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README.Rmd
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---
title: "README"
output:
md_document:
variant: markdown_github
editor_options:
chunk_output_type: console
---
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "##",
fig.path = "man/figures/README-"
)
```
# loadflex: Models and Tools for Watershed Flux Estimates
<span style="color: red;">
In summer or fall 2023, this package will move from
https://github.com/USGS-R/loadflex to
https://github.com/DOI-USGS/loadflex
Please update your links accordingly.
</span>
The `loadflex` R package implements several of the most common methods for modeling and
predicting watershed solute fluxes and concentrations, including interpolation
and regression models, period-weighted averaging, and the composite method.
`loadflex` integrates seamlessly with the USGS's
[rloadest](https://code.usgs.gov/water/analysis-tools/rloadest) package and with native R
regression models. It offers a uniform interface for any model type, with which
you can quickly fit models, generate predictions, and aggregate to monthly or
annual values.
This package has been described in Appling et al. (2015):
> Appling, A. P., Leon, M. C., & McDowell, W. H. (2015). Reducing bias and quantifying uncertainty in watershed flux estimates: The R package `loadflex`. Ecosphere, 6(12), art269. https://doi.org/10.1890/ES14-00517.1
To see the recommended citation for this package, please run `citation('loadflex')` at the R prompt.
```{r eval=TRUE}
citation('loadflex')
```
## Installation
To install the `loadflex` package, use the `remotes` package as follows (running `install.packages('remotes')` first if needed). To use `remotes::install_gitlab()` it is convenient to set a [GitLab Personal Access Token (PAT)](https://docs.gitlab.com/ee/user/profile/personal_access_tokens.html). Similarly, to use `remotes::install_github()` it is convenient to set a [GitHub PAT](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens). There are [several methods](https://usethis.r-lib.org/articles/git-credentials.html) for setting your PATs within R; the simplest is to call `Sys.setenv(GITLAB_PAT="xxxx", GITHUB_PAT="yyyy"),
replacing xxxx and yyyy with the PATs you established on the GitLab and GitHub websites.
You will also need a compiler to install `smwrStats`, `smwrQW`, and `rloadest` -- for Windows, see https://cran.r-project.org/bin/windows/Rtools/rtools43/rtools.html. For Mac, see https://mac.r-project.org/tools/.
```{r eval=FALSE}
library(remotes)
remotes::install_gitlab("water/analysis-tools/smwrData", host = "code.usgs.gov")
remotes::install_gitlab("water/analysis-tools/smwrBase", host = "code.usgs.gov")
remotes::install_gitlab("water/analysis-tools/smwrGraphs", host = "code.usgs.gov")
remotes::install_gitlab("water/analysis-tools/smwrStats", host = "code.usgs.gov") # needs compilation
remotes::install_gitlab("water/analysis-tools/smwrQW", host = "code.usgs.gov") # needs compilation
remotes::install_gitlab("water/analysis-tools/rloadest", host = "code.usgs.gov") # needs compilation
remotes::install_github("appling/unitted")
remotes::install_github("DOI-USGS/EGRET")
remotes::install_github("USGS-R/loadflex") # soon to be "DOI-USGS/loadflex"
```
Also please see the installation FAQ on the wiki
(https://github.com/USGS-R/loadflex/wiki/Installation-FAQ) if you run into trouble.
## Getting Started
To get started, load the package with `library(loadflex)` and type `?loadflex` or `vignette('intro_to_loadflex')`.
## Development and Maintenance Status
`loadflex` is a USGS Archive Research Package:
[](https://owi.usgs.gov/R/packages.html#research)
Project funding has ended and our maintenance time is limited,
but we do attempt to provide bug fixes and lightweight support
as we are able. Submit questions or suggestions to
[https://github.com/USGS-R/loadflex/issues](https://github.com/USGS-R/loadflex/issues).
## Contributing
We want to encourage a warm, welcoming, and safe environment for contributing to this project. See [CODE_OF_CONDUCT.md](https://github.com/USGS-R/streamMetabolizer/blob/main/CODE_OF_CONDUCT.md) for more information.
For technical details on how to contribute, see [CONTRIBUTING.md](https://github.com/USGS-R/streamMetabolizer/blob/main/CONTRIBUTING.md)
## Contributing
We want to encourage a warm, welcoming, and safe environment for contributing to this project. See [CODE_OF_CONDUCT.md](https://github.com/USGS-R/loadflex/blob/main/CODE_OF_CONDUCT.md) for more information.
For technical details on how to contribute, see [CONTRIBUTING.md](https://github.com/USGS-R/loadflex/blob/main/CONTRIBUTING.md)
## Development History
`loadflex` was created 2013-2015 by [Alison Appling](https://github.com/aappling-usgs)
and [Miguel Leon](https://github.com/miguelcleon) with the support of [Bill
McDowell](https://colsa.unh.edu/faculty/mcdowell) and the [McDowell
lab](http://wrrc.unh.edu/mcdowell-lab-current) at the University of New
Hampshire. Funding for the project was provided by the National
Science Foundation, USDA National Institute of Food and Agriculture, and the NH
Agricultural Experiment Station. Funding for the example dataset from the
Lamprey River was provied by the EPA, NH Water Resources Research Center, NH
Agricultural Experiment Station, NH Sea Grant, USGS, and NSF.
Additional development and maintenance in 2016-2017 was done by
[Alison Appling](https://github.com/aappling-usgs),
[Lindsay Platt](https://github.com/lindsayplatt), and
[David Watkins](https://github.com/wdwatkins) with support from the USGS National Water Quality Program and the USGS Office of Water Information.
## Model Archive
The following version of R and package dependencies were used most recently to pass the embedded tests within this package. There is no guarantee of reproducible results using future versions of R or updated versions of package dependencies; however, we aim to test and update future modeling environments.
<!-- Run and paste manually after edits, only when tests pass locally -->
```{r eval=FALSE}
> sessioninfo::session_info()
## (TBD)
```
```{r disclaimer, child="DISCLAIMER.md", eval=TRUE}
```