# General Engine for Eco-Evolutionary Simulations

## Documentation for package ‘gen3sis’ version 1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

apply_ecology | apply_ecology allows the user to define the ecology of the species that takes place within each cell, which define species survival and species abundance.
apply_evolution | apply_evolution allows defining the function that changes the values of traits of a given species at each time step and in each cell. If no operations are provided, traits are not changing.
color_richness | define gen3sis richness color scale
create_ancestor_species | The function create_ancestor_species allows the user to populate the world at the beginning of a simulation.
create_input_config | creates either an empty configuration or a pre-filled configuration object from a config file.
create_input_landscape | create an landscape input from a named list of rasters or raster files
create_species | creates a new species.
evolution_mode_none | evolution_mode_none
gen3sis | gen3sis: General Engine for Eco-Evolutionary Simulations
get_dispersal_values | get_dispersal_values allows the user to generates dispersal value(s) for a given species. The simulation request the user to return a vector of dispersal values with length num_draws.
get_divergence_factor | get_divergence_factor allows the user to define the rate at which geographic clusters accumulate differentiation with each other.
get_divergence_matrix | The function get_divergence_matrix returns the full divergence matrix for a given species (cell x cell).
get_geo_richness | calculate the richness of a list of species over a given landscape
plot_landscape | plot the environment variable of a given landscape
plot_landscape_overview | plot the outline of a given landscape over time
plot_raster_multiple | plot a set of values onto a given landscape
plot_raster_single | plot a single set of values onto a given landscape
plot_richness | plot the richness of the given list of species on a landscape
plot_species_presence | plot a species' presence on a given landscape
plot_summary | plot simulation default summary object
prepare_directories | checks if the necessary directories exist, and otherwise creates them. This function will be called by the simulation, but is made available if the directories should be created manually beforehand, for example to redirect the stdout to a file in the output directory.
run_simulation | run a simulation in gen3sis and return a summary object possibly saving outputs and plots to the output folder.
save_abundance | This function can be called within the observer function to save the species abundances.
save_divergence | This function can be called within the observer function to save the compressed species divergence.
save_landscape | 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_occupancy | This function can be called within the observer function to save the current occupancy pattern
save_phylogeny | This function can be called within the observer function to save the current phylogeny.
save_richness | This function can be called within the observer function to save the current richness pattern
save_species | This function can be called within the observer function to save the full species list.
save_traits | This function can be called within the observer function to save the species traits.
skeleton_config | empty skeleton config
verify_config | This function verifies that all required config fields are provided.
write_config_skeleton | writes out a config skeleton, that is, an empty config file to be edited by the user.