From 39c12fb19f9c6a52e1b6e143bfbdeb56f86e35f4 Mon Sep 17 00:00:00 2001 From: David Blodgett Date: Mon, 14 Sep 2020 08:18:34 -0500 Subject: [PATCH 1/3] check --- R/index_nhdplus.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/R/index_nhdplus.R b/R/index_nhdplus.R index 8f019303..e1c72e31 100644 --- a/R/index_nhdplus.R +++ b/R/index_nhdplus.R @@ -132,8 +132,8 @@ get_flowline_index <- function(flines, points, if (nrow(flines) != nrow(fline_atts)) { flines <- summarize(group_by(select(flines, .data$index), - index), - do_union = FALSE) + .data$index), + do_union = FALSE) flines <- left_join(flines, fline_atts, by = "index") @@ -144,7 +144,7 @@ get_flowline_index <- function(flines, points, "part lines. Check results!!")) st_geometry(flines)[multi] <- lapply(st_geometry(flines)[multi], function(x) { - st_linestring(do.call(rbind, x)) + sf::st_linestring(do.call(rbind, x)) }) flines <- sf::st_zm(sf::st_cast(flines, "LINESTRING", warn = FALSE)) From 7acd1dd5b83eddcfef895028be70549480a2b648 Mon Sep 17 00:00:00 2001 From: David Blodgett Date: Thu, 17 Sep 2020 07:39:50 -0500 Subject: [PATCH 2/3] url fixes for CRAN --- DISCLAIMER.md | 2 +- R/get_nldi.R | 2 +- README.md | 18 ++++++++++++++---- docs/DISCLAIMER.html | 2 +- docs/articles/nhdplusTools.html | 20 ++++++++++---------- docs/articles/nhdplushr.html | 2 +- docs/index.html | 18 +++++++++--------- docs/reference/get_nldi_basin.html | 2 +- man/get_nldi_basin.Rd | 2 +- vignettes/nhdplusTools.Rmd | 2 +- 10 files changed, 40 insertions(+), 30 deletions(-) diff --git a/DISCLAIMER.md b/DISCLAIMER.md index b176f14b..15102f3b 100644 --- a/DISCLAIMER.md +++ b/DISCLAIMER.md @@ -3,7 +3,7 @@ Disclaimer This information is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The information has not received final approval by the U.S. Geological Survey (USGS) and is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the information. -This software is in the public domain because it contains materials that originally came from the U.S. Geological Survey (USGS), an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at https://www.usgs.gov/visual-id/credit_usgs.html#copyright +This software is in the public domain because it contains materials that originally came from the U.S. Geological Survey (USGS), an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at https://www.usgs.gov/information-policies-and-instructions/copyrights-and-credits Although this software program has been used by the USGS, no warranty, expressed or implied, is made by the USGS or the U.S. Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith. This software is provided "AS IS." diff --git a/R/get_nldi.R b/R/get_nldi.R index c35d8371..47bbbf49 100644 --- a/R/get_nldi.R +++ b/R/get_nldi.R @@ -173,7 +173,7 @@ navigate_nldi <- function(nldi_feature, mode = "upstreamMain", #' @title Get NLDI Basin Boundary #' @description Get a basin boundary for a given NLDI feature. #' @details Only resolves to the nearest NHDPlus catchment divide. See: -#' https://owi.usgs.gov/blog/nldi-intro/ for more info on the nldi. +#' https://waterdata.usgs.gov/blog/nldi-intro/ for more info on the nldi. #' @inheritParams navigate_nldi #' @return sf data.frame with result basin boundary #' @export diff --git a/README.md b/README.md index 212a0e66..a7f31347 100644 --- a/README.md +++ b/README.md @@ -123,12 +123,12 @@ relates to handling data and what dependencies are used will be very important. Web services will generally be avoided. However, applications that would require loading significant amounts of data to perform something that can be accomplished with a web service very quickly will be considered. Systems like -the [Network Linked Data Index](https://owi.usgs.gov/blog/nldi-intro/) are +the [Network Linked Data Index](https://waterdata.usgs.gov/blog/nldi-intro/) are used for data discovery. ##### NHDPlus Version Initial package development focused on the [National Seamless NHDPlus](https://www.epa.gov/waterdata/nhdplus-national-data) -database. [NHDPlus High Resolution](https://nhd.usgs.gov/NHDPlus_HR.html) is +database. [NHDPlus High Resolution](https://www.usgs.gov/core-science-systems/ngp/national-hydrography/nhdplus-high-resolution) is also supported. ### Related similar packages: @@ -140,13 +140,23 @@ https://github.com/ropensci/FedData https://github.com/cheginit/hydrodata ... others -- please suggest additions? +### Build notes: +This package uses a convention to avoid building vignettes on CRAN. The `BUILD_VIGNETTES` environment variable must be set to `TRUE`. This is done with a .Renviron file in the package directory with the line `BUILD_VIGNETTES=TRUE`. + +Given this, the package should be built locally to include vignettes using: + +```r +devtools::build_vignettes(install = FALSE) +devtools::build(vignettes = FALSE) +``` + ### Contributing: First, thanks for considering a contribution! I hope to make this package a community created resource for us all to gain from and won't be able to do that without your help! 1) Contributions should be thoroughly tested with [testthat](https://testthat.r-lib.org/). -2) Code style should attempt to follow the [tidyverse style guide.](http://style.tidyverse.org/) +2) Code style should attempt to follow the [tidyverse style guide.](https://style.tidyverse.org/) 3) Please attempt to describe what you want to do prior to contributing by submitting an issue. 4) Please follow the typical github [fork - pull-request workflow.](https://gist.github.com/Chaser324/ce0505fbed06b947d962) 5) Make sure you use roxygen and run Check before contributing. More on this front as the package matures. @@ -161,7 +171,7 @@ Other notes: This information is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The information has not received final approval by the U.S. Geological Survey (USGS) and is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the information. -This software is in the public domain because it contains materials that originally came from the U.S. Geological Survey (USGS), an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at [https://www.usgs.gov/visual-id/credit_usgs.html#copyright](https://www.usgs.gov/visual-id/credit_usgs.html#copyright) +This software is in the public domain because it contains materials that originally came from the U.S. Geological Survey (USGS), an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at [https://www.usgs.gov/information-policies-and-instructions/copyrights-and-credits](https://www.usgs.gov/information-policies-and-instructions/copyrights-and-credits) Although this software program has been used by the USGS, no warranty, expressed or implied, is made by the USGS or the U.S. Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith. diff --git a/docs/DISCLAIMER.html b/docs/DISCLAIMER.html index 3039df1e..89a2775f 100644 --- a/docs/DISCLAIMER.html +++ b/docs/DISCLAIMER.html @@ -145,7 +145,7 @@

Disclaimer

This information is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The information has not received final approval by the U.S. Geological Survey (USGS) and is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the information.

-

This software is in the public domain because it contains materials that originally came from the U.S. Geological Survey (USGS), an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at https://www.usgs.gov/visual-id/credit_usgs.html#copyright

+

This software is in the public domain because it contains materials that originally came from the U.S. Geological Survey (USGS), an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at https://www.usgs.gov/information-policies-and-instructions/copyrights-and-credits

Although this software program has been used by the USGS, no warranty, expressed or implied, is made by the USGS or the U.S. Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith. This software is provided “AS IS.”

diff --git a/docs/articles/nhdplusTools.html b/docs/articles/nhdplusTools.html index c51b24b1..681b589d 100644 --- a/docs/articles/nhdplusTools.html +++ b/docs/articles/nhdplusTools.html @@ -47,7 +47,7 @@
  • - +
  • @@ -59,7 +59,7 @@
  • @@ -93,22 +93,22 @@ - +

    Introduction to nhdplusTools

    - - + + Source: vignettes/nhdplusTools.Rmd
    - - + +

    TL;DR

    @@ -275,7 +275,7 @@

    Web Service Data Subsetting

    -

    nhdplusTools supports discovery and data subsetting using web services made available through the Network Linked Data Index (NLDI) and the National Water Census Geoserver. The code below shows how to use the NLDI functions to build a dataset upstream of our start_comid that we found above.

    +

    nhdplusTools supports discovery and data subsetting using web services made available through the Network Linked Data Index (NLDI) and the National Water Census Geoserver. The code below shows how to use the NLDI functions to build a dataset upstream of our start_comid that we found above.

    The NLDI can be queried with any set of watershed outlet locations that it has in its index. We call these “featureSources”. We can query the NLDI for an identifier of a given feature from any of its “featureSources” and find out what our navigation options are as shown below.

    discover_nldi_sources()$source
 #> [1] "comid"    "huc12pp"  "nwissite" "wade"     "WQP"
@@ -509,7 +509,7 @@
    - + diff --git a/docs/articles/nhdplushr.html b/docs/articles/nhdplushr.html index d9f3e7ef..e0f841bd 100644 --- a/docs/articles/nhdplushr.html +++ b/docs/articles/nhdplushr.html @@ -38,7 +38,7 @@ nhdplusTools - 0.3.14 + 0.3.15
    diff --git a/docs/index.html b/docs/index.html index 1794e1ba..40183f9b 100644 --- a/docs/index.html +++ b/docs/index.html @@ -47,7 +47,7 @@
  • - +
  • @@ -59,7 +59,7 @@
  • @@ -93,7 +93,7 @@

    • - +
    @@ -184,12 +184,12 @@

    Web vs Local Data
    -

    Web services will generally be avoided. However, applications that would require loading significant amounts of data to perform something that can be accomplished with a web service very quickly will be considered. Systems like the Network Linked Data Index are used for data discovery.

    +

    Web services will generally be avoided. However, applications that would require loading significant amounts of data to perform something that can be accomplished with a web service very quickly will be considered. Systems like the Network Linked Data Index are used for data discovery.

    NHDPlus Version
    -

    Initial package development focused on the National Seamless NHDPlus database. NHDPlus High Resolution is also supported.

    +

    Initial package development focused on the National Seamless NHDPlus database. NHDPlus High Resolution is also supported.

    - + diff --git a/docs/reference/get_nldi_basin.html b/docs/reference/get_nldi_basin.html index 08fb3376..b8f2e1c1 100644 --- a/docs/reference/get_nldi_basin.html +++ b/docs/reference/get_nldi_basin.html @@ -173,7 +173,7 @@

    Value

    Details

    Only resolves to the nearest NHDPlus catchment divide. See: -https://owi.usgs.gov/blog/nldi-intro/ for more info on the nldi.

    +https://waterdata.usgs.gov/blog/nldi-intro/ for more info on the nldi.

    Examples

    # \donttest{
diff --git a/man/get_nldi_basin.Rd b/man/get_nldi_basin.Rd
index 62e02887..92ff3dba 100644
--- a/man/get_nldi_basin.Rd
+++ b/man/get_nldi_basin.Rd
@@ -22,7 +22,7 @@ Get a basin boundary for a given NLDI feature.
 }
 \details{
 Only resolves to the nearest NHDPlus catchment divide. See:
-https://owi.usgs.gov/blog/nldi-intro/ for more info on the nldi.
+https://waterdata.usgs.gov/blog/nldi-intro/ for more info on the nldi.
 }
 \examples{
 \donttest{
diff --git a/vignettes/nhdplusTools.Rmd b/vignettes/nhdplusTools.Rmd
index 101a8460..31972f8a 100644
--- a/vignettes/nhdplusTools.Rmd
+++ b/vignettes/nhdplusTools.Rmd
@@ -194,7 +194,7 @@ start_comid
 
 ### Web Service Data Subsetting
 
-`nhdplusTools` supports discovery and data subsetting using web services made available through the [Network Linked Data Index](https://owi.usgs.gov/blog/nldi-intro/) (NLDI) and the [National Water Census Geoserver.](https://labs.waterdata.usgs.gov/geoserver) The code below shows how to use the NLDI functions to build a dataset upstream of our `start_comid` that we found above.
+`nhdplusTools` supports discovery and data subsetting using web services made available through the [Network Linked Data Index](https://waterdata.usgs.gov/blog/nldi-intro/) (NLDI) and the [National Water Census Geoserver.](https://labs.waterdata.usgs.gov/geoserver) The code below shows how to use the NLDI functions to build a dataset upstream of our `start_comid` that we found above.
 
 The NLDI can be queried with any set of watershed outlet locations that it has in its index. We call these "featureSources". We can query the NLDI for an identifier of a given feature from any of its "featureSources" and find out what our navigation options are as shown below.
 ```{r discover_nldi}

From 0186fe55cef359b870be0b66f4a841c407bb63f1 Mon Sep 17 00:00:00 2001
From: David Blodgett 
Date: Thu, 17 Sep 2020 07:50:39 -0500
Subject: [PATCH 3/3] ad islands documentation

---
 R/downloading_tools.R     | 9 +++++++++
 man/download_nhdplusv2.Rd | 8 ++++++++
 2 files changed, 17 insertions(+)

diff --git a/R/downloading_tools.R b/R/downloading_tools.R
index c2b3580c..1a5c7c19 100644
--- a/R/downloading_tools.R
+++ b/R/downloading_tools.R
@@ -3,6 +3,10 @@
 #' The following requirements are needed: p7zip (MacOS), 7zip (windows) Please see:
 #' https://www.epa.gov/waterdata/get-nhdplus-national-hydrography-dataset-plus-data
 #' for more information and metadata about this data.
+#'
+#' Default downloads lower-48 only. See examples for islands. No Alaska data
+#' are available.
+#'
 #' @param outdir The folder path where data should be downloaded and extracted
 #' @param url the location of the online resource
 #' @return the path to the local geodatabase
@@ -10,6 +14,11 @@
 #' @examples
 #' \dontrun{
 #'   download_nhdplusV2("./data/nhd/")
+#'
+#'   download_nhdplusv2(outdir = "./inst/",
+#'       url = paste0("https://s3.amazonaws.com/edap-nhdplus/NHDPlusV21/",
+#'                    "Data/NationalData/NHDPlusV21_NationalData_Seamless",
+#'                    "_Geodatabase_HI_PR_VI_PI_03.7z"))
 #' }
 
 download_nhdplusv2 <- function(outdir,
diff --git a/man/download_nhdplusv2.Rd b/man/download_nhdplusv2.Rd
index 42f2035c..4e373262 100644
--- a/man/download_nhdplusv2.Rd
+++ b/man/download_nhdplusv2.Rd
@@ -23,9 +23,17 @@ This function downloads and decompresses staged seamless NHDPlusV2 data.
 The following requirements are needed: p7zip (MacOS), 7zip (windows) Please see:
 https://www.epa.gov/waterdata/get-nhdplus-national-hydrography-dataset-plus-data
 for more information and metadata about this data.
+
+Default downloads lower-48 only. See examples for islands. No Alaska data
+are available.
 }
 \examples{
 \dontrun{
   download_nhdplusV2("./data/nhd/")
+
+  download_nhdplusV2(outdir = "./data/nhd_islands/",
+      url = paste0("https://s3.amazonaws.com/edap-nhdplus/NHDPlusV21/",
+                   "Data/NationalData/NHDPlusV21_NationalData_Seamless",
+                   "_Geodatabase_HI_PR_VI_PI_03.7z"))
 }
 }