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. |