V1

DESCRIPTION

@@ -72,4 +72,4 @@ BuildVignettes: true
 VignetteBuilder: knitr
 BugReports: https://github.com/DOI-USGS/dataRetrieval/issues
 Roxygen: list(markdown = TRUE)
-Config/roxygen2/version: 8.0.0
+Config/roxygen2/version: 8.1.0

NAMESPACE

@@ -80,12 +80,14 @@ export(whatWQPsamples)
 export(whatWQPsites)
 export(wqp_check_status)
 export(zeroPad)
-importFrom(data.table,":=")
-importFrom(data.table,.BY)
-importFrom(data.table,.EACHI)
-importFrom(data.table,.GRP)
-importFrom(data.table,.I)
-importFrom(data.table,.N)
-importFrom(data.table,.NGRP)
-importFrom(data.table,.SD)
-importFrom(data.table,data.table)
+importFrom(data.table,
+  ":=",
+  .BY,
+  .EACHI,
+  .GRP,
+  .I,
+  .N,
+  .NGRP,
+  .SD,
+  data.table
+)

NEWS.md

@@ -1,12 +1,14 @@
 dataRetrieval 2.7.26
 ===================
+* Switching to v1 of the Water Data APIs.
 * Added suite of read_ngwmn to access new National Groundwater Monitoring
 Network API.
 * Created get_monitoring_location_arguments to help users understand 
 what new optional arguments are available in many of the read_waterdata functions.
 * Added ability to use `...` in the Water Data functions for: daily, latest-continuous, field-measurements, latest-daily, latest-field-measurements, continuous, and peaks. The "..." argument can now accept any parameter that is output from the make_monitoring_location_arguments function.
 * Added "q" argument to read_waterdata_monitoring_location. Full-text search across the most relevant text fields for this collection (e.g. site name, identifier, number, state, county, and site type).
 * Added "skipGeometry" argument to read_waterdata_continuous. Previously geometry wasn't included with continuous data, but now is supported.
+* Deprecated `pcode_to_name` since the service was removed.
 
 dataRetrieval 2.7.25
 ===================

R/AAA.R

@@ -6,7 +6,7 @@ pkg.env <- new.env()
   options(
     "dataRetrieval.nldi_base" = "https://api.water.usgs.gov/nldi/linked-data/"
   )
-  options("dataRetrieval.api_version" = "v0")
+  options("dataRetrieval.api_version" = "v1")
   options("dataRetrieval.api_version_stat" = "v0")
   options("dataRetrieval.attach_request" = TRUE)
   options("dataRetrieval.convertType" = TRUE)
@@ -138,8 +138,7 @@ https://doi-usgs.github.io/dataRetrieval/articles/Status.html"
 
 new_nwis_message <- function() {
   return(
-    "ALERT: All NWIS services are slated for decommission
-and new dataRetrieval functions will be added.
+    "ALERT: All NWIS services are slated for decommission in early 2027.
 For up-to-date information, see: 
 https://doi-usgs.github.io/dataRetrieval/articles/Status.html"
   )

R/citations.R

@@ -23,6 +23,11 @@
 #' print(nwis_citation, style = "citation")
 #' }
 create_NWIS_bib <- function(x) {
+  .Deprecated(
+    package = "dataRetrieval",
+    msg = "NWIS servers are slated for decommission. Please begin to migrate to read_waterdata functions."
+  )
+
   textVersion <- paste0(
     "U.S. Geological Survey, ",
     format(attr(x, "queryTime"), "%Y"),

R/dataRetrieval-package.R

@@ -69,9 +69,6 @@ NULL
 
 #' Data to convert USGS parameter code to characteristic names
 #'
-#' Data pulled from Water Quality Portal on December 20, 2021. The data was pulled from
-#' <https://www.waterqualitydata.us/Codes/public_srsnames/?mimeType=csv>.
-#'
 #' @name pCodeToName
 #' @return pCodeToName data frame with information about USGS parameters and how they
 #' relate to characteristic names (useful for WQP requests).
@@ -208,14 +205,14 @@ NULL
 #               "field-measurements", "latest-daily",
 #               "continuous", "field-measurements-metadata",
 #               "combined-metadata", "channel-measurements", "peaks")
-# 
+#
 # property_list <- list()
 # for(service in services){
 #   property_list[[service]] <- dataRetrieval:::get_properties_for_docs(service)
 # }
 #
 # num_cols <- c("value", "contributing_drainage_area", "drainage_area",
-#               #"altitude_accuracy", 
+#               #"altitude_accuracy",
 #               "well_construction_depth",
 #               "hole_construction_depth", "channel_flow", "channel_width",
 #               "channel_area", "channel_velocity", "channel_location_distance")

R/pcode_to_name.R

@@ -1,64 +1,24 @@
 #' Parameter code to characteristic name
 #'
-#' This function is useful to fine what characteristic name, result sample
-#' fraction, unit code, and other parameters are mapped with USGS parameter
-#' codes. This information is useful for converting workflows from a more
-#' traditional NWIS water quality retrieval to a Water Quality Portal retrieval.
+#' This function no longer works because the underlying service
+#' has been removed. Similar functionality can be found with
+#' `check_waterdata_sample_params`.
 #'
 #' @export
 #' @param parameterCd character that contains the code for a character vector
-#' of 5-digit parameter codes. Default is "all" which will return a complete
-#' list of parameter codes that have been mapped to a characteristic name.
-#' @return a data frame with columns  "parm_cd", "description",
-#' "characteristicname", "measureunitcode", "resultsamplefraction",
-#' "resulttemperaturebasis", "resultstatisticalbasis",  "resulttimebasis",
-#' "resultweightbasis", "resultparticlesizebasis", "last_rev_dt"
+#' of 5-digit parameter codes.
 #' @examples
 #' pcodes <- c("00070", "00075", "00430", "52642")
 #' \donttest{
-#'
-#' all <- pcode_to_name()
-#' some <- pcode_to_name(pcodes)
+#' all_new <- read_waterdata_parameter_codes(parameter_code = pcodes)
+#' ref_list <- check_waterdata_sample_params("reference-list")
+#' ref_list_sm <- ref_list[ref_list$parm_cd %in% pcodes, ]
 #'
 #' }
 pcode_to_name <- function(parameterCd = "all") {
-  parameterCd.orig <- parameterCd
-  parameterCd <- parameterCd[!is.na(parameterCd)]
-
-  url_all <- "https://www.waterqualitydata.us/Codes/public_srsnames/?mimeType=json"
-  doc <- get_nldi_sources(url_all)
-  retval <- doc[["pcodes"]]
-
-  if (all(tolower(parameterCd) != "all")) {
-    retval <- retval[retval$parm_cd %in% parameterCd, ]
-  }
-
-  attr(retval, "url") <- url_all
-
-  if (any(parameterCd != "all")) {
-    if (nrow(retval) != length(unique(parameterCd))) {
-      badPcode <- parameterCd[!(parameterCd %in% retval$parm_cd)]
-      warning(
-        "The following pCodes seem mistyped, and no information was returned: ",
-        paste(badPcode, collapse = ", ")
-      )
-    }
-  }
-
-  if (nrow(retval) != sum(is.na(parameterCd.orig))) {
-    na.params <- data.frame(matrix(
-      ncol = ncol(retval),
-      nrow = sum(is.na(parameterCd.orig))
-    ))
-    names(na.params) <- names(retval)
-    retval <- rbind(retval, na.params)
-  }
-
-  # order by parameterCd.orig
-  if (!isTRUE(parameterCd.orig == "all")) {
-    retval <- retval[match(parameterCd.orig, retval$parm_cd), ]
-    retval$parm_cd <- parameterCd.orig
-  }
-
-  return(retval)
+  .Deprecated(
+    new = "check_waterdata_sample_params",
+    package = "dataRetrieval",
+    msg = "Convert to check_waterdata_sample_params('reference-list')."
+  )
 }

R/readWQPdata.R

@@ -40,8 +40,7 @@
 #' Sampling Activity \tab ActivityWQX3 \tab /wqx3/Activity/search \cr
 #' }
 #'
-#' @param \dots see <https://www.waterqualitydata.us/webservices_documentation> for a complete list of options.
-#' A list of arguments can also be supplied. For more information see the above
+#' @param \dots A list of arguments can also be supplied. For more information see the above
 #' description for this help file. One way to figure out how to construct a WQP query is to go to the "Advanced"
 #' form in the Water Quality Portal. 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

R/read_waterdata_field_measurements.R

@@ -51,7 +51,7 @@
 #' @examplesIf is_dataRetrieval_user()
 #'
 #' \donttest{
-#' site <- "USGS-02238500"
+#' site <- "USGS-14202650"
 #' field_data_sf <- read_waterdata_field_measurements(monitoring_location_id = site)
 #'
 #' groundwater <- read_waterdata_field_measurements(monitoring_location_id = "USGS-375907091432201")

R/read_waterdata_monitoring_location.R

@@ -149,6 +149,7 @@ read_waterdata_monitoring_location <- function(
   bbox = NA,
   skipGeometry = NA,
   ...,
+  convertType = getOption("dataRetrieval.convertType"),
   limit = getOption("dataRetrieval.limit"),
   no_paging = getOption("dataRetrieval.no_paging"),
   chunk_size = getOption("dataRetrieval.site_chunk_size_meta"),
@@ -159,7 +160,6 @@ read_waterdata_monitoring_location <- function(
   rlang::check_dots_empty()
 
   args <- mget(names(formals()))
-  args[["convertType"]] <- FALSE
 
   return_list <- get_ogc_data(args, output_id, service)
 

R/read_waterdata_ts_meta.R

@@ -18,14 +18,6 @@
 #' @param last_modified `r get_ogc_params("time-series-metadata")$last_modified`
 #'
 #' See also Details below for more information.
-#' @param begin_utc `r get_ogc_params("time-series-metadata")$begin_utc`
-#' #'
-#' See also Details below for more information.
-#' @param end_utc `r get_ogc_params("time-series-metadata")$end_utc`
-#'
-#' See also Details below for more information.
-#' @param hydrologic_unit_code `r get_ogc_params("time-series-metadata")$hydrologic_unit_code`
-#' @param state_name `r get_ogc_params("time-series-metadata")$state_name`
 #' @param thresholds `r get_ogc_params("time-series-metadata")$thresholds`
 #' @param unit_of_measure `r get_ogc_params("time-series-metadata")$unit_of_measure`
 #' @param primary
@@ -47,6 +39,12 @@
 #' @param time_series_id `r get_ogc_params("time-series-metadata")$id`
 #' @param \dots Not used. Included to help differentiate official Water Data API arguments
 #' from more seldom used, optional dataRetrieval-specific arguments.
+#' @param begin_utc Deprecated in v1. Use "begin" instead.
+#' @param end_utc Deprecated in v1. Use "end" instead.
+#' @param state_name Deprecated in v1. Use `read_waterdata_combined_meta` for
+#' similar functionality.
+#' @param hydrologic_unit_code Deprecated in v1. Use
+#' `read_waterdata_combined_meta` for similar functionality.
 #' @inheritParams check_arguments_api
 #' @inheritParams check_arguments_non_api
 #'
@@ -63,8 +61,8 @@
 #'                             parameter_code = c("00060", "00010"),
 #'                             properties = c("monitoring_location_id",
 #'                                            "parameter_code",
-#'                                            "begin_utc",
-#'                                            "end_utc",
+#'                                            "begin",
+#'                                            "end",
 #'                                            "time_series_id"),
 #'                             skipGeometry = TRUE)
 #'
@@ -105,6 +103,44 @@ read_waterdata_ts_meta <- function(
   output_id <- "time_series_id"
   rlang::check_dots_empty()
 
+  on.exit(options("dataRetrieval.api_version" = "v1"))
+
+  if (!is.na(state_name)) {
+    warning(
+      "state_name is deprecated starting in v1 of the Water Data APIs.
+Use the function read_waterdata_combined_meta instead.
+Reverting to v0 version of Water Data APIs."
+    )
+    options("dataRetrieval.api_version" = "v0")
+  }
+
+  if (!is.na(hydrologic_unit_code)) {
+    warning(
+      "hydrologic_unit_code is deprecated starting in v1 of the Water Data APIs.
+Use the function read_waterdata_combined_meta instead.
+Reverting to v0 version of Water Data APIs."
+    )
+    options("dataRetrieval.api_version" = "v0")
+  }
+
+  if (!is.na(begin_utc)) {
+    warning(
+      "begin_utc is deprecated starting in v1 of the Water Data APIs.
+Use begin instead.
+Reverting to v0 version of Water Data APIs."
+    )
+    options("dataRetrieval.api_version" = "v0")
+  }
+
+  if (!is.na(end_utc)) {
+    warning(
+      "end_utc is deprecated starting in v1 of the Water Data APIs.
+Use end instead.
+Reverting to v0 version of Water Data APIs."
+    )
+    options("dataRetrieval.api_version" = "v0")
+  }
+
   args <- mget(names(formals()))
   return_list <- get_ogc_data(args, output_id, service)