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# nhdplusTools <img src="man/figures/logo.png" align="right" alt="" width="120" />

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

### Recommended Citation:

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

### Installation:

``` r
install.packages("nhdplusTools")
```

For the latest development:

``` r
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**](https://doi-usgs.github.io/nhdplusTools/articles/nhdplusTools.html).

Detailed documentation of all the package functions can be found at the
[**Reference
page**](https://doi-usgs.github.io/nhdplusTools/reference/).

### 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`](https://github.com/DOI-USGS/hydroloom)

`nhdplusTools` implements a data model consistent with both the
[NHDPlus](https://www.epa.gov/waterdata/nhdplus-national-hydrography-dataset-plus)
dataset and the
[HY_Features](http://opengeospatial.github.io/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.](https://docs.ogc.org/is/14-111r6/14-111r6.html#annexD_1)

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](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://www.usgs.gov/national-hydrography/nhdplus-high-resolution)
is also supported.

### Related similar packages:

<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:

``` r
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](https://code.usgs.gov/water/sbtools/-/blob/v1.1.14/README.md#L113)
- 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.](https://code.usgs.gov/water/sbtools#disclaimer)
- 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`](https://testthat.r-lib.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.

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](https://www.usgs.gov/information-policies-and-instructions/copyrights-and-credits "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](https://i.creativecommons.org/p/zero/1.0/88x31.png)](https://creativecommons.org/publicdomain/zero/1.0/)
