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output: github_document
pagetitle: README
---

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# photosynthesis <img src="man/figures/logo.png" align="right" height="200" width="200"/>

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[![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)
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## 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.
