https://github.com/sustentarea/logonia
🌿 Plant Growth Response Model in NetLogo
https://github.com/sustentarea/logonia
agent-based-modeling climate-change climate-simulations complex-systems complexity-science computer-simulations environmental-sciences historical-climate-data historical-data levelspace logoclim models netlogo parallel-execution plant-growth population-dynamics simulations spatial-analysis time-series worldclim
Last synced: 5 months ago
JSON representation
🌿 Plant Growth Response Model in NetLogo
- Host: GitHub
- URL: https://github.com/sustentarea/logonia
- Owner: sustentarea
- License: gpl-3.0
- Created: 2025-09-06T23:02:34.000Z (6 months ago)
- Default Branch: main
- Last Pushed: 2025-09-29T22:43:58.000Z (5 months ago)
- Last Synced: 2025-09-30T20:59:05.955Z (5 months ago)
- Topics: agent-based-modeling, climate-change, climate-simulations, complex-systems, complexity-science, computer-simulations, environmental-sciences, historical-climate-data, historical-data, levelspace, logoclim, models, netlogo, parallel-execution, plant-growth, population-dynamics, simulations, spatial-analysis, time-series, worldclim
- Language: R
- Homepage:
- Size: 41.3 MB
- Stars: 1
- Watchers: 0
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE.md
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION.cff
- Security: SECURITY.md
- Codemeta: codemeta.json
Awesome Lists containing this project
README
# LogĂ´nia 
[](https://www.repostatus.org/#active)
[](https://www.comses.net/codebases/4f2be13a-3957-4537-bf64-3fad96ba271f/)
[](https://doi.org/10.17605/OSF.IO/TPY7S)
[](https://fairsoftwarechecklist.net/v0.2?f=31&a=30113&i=32300&r=123)
[](https://fair-software.eu)
[](https://www.gnu.org/licenses/gpl-3.0)
## Overview
`LogĂ´nia` is a [NetLogo](https://www.netlogo.org) model that simulates
the growth response of a fictional plant, logĂ´nia, under different
climatic conditions. The model uses climate data from [WorldClim
2.1](https://worldclim.org/) and demonstrates how to integrate the
[`LogoClim`](https://github.com/sustentarea/logoclim) model through the
[`LevelSpace`](https://ccl.northwestern.edu/netlogo/docs/ls.html)
extension.
> If you find this project useful, please consider giving it a star!
> [](https://github.com/sustentarea/logonia/)
## How It Works
`LogĂ´nia` runs on a grid of patches, where each patch represents a piece
of soil that can host a plant. Patches correspond to a specific
geographic area and store historical climate data.
Each simulation step represents *one month*. Over time, plants *grow*,
*reproduce*, and *age*. These processes are controlled by sliders on the
model’s interface. Climate conditions directly influence growth
probability, adding realism and complexity to the simulation.
### Climate Data
The model uses *Historical Monthly Weather Data* from [WorldClim
2.1](https://worldclim.org/) ([Fick & Hijmans,
2017](https://doi.org/10.1002/joc.5086)) for a region of the **Brazilian
Amazon Forest**.
This dataset provides 12 monthly values per year for 1951–2024, based on
[downscaled](https://worldclim.org/data/downscaling.html) data from
[CRU-TS-4.09](https://crudata.uea.ac.uk/cru/data/hrg/cru_ts_4.09/),
developed by the [Climatic Research
Unit](https://www.uea.ac.uk/groups-and-centres/climatic-research-unit)
at the [University of East Anglia](https://www.uea.ac.uk/) ([Harris et
al., 2020](https://doi.org/10.1038/s41597-020-0453-3)). The variables
are: *Average Minimum Temperature (°C)* (**A**), *Average Maximum
Temperature (°C)* (**B**), and *Total Precipitation (mm)* (**C**).
The dataset can be reproduced using [Quarto](https://quarto.org/)
notebooks in the `qmd` folder of the model repository, adapted from
those in the [`LogoClim`](https://github.com/sustentarea/logoclim)
model.
### Energy and Growth Probability
Growth probability is determined by a [logistic
regression](https://en.wikipedia.org/wiki/Logistic_regression) model
that incorporates patch-level climate variables. The probability follows
the equation below:
$$
p(\text{tmin, tmax, prec}) = \cfrac{1}{1 + e^{- (\beta_{0} + \beta_{\text{tmin}} \text{tmin} + \beta_{\text{tmax}} \text{tmax} + \beta_{\text{prec}} \text{prec})}}
$$
A logĂ´nia gains or loses energy at each step according to the following
rules:
- If a random number between `0` and `1` is *less than* or *equal to*
the growth probability for the current patch, the plant gains the
number of energy points defined by the `energy-gain` slider.
- If the probability is *below* `0.25` and does not meet the above
condition, the plant loses `1` energy point.
- Otherwise, its energy remains unchanged.
If a plant gets to `0` points of energy it dies.
### Growth Phases
A logĂ´nia plant develops through three phases: *seedling*, *juvenile*,
and *adult*. Each has distinct shapes and energy thresholds.
As a *seedling*, the logĂ´nia can only grow and age. Once it accumulates
`10` energy points, it becomes a *juvenile*.
As a *juvenile*, it continues to grow and age. When it reaches `30`
energy points, it advances to its final stage: an *adult*.
As an *adult*, the logĂ´nia gains the ability to reproduce.
### Reproduction
Adult plants can reproduce asexually by randomly colonizing unoccupied
patches:
- If an adult has at least `30` energy points, and a random number
between `0` and `1` is *less than* or *equal to* the
`reproduction-rate` slider, a new seedling is created in a randomly
selected patch with `0` age and `1` point of energy.
- If the selected patch is already occupied, the seedling dies
immediately.
When a logĂ´nia occupy a patch, the patch color changes to brown to
indicate it was once taken.
### Senescence
Plants age by `1` month per step. Age is shown by color, fading from
lime to brown. They die when they reach their maximum age of `100`
months or run out of energy.
## How to Use It
> See a showcase of the model at the following link:
> https://youtu.be/kzfTuw9U-wI?si=ztyGvA5_ztb5dew9
### Setup
To get started, ensure you have [NetLogo](https://www.netlogo.org)
installed. This model was developed with NetLogo 7.0.0. Use this version
or newer for best compatibility.
The model relies on the NetLogo extensions
[`LevelSpace`](https://ccl.northwestern.edu/netlogo/docs/ls.html) and
[`String`](https://github.com/NetLogo/String-Extension). These
extensions are installed automatically when the model is run for the
first time.
### Downloading the Model
You can download the latest release of the model from its [GitHub
releases page](https://github.com/sustentarea/logonia/releases/latest).
For the development version, you can clone or download this GitHub
repository directly.
> [!IMPORTANT]
> Download all repository files, not only the `nlogox` folder.
### Running the Model
Once everything is ready, open the `logonia.nlogox` file located in the
`nlogox` folder, click **`Setup`** and then **`Go`** to start. No extra
installation steps are needed.
Refer to the `Info` tab in the model for additional details.
## How to Cite
To cite `LogĂ´nia` please use the following format:
Vartanian, D., Garcia, L., & Carvalho, A. M. (2025). *LogĂ´nia: Plant
growth response model in NetLogo* \[Computer software\].
https://doi.org/10.17605/OSF.IO/TPY7S
A BibTeX entry for LaTeX users is:
``` latex
@Misc{vartanian2025,
title = {LogĂ´nia: Plant growth response model in NetLogo},
author = {{Daniel Vartanian} and {Leandro Garcia} and {Aline Martins de Carvalho}},
year = {2025},
doi = {10.17605/OSF.IO/TPY7S},
note = {Computer software}
}
```
## How to Contribute
[](CODE_OF_CONDUCT.md)
Contributions are welcome! Whether you want to report bugs, suggest
features, or improve the code or documentation, your input is highly
valued. Please check the [issues
tab](https://github.com/sustentarea/logonia/issues) for existing issues
or to open a new one.
## License
[](https://www.gnu.org/licenses/gpl-3.0)
``` text
Copyright (C) 2025 Daniel Vartanian
LogĂ´nia is free software: you can redistribute it and/or modify it under the
terms of the GNU General Public License as published by the Free Software
Foundation, either version 3 of the License, or (at your option) any later
version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
this program. If not, see .
```
## Acknowledgments
We gratefully acknowledge [Stephen E.
Fick](https://orcid.org/0000-0002-3548-6966), [Robert J.
Hijmans](https://orcid.org/0000-0001-5872-2872), and the entire
[WorldClim](https://worldclim.org/) team for their outstanding work in
creating and maintaining the WorldClim datasets.
We also thank the [Climatic Research
Unit](https://www.uea.ac.uk/groups-and-centres/climatic-research-unit)
at the [University of East Anglia](https://www.uea.ac.uk/) and the UK
[Met Office](https://www.metoffice.gov.uk/) for providing the
[CRU-TS-4.09](https://crudata.uea.ac.uk/cru/data/hrg/cru_ts_4.09/)
dataset, a key source of historical climate data.
This work was developed with support from the
Sustentarea
Research and Extension Center at the University of SĂŁo Paulo (USP).
This work was supported by the Department of Science and
Technology of the Secretariat of Science, Technology, and Innovation
and of the Health Economic-Industrial Complex (SECTICS) of the Ministry of Health
of Brazil, and the National Council for Scientific and
Technological Development (CNPq) (grant no. 444588/2023-0).