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https://github.com/traitecoevo/plant
Trait-Driven Models of Ecology and Evolution :evergreen_tree:
https://github.com/traitecoevo/plant
c-plus-plus demography dynamic ecology evolution forests plant-physiology r science-research simulation trait
Last synced: 2 months ago
JSON representation
Trait-Driven Models of Ecology and Evolution :evergreen_tree:
- Host: GitHub
- URL: https://github.com/traitecoevo/plant
- Owner: traitecoevo
- Created: 2013-04-16T00:30:53.000Z (almost 12 years ago)
- Default Branch: develop
- Last Pushed: 2024-07-10T09:03:14.000Z (7 months ago)
- Last Synced: 2024-10-29T22:31:47.888Z (3 months ago)
- Topics: c-plus-plus, demography, dynamic, ecology, evolution, forests, plant-physiology, r, science-research, simulation, trait
- Language: C++
- Homepage: https://traitecoevo.github.io/plant
- Size: 24.5 MB
- Stars: 53
- Watchers: 12
- Forks: 20
- Open Issues: 70
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- open-sustainable-technology - plant - A package for modeling forest trait ecology and evolution. (Biosphere / Plants and Vegetation)
README
# plant: A package for modelling forest trait ecology and evolution
[](https://github.com/traitecoevo/plant/master)
[](https://codecov.io/gh/traitecoevo/plant?branch=master)
The plant package for R is an extensible framework for modelling size- and trait-structured demography, ecology and evolution in simulated forests. At its core, plant is an individual-based model where plant physiology and demography are mediated by traits. Individual plants from multiple species can be grown in isolation, in patches of competing plants or in metapopulations under a disturbance regime. These dynamics can be integrated into metapopulation-level estimates of invasion fitness and vegetation structure. Accessed from R, the core routines in plant are written in C++. The package provides for alternative physiology models and for capturing trade-offs among parameters. A detailed test suite is provided to ensure correct behaviour of the code.
## Citation
Falster DS, FitzJohn RG, Brännström Å, Dieckmann U, Westoby M (2016) plant: A package for modelling forest trait ecology & evolution. *Methods in Ecology and Evolution* 7: 136-146. doi: [10.1111/2041-210X.12525](http://doi.org/10.1111/2041-210X.12525)
## Documentation
An overview of the plant package is given by the above publication. Further background on the default `FF16` growth model is available in Falster *et al* 2011 ([10.1111/j.1365-2745.2010.01735.x](http://doi.org/10.1111/j.1365-2745.2010.01735.x)) and Falster *et al* 2017 ([10.1101/083451](http://doi.org/10.1101/083451)).
`plant` comes with a lot of documentation, available at [https://traitecoevo.github.io/plant/](https://traitecoevo.github.io/plant/). Initial versions for some of the material there was also included as supplementary material with the publication about plant, which can be accessed [here](http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12525/abstract#footer-support-info).
## Package structure
Plant is a complex package, using [c++14](https://en.wikipedia.org/wiki/C%2B%2B14) behind the scenes for speed with [R6 classes](https://cran.r-project.org/web/packages/R6/vignettes/Introduction.html) (via the [Rcpp](https://cran.r-project.org/web/packages/Rcpp/index.html) and [RcppR6](https://github.com/richfitz/RcppR6) packages). In this blog post, Rich FitzJohn and I describe the [key technologies used to build the plant package](https://methodsblog.wordpress.com/2016/02/23/plant/).
If you are interested in developing plant you should read the Developer Notes.
## Installation
**Requirements**
- You must be using R 4.1.0 or newer. At this stage the package is not on CRAN. You're options for installing are described below.
- Installation requires a [c++14](https://en.wikipedia.org/wiki/C%2B%2B14) compatible C compiler (OSX >= 10.10/Yosemite satisfies this, as do standard linux Ubuntu 12.04 and 14.04). On Windows machines you will need to install [Rtools](http://cran.r-project.org/bin/windows/Rtools/). When I tried this in [Rstudio](https://www.rstudio.com/), the program [automagically](https://en.oxforddictionaries.com/definition/automagically) sensed the absence of a compiler and asked if I wanted to install Rtools. Click `Yes`!
**Option 1, using `remotes::install_github`**
The `plant` package can be installed direct from github using the [`remotes`](https://cran.r-project.org/web/packages/remotes/index.html) package:
```r
remotes::install_github("traitecoevo/plant", dependencies=TRUE)
```
To install a specific (older) release, decide for the version number that you want to install in https://github.com/traitecoevo/plant/releases e.g.
```r
remotes::install_github("traitecoevo/[email protected]", dependencies=TRUE)
```
with `"v1.0.0"` replaced by the appropriate version number. Note, the latest version of `plant` resides on the `develop` branch, which is sporadically released. `plant` follows [semantic versioning](https://semver.org/) meaning that major version indicate a potential break in backward compatibility.
**Option 2, building from source**
If familiar with [git](https://git-scm.com/) you might find it easiest to build `plant` directly from the source code. This is most useful if developing new models or strategies, or to contribute new features.
First, clone the `plant` repository
```
git clone https://github.com/traitecoevo/plant
```
Open an R session in the folder, then to install dependencies run
```
devtools::install_deps()
```
Then to compile the project
```
devtools::install()
```
or
```
devtools::load_all()
```
## Usage
Here are some example publications using plant:
- Falster DS, FitzJohn RG, Brännström Å, Dieckmann U, Westoby M (2016) plant: A package for modelling forest trait ecology & evolution. *Methods in Ecology and Evolution* 7: 136-146. DOI: [10.1111/2041-210X.12525](http://doi.org/10.1111/2041-210X.12525) code: [github](https://github.com/traitecoevo/plant_paper)
- Falster DS, Duursma RA, FitzJohn RG (2018) How functional traits influence plant growth and shade tolerance across the life cycle. *Proceedings of the National Academy of Sciences* 115: E6789–E6798. DOI: [10.1073/pnas.1714044115](http://doi.org/10.1073/pnas.1714044115) code: [github](https://github.com/traitecoevo/growth_trajectories)
- Falster DS, Kunstler GK, FitzJohn RG, Westoby M (2021) Emergent shapes of trait-based competition functions from resource-based models: a Gaussian is not normal in plant communities. *The American Naturalist* 198: 256–267. DOI: [10.1086/714868](http://doi.org/10.1086/714868) code: [github](https://github.com/traitecoevo/competition_kernels)