more CRAN fixes

DOI-USGS · Aug 22, 2019 · 07afb79 · 07afb79
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -3,7 +3,7 @@ Type: Package
 Title: Tools for Using NHDPlus Data
 Version: 0.3.7
 Authors@R: person("David", "Blodgett", role = c("aut", "cre"), email = "[email protected]")
-Description: Tools for traversing and working with NHDPlus data.
+Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
 URL: https://github.com/usgs-r/nhdplusTools
 BugReports: https://github.com/usgs-r/nhdplusTools/issues
 Depends:

diff --git a/R/get_nhdplus.R b/R/get_nhdplus.R
@@ -9,18 +9,12 @@
 #' @return integer COMID
 #' @export
 #' @examples
-#' \dontrun{
 #' point <- sf::st_sfc(sf::st_point(c(-76.87479, 39.48233)), crs = 4326)
 #' discover_nhdplus_id(point)
 #'
-#' discover_nldi_sources()
-#'
-#' nldi_huc12 <- list(featureSource = "huc12pp", featureID = "070700051701")
-#' discover_nhdplus_id(nldi_feature = nldi_huc12)
-#'
 #' nldi_nwis <- list(featureSource = "nwissite", featureID = "USGS-08279500")
 #' discover_nhdplus_id(nldi_feature = nldi_nwis)
-#' }
+#'
 discover_nhdplus_id <- function(point = NULL, nldi_feature = NULL) {
 
   if (!is.null(point)) {
@@ -246,6 +240,7 @@ download_nhdplushr <- function(nhd_dir, hu_list, download_files = TRUE) {
 #' @export
 #' @examples
 #' \dontrun{
+#' # Not run because this will download a lot of data for the user.
 #' download_dir <- download_nhdplushr("./", c("0302", "0303"))
 #' get_nhdplushr(download_dir, "nhdplus_0302-03.gpkg")
 #' }

diff --git a/R/get_nldi.R b/R/get_nldi.R
@@ -55,17 +55,11 @@ discover_nldi_navigation <- function(nldi_feature, tier = "prod") {
 #' @export
 #' @importFrom utils tail
 #' @examples
-#' \dontrun{
+#' \dontrun{ # Long running example
 #' library(sf)
 #' library(dplyr)
 #'
-#' discover_nldi_sources()
-#'
-#' nldi_nwis <- list(featureSource = "nwissite", featureID = "USGS-08279500")
-#'
-#' nav_options <- discover_nldi_navigation(nldi_nwis)
-#'
-#' nav_options
+#' nldi_nwis <- list(featureSource = "nwissite", featureID = "USGS-05428500")
 #'
 #' navigate_nldi(nldi_feature = nldi_nwis,
 #'               mode = "upstreamTributaries",
@@ -79,25 +73,7 @@ discover_nldi_navigation <- function(nldi_feature, tier = "prod") {
 #'   st_geometry() %>%
 #'   plot(col = "blue", add = TRUE)
 #'
-#' navigate_nldi(nldi_feature = nldi_nwis,
-#'               mode = nav_options[["downstreamMain"]],
-#'               data_source = "",
-#'               distance_km = 40) %>%
-#'   st_geometry() %>%
-#'   plot(col = "red", add = TRUE)
-#'
-#' navigate_nldi(nldi_feature = nldi_nwis,
-#'               mode = "UM", data_source = "nwissite",
-#'               distance_km = 0) %>%
-#'   st_geometry() %>%
-#'   plot(col = "red", add = TRUE)
 #'
-#' navigate_nldi(nldi_feature = nldi_nwis,
-#'               mode = "UT",
-#'               data_source = "huc12pp") %>%
-#'   st_geometry() %>%
-#'   plot(col = rgb(255, 205, 205, 100, maxColorValue = 255),
-#'        pch = 18, add = TRUE)
 #'
 #' nwissite <- navigate_nldi(nldi_feature = nldi_nwis,
 #'                           mode = "UT",
@@ -108,6 +84,7 @@ discover_nldi_navigation <- function(nldi_feature, tier = "prod") {
 #'
 #' nwissite
 #' }
+#'
 navigate_nldi <- function(nldi_feature, mode = "upstreamMain",
                           data_source = "comid", distance_km = NULL,
                           tier = "prod") {
@@ -150,22 +127,18 @@ navigate_nldi <- function(nldi_feature, mode = "upstreamMain",
 #' @return sf data.frame with result basin boundary
 #' @export
 #' @examples
-#' \dontrun{
 #' library(sf)
 #' library(dplyr)
 #'
-#' discover_nldi_sources()
-#'
-#' nldi_nwis <- list(featureSource = "nwissite", featureID = "USGS-08279500")
+#' nldi_nwis <- list(featureSource = "nwissite", featureID = "USGS-05428500")
 #'
 #' basin <- get_nldi_basin(nldi_feature = nldi_nwis)
 #'
 #' basin %>%
 #'  st_geometry() %>%
 #'  plot()
 #'
-#'  basin
-#'  }
+#' basin
 #'
 get_nldi_basin <- function(nldi_feature,
                           tier = "prod") {

diff --git a/R/subset_nhdplus.R b/R/subset_nhdplus.R
@@ -27,30 +27,7 @@
 #' @return path to the saved subset geopackage
 #' @export
 #' @examples
-#' \dontrun{
-#' # NHDPlusHR
-#' temp_dir <- tempdir()
-#' temp_file <- tempfile(fileext = ".zip", tmpdir = temp_dir)
-#' download.file("https://usgs-r.github.io/nhdplusTools/data/03_sub.zip",
-#'               temp_file)
-#' unzip(temp_file, exdir = temp_dir)
-#'
-#' hr_data <- get_nhdplushr(temp_dir,
-#'                          out_gpkg = file.path(temp_dir, "nhd_hr.gpkg"),
-#'                          layers = NULL)
-#' flowlines <- sf::read_sf(hr_data, "NHDFlowline")
-#'
-#' up_ids <- get_UT(flowlines, 15000500028335)
-#'
-#' sub_nhdhr <- subset_nhdplus(up_ids, file.path(temp_dir, "sub.gpkg"),
-#'                       hr_data, overwrite = TRUE)
-#'
-#' sf::st_layers(sub_nhdhr)
-#'
-#' sub_flowline <- sf::read_sf(sub_nhdhr, "NHDFlowline")
-#' plot(sf::st_geometry(flowlines), lwd = 0.5)
-#' plot(sf::st_geometry(sub_flowline), lwd = 0.6, col = "red", add = TRUE)
-#'
+#' \dontrun{ # long running example
 #' sample_data <- system.file("extdata/sample_natseamless.gpkg",
 #'                            package = "nhdplusTools")
 #'
@@ -104,6 +81,29 @@
 #'                status = TRUE)
 #'
 #' sf::st_layers(output_file)
+#'
+#' # NHDPlusHR
+#' temp_dir <- tempdir()
+#' temp_file <- tempfile(fileext = ".zip", tmpdir = temp_dir)
+#' download.file("https://usgs-r.github.io/nhdplusTools/data/03_sub.zip",
+#'               temp_file)
+#' unzip(temp_file, exdir = temp_dir)
+#'
+#' hr_data <- get_nhdplushr(temp_dir,
+#'                          out_gpkg = file.path(temp_dir, "nhd_hr.gpkg"),
+#'                          layers = NULL)
+#' flowlines <- sf::read_sf(hr_data, "NHDFlowline")
+#'
+#' up_ids <- get_UT(flowlines, 15000500028335)
+#'
+#' sub_nhdhr <- subset_nhdplus(up_ids, file.path(temp_dir, "sub.gpkg"),
+#'                       hr_data, overwrite = TRUE)
+#'
+#' sf::st_layers(sub_nhdhr)
+#'
+#' sub_flowline <- sf::read_sf(sub_nhdhr, "NHDFlowline")
+#' plot(sf::st_geometry(flowlines), lwd = 0.5)
+#' plot(sf::st_geometry(sub_flowline), lwd = 0.6, col = "red", add = TRUE)
 #' }
 #'
 
@@ -290,11 +290,10 @@ intersection_write <- function(layer_name, data_path, envelope,
 #' @return list containing paths to the .rds files.
 #' @export
 #' @examples
-#' \dontrun{
-#' stage_national_data()
+#' sample_data <- system.file("extdata/sample_natseamless.gpkg",
+#'                            package = "nhdplusTools")
 #'
-#' stage_national_data(include = c("attributes", "flowlines","catchment"))
-#' }
+#' stage_national_data(nhdplus_data = sample_data, output_path = tempdir())
 #'
 stage_national_data <- function(include = c("attribute",
                                             "flowline",

diff --git a/man/discover_nhdplus_id.Rd b/man/discover_nhdplus_id.Rd
diff --git a/man/get_nhdplushr.Rd b/man/get_nhdplushr.Rd
diff --git a/man/get_nldi_basin.Rd b/man/get_nldi_basin.Rd
diff --git a/man/navigate_nldi.Rd b/man/navigate_nldi.Rd
diff --git a/man/stage_national_data.Rd b/man/stage_national_data.Rd
diff --git a/man/subset_nhdplus.Rd b/man/subset_nhdplus.Rd
diff --git a/vignettes/nhdplusTools.Rmd b/vignettes/nhdplusTools.Rmd
@@ -15,6 +15,7 @@ knitr::opts_chunk$set(
   fig.width=6, 
   fig.height=4
 )
+oldoption <- options(scipen = 9999)
 options(scipen = 9999)
 ```
 
@@ -330,3 +331,7 @@ For more info about `get_flowline_index()` see the article `vignette("point_inde
 ## Refactoring
 
 The NHDPlus tools package has been developed in support of an experimental NHDPlus refactoring workflow to normalize the size of catchments and resolve particular network locations. If this work is of interest, it can be found in the network_refactor branch of this repository.
+
+```{r teardown, include=FALSE}
+options(oldoption)
+```