{ "_id": "6a197acaacfb0bcc41df550b", "Package": "gen3sis", "Type": "Package", "Title": "General Engine for Eco-Evolutionary Simulations", "Version": "1.6.0", "Date": "2025-09-01", "Authors@R": "c(\nperson(\"ETH Zürich\", role=c(\"cph\")),\nperson(\"Oskar\", \"Hagen\", email = \"oskar@hagen.bio\", role = c(\"aut\", \"cre\"), comment = \"Landscape Ecology, WSL and ETH Zürich, Switzerland\"),\nperson(\"Benjamin\", \"Flück\", email=\"benjamin.flueck@alumni.ethz.ch\", role = c(\"aut\"), comment = \"Landscape Ecology, WSL and ETH Zürich, Switzerland\"),\nperson(\"Fabian\", \"Fopp\", email=\"fabian.fopp@usys.ethz.ch\", role = c(\"aut\"), comment = \"Landscape Ecology, WSL and ETH Zürich, Switzerland\"),\nperson(c(\"Juliano\",\"S.\"), \"Cabral\", email = \"juliano.sarmento_cabral@uni-wuerzburg.de\", role = c(\"aut\"), comment = \"Ecosystem Modeling, Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany\"),\nperson(\"Florian\", \"Hartig\", email = \"florian.hartig@biologie.uni-regensburg.de\", role = c(\"aut\"), comment = \"Theoretical Ecology, University of Regensburg, Regensburg, Germany\"),\nperson(\"Mikael\", \"Pontarp\", email = \"mikael.pontarp@biol.lu.se\", role = c(\"aut\"), comment = \"Department of Biology, Lund University, Lund, Sweden\"),\nperson(\"Charles\", \"Novaes de Santana \", email = \"charles.novaes@usys.ethz.ch\", role = c(\"ctb\"), comment = \"Landscape Ecology, WSL and ETH Zürich, Switzerland\"),\nperson(c(\"Thiago\", \"F.\"), \"Rangel\", email = \"rangel.tf@gmail.com\", role = c(\"aut\"), comment = \"Department of Ecology, Universidade Federal de Goiás, Goiás, Brazil\"),\nperson(\"Theo\", \"Gaboriau\", email = \"theo.gaboriau@unil.ch\", role = c(\"ctb\"), comment = \"Depatment of Computational Biology, Lausanne University, Switzerland\"),\nperson(\"Loïc\", \"Pellissier\", email = \"loic.pellissier@usys.ethz.ch\", role = c(\"aut\",\"ths\"), comment = \"Landscape Ecology, WSL and ETH Zürich, Switzerland\"))", "Description": "Contains an engine for spatially-explicit eco-evolutionary\nmechanistic models with a modular implementation and several\nsupport functions. It allows exploring the consequences of\necological and macroevolutionary processes across realistic or\ntheoretical spatio-temporal landscapes on biodiversity patterns\nas a general term. Reference: Oskar Hagen, Benjamin Flueck,\nFabian Fopp, Juliano S. Cabral, Florian Hartig, Mikael Pontarp,\nThiago F. Rangel, Loic Pellissier (2021) \"gen3sis: A general\nengine for eco-evolutionary simulations of the processes that\nshape Earth's biodiversity\" .", "License": "GPL-3", "Encoding": "UTF-8", "URL": "https://github.com/project-Gen3sis/R-package", "BugReports": "https://github.com/project-Gen3sis/R-package/issues", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libgdal-dev gdal-bin libgeos-dev libglpk-dev\nlibicu-dev libxml2-dev libproj-dev libsqlite3-dev", "Repository": "https://project-gen3sis.r-universe.dev", "Date/Publication": "2025-09-01 14:13:51 UTC", "RemoteUrl": "https://github.com/project-gen3sis/r-package", "RemoteRef": "HEAD", "RemoteSha": "cf76a62a5a6d45324c5f4b51d83edf839d7cb017", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-29 10:20:00 UTC", "User": "root" }, "Author": "ETH Zürich [cph],\nOskar Hagen [aut, cre] (Landscape Ecology, WSL and ETH Zürich,\nSwitzerland),\nBenjamin Flück [aut] (Landscape Ecology, WSL and ETH Zürich,\nSwitzerland),\nFabian Fopp [aut] (Landscape Ecology, WSL and ETH Zürich, Switzerland),\nJuliano S. Cabral [aut] (Ecosystem Modeling, Center for Computational\nand Theoretical Biology, University of Würzburg, Würzburg, Germany),\nFlorian Hartig [aut] (Theoretical Ecology, University of Regensburg,\nRegensburg, Germany),\nMikael Pontarp [aut] (Department of Biology, Lund University, Lund,\nSweden),\nCharles Novaes de Santana [ctb] (Landscape Ecology, WSL and ETH Zürich,\nSwitzerland),\nThiago F. Rangel [aut] (Department of Ecology, Universidade Federal de\nGoiás, Goiás, Brazil),\nTheo Gaboriau [ctb] (Depatment of Computational Biology, Lausanne\nUniversity, Switzerland),\nLoïc Pellissier [aut, ths] (Landscape Ecology, WSL and ETH Zürich,\nSwitzerland)", "Maintainer": "Oskar Hagen ", "MD5sum": "4748ff46f61179e52f0e6cd0021b9f2d", "_user": "project-gen3sis", "_type": "src", "_file": "gen3sis_1.6.0.tar.gz", "_fileid": "7b3805bafc51de44a5c85fdf831122994ca54f909022b24e06dbbbe0bf2d2602", "_filesize": 3429973, "_sha256": "7b3805bafc51de44a5c85fdf831122994ca54f909022b24e06dbbbe0bf2d2602", "_created": "2026-05-29T10:20:00.000Z", "_published": "2026-05-29T11:38:50.145Z", "_distro": "noble", "_jobs": [ { "job": 78482281571, "time": 265, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7288516384" }, { "job": 78482281597, "time": 304, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7288528490" }, { "job": 78482281581, "time": 251, "config": 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"extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/project-gen3sis/r-package", "_realowner": "project-gen3sis", "_cranurl": true, "_releases": [ { "version": "1.0", "date": "2020-07-10" }, { "version": "1.1", "date": "2020-08-29" }, { "version": "1.2", "date": "2020-12-16" }, { "version": "1.3", "date": "2021-07-12" }, { "version": "1.4", "date": "2021-10-27" }, { "version": "1.5.11", "date": "2023-11-22" }, { "version": "1.6.0", "date": "2025-09-01" } ], "_exports": [ "apply_ecology", "apply_evolution", "color_richness", "color_richness_non_CVDCBP", "create_ancestor_species", "create_input_config", "create_input_landscape", "create_species", "evolution_mode_none", "get_dispersal_values", "get_divergence_factor", "get_divergence_matrix", "get_geo_richness", "plot_landscape", "plot_landscape_overview", "plot_ranges", "plot_raster_multiple", "plot_raster_single", "plot_richness", "plot_species_abundance", "plot_species_presence", "plot_summary", "prepare_directories", "run_simulation", "save_abundance", "save_divergence", "save_landscape", "save_occupancy", "save_phylogeny", "save_richness", "save_species", "save_traits", "verify_config", "write_config_skeleton" ], "_help": [ { "page": "apply_ecology", "title": "Allows the user to define the ecological consequences for species within each site, defining thus species survival and abundance", "topics": [ "apply_ecology" ] }, { "page": "apply_evolution", "title": "Allows defining the function that changes the values of traits of a given species at each time-step and in each site. If no operations are provided, traits are not changing", "topics": [ "apply_evolution" ] }, { "page": "color_richness", "title": "Define gen3sis richness color scale which is colour-vision deficient and colour-blind people safe based on scientific colour maps by Fabio Crameri", "topics": [ "color_richness" ] }, { "page": "color_richness_non_CVDCBP", "title": "Define gen3sis richness color scale for non colour-vision deficient and colour-blind people", "topics": [ "color_richness_non_CVDCBP" ] }, { "page": "create_ancestor_species", "title": "Allows the user to populate the world at the beginning of a simulation", "topics": [ "create_ancestor_species" ] }, { "page": "create_input_config", "title": "Creates either an empty configuration or a pre-filled configuration object from a config file", "topics": [ "create_input_config" ] }, { "page": "create_input_landscape", "title": "create an landscape input from a named list of rasters or raster files", "topics": [ "create_input_landscape" ] }, { "page": "create_species", "title": "Creates a new species", "topics": [ "create_species" ] }, { "page": "evolution_mode_none", "title": "No evolution considered", "topics": [ "evolution_mode_none" ] }, { "page": "gen3sis", "title": "gen3sis: General Engine for Eco-Evolutionary Simulations", "concept": [ "gen3sis modeling eco-evolutionary macroevolution macroecology mechanisms" ], "topics": [ "gen3sis-package", "gen3sis" ] }, { "page": "get_dispersal_values", "title": "Allows the user to generate dispersal value(s) for a given species. The simulation request the user to return a vector of dispersal values with length specified by the num_draws parameter", "topics": [ "get_dispersal_values" ] }, { "page": "get_divergence_factor", "title": "Allows the user to define the rate at which geographic clusters accumulate differentiation with each other.", "topics": [ "get_divergence_factor" ] }, { "page": "get_divergence_matrix", "title": "Returns the full divergence matrix for a given species (site x site).", "topics": [ "get_divergence_matrix" ] }, { "page": "get_geo_richness", "title": "calculate the richness of a list of species over a given landscape", "topics": [ "get_geo_richness" ] }, { "page": "plot_landscape", "title": "Plot the environment variable of a given landscape", "topics": [ "plot_landscape" ] }, { "page": "plot_landscape_overview", "title": "Plot the outline of a given landscape over time", "topics": [ "plot_landscape_overview" ] }, { "page": "plot_ranges", "title": "Plot species ranges of the given list of species on a landscape", "topics": [ "plot_ranges" ] }, { "page": "plot_raster_multiple", "title": "Plot a set of values onto a given landscape", "topics": [ "plot_raster_multiple" ] }, { "page": "plot_raster_single", "title": "Plot a single set of values onto a given landscape", "topics": [ "plot_raster_single" ] }, { "page": "plot_richness", "title": "Plot the richness of the given list of species on a landscape", "topics": [ "plot_richness" ] }, { "page": "plot_species_abundance", "title": "Plot a species' abundance on a given landscape", "topics": [ "plot_species_abundance" ] }, { "page": "plot_species_presence", "title": "Plot a species' presence on a given landscape", "topics": [ "plot_species_presence" ] }, { "page": "plot_summary", "title": "Plot simulation default summary object", "topics": [ "plot_summary" ] }, { "page": "prepare_directories", "title": "Checks if the necessary directories exist, and otherwise creates them", "topics": [ "prepare_directories" ] }, { "page": "run_simulation", "title": "Run a simulation in gen3sis and return a summary object possibly saving outputs and plots to the output folder", "topics": [ "run_simulation" ] }, { "page": "save_abundance", "title": "This function can be called within the observer function to save the species abundances.", "topics": [ "save_abundance" ] }, { "page": "save_divergence", "title": "This function can be called within the observer function to save the compressed species divergence.", "topics": [ "save_divergence" ] }, { "page": "save_landscape", "title": "This function can be called within the observer function to save the current landscape, can be called independently by the user and is called by other observer functions relying on the landscape to be present (e.g. save_species)", "topics": [ "save_landscape" ] }, { "page": "save_occupancy", "title": "This function can be called within the observer function to save the current occupancy pattern", "topics": [ "save_occupancy" ] }, { "page": "save_phylogeny", "title": "This function can be called within the observer function to save the current phylogeny.", "topics": [ "save_phylogeny" ] }, { "page": "save_richness", "title": "This function can be called within the observer function to save the current richness pattern", "topics": [ "save_richness" ] }, { "page": "save_species", "title": "This function can be called within the observer function to save the full species list.", "topics": [ "save_species" ] }, { "page": "save_traits", "title": "This function can be called within the observer function to save the species traits.", "topics": [ "save_traits" ] }, { "page": "verify_config", "title": "Verifies if all required config fields are provided", "topics": [ "verify_config" ] }, { "page": "write_config_skeleton", "title": "Writes out a config skeleton", "topics": [ "write_config_skeleton" ] } ], "_readme": "https://github.com/project-gen3sis/r-package/raw/HEAD/README.md", "_rundeps": [ "BH", "cli", "cpp11", "gdistance", "glue", "igraph", "lattice", "lifecycle", "magrittr", "Matrix", "pkgconfig", "raster", "Rcpp", "rlang", "sp", "stringi", "stringr", "terra", "vctrs" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "introduction.Rmd", "filename": "introduction.html", "title": "Introducing gen3sis ", "engine": "knitr::rmarkdown", "headings": [ "1. Set-up", "Landscape", "Configuration", "2. Run", "3. Visualize", "4. Analyze" ], "created": "2020-04-01 09:48:10", "modified": "2021-10-25 19:16:22", "commits": 99 }, { "source": "create_input_landscape.Rmd", "filename": "create_input_landscape.html", "title": "Creating landscapes (gen3sis input) ", "engine": "knitr::rmarkdown", "headings": [ "Creating the environmental rasters bricks", "Creating a list with the environmental raster bricks", "Defining a cost function", "Further useful arguments", "Create input files" ], "created": "2020-06-19 13:59:59", "modified": "2020-12-19 20:46:33", "commits": 23 }, { "source": "create_config.Rmd", "filename": "create_config.html", "title": "Creating configurations (gen3sis input) ", "engine": "knitr::rmarkdown", "headings": [ "1. Create an empty config", "Content of config_empty.R", "Version: 1.0", "Author:", "Date:", "Landscape:", "Publications:", "Description:", "set the random seed for the simulation.", "set the starting time step or leave NA to use the earliest/highest time-step.", "set the end time step or leave as NA to use the latest/lowest time-step (0).", "maximum total number of species in the simulation before it is aborted.", "maximum number of species within one cell before the simulation is aborted.", "a list of traits to include with each species.", "a \"dispersal\" trait is implicitly added in any case.", "ranges to scale the input environments with:", "not listed variable: no scaling takes place", "listed, set to NA: env. variable will be scaled from [min, max] to [0, 1]", "listed with a given range r: env. variable will be scaled from [r1, r2] to [0, 1]", "the list of all species can be found in data$all_species.", "the current landscape can be found in data$landscape.", "the initial abundance of a newly colonized cell, both during setup and later when", "colonizing a cell during the dispersal.", "place species in the landscape:", "Dispersal", "the maximum range to consider when calculating the distances from local distance inputs.", "returns n dispersal values.", "Speciation", "threshold for genetic distance after which a speciation event takes place.", "factor by which the divergence is increased between geographically isolated population.", "can also be a matrix between the different population clusters.", "Evolution", "mutate the traits of a species and return the new traits matrix.", "Ecology", "called for every cell with all occurring species, this function calculates abundances and/or who survives for each sites", "returns a vector of abundances.", "set the abundance to 0 for every species supposed to die.", "2. Explain example config", "Content of config_.empty_southamerica.R", "Metadata", "Author: Oskar Hagen", "Date: 26.10.2020", "Landscape: SouthAmerica", "Publications: R-package gen3sis", "Description: Example config used at the introduction vignette and similar to case study global configs in Hagen et al. 2020.", "O. Hagen, B. Flück, F. Fopp, J.S. Cabral, F. Hartig, M. Pontarp, T.F. Rangel, L. Pellissier. gen3sis: the general engine for eco-evolutionary simulations on the origins of biodiversity.", "Settings", "Observer", "Initialization", "Core Processes", "mutate the traits of a species and return the new traits matrix", "3. Modify a config" ], "created": "2020-04-03 09:54:07", "modified": "2021-10-11 20:33:27", "commits": 30 }, { "source": "design_landscape.Rmd", "filename": "design_landscape.html", "title": "Example designing landscapes ", "engine": "knitr::rmarkdown", "headings": [ "Create your landscape grid", "Add environmental characteristics", "Add a cost function" ], "created": "2020-06-19 14:16:16", "modified": "2020-12-15 15:52:29", "commits": 9 } ], "_score": 7.999095726707057, "_indexed": true, "_nocasepkg": "gen3sis", "_universes": [ "project-gen3sis" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.6.0", "date": "2026-05-29T10:22:46.000Z", "distro": "noble", "arch": "aarch64", "commit": "cf76a62a5a6d45324c5f4b51d83edf839d7cb017", "fileid": "2b1bad9e4f6b28837d1fa0e751befc778a16cac38ac6c8ac245f13f71aaca405", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/project-gen3sis/actions/runs/26631625682" }, { "r": "4.7.0", "os": "linux", "version": "1.6.0", "date": "2026-05-29T10:23:00.000Z", "distro": "noble", "arch": "x86_64", "commit": "cf76a62a5a6d45324c5f4b51d83edf839d7cb017", "fileid": "45c5b75d528668c2058fd446ea44239659104c21c37399589dfc9c4df67a5231", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/project-gen3sis/actions/runs/26631625682" }, { "r": "4.6.0", "os": "linux", "version": "1.6.0", "date": "2026-05-29T10:22:56.000Z", "distro": "noble", "arch": "aarch64", "commit": "cf76a62a5a6d45324c5f4b51d83edf839d7cb017", "fileid": "70af158190112d9f5d0b8357e1ccf48332b96a61c2101180e84d06878323998f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/project-gen3sis/actions/runs/26631625682" }, { "r": "4.6.0", "os": "linux", "version": "1.6.0", "date": "2026-05-29T10:22:59.000Z", "distro": "noble", "arch": "x86_64", "commit": "cf76a62a5a6d45324c5f4b51d83edf839d7cb017", "fileid": "8e1deb30c3371703ea18697e979dd4ecdf00b7154b351eef9a32cc12586fba99", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/project-gen3sis/actions/runs/26631625682" }, { "r": "4.5.3", "os": "mac", "version": "1.6.0", "date": "2026-05-29T11:36:41.000Z", "arch": "aarch64", "commit": "cf76a62a5a6d45324c5f4b51d83edf839d7cb017", "fileid": "f92af22cd64daf6fdfad2a364b0574dd8891e49c1c2a169205a187061b0adfae", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/project-gen3sis/actions/runs/26631625682" }, { "r": "4.5.3", "os": "mac", "version": "1.6.0", "date": "2026-05-29T10:23:50.000Z", "arch": "x86_64", "commit": "cf76a62a5a6d45324c5f4b51d83edf839d7cb017", "fileid": "5fca596b95ea677bd083463b7991e063891b39563469cd103d5e2c027eeaa66e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/project-gen3sis/actions/runs/26631625682" }, { "r": "4.6.0", "os": "mac", "version": "1.6.0", "date": "2026-05-29T11:37:05.000Z", "arch": "aarch64", "commit": "cf76a62a5a6d45324c5f4b51d83edf839d7cb017", "fileid": "24dc985374ac0d57c622441e23a7d8cfe429762f6457517c4d5ddd575e721fa8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/project-gen3sis/actions/runs/26631625682" }, { "r": "4.6.0", "os": "mac", "version": "1.6.0", "date": "2026-05-29T10:24:33.000Z", "arch": "x86_64", "commit": "cf76a62a5a6d45324c5f4b51d83edf839d7cb017", "fileid": "1860ec2e9752ffc8a5c38f3a01f021decee8f55f419d300f8e6f2160a05d0501", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/project-gen3sis/actions/runs/26631625682" }, { "r": "4.6.0", "os": "wasm", "version": "1.6.0", "date": "2026-05-29T10:23:00.000Z", "arch": "emscripten", "commit": "cf76a62a5a6d45324c5f4b51d83edf839d7cb017", "fileid": "32b77f810d6ad887198545cfd17fad510afaeb00a6d16f64799ea89209364499", "status": "success", "buildurl": "https://github.com/r-universe/project-gen3sis/actions/runs/26631625682" }, { "r": "4.7.0", "os": "win", "version": "1.6.0", "date": "2026-05-29T10:22:01.000Z", "arch": "x86_64", "commit": "cf76a62a5a6d45324c5f4b51d83edf839d7cb017", "fileid": "88a4fae033f2f437c849bf0754afd440e4faf538b5cc6a0deb9145fb1668c7ad", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/project-gen3sis/actions/runs/26631625682" }, { "r": "4.5.3", "os": "win", "version": "1.6.0", "date": "2026-05-29T10:22:06.000Z", "arch": "x86_64", "commit": "cf76a62a5a6d45324c5f4b51d83edf839d7cb017", "fileid": "7b270faa59dd043e5c20caf9b22ebb98da833a1405bb01ffc86ba19b90c7ded5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/project-gen3sis/actions/runs/26631625682" }, { "r": "4.6.0", "os": "win", "version": "1.6.0", "date": "2026-05-29T10:22:01.000Z", "arch": "x86_64", "commit": "cf76a62a5a6d45324c5f4b51d83edf839d7cb017", "fileid": "e572a5ce70712354f19e3f1531581aacc23c6068124350d8704194f8d3d38190", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/project-gen3sis/actions/runs/26631625682" } ] }