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#' @name whatWQPsamples
#' @rdname wqpSpecials
#' @export
#' @return A data frame with information on the sampling activity
#' available from the Water Quality Portal for the query parameters.
#' @examples
#' \donttest{
#'
#' site1 <- whatWQPsamples(siteid = "USGS-01594440")
#'
#' type <- "Stream"
#'
#' sites <- whatWQPsamples(countycode = "US:55:025", siteType = type)
#'
#' lakeSites_samples <- whatWQPsamples(siteType = "Lake, Reservoir, Impoundment",
#' countycode = "US:55:025")
#' }
whatWQPsamples <- function(...,
convertType = TRUE,
legacy = TRUE) {
values <- readWQPdots(..., legacy = legacy)
values <- values[["values"]]
if ("tz" %in% names(values)) {
values <- values[!(names(values) %in% "tz")]
}
if ("service" %in% names(values)) {
values <- values[!(names(values) %in% "service")]
}
if(legacy){
baseURL <- httr2::request(pkg.env[["Activity"]])
} else {
baseURL <- httr2::request(pkg.env[["ActivityWQX3"]])
}
POST = FALSE
if(!legacy){
baseURL <- httr2::req_url_query(baseURL, !!!values,
.multi = "explode")
} else {
if("siteid" %in% names(values)){
if(length(values[["siteid"]]) > 1){
sites <- values[["siteid"]]
POST <- nchar(paste0(sites, collapse = "")) > 2048
baseURL <- get_or_post(baseURL, POST = POST,
siteid = sites,
.multi = function(x) paste0(x, collapse = ";"))
values <- values[names(values) != "siteid"]
}
}
baseURL <- get_or_post(baseURL,
POST = POST,
!!!values,
.multi = "explode")
}
retval <- importWQP(baseURL,
convertType = convertType)
if(!is.null(retval)){
attr(retval, "legacy") <- legacy
attr(retval, "queryTime") <- Sys.time()
attr(retval, "url") <- baseURL$url
if(legacy){
wqp_message()
} else {
wqp_message_beta()
attr(retval, "wqp-request-id") <- attr(retval, "headerInfo")$`wqp-request-id`
}
}
return(retval)
}
#' @name whatWQPmetrics
#' @rdname wqpSpecials
#' @export
#' @examples
#' \donttest{
#'
#' type <- "Stream"
#'
#' sites <- whatWQPmetrics(countycode = "US:55:025", siteType = type)
#' lakeSites_metrics <- whatWQPmetrics(siteType = "Lake, Reservoir, Impoundment",
#' countycode = "US:55:025")
#' }
whatWQPmetrics <- function(...,
convertType = TRUE) {
values <- readWQPdots(..., legacy = TRUE)
values <- values[["values"]]
if ("tz" %in% names(values)) {
values <- values[!(names(values) %in% "tz")]
}
if ("service" %in% names(values)) {
values <- values[!(names(values) %in% "service")]
}
POST <- FALSE
baseURL <- httr2::request(pkg.env[["ActivityMetric"]])
if("siteid" %in% names(values)){
if(length(values[["siteid"]]) > 1){
sites <- values[["siteid"]]
POST <- nchar(paste0(sites, collapse = "")) > 2048
baseURL <- get_or_post(baseURL, POST = POST,
siteid = sites,
.multi = function(x) paste0(x, collapse = ";"))
values <- values[names(values) != "siteid"]
}
}
baseURL <- get_or_post(baseURL,
POST = POST,
!!!values,
.multi = "explode")
withCallingHandlers(
{
retval <- importWQP(baseURL,
convertType = convertType
)
},
warning = function(w) {
if (any(grepl("Number of rows returned not matched in header", w))) {
invokeRestart("muffleWarning")
}
}
)
if(is.null(retval)){
return(NULL)
} else {
wqp_message()
attr(retval, "queryTime") <- Sys.time()
attr(retval, "url") <- baseURL$url
return(retval)
}
}
#' Data Available from Water Quality Portal
#'
#' Returns a list of sites from the Water Quality Portal web service. This function gets
#' the data from: <https://www.waterqualitydata.us>.
#' Arguments to the function should be based on
#' <https://www.waterqualitydata.us/webservices_documentation>.
#' The information returned from whatWQPdata describes the
#' available data at the WQP sites, and some metadata on the sites themselves.
#' For example, a row is returned for each individual site that fulfills this
#' query. In that we can learn how many sampling activities and results
#' are available for the query. It does not break those results down by any finer
#' grain. For example, if you ask for "Nutrients" (characteristicGroup), you will
#' not learn what specific nutrients are available at that site. For that
#' kind of data discovery see `readWQPsummary`.
#'
#' @param \dots see <https://www.waterqualitydata.us/webservices_documentation> for
#' a complete list of options. A list of arguments can also be supplied.
#' One way to figure out how to construct a WQP query is to go to the "Advanced"
#' form in the Water Quality Portal:
#' <https://www.waterqualitydata.us/#mimeType=csv&providers=NWIS&providers=STORET>
#' 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).
#' @param 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.
#' @keywords data import WQP web service
#' @return A data frame that returns basic data availability such as
#' sites, number of results, and number of sampling activities from the
#' query parameters for the Water Quality Portal.
#'
#' @export
#' @seealso whatWQPsites readWQPsummary readWQPdata
#' @examplesIf is_dataRetrieval_user()
#' \donttest{
#' site1 <- whatWQPdata(siteid = "USGS-01594440")
#'
#' type <- "Stream"
#' sites <- whatWQPdata(countycode = "US:55:025", siteType = type)
#'
#' lakeSites <- whatWQPdata(siteType = "Lake, Reservoir, Impoundment",
#' countycode = "US:55:025")
#' lakeSites_chars <- whatWQPdata(
#' siteType = "Lake, Reservoir, Impoundment",
#' countycode = "US:55:025", convertType = FALSE)
#' }
#'
#' bbox <- c(-86.9736, 34.4883, -86.6135, 34.6562)
#' what_bb <- whatWQPdata(bBox = bbox)
#'
whatWQPdata <- function(...,
convertType = TRUE) {
values <- readWQPdots(..., legacy = TRUE)
values <- values[["values"]]
if (any(c("tz", "service", "mimeType") %in% names(values))){
values <- values[!(names(values) %in% c("tz", "service", "mimeType"))]
}
POST <- FALSE
baseURL <- httr2::request(pkg.env[["Station"]])
if("siteid" %in% names(values)){
if(length(values[["siteid"]]) > 1){
sites <- values[["siteid"]]
POST <- nchar(paste0(sites, collapse = "")) > 2048
baseURL <- get_or_post(baseURL, POST = POST,
siteid = sites,
.multi = function(x) paste0(x, collapse = ";"))
values <- values[names(values) != "siteid"]
}
}
baseURL <- get_or_post(req = baseURL,
POST = POST,
!!!values,
.multi = "explode")
baseURL <- get_or_post(baseURL,
POST = POST,
mimeType = "geojson")
# Not sure if there's a geojson option with WQX3
wqp_message()
doc <- getWebServiceData(baseURL)
if (is.null(doc)) {
return(invisible(NULL))
}
headerInfo <- attr(doc, "headerInfo")
if (headerInfo$`total-site-count` == 0) {
y <- data.frame(
total_type = character(),
lat = numeric(),
lon = numeric(),
ProviderName = character(),
OrganizationIdentifier = character(),
OrganizationFormalName = character(),
MonitoringLocationIdentifier = character(),
MonitoringLocationName = character(),
MonitoringLocationTypeName = character(),
ResolvedMonitoringLocationTypeName = character(),
HUCEightDigitCode = character(),
siteUrl = character(),
activityCount = numeric(),
resultCount = numeric(),
StateName = character(),
CountyName = character(),
stringsAsFactors = FALSE
)
if (!convertType) {
y <- data.frame(lapply(y, as.character), stringsAsFactors = FALSE)
}
} else {
features <- doc[["features"]]
y <- data.frame(matrix(NA, nrow = length(features), ncol = 15))
names(y) <- c(names(features[[1]][["properties"]]),
"lat", "lon")
for(i in seq_along(features)){
single_feature <- features[[i]][["properties"]]
single_feature[["lat"]] <- unlist(features[[i]][["geometry"]][["coordinates"]][2])
single_feature[["lon"]] <- unlist(features[[i]][["geometry"]][["coordinates"]][1])
y[i,] <- single_feature
}
if (convertType) {
y[, grep("Count$", names(y))] <- sapply(y[, grep("Count$", names(y))], as.numeric)
}
names(y)[names(y) == "type"] <- paste("type",
letters[seq_along(names(y)[names(y) == "type"])],
sep = "_"
)
if (all(c("type_a", "type_b", "features.type") %in% names(y))) {
y$total_type <- paste(y$type_a, y$features.type, y$type_b)
y$type_a <- NULL
if (all(y$type_b == "Point")) {
y$lon <- sapply(y$coordinates, function(x) x[[1]][1])
y$lat <- sapply(y$coordinates, function(x) x[[2]][1])
}
y$type_b <- NULL
y$coordinates <- NULL
y$features.type <- NULL
y <- y[, c("total_type", "lat", "lon", names(y)[!(names(y) %in% c("total_type", "lat", "lon"))])]
}
}
if (!convertType) {
y <- data.frame(lapply(y, as.character), stringsAsFactors = FALSE)
}
attr(y, "queryTime") <- Sys.time()
attr(y, "url") <- baseURL
return(y)
}
get_or_post <- function(req, POST = FALSE, ...){
if(POST){
req <- httr2::req_body_form(req, ...)
} else {
req <- httr2::req_url_query(req, ...)
}
return(req)
}
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