tests and documentation

NAMESPACE

@@ -7,7 +7,7 @@ export(constructWQPURL)
 export(countyCd)
 export(countyCdLookup)
 export(getWebServiceData)
-export(importNGMWN_wml2)
+export(importNGWMN_wml2)
 export(importRDB1)
 export(importWQP)
 export(importWaterML1)

R/importNGWMN_wml2.R

@@ -6,7 +6,7 @@
 #' @param input character or raw, containing the url for the retrieval or a path to the data file, or raw XML.
 #' @param asDateTime logical, if \code{TRUE} returns date and time as POSIXct, if \code{FALSE}, character
 #' @param tz character to set timezone attribute of datetime. Default is an empty quote, which converts the 
-#' datetimes to UTC (properly accounting for daylight savings times based on the data's provided tz_cd column).
+#' datetimes to UTC (properly accounting for daylight savings times based on the data's provided time zone offset).
 #' Possible values to provide are "America/New_York","America/Chicago", "America/Denver","America/Los_Angeles",
 #' "America/Anchorage","America/Honolulu","America/Jamaica","America/Managua","America/Phoenix", and "America/Metlakatla"
 #' @return mergedDF a data frame source, time, value, uom, uomTitle, comment, gmlID
@@ -20,9 +20,12 @@
 #' \dontrun{
 #' url <- "http://cida.usgs.gov/ngwmn_cache/sos?request=GetObservation&service=SOS&version=2.0.0&observedProperty=urn:ogc:def:property:OGC:GroundWaterLevel&responseFormat=text/xml&featureOfInterest=VW_GWDP_GEOSERVER.USGS.403836085374401"
 #' data <- importNGWMN_wml2(url)
+#' 
+#' url <- "http://cida.usgs.gov/ngwmn_cache/sos?request=GetObservation&service=SOS&version=2.0.0&observedProperty=urn:ogc:def:property:OGC:GroundWaterLevel&responseFormat=text/xml&featureOfInterest=VW_GWDP_GEOSERVER.USGS.474011117072901"
+#' data <- importNGWMN_wml2(url)
 #' }
-importNGMWN_wml2 <- function(input, asDateTime=FALSE, tz=""){
-  #TODO: update documentation
+#' 
+importNGWMN_wml2 <- function(input, asDateTime=FALSE, tz=""){
   if(tz != ""){
     tz <- match.arg(tz, c("America/New_York","America/Chicago",
                           "America/Denver","America/Los_Angeles",
@@ -91,6 +94,7 @@ importNGMWN_wml2 <- function(input, asDateTime=FALSE, tz=""){
     }
     attr(mergedDF, "gml:identifier") <- xml_text(xml_find_all(returnedDoc, ".//gml:identifier")) 
     attr(mergedDF, "generationDate") <- xml_text(xml_find_all(returnedDoc, ".//wml2:generationDate")) 
+    mergedDF$value[mergedDF$value == -999999.0] <- NA
     
   }else if(response == "GetFeatureOfInterestResponse"){
     site <- xml_text(xml_find_all(returnedDoc,".//gml:identifier"))
@@ -107,18 +111,15 @@ importNGMWN_wml2 <- function(input, asDateTime=FALSE, tz=""){
     siteLocs <- data.frame(lat=siteLocs[[1]][1], lon=siteLocs[[1]][2], stringsAsFactors = FALSE)
     mergedDF <- cbind.data.frame(site, description = siteDesc, siteLocs, stringsAsFactors = FALSE) 
   }
-  else if(response == "ExceptionReport"){
-    #TODO: what happens if exception?
+  else{
+    stop("Unrecognized response from the web service")
   }
   return(mergedDF)
   
 }
 
-
 #replace blank cells with NAs
 removeBlanks <- function(input){
   input <- sapply(input, function(f){is.na(f)<-which(f == '');f})
   return(input)
 }
-
-

R/readNGWMNdata.R

-#' import data from the National Groundwater Monitoring Network \link{http://cida.usgs.gov/ngwmn/}
-#' Only water level data and site metadata is currently available through the web service.  
-#' @param asDateTime logical 
-#' @param featureID character
-#' @param request character
+#' import data from the National Groundwater Monitoring Network \link{http://cida.usgs.gov/ngwmn/}.
+#' 
+#' Only water level data is currently available through the web service.  
+#' @param asDateTime logical if \code{TRUE}, will convert times to POSIXct format.  Currently defaults to 
+#' \code{FALSE} since time zone information is not included.  
+#' @param featureID character Vector of feature IDs in the formatted with agency code and site number 
+#' separated by a period, e.g. \code{USGS.404159100494601}.
+#' @param request character Identifies which web service to access.  Only \code{observation} is currently 
+#' supported, which retrieves all water level for each site.   
 #' @import utils
 #' @importFrom dplyr mutate
 #' @importFrom dplyr bind_rows
 #' @export
 #' 
-#TODO: documentation once more solidified
-readNGWMNdata <- function(featureID, request = "observation", asDateTime = TRUE){
+#' @examples 
+#' \dontrun{
+#' #one site
+#' site <- "USGS.430427089284901"
+#' oneSite <- readNGWMNdata(featureID = site)
+#' 
+#' #multiple sites
+#' sites <- c("USGS.272838082142201","USGS.404159100494601", "USGS.401216080362703")
+#' multiSiteData <- readNGWMNdata(sites)
+#' 
+#' #non-USGS site
+#' site <- "MBMG.892195"
+#' data <- readNGWMNdata(featureID = site)
+#' 
+#' #site with no data returns empty data frame
+#' noDataSite <- "UTGS.401544112060301"
+#' noDataSite <- readNGWMNdata(featureID = noDataSite, request = "observation")
+#' }
+#' 
+
+readNGWMNdata <- function(featureID, request = "observation", asDateTime = FALSE){
   
   match.arg(request, c("observation", "featureOfInterest"))
+  if(asDateTime){
+    warning("Times zones will be incorrect.  This will be fixed in the future")
+  }
   
   if(request == "observation"){
     allObs <- NULL
@@ -25,17 +51,15 @@ readNGWMNdata <- function(featureID, request = "observation", asDateTime = TRUE)
       if(is.null(allObs)){
         allObs <- obsFID
         allSites <- siteFID
+        allAttrs <- saveAttrs(attrs, allObs)
       }else{
-        #TODO: can attaching attributes wait till the end?
         obsFIDatt <- saveAttrs(attrs, obsFID)
-        allAttrs <- saveAttrs(attrs, allObs)
-        allObs <- removeAttrs(attrs, allObs)
         obsFID <- removeAttrs(attrs, obsFID)
         allAttrs <- bind_rows(allAttrs, obsFIDatt)
         allObs <- bind_rows(allObs, obsFID)
-        attributes(allObs) <- c(attributes(allObs),as.list(allAttrs))
         allSites <- bind_rows(allSites, siteFID)
       }
+      attributes(allObs) <- c(attributes(allObs),as.list(allAttrs))
       attr(allObs, "siteInfo") <- allSites
       returnData <- allObs
     }
@@ -49,7 +73,7 @@ retrieveObservation <- function(featureID, asDateTime, attrs){
   baseURL <- "http://cida.usgs.gov/ngwmn_cache/sos?request=GetObservation&service=SOS&version=2.0.0&observedProperty=urn:ogc:def:property:OGC:GroundWaterLevel&responseFormat=text/xml&featureOfInterest=VW_GWDP_GEOSERVER."
   url <- paste0(baseURL, featureID)
   
-  returnData <- importNGMWN_wml2(url, asDateTime)
+  returnData <- importNGWMN_wml2(url, asDateTime)
   if(nrow(returnData) == 0){
     #need to add NA attributes, so they aren't messed up when stored as DFs
     attr(returnData, "gml:identifier") <- NA
@@ -75,7 +99,7 @@ retrieveObservation <- function(featureID, asDateTime, attrs){
 retrieveFeatureOfInterest <- function(featureID){
   baseURL <- "http://cida.usgs.gov/ngwmn_cache/sos?request=GetFeatureOfInterest&service=SOS&version=2.0.0&observedProperty=urn:ogc:def:property:OGC:GroundWaterLevel&responseFormat=text/xml&featureOfInterest=VW_GWDP_GEOSERVER."
   url <- paste0(baseURL, featureID)
-  siteDF <- importNGMWN_wml2(url, asDateTime)
+  siteDF <- importNGWMN_wml2(url, asDateTime)
   return(siteDF)
 }
 

man/importNGMWN_wml2.Rd → man/importNGWMN_wml2.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/importNGWMN_wml2.R
-\name{importNGMWN_wml2}
-\alias{importNGMWN_wml2}
+\name{importNGWMN_wml2}
+\alias{importNGWMN_wml2}
 \title{Function to return data from the National Ground Water Monitoring Network waterML2 format}
 \usage{
-importNGMWN_wml2(input, asDateTime = FALSE, tz = "")
+importNGWMN_wml2(input, asDateTime = FALSE, tz = "")
 }
 \arguments{
 \item{input}{character or raw, containing the url for the retrieval or a path to the data file, or raw XML.}
@@ -12,7 +12,7 @@ importNGMWN_wml2(input, asDateTime = FALSE, tz = "")
 \item{asDateTime}{logical, if \code{TRUE} returns date and time as POSIXct, if \code{FALSE}, character}
 
 \item{tz}{character to set timezone attribute of datetime. Default is an empty quote, which converts the 
-datetimes to UTC (properly accounting for daylight savings times based on the data's provided tz_cd column).
+datetimes to UTC (properly accounting for daylight savings times based on the data's provided time zone offset).
 Possible values to provide are "America/New_York","America/Chicago", "America/Denver","America/Los_Angeles",
 "America/Anchorage","America/Honolulu","America/Jamaica","America/Managua","America/Phoenix", and "America/Metlakatla"}
 }
@@ -27,6 +27,10 @@ but the general functionality is correct.
 \dontrun{
 url <- "http://cida.usgs.gov/ngwmn_cache/sos?request=GetObservation&service=SOS&version=2.0.0&observedProperty=urn:ogc:def:property:OGC:GroundWaterLevel&responseFormat=text/xml&featureOfInterest=VW_GWDP_GEOSERVER.USGS.403836085374401"
 data <- importNGWMN_wml2(url)
+
+url <- "http://cida.usgs.gov/ngwmn_cache/sos?request=GetObservation&service=SOS&version=2.0.0&observedProperty=urn:ogc:def:property:OGC:GroundWaterLevel&responseFormat=text/xml&featureOfInterest=VW_GWDP_GEOSERVER.USGS.474011117072901"
+data <- importNGWMN_wml2(url)
 }
+
 }
 

man/readNGWMNdata.Rd

@@ -2,20 +2,41 @@
 % Please edit documentation in R/readNGWMNdata.R
 \name{readNGWMNdata}
 \alias{readNGWMNdata}
-\title{import data from the National Groundwater Monitoring Network \link{http://cida.usgs.gov/ngwmn/}
-Only water level data and site metadata is currently available through the web service.}
+\title{import data from the National Groundwater Monitoring Network \link{http://cida.usgs.gov/ngwmn/}.}
 \usage{
-readNGWMNdata(featureID, request = "observation", asDateTime = TRUE)
+readNGWMNdata(featureID, request = "observation", asDateTime = FALSE)
 }
 \arguments{
-\item{featureID}{character}
+\item{featureID}{character Vector of feature IDs in the formatted with agency code and site number 
+separated by a period, e.g. \code{USGS.404159100494601}.}
 
-\item{request}{character}
+\item{request}{character Identifies which web service to access.  Only \code{observation} is currently 
+supported, which retrieves all water level for each site.}
 
-\item{asDateTime}{logical}
+\item{asDateTime}{logical if \code{TRUE}, will convert times to POSIXct format.  Currently defaults to 
+\code{FALSE} since time zone information is not included.}
 }
 \description{
-import data from the National Groundwater Monitoring Network \link{http://cida.usgs.gov/ngwmn/}
-Only water level data and site metadata is currently available through the web service.
+Only water level data is currently available through the web service.
+}
+\examples{
+\dontrun{
+#one site
+site <- "USGS.430427089284901"
+oneSite <- readNGWMNdata(featureID = site)
+
+#multiple sites
+sites <- c("USGS.272838082142201","USGS.404159100494601", "USGS.401216080362703")
+multiSiteData <- readNGWMNdata(sites)
+
+#non-USGS site
+site <- "MBMG.892195"
+data <- readNGWMNdata(featureID = site)
+
+#site with no data returns empty data frame
+noDataSite <- "UTGS.401544112060301"
+noDataSite <- readNGWMNdata(featureID = noDataSite, request = "observation")
+}
+
 }
 

tests/testthat/tests_general.R

@@ -97,3 +97,4 @@ test_that("Dates with no days can be handled", {
   testthat::skip_on_cran()
   expect_error(readNWISgwl("425957088141001", startDate = "1980-01-01"))
  })
+

tests/testthat/tests_imports.R

@@ -173,3 +173,12 @@ test_that("External WQP tests", {
   STORETdata <- importWQP(STORETex)
   expect_is(STORETdata$ActivityStartDateTime, 'POSIXct')
 })
+
+context("importNGWMN_wml2")
+test_that("External NGMMN import tests", {
+  testthat::skip_on_cran()
+  url <- "http://cida.usgs.gov/ngwmn_cache/sos?request=GetObservation&service=SOS&version=2.0.0&observedProperty=urn:ogc:def:property:OGC:GroundWaterLevel&responseFormat=text/xml&featureOfInterest=VW_GWDP_GEOSERVER.USGS.403836085374401"
+  data <- importNGWMN_wml2(url)
+  expect_true(is.numeric(data$value))
+  expect_true(nrow(data) > 0)
+})

tests/testthat/tests_userFriendly_fxns.R

@@ -215,3 +215,18 @@ test_that("state county tests",{
   fromIDs <- countyCdLookup(state = 13, county = 5, output = "fullName")
   expect_equal(fromIDs, "Bacon County")
 })
+
+test_that("NGWMN functions working", {
+  noDataSite <- "UTGS.401544112060301"
+  noDataSite <- readNGWMNdata(featureID = noDataSite, request = "observation")
+  expect_true(is.data.frame(noDataSite))
+  
+  #one site
+  site <- "USGS.430427089284901"
+  oneSite <- readNGWMNdata(featureID = site)
+  expect_true(is.numeric(oneSite$value))
+  expect_true(is.character(oneSite$site))
+  expect_true(nrow(oneSite) > 0)
+  
+  
+})