README.md

In USGS-R/streamMetabolizer: Models for Estimating Aquatic Photosynthesis and Respiration

streamMetabolizer: Models for Estimating Aquatic Photosynthesis and Respiration

! In summer or fall 2023, this package will move from
! https://github.com/USGS-R/streamMetabolizer to
! https://github.com/DOI-USGS/streamMetabolizer.
! Please update your links accordingly.

The streamMetabolizer R package uses inverse modeling to estimate aquatic photosynthesis and respiration (collectively, metabolism) from time series data on dissolved oxygen, water temperature, depth, and light. The package assists with data preparation, handles data gaps during modeling, and provides tabular and graphical reports of model outputs. Several time-honored methods are implemented along with many promising new variants that produce more accurate and precise metabolism estimates.

This package has been described, with special focus on the Bayesian model options, by Appling et al. 2018a. An application to 356 streams across the U.S. is described in Appling et al. 2018b.

Appling, A. P., Hall, R. O., Yackulic, C. B., & Arroita, M. (2018a). Overcoming equifinality: Leveraging long time series for stream metabolism estimation. Journal of Geophysical Research: Biogeosciences, 123(2), 624–645. https://doi.org/10.1002/2017JG004140

Appling, A. P., Read, J. S., Winslow, L. A., Arroita, M., Bernhardt, E. S., Griffiths, N. A., Hall, R. O., Harvey, J. W., Heffernan, J. B., Stanley, E. H., Stets, E. G., & Yackulic, C. B. (2018b). The metabolic regimes of 356 rivers in the United States. Scientific Data, 5(1), 180292. https://doi.org/10.1038/sdata.2018.292

To see the recommended citation for this package, please run citation('streamMetabolizer') at the R prompt.

citation('streamMetabolizer')
## 
## To cite streamMetabolizer in publications, please use:
## 
##   Appling, Alison P., Robert O. Hall, Charles B. Yackulic, and Maite
##   Arroita. “Overcoming Equifinality: Leveraging Long Time Series for
##   Stream Metabolism Estimation.” Journal of Geophysical Research:
##   Biogeosciences 123, no. 2 (February 2018): 624–45.
##   https://doi.org/10.1002/2017JG004140.
## 
## A BibTeX entry for LaTeX users is
## 
##   @Article{,
##     author = {Alison P. Appling and Robert O. {Hall Jr.} and Charles B. Yackulic and Maite Arroita},
##     title = {Overcoming Equifinality: Leveraging Long Time Series for Stream Metabolism Estimation},
##     journal = {Journal of Geophysical Research: Biogeosciences},
##     year = {2018},
##     volume = {123},
##     number = {2},
##     doi = {10.1002/2017JG004140},
##     url = {https://github.com/USGS-R/streamMetabolizer},
##   }

Installation

To install the streamMetabolizer package, use the remotes package (running install.packages('remotes') first if needed). To use remotes::install_github() it is convenient to set a GitHub Personal Access Token (PAT). There are several methods for setting your PATs within R; the simplest is to call `Sys.setenv(GITHUB_PAT=“yyyy”), replacing yyyy with the PAT you established on the GitHub website.

You may first need to install the unitted dependency:

remotes::install_github('appling/unitted')

You can then install the most cutting edge version of streamMetabolizer with this command:

remotes::install_github(
  "USGS-R/streamMetabolizer", # soon to be "DOI-USGS/streamMetabolizer"
  build_vignettes = TRUE)

Software dependencies for Bayesian models

The major dependency for Bayesian models is the rstan package, and installation of that package is rarely as simple as a call to install.packages(). Start at the rstan wiki page for the most up-to-date installation instructions, which differ by operating system.

Getting started

After installing and loading streamMetabolizer, run vignette() in R to see tutorials on getting started and customizing your metabolism models.

vignette(package='streamMetabolizer')
## displays a list of available vignettes

vignette('get_started', package='streamMetabolizer')
## displays an html or pdf rendering of the 'get_started' vignette

You can also view pre-built html versions of these vignettes in the “inst/doc” folder in the source code, e.g., inst/doc/get_started.html, which you can download and then open in a browser.

Development and Maintenance Status

streamMetabolizer is a USGS Archive Research Package:

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/streamMetabolizer/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

Development History

streamMetabolizer was developed 2015-2018 with support from the USGS Powell Center (through a working group on Continental Patterns of Stream Metabolism), 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()

## ─ Session info ───────────────────────────────────────────────────────────────────────────────────
##  setting  value
##  version  R version 4.2.3 (2023-03-15)
##  os       macOS Ventura 13.4.1
##  system   x86_64, darwin17.0
##  ui       RStudio
##  language (EN)
##  collate  en_US.UTF-8
##  ctype    en_US.UTF-8
##  tz       America/New_York
##  date     2023-07-02
##  rstudio  2023.06.0+421 Mountain Hydrangea (desktop)
##  pandoc   3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
## 
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────
##  package           * version  date (UTC) lib source
##  cli                 3.6.1    2023-03-23 [1] CRAN (R 4.2.0)
##  deSolve             1.35     2023-03-12 [1] CRAN (R 4.2.0)
##  digest              0.6.32   2023-06-26 [1] CRAN (R 4.2.0)
##  dplyr               1.1.2    2023-04-20 [1] CRAN (R 4.2.0)
##  evaluate            0.21     2023-05-05 [1] CRAN (R 4.2.0)
##  fansi               1.0.4    2023-01-22 [1] CRAN (R 4.2.0)
##  fastmap             1.1.1    2023-02-24 [1] CRAN (R 4.2.0)
##  generics            0.1.3    2022-07-05 [1] CRAN (R 4.2.0)
##  glue                1.6.2    2022-02-24 [1] CRAN (R 4.2.0)
##  htmltools           0.5.5    2023-03-23 [1] CRAN (R 4.2.0)
##  knitr               1.43     2023-05-25 [1] CRAN (R 4.2.0)
##  LakeMetabolizer     1.5.5    2022-11-15 [1] CRAN (R 4.2.0)
##  lazyeval            0.2.2    2019-03-15 [1] CRAN (R 4.2.0)
##  lifecycle           1.0.3    2022-10-07 [1] CRAN (R 4.2.0)
##  lubridate           1.9.2    2023-02-10 [1] CRAN (R 4.2.0)
##  magrittr            2.0.3    2022-03-30 [1] CRAN (R 4.2.0)
##  pillar              1.9.0    2023-03-22 [1] CRAN (R 4.2.0)
##  pkgconfig           2.0.3    2019-09-22 [1] CRAN (R 4.2.0)
##  plyr                1.8.8    2022-11-11 [1] CRAN (R 4.2.0)
##  purrr               1.0.1    2023-01-10 [1] CRAN (R 4.2.0)
##  R6                  2.5.1    2021-08-19 [1] CRAN (R 4.2.0)
##  Rcpp                1.0.10   2023-01-22 [1] CRAN (R 4.2.0)
##  rLakeAnalyzer       1.11.4.1 2019-06-09 [1] CRAN (R 4.2.0)
##  rlang               1.1.1    2023-04-28 [1] CRAN (R 4.2.0)
##  rmarkdown           2.22     2023-06-01 [1] CRAN (R 4.2.0)
##  rstudioapi          0.14     2022-08-22 [1] CRAN (R 4.2.0)
##  sessioninfo         1.2.2    2021-12-06 [1] CRAN (R 4.2.0)
##  streamMetabolizer * 0.12.1   2023-07-02 [1] local
##  tibble              3.2.1    2023-03-20 [1] CRAN (R 4.2.0)
##  tidyr               1.3.0    2023-01-24 [1] CRAN (R 4.2.0)
##  tidyselect          1.2.0    2022-10-10 [1] CRAN (R 4.2.0)
##  timechange          0.2.0    2023-01-11 [1] CRAN (R 4.2.0)
##  unitted             0.2.9    2023-06-05 [1] Github (appling/unitted@d1f1172)
##  utf8                1.2.3    2023-01-31 [1] CRAN (R 4.2.0)
##  vctrs               0.6.3    2023-06-14 [1] CRAN (R 4.2.0)
##  xfun                0.39     2023-04-20 [1] CRAN (R 4.2.0)
##  yaml                2.3.7    2023-01-23 [1] CRAN (R 4.2.0)
## 
##  [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library

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.

USGS-R/streamMetabolizer documentation built on Aug. 15, 2023, 7:50 a.m.