photosynthesis

An R package with modeling tools for C3 photosynthesis, as well as analytical tools for curve-fitting plant ecophysiology responses.
https://github.com/cdmuir/photosynthesis

Category: Biosphere
Sub Category: Plants and Vegetation

Last synced: about 10 hours ago
JSON representation

Repository metadata

Tools for Plant Ecophysiology & Modeling

• Host: GitHub
• URL: https://github.com/cdmuir/photosynthesis
• Owner: cdmuir
• License: other
• Created: 2018-11-11T23:46:12.000Z (about 7 years ago)
• Default Branch: main
• Last Pushed: 2025-03-07T18:39:05.000Z (10 months ago)
• Last Synced: 2025-12-08T08:46:21.490Z (19 days ago)
• Language: R
• Homepage:
• Size: 20.1 MB
• Stars: 39
• Watchers: 4
• Forks: 8
• Open Issues: 1
• Releases: 10
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • License: LICENSE

README.Rmd

          ---
output: github_document
pagetitle: README
---



```{r echo=FALSE}
knitr::opts_chunk$set(
  warning = FALSE,
  message = FALSE,
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```
# photosynthesis 


[![CRAN status](https://www.r-pkg.org/badges/version/photosynthesis)](https://cran.r-project.org/package=photosynthesis)
[![](https://cranlogs.r-pkg.org/badges/photosynthesis)](https://cran.r-project.org/package=photosynthesis)
[![R-CMD-check](https://github.com/cdmuir/photosynthesis/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/cdmuir/photosynthesis/actions/workflows/R-CMD-check.yaml)


## Model C3 Photosynthesis

## Description

**photosynthesis** is an R package with modeling tools for C3 photosynthesis, as well as analytical tools for curve-fitting plant ecophysiology responses. It uses the R package [**units**](https://CRAN.R-project.org/package=units) to ensure that parameters are properly specified and transformed before calculations. 

## Get **photosynthesis**

From CRAN

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

or from GitHub

```r
install.packages("remotes")
remotes::install_github("cdmuir/photosynthesis")
```

And load `photosynthesis`

```r
library("photosynthesis")
```

## Vignettes

See the following vignettes for examples of what **photosynthesis** can do:

* [Introduction to the photosynthesis package][photosynthesis-introduction]
* [Modeling C3 Photosynthesis: recommendations for common scenarios][modeling-recommendations]
* [Fitting light response curves][light-response]
* [Fitting CO2 response curves][co2-response]
* [Fitting temperature response curves][temperature-response]
* [Fitting stomatal conductance models][stomatal-conductance]
* [Fitting light respiration][light-respiration]
* [Fitting mesophyll conductance][mesophyll-conductance]
* [Fitting pressure-volume curves][pressure-volume]
* [Fitting hydraulic vulnerability curves][hydraulic-vulnerability]
* [Sensitivity Analysis][sensitivity-analysis]

[photosynthesis-introduction]: https://cdmuir.github.io/photosynthesis/articles/photosynthesis-introduction.html
[modeling-recommendations]: https://cdmuir.github.io/photosynthesis/articles/modeling-recommendations.html
[light-response]: https://cdmuir.github.io/photosynthesis/articles/light-response.html
[co2-response]: https://cdmuir.github.io/photosynthesis/articles/co2-response.html
[temperature-response]: https://cdmuir.github.io/photosynthesis/articles/temperature-response.html
[stomatal-conductance]: https://cdmuir.github.io/photosynthesis/articles/stomatal-conductance.html
[light-respiration]: https://cdmuir.github.io/photosynthesis/articles/light-respiration.html
[mesophyll-conductance]: https://cdmuir.github.io/photosynthesis/articles/mesophyll-conductance.html
[pressure-volume]: https://cdmuir.github.io/photosynthesis/articles/pressure-volume.html
[hydraulic-vulnerability]: https://cdmuir.github.io/photosynthesis/articles/hydraulic-vulnerability.html
[sensitivity-analysis]: https://cdmuir.github.io/photosynthesis/articles/sensitivity-analysis.html

## Contributors

* [Joseph Stinziano](https://github.com/jstinzi)
* [Chris Muir](https://github.com/cdmuir)
* Cassaundra Roback
* Demi Sargent
* Bridget Murphy
* Patrick Hudson

## Comments and contributions

We welcome comments, criticisms, and especially contributions!
GitHub issues are the preferred way to report bugs, ask questions, or request new features.
You can submit issues here:

https://github.com/cdmuir/photosynthesis/issues

## Meta

* Please [report any issues or bugs](https://github.com/cdmuir/photosynthesis/issues).
* License: MIT
* Get citation information for **photosynthesis** in R doing `citation(package = 'photosynthesis')`
* Please note that this project is released with a [Contributor Code of Conduct](https://github.com/cdmuir/photosynthesis/blob/master/CONDUCT.md). By participating in this project you agree to abide by its terms.

        

---

Owner metadata

• Name: Chris Muir
• Login: cdmuir
• Email:
• Kind: user
• Description: Assistant Professor at the University of Wisconsin - Madison. My lab works on evolution, plant ecophysiology, and biostatistics.
• Website: cdmuir.netlify.app
• Location: Madison, WI
• Twitter:
• Company: University of Wisconsin
• Icon url: https://avatars.githubusercontent.com/u/5565889?u=2d942d82eb624045525f5f0c16f818ffbbfba3a3&v=4
• Repositories: 26
• Last ynced at: 2025-10-14T21:12:29.263Z
• Profile URL: https://github.com/cdmuir

---

GitHub Events

Total

• Issues event: 2
• Watch event: 5
• Push event: 6
• Pull request review event: 1
• Pull request event: 2
• Fork event: 2

Last Year

• Issues event: 2
• Watch event: 3
• Push event: 1
• Pull request review event: 1
• Pull request event: 2
• Fork event: 2

---

Committers metadata

Last synced: 2 days ago

Name	Email	Commits
cdmuir	c****r@g****m	142
Joseph Ronald Stinziano	j****o@g****m	8
Iñaki Úcar	i****r@f****g	1
Muir Lab	m****b@M****l	1
Chris Muir	c****r@d****u	1

Committer domains:

• dhcp-168-105-223-208.wireless.manoa.hawaii.edu: 1
• fedoraproject.org: 1

---

Issue and Pull Request metadata

Last synced: 4 months ago

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/cdmuir/photosynthesis

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Package metadata

• Total packages: 2
• Total downloads:
  • cran: 1,281 last-month
• Total docker downloads: 21,613
• Total dependent packages: 1 (may contain duplicates)
• Total dependent repositories: 1 (may contain duplicates)
• Total versions: 21
• Total maintainers: 1

---

Dependencies

Score: 15.337122216031794