISpCode(pcodes)
-        names(paramINFO)["parameter_cd" == names(paramINFO)] <- "parameterCd"
+      if(all(c("CharacteristicName","USGSPCode",
+               "ResultMeasure.MeasureUnitCode","ResultSampleFractionText") %in% names(retval))){
+        retvalVariableInfo <- retval[,c("CharacteristicName","USGSPCode",
+                                        "ResultMeasure.MeasureUnitCode","ResultSampleFractionText")]
+        retvalVariableInfo <- unique(retvalVariableInfo)
+        
+        variableInfo <- data.frame(characteristicName=retval$CharacteristicName,
+                                   parameterCd=retval$USGSPCode,
+                                   param_units=retval$ResultMeasure.MeasureUnitCode,
+                                   valueType=retval$ResultSampleFractionText,
+                                   stringsAsFactors=FALSE)
        
-        pCodeToName <- pCodeToName
-        varExtras <- pCodeToName[pCodeToName$parm_cd %in% unique(variableInfo$parameterCd[!is.na(variableInfo$parameterCd)]),]
-        names(varExtras)[names(varExtras) == "parm_cd"] <- "parameterCd"
-        variableInfo <- merge(variableInfo, varExtras, by="parameterCd", all = TRUE)
-        variableInfo <- merge(variableInfo, paramINFO, by="parameterCd", all = TRUE)
-        variableInfo <- unique(variableInfo)
+        if(!anyNA(variableInfo$parameterCd)){
+          pcodes <- unique(variableInfo$parameterCd[!is.na(variableInfo$parameterCd)])
+          pcodes <- pcodes["" != pcodes]
+          paramINFO <- readNWISpCode(pcodes)
+          names(paramINFO)["parameter_cd" == names(paramINFO)] <- "parameterCd"
+          
+          pCodeToName <- pCodeToName
+          varExtras <- pCodeToName[pCodeToName$parm_cd %in% unique(variableInfo$parameterCd[!is.na(variableInfo$parameterCd)]),]
+          names(varExtras)[names(varExtras) == "parm_cd"] <- "parameterCd"
+          variableInfo <- merge(variableInfo, varExtras, by="parameterCd", all = TRUE)
+          variableInfo <- merge(variableInfo, paramINFO, by="parameterCd", all = TRUE)
+          variableInfo <- unique(variableInfo)
+        }
+        attr(retval, "variableInfo") <- variableInfo
      }
-      
-      attr(retval, "siteInfo") <- siteInfo
-      attr(retval, "variableInfo") <- variableInfo
-      
+
    } else {
      if(!ignore_attributes){
        message("The following url returned no data:\n")

--- a/R/readWQPdots.R
+++ b/R/readWQPdots.R
@@ -23,7 +23,7 @@ readWQPdots <- function(...){
    service <- "Result"
  }
  
-  match.arg(service, c("Result", "Station", "Activity",
+  match.arg(service, c("Result", "Station", "Activity", "Organization",
                       "ActivityMetric", "SiteSummary",
                       "Project", "ProjectMonitoringLocationWeighting",
                       "ResultDetectionQuantitationLimit", "BiologicalMetric"))

--- a/R/setAccess.R
+++ b/R/setAccess.R
@@ -65,7 +65,8 @@ setAccess = function(access="public"){
  pkg.env$ProjectMonitoringLocationWeighting = "https://www.waterqualitydata.us/data/ProjectMonitoringLocationWeighting/search"
  pkg.env$ResultDetectionQuantitationLimit = "https://www.waterqualitydata.us/data/ResultDetectionQuantitationLimit/search"
  pkg.env$BiologicalMetric = "https://www.waterqualitydata.us/data/BiologicalMetric/search"
-  
+  pkg.env$Organization = "https://www.waterqualitydata.us/data/Organization/search"
+
  pkg.env$NGWMN = "https://cida.usgs.gov/ngwmn_cache/sos"

 }

--- a/man/readWQPdata.Rd
+++ b/man/readWQPdata.Rd
@@ -146,6 +146,54 @@ dailyLexingtonVA <- readWQPdata(statecode = "Virginia",
                                countycode="Lexington", 
                                parameterCd = "00010") 
                                
+# 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",
+                         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",
+                           dataProfile = "narrowResult",
+                           service = "Result")
+                           
+# 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")
 }
 \dontshow{\}) # examplesIf}
 }

--- a/tests/testthat/tests_general.R
+++ b/tests/testthat/tests_general.R
@@ -421,6 +421,77 @@ test_that("internal functions",{

 })

+test_that("profiles", {
+  # Data profiles: "Organization Data"
+  org_data <- readWQPdata(statecode = "WI",
+                          countycode = "Dane",
+                          service = "Organization")
+  expect_true(all(c("OrganizationIdentifier",
+                    "OrganizationFormalName") %in% names(org_data)))
+  
+  # Data profiles: "Site Data Only"
+  site_data <- readWQPdata(statecode = "WI",
+                           countycode = "Dane",
+                           service = "Station")
+  expect_true(all(c("ProviderName", "MonitoringLocationIdentifier") %in% names(site_data)))
+  
+  # Data profiles: "Project Data"
+  project_data <- readWQPdata(statecode = "WI",
+                              countycode = "Dane",
+                              service = "Project")
+  expect_true(all(c("OrganizationIdentifier",
+                    "OrganizationFormalName") %in% names(project_data)))
+  
+  # Data profiles: "Project Monitoring Location Weighting Data"
+  proj_mlwd <- readWQPdata(statecode = "WI",
+                           countycode = "Dane",
+                           service = "ProjectMonitoringLocationWeighting")
+  
+  expect_true(all(c("OrganizationIdentifier",
+                    "OrganizationFormalName") %in% names(proj_mlwd)))
+  
+  # Data profiles: "Sample Results (physical/chemical metadata)":
+  samp_data <- readWQPdata(siteid = "USGS-04024315",
+                           dataProfile = "resultPhysChem",
+                           service = "Result")
+  expect_true(all(c("OrganizationIdentifier",
+                    "OrganizationFormalName") %in% names(samp_data)))
+  
+  # Data profiles: "Sample Results (biological metadata)"
+  samp_bio <- readWQPdata(siteid="USGS-04024315",
+                          dataProfile = "biological",
+                          service = "Result")
+  
+  expect_true(all(c("OrganizationIdentifier",
+                    "OrganizationFormalName") %in% names(samp_bio)))
+  
+  # Data profiles: "Sample Results (narrow)"
+  samp_narrow <- readWQPdata(siteid="USGS-04024315",
+                             dataProfile = "narrowResult",
+                             service = "Result")
+  expect_true(all(c("OrganizationIdentifier",
+                    "OrganizationFormalName") %in% names(samp_narrow)))
+  
+  # Data profiles: "Sampling Activity"
+  samp_activity <- readWQPdata(siteid="USGS-04024315",
+                               dataProfile = "activityAll",
+                               service = "Activity")
+  expect_true(all(c("OrganizationIdentifier",
+                    "OrganizationFormalName") %in% names(samp_activity)))
+  
+  # Data profile: "Sampling Activity Metrics"
+  act_metrics <- readWQPdata(statecode = "WI",
+                             countycode = "Dane",
+                             service = "ActivityMetric")
+  expect_true(all(c("OrganizationIdentifier",
+                    "OrganizationFormalName") %in% names(act_metrics)))
+  
+  # Data profile: "Result Detection Quantitation Limit Data"
+  dl_data <- readWQPdata(siteid="USGS-04024315",
+                         service = "ResultDetectionQuantitationLimit")
+  expect_true(all(c("OrganizationIdentifier",
+                    "OrganizationFormalName") %in% names(dl_data)))
+})

 test_that("readWQPsummary", {
  testthat::skip_on_cran()