Package: gen3sis 1.6.0

Oskar Hagen

gen3sis: General Engine for Eco-Evolutionary Simulations

Contains an engine for spatially-explicit eco-evolutionary mechanistic models with a modular implementation and several support functions. It allows exploring the consequences of ecological and macroevolutionary processes across realistic or theoretical spatio-temporal landscapes on biodiversity patterns as a general term. Reference: Oskar Hagen, Benjamin Flueck, Fabian Fopp, Juliano S. Cabral, Florian Hartig, Mikael Pontarp, Thiago F. Rangel, Loic Pellissier (2021) "gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth's biodiversity" <doi:10.1371/journal.pbio.3001340>.

Authors:ETH Zürich [cph], Oskar Hagen [aut, cre], Benjamin Flück [aut], Fabian Fopp [aut], Juliano S. Cabral [aut], Florian Hartig [aut], Mikael Pontarp [aut], Charles Novaes de Santana [ctb], Thiago F. Rangel [aut], Theo Gaboriau [ctb], Loïc Pellissier [aut, ths]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gen3sis/json (API)

# Install 'gen3sis' in R:
install.packages('gen3sis', repos = c('https://project-gen3sis.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/project-gen3sis/r-package/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

biodiversityecologyevolutionmechanisticmodelmodelingsimulationcpp

8.10 score 36 stars 92 scripts 1.1k downloads 1 mentions 34 exports 19 dependencies

Last updated from:cf76a62a5a. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK319
linux-devel-x86_64OK321
source / vignettesOK246
linux-release-arm64OK292
linux-release-x86_64OK287
macos-release-arm64OK258
macos-release-x86_64OK355
macos-oldrel-arm64OK250
macos-oldrel-x86_64OK550
windows-develOK273
windows-releaseOK291
windows-oldrelOK281
wasm-releaseOK187

Exports:apply_ecologyapply_evolutioncolor_richnesscolor_richness_non_CVDCBPcreate_ancestor_speciescreate_input_configcreate_input_landscapecreate_speciesevolution_mode_noneget_dispersal_valuesget_divergence_factorget_divergence_matrixget_geo_richnessplot_landscapeplot_landscape_overviewplot_rangesplot_raster_multipleplot_raster_singleplot_richnessplot_species_abundanceplot_species_presenceplot_summaryprepare_directoriesrun_simulationsave_abundancesave_divergencesave_landscapesave_occupancysave_phylogenysave_richnesssave_speciessave_traitsverify_configwrite_config_skeleton

Dependencies:BHclicpp11gdistanceglueigraphlatticelifecyclemagrittrMatrixpkgconfigrasterRcpprlangspstringistringrterravctrs

Introducing gen3sis
1. Set-up | Landscape | Configuration | 2. Run | 3. Visualize | 4. Analyze
Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2021-10-25
Started: 2020-04-01

Creating configurations (gen3sis input)
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
Rendered fromcreate_config.Rmdusingknitr::rmarkdown

Last update: 2021-10-11
Started: 2020-04-03

Creating landscapes (gen3sis input)
Creating the environmental rasters bricks | Creating a list with the environmental raster bricks | Defining a cost function | Further useful arguments | Create input files
Rendered fromcreate_input_landscape.Rmdusingknitr::rmarkdown

Last update: 2020-12-19
Started: 2020-06-19

Example designing landscapes
Create your landscape grid | Add environmental characteristics | Add a cost function
Rendered fromdesign_landscape.Rmdusingknitr::rmarkdown

Last update: 2020-12-15
Started: 2020-06-19

Readme and manuals

Help Manual

Help pageTopics
Allows the user to define the ecological consequences for species within each site, defining thus species survival and abundanceapply_ecology
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 changingapply_evolution
Define gen3sis richness color scale which is colour-vision deficient and colour-blind people safe based on scientific colour maps by Fabio Cramericolor_richness
Define gen3sis richness color scale for non colour-vision deficient and colour-blind peoplecolor_richness_non_CVDCBP
Allows the user to populate the world at the beginning of a simulationcreate_ancestor_species
Creates either an empty configuration or a pre-filled configuration object from a config filecreate_input_config
create an landscape input from a named list of rasters or raster filescreate_input_landscape
Creates a new speciescreate_species
No evolution consideredevolution_mode_none
gen3sis: General Engine for Eco-Evolutionary Simulationsgen3sis-package gen3sis
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 parameterget_dispersal_values
Allows the user to define the rate at which geographic clusters accumulate differentiation with each other.get_divergence_factor
Returns the full divergence matrix for a given species (site x site).get_divergence_matrix
calculate the richness of a list of species over a given landscapeget_geo_richness
Plot the environment variable of a given landscapeplot_landscape
Plot the outline of a given landscape over timeplot_landscape_overview
Plot species ranges of the given list of species on a landscapeplot_ranges
Plot a set of values onto a given landscapeplot_raster_multiple
Plot a single set of values onto a given landscapeplot_raster_single
Plot the richness of the given list of species on a landscapeplot_richness
Plot a species' abundance on a given landscapeplot_species_abundance
Plot a species' presence on a given landscapeplot_species_presence
Plot simulation default summary objectplot_summary
Checks if the necessary directories exist, and otherwise creates themprepare_directories
Run a simulation in gen3sis and return a summary object possibly saving outputs and plots to the output folderrun_simulation
This function can be called within the observer function to save the species abundances.save_abundance
This function can be called within the observer function to save the compressed species divergence.save_divergence
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)save_landscape
This function can be called within the observer function to save the current occupancy patternsave_occupancy
This function can be called within the observer function to save the current phylogeny.save_phylogeny
This function can be called within the observer function to save the current richness patternsave_richness
This function can be called within the observer function to save the full species list.save_species
This function can be called within the observer function to save the species traits.save_traits
Verifies if all required config fields are providedverify_config
Writes out a config skeletonwrite_config_skeleton