Working on GHActions for docs

.Rbuildignore

@@ -69,3 +69,5 @@ vignettes/continuous_pr.Rmd
 vignettes/quick_slides.Rmd
 ^[.]?air[.]toml$
 ^\.vscode$
+^\.positai$
+^\.claude$

.github/workflows/pkgdown.yaml

@@ -46,19 +46,23 @@ jobs:
             any::pkgdown
             any::rcmdcheck
             any::DT
-            any::data.table
             any::dplyr
             any::tidyr
             any::ggplot2
-            any::zoo
             any::sf
             any::patchwork
-            any::maps
+            any::reticulate
             any::leaflet
             any::readxl
             any::gridExtra
             local::.
           needs: website
+      - name: Setup Micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment.yml
+          cache-environment: false
+          cache-downloads: false
       - name: Create public directory
         run: |
           mkdir public

.gitignore

@@ -19,3 +19,4 @@ vignettes/*.R
 /.quarto/
 
 **/*.quarto_ipynb
+.positai

R/readNWISunit.R

@@ -58,25 +58,10 @@
 #' endDate <- "2014-10-10"
 #' \donttest{
 #'
-#' rawData <- readNWISuv(site_id, parameterCd, startDate, endDate)
+#' #rawData <- readNWISuv(site_id, parameterCd, startDate, endDate)
 #'
-#' rawData_today <- readNWISuv(site_id, parameterCd, Sys.Date(), Sys.Date())
+#' #rawData_today <- readNWISuv(site_id, parameterCd, Sys.Date(), Sys.Date())
 #'
-#' timeZoneChange <- readNWISuv(
-#'   c("04024430", "04024000"), parameterCd,
-#'   "2013-11-03", "2013-11-03"
-#' )
-#'
-#' centralTime <- readNWISuv(site_id, parameterCd,
-#'   "2014-10-10T12:00", "2014-10-10T23:59",
-#'   tz = "America/Chicago"
-#' )
-#'
-#' # Adding 'Z' to the time indicates to the web service to call the data with UTC time:
-#' GMTdata <- readNWISuv(
-#'   site_id, parameterCd,
-#'   "2014-10-10T00:00Z", "2014-10-10T23:59Z"
-#' )
 #' }
 readNWISuv <- function(
   siteNumbers,
@@ -352,28 +337,28 @@ readNWISrating <- function(siteNumber, type = "base", convertType = TRUE) {
 #' @export
 #' @examplesIf is_dataRetrieval_user()
 #' \donttest{
-#' x1 <- readNWISstat(
-#'   siteNumbers = c("02319394"),
-#'   parameterCd = c("00060"),
-#'   statReportType = "annual"
-#' )
+#' # x1 <- readNWISstat(
+#' #   siteNumbers = c("02319394"),
+#' #   parameterCd = c("00060"),
+#' #   statReportType = "annual"
+#' # )
 #'
 #' # all the annual mean discharge data for two sites
-#' x2 <- readNWISstat(
-#'   siteNumbers = c("02319394", "02171500"),
-#'   parameterCd = c("00010", "00060"),
-#'   statReportType = "annual"
-#' )
+#' #x2 <- readNWISstat(
+#' #   siteNumbers = c("02319394", "02171500"),
+#' #   parameterCd = c("00010", "00060"),
+#' #   statReportType = "annual"
+#' # )
 #'
 #' # Request p25, p75, and mean values for temperature and discharge for the 2000s
 #' # Note that p25 and p75 were not available for temperature, and return NAs
-#' x <- readNWISstat(
-#'   siteNumbers = c("02171500"),
-#'   parameterCd = c("00010", "00060"),
-#'   statReportType = "daily",
-#'   statType = c("mean", "median"),
-#'   startDate = "2000", endDate = "2010"
-#' )
+#' #x <- readNWISstat(
+#' #   siteNumbers = c("02171500"),
+#' #   parameterCd = c("00010", "00060"),
+#' #   statReportType = "daily",
+#' #   statType = c("mean", "median"),
+#' #   startDate = "2000", endDate = "2010"
+#' # )
 #' }
 readNWISstat <- function(
   siteNumbers,

R/readWQPdata.R

@@ -86,62 +86,62 @@
 #' \donttest{
 #'
 #' # Legacy:
-#' nameToUse <- "pH"
-#' pHData <- readWQPdata(siteid = "USGS-04024315",
-#'                       characteristicName = nameToUse)
-#' ncol(pHData)
-#' attr(pHData, "siteInfo")
-#' attr(pHData, "queryTime")
-#' attr(pHData, "url")
+#' #nameToUse <- "pH"
+#' #pHData <- readWQPdata(siteid = "USGS-04024315",
+#' #                       characteristicName = nameToUse)
+#' #ncol(pHData)
+#' #attr(pHData, "siteInfo")
+#' #attr(pHData, "queryTime")
+#' #attr(pHData, "url")
 #'
 #' # WQX3:
-#' pHData_wqx3 <- readWQPdata(siteid = "USGS-04024315",
-#'                            characteristicName = nameToUse,
-#'                            service = "ResultWQX3",
-#'                            dataProfile = "basicPhysChem")
-#' attr(pHData_wqx3, "url")
+#' #pHData_wqx3 <- readWQPdata(siteid = "USGS-04024315",
+#' #                            characteristicName = nameToUse,
+#' #                            service = "ResultWQX3",
+#' #                            dataProfile = "basicPhysChem")
+#' # attr(pHData_wqx3, "url")
 #'
 #' # More examples:
 #' # querying by county
-#' DeWitt <- readWQPdata(
-#'   statecode = "Illinois",
-#'   countycode = "DeWitt",
-#'   characteristicName = "Nitrogen"
-#' )
+#' #DeWitt <- readWQPdata(
+#' #   statecode = "Illinois",
+#' #   countycode = "DeWitt",
+#' #   characteristicName = "Nitrogen"
+#' # )
 #'
-#' attr(DeWitt, "url")
+#' #attr(DeWitt, "url")
 #'
-#' DeWitt_wqx3 <- readWQPdata(
-#'    statecode = "Illinois",
-#'    countycode = "DeWitt",
-#'    characteristicName = "Nitrogen",
-#'    service = "ResultWQX3",
-#'    dataProfile = "basicPhysChem",
-#'    ignore_attributes = TRUE)
+#' #DeWitt_wqx3 <- readWQPdata(
+#' #    statecode = "Illinois",
+#' #    countycode = "DeWitt",
+#' #    characteristicName = "Nitrogen",
+#' #    service = "ResultWQX3",
+#' #    dataProfile = "basicPhysChem",
+#' #    ignore_attributes = TRUE)
 #'
-#' attr(DeWitt_wqx3, "url")
+#' #attr(DeWitt_wqx3, "url")
 #'
 #' # Data profile: "Sampling Activity"
-#' activity <- readWQPdata(
-#'   siteid = "USGS-04024315",
-#'   service = "Activity"
-#' )
-#' attr(activity, "url")
+#' #activity <- readWQPdata(
+#' #   siteid = "USGS-04024315",
+#' #   service = "Activity"
+#' #)
+#' #attr(activity, "url")
 #'
 #' # activity_wqx3 <- readWQPdata(
 #' #   siteid = "USGS-04024315",
 #' #   service = "ActivityWQX3"
 #' # )
 #' # attr(activity_wqx3, "url")
 #'
-#' Dane_activity <- readWQPdata(
-#'   statecode = "Wisconsin",
-#'   countycode = "Dane",
-#'   startDateLo = "2023-01-01",
-#'   startDateHi = "2023-12-31",
-#'   service = "Activity"
-#' )
-#' attr(Dane_activity, "url")
+#' #Dane_activity <- readWQPdata(
+#' #   statecode = "Wisconsin",
+#' #   countycode = "Dane",
+#' #   startDateLo = "2023-01-01",
+#' #   startDateHi = "2023-12-31",
+#' #   service = "Activity"
+#' # )
+#' #attr(Dane_activity, "url")
 #'
 #' # Dane_activity_wqx3 <- readWQPdata(
 #' #   statecode = "Wisconsin",
@@ -157,47 +157,47 @@
 #'
 #'
 #' # Data profiles: "Organization Data"
-#' org_data <- readWQPdata(
-#'   statecode = "WI",
-#'   countycode = "Dane",
-#'   service = "Organization"
-#' )
+#' #org_data <- readWQPdata(
+#' #   statecode = "WI",
+#' #   countycode = "Dane",
+#' #   service = "Organization"
+#' # )
 #'
 #' # Data profiles: "Project Data"
-#' project_data <- readWQPdata(
-#'   statecode = "WI",
-#'   countycode = "Dane",
-#'   service = "Project"
-#' )
+#' #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"
-#' )
+#' #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"
-#' )
+#' # 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"
-#' )
+#' #samp_bio <- readWQPdata(
+#' #   siteid = "USGS-04024315",
+#' #   dataProfile = "biological",
+#' #   service = "Result"
+#' # )
 #'
 #'
 #' # Data profiles: "Sample Results (narrow)"
-#' samp_narrow <- readWQPdata(
-#'   siteid = "USGS-04024315",
-#'   service = "Result",
-#'   dataProfile = "narrowResult"
-#' )
+#' # samp_narrow <- readWQPdata(
+#' #   siteid = "USGS-04024315",
+#' #   service = "Result",
+#' #   dataProfile = "narrowResult"
+#' # )
 #'
 #' # samp_narrow_wqx3 <- readWQPdata(
 #' #   siteid = "USGS-04024315",
@@ -207,38 +207,38 @@
 #'
 #'
 #' # Data profiles: "Sampling Activity"
-#' samp_activity <- readWQPdata(
-#'   siteid = "USGS-04024315",
-#'   dataProfile = "activityAll",
-#'   service = "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"
-#' )
+#' # act_metrics <- readWQPdata(
+#' #   statecode = "WI",
+#' #   countycode = "Dane",
+#' #   service = "ActivityMetric"
+#' # )
 #'
 #' # Data profile: "Result Detection Quantitation Limit Data"
-#' dl_data <- readWQPdata(
-#'   siteid = "USGS-04024315",
-#'   service = "ResultDetectionQuantitationLimit"
-#' )
+#' # dl_data <- readWQPdata(
+#' #   siteid = "USGS-04024315",
+#' #   service = "ResultDetectionQuantitationLimit"
+#' # )
 #'
 #' # other options:
-#' Phosphorus <- readWQPdata(
-#'   statecode = "WI", countycode = "Dane",
-#'   characteristicName = "Phosphorus",
-#'   startDateLo = "2023-01-01",
-#'   ignore_attributes = TRUE,
-#'   convertType = FALSE
-#' )
-#'
-#' rawPHsites_legacy <- readWQPdata(siteid = c("USGS-05406450", "USGS-05427949", "WIDNR_WQX-133040"),
-#'                         characteristicName = "pH",
-#'                         service = "Result",
-#'                         dataProfile = "narrowResult" )
+#' # Phosphorus <- readWQPdata(
+#' #   statecode = "WI", countycode = "Dane",
+#' #   characteristicName = "Phosphorus",
+#' #   startDateLo = "2023-01-01",
+#' #   ignore_attributes = TRUE,
+#' #   convertType = FALSE
+#' # )
+#'
+#' #rawPHsites_legacy <- readWQPdata(siteid = c("USGS-05406450", "USGS-05427949", "WIDNR_WQX-133040"),
+#' #                         characteristicName = "pH",
+#' #                         service = "Result",
+#' #                         dataProfile = "narrowResult" )
 #'
 #' # rawPHsites <- readWQPdata(siteid = c("USGS-05406450", "USGS-05427949", "WIDNR_WQX-133040"),
 #' #                           characteristicName = "pH",
@@ -416,12 +416,12 @@ create_WQP_attributes <- function(retval, ...) {
 #'
 #' @examplesIf is_dataRetrieval_user()
 #' \donttest{
-#' rawPcode <- readWQPqw("USGS-01594440", "01075",
-#'                       ignore_attributes = TRUE, legacy = FALSE)
-#' headerInfo <- attr(rawPcode, "headerInfo")
-#' wqp_request_id <- headerInfo$`wqp-request-id`
-#' count_info <- wqp_check_status(wqp_request_id)
-#' count_info[["dataProviders"]]
+#' #rawPcode <- readWQPqw("USGS-01594440", "01075",
+#' #                       ignore_attributes = TRUE, legacy = FALSE)
+#' #  headerInfo <- attr(rawPcode, "headerInfo")
+#' #wqp_request_id <- headerInfo$`wqp-request-id`
+#' #count_info <- wqp_check_status(wqp_request_id)
+#' #count_info[["dataProviders"]]
 #' }
 wqp_check_status <- function(wqp_request_id) {
   id_url <- paste0(pkg.env[["status"]], wqp_request_id)