Adding waterdata functions

.Rbuildignore

@@ -90,6 +90,7 @@ vignettes/Status.Rmd
 vignettes/long_to_wide.Rmd
 vignettes/join_by_closest.Rmd
 vignettes/wqx3_development_plan.Rmd
+vignettes/read_waterdata_functions.Rmd
 vignettes/dataretrieval_discrete_changes_images/*
 ^ci$
 ^public$

.github/workflows/R-CMD-check.yaml

@@ -24,6 +24,7 @@ jobs:
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      API_USGS_PAT: ${{ secrets.API_USGS_PAT }}
       R_KEEP_PKG_SOURCE: yes
       CUSTOM_DR_UA: 'GitHub_CI'
 

.github/workflows/pkgdown.yaml

@@ -28,6 +28,7 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      API_USGS_PAT: ${{ secrets.API_USGS_PAT }}
       CUSTOM_DR_UA: 'GitHub_CI'
     steps:
       - uses: actions/checkout@581d62f320f2a4043a1ea6ac77290c60d27485cc

.github/workflows/test-coverage.yaml

@@ -14,6 +14,7 @@ jobs:
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      API_USGS_PAT: ${{ secrets.API_USGS_PAT }}
       R_KEEP_PKG_SOURCE: yes
       CUSTOM_DR_UA: 'GitHub_CI'
 

.gitlab-ci.yml

@@ -31,6 +31,7 @@ variables:
   NOT_CRAN: "true"
   PAGES_OUTDIR: "$CI_PROJECT_DIR/public"
   CUSTOM_DR_UA: "GitLab_CI"
+  API_USGS_PAT: "${API_USGS_PAT}"
 
 build-image:
   stage: build
@@ -98,6 +99,7 @@ pages:
   cache: []
   script:
     - Rscript -e 'pkgdown::build_site(override = list(destination = "public"))'
+    - Rscript -e 'file.copy(from = "./public/articles/logo.png", to = "./public/reference/logo.png")'
   artifacts:
     paths:
       - $PAGES_OUTDIR

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dataRetrieval
 Type: Package
 Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality Data
-Version: 2.7.18.9002
+Version: 2.7.19
 Authors@R: c(
     person("Laura", "DeCicco", role = c("aut","cre"),
             email = "ldecicco@usgs.gov",
@@ -26,36 +26,46 @@ Authors@R: c(
             comment=c(ORCID = "0000-0003-2521-5043")),
     person("Lee", "Stanish", role="ctb",
             email = "lstanish@usgs.gov",
-            comment=c(ORCID = "0000-0002-9775-6861")))
+            comment=c(ORCID = "0000-0002-9775-6861")),
+    person("Joeseph", "Zemmels", role="ctb",
+            email = "jzemmels@usgs.gov",
+            comment=c(ORCID = "0009-0008-1463-6313")),
+    person("Elise", "Hinman", role="ctb",
+            email = "ehinman@usgs.gov",
+            comment=c(ORCID = "0000-0001-5396-1583")),  
+    person("Michael", "Mahoney", role="ctb",
+            email = "mjmahoney@usgs.gov",
+            comment=c(ORCID = "0000-0003-2402-304X"))  
+            )
 Description: Collection of functions to help retrieve U.S. Geological Survey
     and U.S. Environmental Protection Agency water quality and
-    hydrology data from web services. Data are discovered from 
-    National Water Information System <https://waterservices.usgs.gov/> and <https://waterdata.usgs.gov/nwis>. 
-    Water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.
+    hydrology data from web services. 
 License: CC0
 Copyright: This software is in the public domain because it contains materials
     that originally came from the United States Geological Survey, an agency of
     the United States Department of Interior. 
 Depends:
     R (>= 4.1.0)
 Imports:
-    curl,
+    curl (>= 6.0.0),
     lubridate (>= 1.5.0),
     stats,
     utils,
     xml2,
     readr (>= 1.4.0),
     jsonlite,
-    httr2
+    httr2,
+    whisker,
+    sf
 Suggests:
     covr,
     dplyr,
     knitr,
     rmarkdown,
-    sf,
     testthat
 Encoding: UTF-8
 BuildVignettes: true
 VignetteBuilder: knitr
 BugReports: https://github.com/DOI-USGS/dataRetrieval/issues
 RoxygenNote: 7.3.2
+Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -3,11 +3,13 @@
 export(addWaterYear)
 export(calcWaterYear)
 export(checkWQPdates)
-export(check_param)
+export(check_OGC_requests)
+export(check_waterdata_sample_params)
 export(constructNWISURL)
 export(constructUseURL)
 export(constructWQPURL)
-export(construct_USGS_sample_request)
+export(construct_api_requests)
+export(construct_waterdata_sample_request)
 export(countyCd)
 export(countyCdLookup)
 export(create_NWIS_bib)
@@ -43,11 +45,17 @@ export(readWQPdata)
 export(readWQPqw)
 export(readWQPsummary)
 export(read_USGS_samples)
+export(read_waterdata)
+export(read_waterdata_daily)
+export(read_waterdata_monitoring_location)
+export(read_waterdata_samples)
+export(read_waterdata_ts_meta)
 export(renameNWISColumns)
 export(setAccess)
 export(stateCd)
 export(stateCdLookup)
 export(summarize_USGS_samples)
+export(summarize_waterdata_samples)
 export(whatNWISdata)
 export(whatNWISsites)
 export(whatWQPdata)

NEWS

@@ -1,3 +1,12 @@
+dataRetrieval 2.7.19
+===================
+* Added read_waterdata_daily, read_waterdata_monitoring_location, read_waterdata_ts_meta to access
+new USGS web services.
+* Added whisker and sf as dependencies.
+* Renamed read_USGS_samples to read_waterdata_samples.
+* Renamed summarize_USGS_samples to summarize_waterdata_samples.
+* Added warning to setAccess for non-public endpoints.
+
 dataRetrieval 2.7.18
 ===================
 * Switched from httr to httr2

R/AAA.R

@@ -4,6 +4,7 @@ pkg.env <- new.env()
   suppressMessages(setAccess("public"))
   pkg.env$nldi_base <- "https://api.water.usgs.gov/nldi/linked-data/"
   pkg.env$local_sf <- requireNamespace("sf", quietly = TRUE)
+  options("dataRetrieval" = list("api_version" = "v0"))
 }
 
 
@@ -51,3 +52,11 @@ discrete water quality data newer than March 11, 2024.
 For additional details, see:
 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.
+For up-to-date information, see: 
+https://doi-usgs.github.io/dataRetrieval/articles/Status.html")
+}
+

R/checkWQPdates.R

@@ -1,7 +1,7 @@
 #' Date Check for Water Quality Portal
 #'
-#' Checks date format for inputs to the Water Quality Portal. Used in \code{readWQPqw}
-#' and \code{readWQPdata}.
+#' Checks date format for inputs to the Water Quality Portal. Used in `readWQPqw`
+#' and `readWQPdata`.
 #'
 #' @param values named list with arguments to send to the Water Quality Portal
 #' @return values named list with corrected arguments to send to the Water Quality Portal

R/citations.R

@@ -2,7 +2,7 @@
 #'
 #' Uses attributes from the NWIS functions to create data citations.
 #' 
-#' See \code{?bibentry} for more information.
+#' See `?bibentry` for more information.
 #'
 #' @param x Any data returned from an NWIS function, must
 #' include "queryTime" and "url" attributes, which should
@@ -48,7 +48,7 @@ create_NWIS_bib <- function(x){
 #'
 #' Uses attributes from the WQP functions to create data citations.
 #' 
-#' See \code{?bibentry} for more information.
+#' See `?bibentry` for more information.
 #'
 #' @param x Any data returned from an NWIS function, must
 #' include "queryTime" and "url" attributes, which should

R/constructNWISURL.R

@@ -22,21 +22,21 @@
 #' momentary problem with the internet connection). It is possible to safely use the "tsv" option,
 #' but the user must carefully check the results to see if the data returns matches
 #' what is expected. The default is therefore "xml".
-#' @param expanded logical defaults to \code{TRUE}. If \code{TRUE}, retrieves additional
+#' @param expanded logical defaults to `TRUE`. If `TRUE`, retrieves additional
 #' information, only applicable for qw data.
 #' @param ratingType can be "base", "corr", or "exsa". Only applies to rating curve data.
 #' @param statReportType character Only used for statistics service requests.  Time
 #' division for statistics: daily, monthly, or annual.  Default is daily.
 #' Note that daily provides statistics for each calendar day over the specified
 #' range of water years, i.e. no more than 366 data points will be returned for
-#' each site/parameter.  Use \code{readNWISdata} or \code{readNWISdv} for daily averages.
+#' each site/parameter.  Use `readNWISdata` or `readNWISdv` for daily averages.
 #' Also note that "annual" returns statistics for the calendar year.  Use
-#' \code{readNWISdata} for water years. Monthly and yearly
+#' `readNWISdata` for water years. Monthly and yearly
 #' provide statistics for each month and year within the range individually.
 #' @param statType character Only used for statistics service requests. Type(s)
 #' of statistics to output for daily values.  Default is mean, which is the only
 #' option for monthly and yearly report types. See the statistics service documentation
-#' at \url{https://waterservices.usgs.gov/docs/statistics/} for a
+#' at <https://waterservices.usgs.gov/docs/statistics/> for a
 #' full list of codes.
 #' @keywords data import USGS web service
 #' @return url string
@@ -304,7 +304,7 @@ constructNWISURL <- function(siteNumbers,
 
 #' Construct WQP url for data retrieval
 #'
-#' Construct WQP url for data retrieval. This function gets the data from here: \url{https://www.waterqualitydata.us}
+#' Construct WQP url for data retrieval. This function gets the data from here: <https://www.waterqualitydata.us>
 #'
 #' @param siteNumbers string or vector of strings USGS site number.  
 #' @param parameterCd string or vector of USGS parameter code.  This is usually an 5 digit number.
@@ -433,7 +433,7 @@ constructWQPURL <- function(siteNumbers,
 
 #' Construct URL for NWIS water use data service
 #'
-#' Reconstructs URLs to retrieve data from here: \url{https://waterdata.usgs.gov/nwis/wu}
+#' Reconstructs URLs to retrieve data from here: <https://waterdata.usgs.gov/nwis/wu>
 #'
 #' @param years integer Years for data retrieval. Must be years ending in 0 or 5,
 #' or "ALL", which retrieves all available years.
@@ -490,4 +490,4 @@ constructUseURL <- function(years, stateCd, countyCd, categories) {
                                   .multi = "comma")
 
   return(baseURL)
-}
+}