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README.Rmd
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README.Rmd
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---
output: github_document
pagetitle: README
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r echo=FALSE}
knitr::opts_chunk$set(
warning = FALSE,
message = FALSE,
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# photosynthesis <img src="man/figures/logo.png" align="right" height="200" width="200"/>
<!-- badges: start -->
[](https://cran.r-project.org/package=photosynthesis)
[](https://cran.r-project.org/package=photosynthesis)
[](https://github.com/cdmuir/photosynthesis/actions/workflows/R-CMD-check.yaml)
<!-- badges: end -->
## 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.