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Please edit that file --\u003e\n\n# [DynACof](https://vezy.github.io/DynACof): The Dynamic Agroforestry Coffee Crop Model \u003cimg src=\"man/figures/logo.png\" alt=\"\" width=\"300\" align=\"right\" /\u003e\n\n\u003c!-- badges: start --\u003e\n\n[![Project Status: Active – The project has reached a stable, usable\nstate and is being actively\ndeveloped.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)\n[![R-CMD-check](https://github.com/VEZY/DynACof/workflows/R-CMD-check/badge.svg)](https://github.com/VEZY/DynACof/actions)\n[![Join the chat at\nhttps://gitter.im/DynACof/Lobby\\#](https://badges.gitter.im/DynACof/Lobby.svg?token=1d2e733532f5122f05de\u0026branch=master)](https://gitter.im/DynACof/Lobby?utm_source=badge\u0026utm_medium=badge\u0026utm_campaign=pr-badge\u0026utm_content=badge)\n[![License: GPL\nv3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1256816.svg)](https://doi.org/10.5281/zenodo.1256816)\n\u003c!-- badges: end --\u003e\n\n## Overview\n\nThe [DynACof](https://vezy.github.io/DynACof) process-based model\ncomputes plot-scale Net Primary Productivity, carbon allocation, growth,\nyield, energy, and water balance of coffee plantations according to\nmanagement, while accounting for spatial effects using metamodels from\nthe 3D process-based [MAESPA](https://maespa.github.io/). The model also\nuses coffee bud and fruit cohorts for reproductive development to better\nrepresent fruit carbon demand distribution along the year.\n\nA research article presenting and evaluating the model is published in\nVezy et al. (2020). The official website is available\n[here](https://vezy.github.io/DynACof).\n\nDynACof is also available as a [Julia](https://julialang.org/) package.\nUse this one for better performance (\\~100x). Its repository is\navailable [here](https://github.com/VEZY/DynACof.jl), and the\ndocumentation is available\n[here](https://vezy.github.io/DynACof.jl/dev/). The Julia version is\nalso available from the R package. See [the\nvignette](https://vezy.github.io/DynACof/articles/julia-version.html)\nfor more details. Note that the input parameter files are different from\nthe R-version. They are accessible in the\n[DynACof.jl\\_inputs](https://github.com/VEZY/DynACof.jl_inputs)\nrepository.\n\n## Installation\n\nThe development version from [GitHub](https://github.com/) can be\ninstalled with:\n\n``` r\n# install.packages(\"devtools\")\ndevtools::install_github(\"VEZY/DynACof\")\n```\n\nOr using the lightweight\n[remotes](https://github.com/r-lib/remotes#readme) package:\n\n``` r\n# install.packages(\"remotes\")\nremotes::install_github(\"VEZY/DynACof\")\n```\n\nThe package is tested routinely to pass all\n[CRAN](https://CRAN.R-project.org) tests using Travis-CI (linux) and\nAppVeyor (Windows), but is not released to the CRAN servers because we\nbelieve DynACof users are not widespread enough to bother CRAN people\nand use their free server time.\n\n## Example\n\nThis is a basic example using all defaults (parameters and meteorology)\nover 2 years :\n\n``` r\nrm(list = ls())\nlibrary(\"DynACof\")\nSys.setenv(TZ=\"UTC\")\nDynACof(Period= as.POSIXct(c(\"1979-01-01\", \"1980-12-31\")))\n```\n\nTo use your own data, you have to tell DynACof where to find it using\n`Inpath` parameter, and what are the file names with the `FileName`\nparameter list. A separate [Github\nrepository](https://github.com/VEZY/DynACof_inputs) is available for\ninput files templates, and some help on how to proceed.\n\nExample using custom input parameter files:\n\n``` r\nrm(list = ls())\nlibrary(\"DynACof\")\nSys.setenv(TZ=\"UTC\")\nDynACof(WriteIt = T, Period = as.POSIXct(c(\"1979-01-01\", \"1980-12-31\")),\n        Inpath = \"1-Input/Aquiares/\", Simulation_Name = \"Test1\",\n        FileName = list(Site = \"1-Site.R\", Meteo =\"2-Meteorology.txt\",\n                        Soil = \"3-Soil.R\",Coffee = \"4-Coffee.R\", Tree = NULL))\n```\n\nNote that the Meteo file can be of any regular format because the model\nuses the `data.table::fread` function internally.\n\n## Notes\n\nThe model first computes the shade tree, then the coffee and then the\nsoil. So if you need to update the metamodels, please keep in mind that\nthe state of soil of a given day is only accessible on the next day for\nthe tree and the coffee, unless the code is updated too. The model is\nimplemented like this for simplicity, based on the hypothesis that the\nsoil has a rather slow dynamic compared to plants dynamics.\n\n## Code of conduct\n\nPlease note that this project is released with a [Contributor Code of\nConduct](CODE_OF_CONDUCT.md). By participating in this project you agree\nto abide by its terms.\n\n## Acknowledgments\n\nThe DynACof model was mainly developed thanks to the MACCAC project,\nwhich was funded by the french ANR (Agence Nationale de la Recherche).\nThe authors were funded by [CIRAD](https://www.cirad.fr/) and\n[INRAE](https://www.inrae.fr/). The authors are grateful for the support\nof the [Aquiares farm](https://aquiares.com/) and the\n[CATIE](https://www.catie.ac.cr/) for the long-term coffee agroforestry\ntrial, the SOERE F-ORE-T which is supported annually by Ecofor, Allenvi\nand the French national research infrastructure\n[ANAEE-F](http://www.anaee-france.fr/fr/); the CIRAD-IRD-SAFSE project\n(France) and the PCP platform of CATIE. CoffeeFlux observatory was\nsupported and managed by CIRAD researchers. We are grateful to the staff\nfrom Costa-Rica, in particular Alvaro Barquero, Alejandra Barquero,\nJenny Barquero, Alexis Perez, Guillermo Ramirez, Rafael Acuna, Manuel\nJara, Alonso Barquero for their technical and field support.\n\nMACACC project: ANR-13-AGRO-0005, Viabilité et Adaptation des\nEcosystèmes Productifs, Territoires et Ressources face aux Changements\nGlobaux, AGROBIOSPHERE 2013 program.\n\n-----\n\n\u003csub\u003eThe DynACof logo was made using\n\u003ca href=\"http://logomakr.com\" title=\"Logo Makr\"\u003eLogoMakr.com\u003c/a\u003e \u003c/sub\u003e\n\n## References\n\n\u003cdiv id=\"refs\" class=\"references hanging-indent\"\u003e\n\n\u003cdiv id=\"ref-vezyDynACofProcessbasedModel2020\"\u003e\n\nVezy, R., le Maire, G., Christina, M., Georgiou, S., Imbach, P.,\nHidalgo, H.G., Alfaro, E.J., Blitz-Frayret, C., Charbonnier, F., Lehner,\nP., Loustau, D., Roupsard, O., 2020. DynACof: A process-based model to\nstudy growth, yield and ecosystem services of coffee agroforestry\nsystems. Environmental Modelling \u0026 Software 124, 104609.\n\u003chttps://doi.org/10.1016/j.envsoft.2019.104609\u003e\n\n\u003c/div\u003e\n\n\u003c/div\u003e\n","funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.1256816","https://doi.org/10.1016/j.envsoft.2019.104609"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://ost.ecosyste.ms/api/v1/projects/20363","html_url":"https://ost.ecosyste.ms/projects/20363"}