{"id":31576196,"url":"https://github.com/sustentarea/logonia","last_synced_at":"2025-10-05T17:17:58.108Z","repository":{"id":313744390,"uuid":"1051878166","full_name":"sustentarea/logonia","owner":"sustentarea","description":"🌿 Plant Growth Response Model in NetLogo","archived":false,"fork":false,"pushed_at":"2025-09-29T22:43:58.000Z","size":43318,"stargazers_count":1,"open_issues_count":1,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-09-30T20:59:05.955Z","etag":null,"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"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sustentarea.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":"SECURITY.md","support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":"codemeta.json","zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-09-06T23:02:34.000Z","updated_at":"2025-09-29T22:44:02.000Z","dependencies_parsed_at":"2025-09-08T08:29:49.832Z","dependency_job_id":null,"html_url":"https://github.com/sustentarea/logonia","commit_stats":null,"previous_names":["sustentarea/logonia"],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/sustentarea/logonia","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sustentarea%2Flogonia","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sustentarea%2Flogonia/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sustentarea%2Flogonia/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sustentarea%2Flogonia/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sustentarea","download_url":"https://codeload.github.com/sustentarea/logonia/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sustentarea%2Flogonia/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":278486308,"owners_count":25994945,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-05T02:00:06.059Z","response_time":54,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["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"],"created_at":"2025-10-05T17:17:30.552Z","updated_at":"2025-10-05T17:17:58.094Z","avatar_url":"https://github.com/sustentarea.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Logônia \u003cimg src=\"images/logo.png\" align=\"right\" width=\"120\" /\u003e\n\n\u003c!-- Quarto render --\u003e\n\n\u003c!-- badges: start --\u003e\n[![Project Status: Active - The project has reached a stable, usable\nstate and is being actively\ndeveloped.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![](https://img.shields.io/badge/CoMSES%20Network-1.1.0-1284C5.svg)](https://www.comses.net/codebases/4f2be13a-3957-4537-bf64-3fad96ba271f/)\n[![](https://img.shields.io/badge/OSF%20DOI-10.17605/OSF.IO/TPY7S-1284C5.svg)](https://doi.org/10.17605/OSF.IO/TPY7S)\n[![FAIR checklist\nbadge](https://img.shields.io/badge/fairsoftwarechecklist.net--00a7d9)](https://fairsoftwarechecklist.net/v0.2?f=31\u0026a=30113\u0026i=32300\u0026r=123)\n[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)\n[![License:\nGPLv3](https://img.shields.io/badge/license-GPLv3-bd0000.svg)](https://www.gnu.org/licenses/gpl-3.0)\n\u003c!-- badges: end --\u003e\n\n## Overview\n\n`Logônia` is a [NetLogo](https://www.netlogo.org) model that simulates\nthe growth response of a fictional plant, logônia, under different\nclimatic conditions. The model uses climate data from [WorldClim\n2.1](https://worldclim.org/) and demonstrates how to integrate the\n[`LogoClim`](https://github.com/sustentarea/logoclim) model through the\n[`LevelSpace`](https://ccl.northwestern.edu/netlogo/docs/ls.html)\nextension.\n\n\u003e If you find this project useful, please consider giving it a star!\n\u003e [![GitHub repo\n\u003e stars](https://img.shields.io/github/stars/sustentarea/logonia)](https://github.com/sustentarea/logonia/)\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"images/logonia-interface.gif\" /\u003e\n\u003c/p\u003e\n\n## How It Works\n\n`Logônia` runs on a grid of patches, where each patch represents a piece\nof soil that can host a plant. Patches correspond to a specific\ngeographic area and store historical climate data.\n\nEach simulation step represents *one month*. Over time, plants *grow*,\n*reproduce*, and *age*. These processes are controlled by sliders on the\nmodel’s interface. Climate conditions directly influence growth\nprobability, adding realism and complexity to the simulation.\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"images/logonia-evolution.svg\" height=125px /\u003e\n\u003c/p\u003e\n\n### Climate Data\n\nThe model uses *Historical Monthly Weather Data* from [WorldClim\n2.1](https://worldclim.org/) ([Fick \u0026 Hijmans,\n2017](https://doi.org/10.1002/joc.5086)) for a region of the **Brazilian\nAmazon Forest**.\n\nThis dataset provides 12 monthly values per year for 1951–2024, based on\n[downscaled](https://worldclim.org/data/downscaling.html) data from\n[CRU-TS-4.09](https://crudata.uea.ac.uk/cru/data/hrg/cru_ts_4.09/),\ndeveloped by the [Climatic Research\nUnit](https://www.uea.ac.uk/groups-and-centres/climatic-research-unit)\nat the [University of East Anglia](https://www.uea.ac.uk/) ([Harris et\nal., 2020](https://doi.org/10.1038/s41597-020-0453-3)). The variables\nare: *Average Minimum Temperature (°C)* (**A**), *Average Maximum\nTemperature (°C)* (**B**), and *Total Precipitation (mm)* (**C**).\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"images/worldclim-animation.gif\" height=150px /\u003e\n\u003c/p\u003e\n\nThe dataset can be reproduced using [Quarto](https://quarto.org/)\nnotebooks in the `qmd` folder of the model repository, adapted from\nthose in the [`LogoClim`](https://github.com/sustentarea/logoclim)\nmodel.\n\n### Energy and Growth Probability\n\nGrowth probability is determined by a [logistic\nregression](https://en.wikipedia.org/wiki/Logistic_regression) model\nthat incorporates patch-level climate variables. The probability follows\nthe equation below:\n\n$$\np(\\text{tmin, tmax, prec}) = \\cfrac{1}{1 + e^{- (\\beta_{0} + \\beta_{\\text{tmin}} \\text{tmin} + \\beta_{\\text{tmax}} \\text{tmax} + \\beta_{\\text{prec}} \\text{prec})}}\n$$\n\nA logônia gains or loses energy at each step according to the following\nrules:\n\n- If a random number between `0` and `1` is *less than* or *equal to*\n  the growth probability for the current patch, the plant gains the\n  number of energy points defined by the `energy-gain` slider.\n- If the probability is *below* `0.25` and does not meet the above\n  condition, the plant loses `1` energy point.\n- Otherwise, its energy remains unchanged.\n\nIf a plant gets to `0` points of energy it dies.\n\n### Growth Phases\n\nA logônia plant develops through three phases: *seedling*, *juvenile*,\nand *adult*. Each has distinct shapes and energy thresholds.\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"images/logonia-shapes.svg\" height=125px /\u003e\n\u003c/p\u003e\n\nAs a *seedling*, the logônia can only grow and age. Once it accumulates\n`10` energy points, it becomes a *juvenile*.\n\nAs a *juvenile*, it continues to grow and age. When it reaches `30`\nenergy points, it advances to its final stage: an *adult*.\n\nAs an *adult*, the logônia gains the ability to reproduce.\n\n### Reproduction\n\nAdult plants can reproduce asexually by randomly colonizing unoccupied\npatches:\n\n- If an adult has at least `30` energy points, and a random number\n  between `0` and `1` is *less than* or *equal to* the\n  `reproduction-rate` slider, a new seedling is created in a randomly\n  selected patch with `0` age and `1` point of energy.\n- If the selected patch is already occupied, the seedling dies\n  immediately.\n\nWhen a logônia occupy a patch, the patch color changes to brown to\nindicate it was once taken.\n\n### Senescence\n\nPlants age by `1` month per step. Age is shown by color, fading from\nlime to brown. They die when they reach their maximum age of `100`\nmonths or run out of energy.\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"images/logonia-aging.svg\" height=125px /\u003e\n\u003c/p\u003e\n\n## How to Use It\n\n\u003e See a showcase of the model at the following link:\n\u003e https://youtu.be/kzfTuw9U-wI?si=ztyGvA5_ztb5dew9\n\n### Setup\n\nTo get started, ensure you have [NetLogo](https://www.netlogo.org)\ninstalled. This model was developed with NetLogo 7.0.0. Use this version\nor newer for best compatibility.\n\nThe model relies on the NetLogo extensions\n[`LevelSpace`](https://ccl.northwestern.edu/netlogo/docs/ls.html) and\n[`String`](https://github.com/NetLogo/String-Extension). These\nextensions are installed automatically when the model is run for the\nfirst time.\n\n### Downloading the Model\n\nYou can download the latest release of the model from its [GitHub\nreleases page](https://github.com/sustentarea/logonia/releases/latest).\nFor the development version, you can clone or download this GitHub\nrepository directly.\n\n\u003e [!IMPORTANT]\n\u003e Download all repository files, not only the `nlogox` folder.\n\n### Running the Model\n\nOnce everything is ready, open the `logonia.nlogox` file located in the\n`nlogox` folder, click **`Setup`** and then **`Go`** to start. No extra\ninstallation steps are needed.\n\nRefer to the `Info` tab in the model for additional details.\n\n## How to Cite\n\nTo cite `Logônia` please use the following format:\n\nVartanian, D., Garcia, L., \u0026 Carvalho, A. M. (2025). *Logônia: Plant\ngrowth response model in NetLogo* \\[Computer software\\].\nhttps://doi.org/10.17605/OSF.IO/TPY7S\n\nA BibTeX entry for LaTeX users is:\n\n``` latex\n@Misc{vartanian2025,\n  title = {Logônia: Plant growth response model in NetLogo},\n  author = {{Daniel Vartanian} and {Leandro Garcia} and {Aline Martins de Carvalho}},\n  year = {2025},\n  doi = {10.17605/OSF.IO/TPY7S},\n  note = {Computer software}\n}\n```\n\n## How to Contribute\n\n[![](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CODE_OF_CONDUCT.md)\n\nContributions are welcome! Whether you want to report bugs, suggest\nfeatures, or improve the code or documentation, your input is highly\nvalued. Please check the [issues\ntab](https://github.com/sustentarea/logonia/issues) for existing issues\nor to open a new one.\n\n## License\n\n[![](https://img.shields.io/badge/license-GPLv3-bd0000.svg)](https://www.gnu.org/licenses/gpl-3.0)\n\n``` text\nCopyright (C) 2025 Daniel Vartanian\n\nLogônia is free software: you can redistribute it and/or modify it under the\nterms of the GNU General Public License as published by the Free Software\nFoundation, either version 3 of the License, or (at your option) any later\nversion.\n\nThis program is distributed in the hope that it will be useful, but WITHOUT ANY\nWARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\nPARTICULAR PURPOSE. See the GNU General Public License for more details.\n\nYou should have received a copy of the GNU General Public License along with\nthis program. If not, see \u003chttps://www.gnu.org/licenses/\u003e.\n```\n\n## Acknowledgments\n\nWe gratefully acknowledge [Stephen E.\nFick](https://orcid.org/0000-0002-3548-6966), [Robert J.\nHijmans](https://orcid.org/0000-0001-5872-2872), and the entire\n[WorldClim](https://worldclim.org/) team for their outstanding work in\ncreating and maintaining the WorldClim datasets.\n\nWe also thank the [Climatic Research\nUnit](https://www.uea.ac.uk/groups-and-centres/climatic-research-unit)\nat the [University of East Anglia](https://www.uea.ac.uk/) and the UK\n[Met Office](https://www.metoffice.gov.uk/) for providing the\n[CRU-TS-4.09](https://crudata.uea.ac.uk/cru/data/hrg/cru_ts_4.09/)\ndataset, a key source of historical climate data.\n\n\u003ctable\u003e\n  \u003ctr\u003e\n    \u003ctd width=\"30%\"\u003e\n      \u003cbr/\u003e\n      \u003cbr/\u003e\n      \u003cp align=\"center\"\u003e\n        \u003ca href=\"https://www.fsp.usp.br/sustentarea/\"\u003e\n          \u003cimg src=\"images/sustentarea-logo.svg\" width=\"125\"/\u003e\n        \u003c/a\u003e\n      \u003c/p\u003e\n      \u003cbr/\u003e\n    \u003c/td\u003e\n    \u003ctd width=\"70%\"\u003e\n      \u003cp\u003e\n        This work was developed with support from the \n        \u003ca href=\"https://www.fsp.usp.br/sustentarea/\"\u003eSustentarea\u003c/a\u003e\n         Research and Extension Center at the University of São Paulo (\u003ca href=\"https://www5.usp.br/\"\u003eUSP\u003c/a\u003e).\n      \u003c/p\u003e\n    \u003c/td\u003e\n  \u003c/tr\u003e\n\u003c/table\u003e\n\n\u003ctable\u003e\n  \u003ctr\u003e\n    \u003ctd width=\"30%\"\u003e\n      \u003cbr/\u003e\n      \u003cp align=\"center\"\u003e\n        \u003ca href=\"https://www.gov.br/cnpq/\"\u003e\n          \u003cimg src=\"images/cnpq-logo.svg\" width=\"150\"/\u003e\n        \u003c/a\u003e\n      \u003c/p\u003e\n      \u003cbr/\u003e\n    \u003c/td\u003e\n    \u003ctd width=\"70%\"\u003e\n      \u003cp\u003e\n        This work was supported by the Department of Science and \n        Technology of the Secretariat of Science, Technology, and Innovation \n        and of the Health Economic-Industrial Complex (\u003ca href=\"https://www.gov.br/saude/pt-br/composicao/sectics/\"\u003eSECTICS\u003c/a\u003e)  of the \u003ca href=\"https://www.gov.br/saude/pt-br/composicao/sectics/\"\u003eMinistry of Health\u003c/a\u003e \n        of Brazil, and the National Council for Scientific and \n        Technological Development (\u003ca href=\"https://www.gov.br/cnpq/\"\u003eCNPq\u003c/a\u003e) (grant no. 444588/2023-0).\n      \u003c/p\u003e\n    \u003c/td\u003e\n  \u003c/tr\u003e\n\u003c/table\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsustentarea%2Flogonia","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsustentarea%2Flogonia","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsustentarea%2Flogonia/lists"}