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photosynthesis

Tools for Plant Ecophysiology & Modeling

https://github.com/cdmuir/photosynthesis

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 5 committers (20.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.3%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Tools for Plant Ecophysiology & Modeling

Basic Info
  • Host: GitHub
  • Owner: cdmuir
  • License: other
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 20.1 MB
Statistics
  • Stars: 38
  • Watchers: 4
  • Forks: 8
  • Open Issues: 1
  • Releases: 10
Created over 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog 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

  • Name: Chris Muir
  • Login: cdmuir
  • Kind: user
  • Location: Madison, WI
  • Company: University of Wisconsin

Assistant Professor at the University of Wisconsin - Madison. My lab works on evolution, plant ecophysiology, and biostatistics.

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

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 153
  • Total Committers: 5
  • Avg Commits per committer: 30.6
  • Development Distribution Score (DDS): 0.072
Past Year
  • Commits: 6
  • Committers: 2
  • Avg Commits per committer: 3.0
  • Development Distribution Score (DDS): 0.167
Top Committers
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 (Top 20 + Academic)
dhcp-168-105-223-208.wireless.manoa.hawaii.edu: 1 fedoraproject.org: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 17
  • Total pull requests: 3
  • Average time to close issues: 4 months
  • Average time to close pull requests: 5 days
  • Total issue authors: 14
  • Total pull request authors: 2
  • Average comments per issue: 1.35
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 2
  • Average time to close issues: 22 days
  • Average time to close pull requests: about 7 hours
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • HenrikBengtsson (3)
  • cdmuir (2)
  • Dom3442 (1)
  • AleMorales (1)
  • mollyng (1)
  • samanthastutz (1)
  • jcmtkfmeckm (1)
  • Enchufa2 (1)
  • gonzalodqa (1)
  • Marandola12 (1)
  • ginavong (1)
  • lionel- (1)
  • hoganhaben (1)
Pull Request Authors
  • Enchufa2 (2)
  • cdmuir (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cran 301 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
proxy.golang.org: github.com/cdmuir/photosynthesis
  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 10 months ago
cran.r-project.org: photosynthesis

Tools for Plant Ecophysiology & Modeling

  • Versions: 11
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 301 Last month
  • Docker Downloads: 21,613
Rankings
Docker downloads count: 0.4%
Forks count: 9.7%
Stargazers count: 10.7%
Average: 15.9%
Downloads: 22.4%
Dependent repos count: 24.3%
Dependent packages count: 27.9%
Maintainers (1)
cdmuir@wisc.edu
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0.0 depends
  • ggplot2 >= 3.3.0 depends
  • minpack.lm >= 1.2 depends
  • units >= 0.6.6 depends
  • checkmate >= 2.0.0 imports
  • crayon >= 1.3.4 imports
  • dplyr >= 0.8.5 imports
  • furrr >= 0.1.0 imports
  • glue >= 1.4.0 imports
  • grDevices >= 4.0.0 imports
  • graphics >= 4.0.0 imports
  • gunit >= 1.0.0 imports
  • magrittr >= 1.5.0 imports
  • methods >= 3.5.0 imports
  • nlme >= 3.1 imports
  • pkgnet >= 0.4.1 imports
  • purrr >= 0.3.3 imports
  • rlang >= 0.4.6 imports
  • stats >= 4.0.0 imports
  • stringr >= 1.4.0 imports
  • tealeaves >= 1.0.5 imports
  • tidyselect >= 1.0.0 imports
  • utils >= 4.0.0 imports
  • future * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
  • tidyr * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/rhub.yaml actions
  • r-hub/actions/checkout v1 composite
  • r-hub/actions/platform-info v1 composite
  • r-hub/actions/run-check v1 composite
  • r-hub/actions/setup v1 composite
  • r-hub/actions/setup-deps v1 composite
  • r-hub/actions/setup-r v1 composite