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loadflex: Models and Tools for Watershed Flux Estimates

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.

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 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.

citation('loadflex')
## 
## To cite package 'loadflex' in publications use:
## 
##   Appling, A. P., M. C. Leon, and W. H. McDowell. 2015. Reducing bias
##   and quantifying uncertainty in watershed flux estimates: the R
##   package loadflex. Ecosphere 6(12):269.
##   https://doi.org/10.1890/ES14-00517.1
## 
## A BibTeX entry for LaTeX users is
## 
##   @Article{,
##     title = {Reducing bias and quantifying uncertainty in watershed flux estimates: the R package loadflex},
##     author = {Alison P. Appling and Miguel C. Leon and William H. McDowell},
##     year = {2015},
##     journal = {Ecosphere},
##     volume = {6},
##     number = {12},
##     pages = {art269},
##     doi = {10.1890/ES14-00517.1},
##     url = {http://www.esajournals.org/doi/full/10.1890/ES14-00517.1},
##   }

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). Similarly, to use remotes::install_github() it is convenient to set a GitHub PAT. There are several methods 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/.

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: USGS Status

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.

Contributing

We want to encourage a warm, welcoming, and safe environment for contributing to this project. See CODE_OF_CONDUCT.md for more information.

For technical details on how to contribute, see CONTRIBUTING.md

Contributing

We want to encourage a warm, welcoming, and safe environment for contributing to this project. See CODE_OF_CONDUCT.md for more information.

For technical details on how to contribute, see CONTRIBUTING.md

Development History

loadflex was created 2013-2015 by Alison Appling and Miguel Leon with the support of Bill McDowell and the McDowell lab 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, Lindsay Platt, and David Watkins 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.

> sessioninfo::session_info()

## (TBD)

Disclaimer

This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The software has not received final approval by the U.S. Geological Survey (USGS). No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. The software 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 software.