plant
A package for modeling forest trait ecology and evolution.
https://github.com/traitecoevo/plant
Category: Biosphere
Sub Category: Plants and Vegetation
Keywords
c-plus-plus demography dynamic ecology evolution forests plant-physiology r science-research simulation trait
Keywords from Contributors
geo
Last synced: about 4 hours ago
JSON representation
Repository metadata
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 (about 12 years ago)
- Default Branch: develop
- Last Pushed: 2025-03-09T10:54:04.000Z (about 2 months ago)
- Last Synced: 2025-04-17T22:59:18.924Z (10 days 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: 11
- Forks: 20
- Open Issues: 70
- Releases: 7
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
README.md
plant: A package for modelling forest trait ecology and evolution
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
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) and Falster et al 2017 (10.1101/083451).
plant comes with a lot of documentation, available at 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.
Package structure
Plant is a complex package, using c++14 behind the scenes for speed with R6 classes (via the Rcpp and RcppR6 packages). In this blog post, Rich FitzJohn and I describe the key technologies used to build the plant package.
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 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. When I tried this in Rstudio, the program 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 package:
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.
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 meaning that major version indicate a potential break in backward compatibility.
Option 2, building from source
If familiar with git 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 code: github
- 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 code: github
- 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 code: github
Owner metadata
- Name: Trait Ecology and Evolution
- Login: traitecoevo
- Email:
- Kind: organization
- Description:
- Website:
- Location: Australia
- Twitter:
- Company:
- Icon url: https://avatars.githubusercontent.com/u/11747619?v=4
- Repositories: 64
- Last ynced at: 2023-06-03T21:10:14.705Z
- Profile URL: https://github.com/traitecoevo
GitHub Events
Total
- Push event: 1
Last Year
- Push event: 1
Committers metadata
Last synced: 6 days ago
Total Commits: 1,508
Total Committers: 9
Avg Commits per committer: 167.556
Development Distribution Score (DDS): 0.275
Commits in past year: 13
Committers in past year: 2
Avg Commits per committer in past year: 6.5
Development Distribution Score (DDS) in past year: 0.077
| Name | Commits | |
|---|---|---|
| Rich FitzJohn | r****n@g****m | 1093 |
| Daniel Falster | d****r@m****u | 279 |
| Rafael Schouten | r****n@g****m | 57 |
| johnWilshire | j****e@g****m | 34 |
| Andrew O'Reilly-Nugent | a****t@g****m | 28 |
| Mitchell Henry | m****4@g****m | 9 |
| Felix Lawrence | f****e@n****u | 4 |
| Becca-90 | 8****0 | 2 |
| itowers1 | 3****1 | 2 |
Committer domains:
- nicta.com.au: 1
- mq.edu.au: 1
Issue and Pull Request metadata
Last synced: 1 day ago
Total issues: 341
Total pull requests: 96
Average time to close issues: about 1 year
Average time to close pull requests: 26 days
Total issue authors: 14
Total pull request authors: 8
Average comments per issue: 2.02
Average comments per pull request: 3.23
Merged pull request: 71
Bot issues: 0
Bot pull requests: 0
Past year issues: 40
Past year pull requests: 8
Past year average time to close issues: 6 days
Past year average time to close pull requests: 4 days
Past year issue authors: 4
Past year pull request authors: 2
Past year average comments per issue: 0.15
Past year average comments per pull request: 0.5
Past year merged pull request: 7
Past year bot issues: 0
Past year bot pull requests: 0
Top Issue Authors
- dfalster (135)
- richfitz (134)
- aornugent (25)
- rafaqz (24)
- itowers1 (10)
- foxeswithdata (3)
- kunstler (2)
- Becca-90 (2)
- fjrrobinson (1)
- johnWilshire (1)
- eebutler (1)
- hrlai (1)
- pzylstra (1)
- hol430 (1)
Top Pull Request Authors
- aornugent (36)
- dfalster (31)
- rafaqz (13)
- devmitch (9)
- johnWilshire (2)
- Becca-90 (2)
- itowers1 (2)
- richfitz (1)
Top Issue Labels
- documentation (27)
- epic (18)
- wontfix (13)
- bug (10)
- enhancement (9)
- performance (9)
- fixed_on_development (9)
- testing (8)
- low priority (7)
- easy (5)
- blocked (4)
- task (4)
- question (3)
- ready (3)
- on hold (1)
- duplicate (1)
- help (1)
- planning (1)
Top Pull Request Labels
- epic (3)
Dependencies
- actions/checkout v3 composite
- r-lib/actions/check-r-package v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
- actions/checkout v3 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
- R >= 3.3.0 depends
- BB * imports
- R6 * imports
- Rcpp * imports
- crayon * imports
- dplyr * imports
- loggr * imports
- magrittr * imports
- nleqslv * imports
- purrr * imports
- rlang * imports
- tibble * imports
- tidyr * imports
- RcppR6 >= 0.2.3 suggests
- bench * suggests
- deSolve * suggests
- ggplot2 * suggests
- ggridges * suggests
- kableExtra * suggests
- knitr * suggests
- markdown * suggests
- numDeriv * suggests
- parallel * suggests
- patchwork * suggests
- rmarkdown * suggests
- testthat * suggests
Score: 7.009408932708636