nhdplusTools

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nhdplusTools: Tools for Accessing and Working with the NHDPlus and other US hydrographic data. 

  Blodgett, D., Johnson, J.M., 2022, nhdplusTools: Tools for
  Accessing and Working with the NHDPlus,
  https://doi.org/10.5066/P97AS8JD

Installation: 

install.packages("nhdplusTools")

For the latest development:

install.packages("remotes")
remotes::install_github("DOI-USGS/nhdplusTools")

Resources

For data discovery and access in a U.S. context, start with the Getting Started page.

Detailed documentation of all the package functions can be found at the Reference page.

Data:

nhdplusTools, is designed to provide easy access to data associated with the U.S. National Hydrography Dataset. Many functions provided in nhdplusTools are thin wrappers around functions that have been migrated to hydroloom.

Package Vision

The nhdplusTools package is intended to provide a reusable set of tools to subset, relate data to, and generate network attributes for U.S. NHDPlus data.

General, globally applicable functionality has been moved to hydroloom

nhdplusTools implements a data model consistent with both the NHDPlus dataset and the HY_Features data model. The package aims to provide a set of tools that can be used to build workflows using NHDPlus data.

This vision is intended as a guide to contributors – conveying what kinds of contributions are of interest to the package’s long term vision. It is a reflection of the current thinking and is open to discussion and modification.

Functional Vision

The following describe a vision for the functionality that should be included in the package in the long run.

Subsetting

The NHDPlus is a very large dataset both spatially and in terms of the number of attributes it contains. Subsetting utilities will provide network location discovery, network navigation, and data export utilities to generate spatial and attribute subsets of the NHDPlus dataset.

Indexing

One of the most important roles of the NHDPlus is as a connecting network for ancillary data and models. The first step in any workflow that uses the network like this is indexing relevant data to the network. A number of methods for indexing exist, they can be broken into two main categories: linear referencing and catchment indexing. Both operate on features represented by points, lines, and polygons. nhdplusTools should eventually support both linear and catchment indexing.

Data Model

Given that nhdplusTools is focused on working with NHDPlus data, the NHDPlus data model will largely govern the data model the package is designed to work with. That said, much of the package functionality also uses concepts from the HY_Features standard.

Note: The HY_Features standard is based on the notion that a “catchment” is a holistic feature that can be “realized” (some might say modeled) in a number of ways. In other words, a catchment can only be characterized fully through a collection of different conceptual representations. In NHDPlus, the “catchment” feature is the polygon feature that describes the drainage divide around the hydrologic unit that contributes surface flow to a given NHD flowline. While this may seem like a significant difference, in reality, the NHDPlus COMID identifier lends itself very well to the HY_Features catchment concept. The COMID is used as an identifier for the catchment polygon, the flowline that connects the catchment inlet and outlet, and value added attributes that describe characteristics of the catchment’s interior. In this way, the COMID identifier is actually an identifier for a collection of data that together fully describe an NHDPlus catchment. See the NHDPlus mapping to HY_Features in the HY_Features specification.

Below is a description of the scope of data used by the nhdplusTools package. While other data and attributes may come into scope, it should only be done as a naive pass-through, as in data subsetting, or with considerable deliberation.

Flowlines and Waterbodies

Flowline geometry is a mix of 1-d streams and 1-d “artificial paths”. In order to complete the set of features meant to represent water, we need to include waterbody polygons.

Catchment Polygons

Catchment polygons are the result of a complete elevation derived hydrography process with hydro-enforcement applied with both Watershed Boundary Dataset Hydrologic Units and NHD reaches.

Network Attributes

The NHDPlus includes numerous attributes that are built using the network and allow a wide array of capabilities that would require excessive iteration or sophisticated and complex graph-oriented data structures and algorithms.

Architecture

The NHDPlus is a very large dataset. The architecture of this package as it relates to handling data and what dependencies are used will be very important.

Web vs Local Data

nhdplusTools offers a mix of web service and local data functionality. Web services have generally been avoided for large processes. However, applications that would require loading significant amounts of data to perform something that can be accomplished with a web service very quickly are supported. 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.

https://github.com/mbtyers/riverdist
https://github.com/jsta/nhdR
https://github.com/lawinslow/hydrolinks
https://github.com/mikejohnson51/HydroData
https://github.com/ropensci/FedData
https://github.com/hyriver/pygeohydro … 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:

devtools::build()

Check notes:

In addition to typical R package checking, a Dockerfile is included in this repository. Once built, it can be run with the following command.

docker build -t nhdplustools_test .

docker run --rm -it -v $PWD:/src nhdplustools_test /bin/bash -c "cp -r /src/* /check/ && cp /src/.Rbuildignore /check/ && cd /check && Rscript -e 'devtools::build()' && R CMD check --as-cran ../nhdplusTools_*"

Release procedure:

  • ensure all checks pass and code coverage is adequate.
  • ensure news has been updated
  • convert disclaimer to released form
  • update version in inst/CITATION file
  • update version in code.json file
  • Build source package and upload to CRAN
  • Once a new version has been accepted by cran,
  • ensure pkgdown is up to date
  • commit, push, and PR/MR changes
  • create release page and tag
  • attach cran tar.gz to release page
  • update DOI to point to release page
  • switch README disclaimer back to “dev” mode.
  • Update version in Description.
  • push an PR/MR changes.

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.
  2. Code style should attempt to follow the tidyverse style guide.
  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.
  5. Make sure you use roxygen and run Check before contributing. More on this front as the package matures.

Other notes: - consider running lintr prior to contributing. - consider running goodpractice::gp() on the package before contributing. - consider running devtools::spell_check() if you wrote documentation. - this package uses pkgdown. Running pkgdown::build_site() will refresh it.

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.

From: https://www.usgs.gov/office-of-science-quality-and-integrity/fundamental-science-practices#5

This software is in the public domain because it contains materials that originally came from the U.S. Geological Survey, an agency of the United States Department of Interior. For more information, see the official USGS copyright policy

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.”

CC0