# General Engine for Eco-Evolutionary Simulations

## Documentation for package ‘gen3sis’ version 1.5.11

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

## Help Pages

apply_ecology | Allows the user to define the ecological consequences for species within each site, defining thus species survival and abundance
apply_evolution | 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
color_richness | Define gen3sis richness color scale which is colour-vision deficient and colour-blind people safe based on scientific colour maps by Fabio Crameri
color_richness_non_CVDCBP | Define gen3sis richness color scale for non colour-vision deficient and colour-blind people
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 | No evolution considered
gen3sis | gen3sis: General Engine for Eco-Evolutionary Simulations
get_dispersal_values | 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
get_divergence_factor | Allows the user to define the rate at which geographic clusters accumulate differentiation with each other.
get_divergence_matrix | Returns the full divergence matrix for a given species (site x site).
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_ranges | Plot species ranges of the given list of species on a landscape
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_abundance | Plot a species' abundance on a given 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
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 | Verifies if all required config fields are provided
write_config_skeleton | Writes out a config skeleton