Man pages for gen3sis
General Engine for Eco-Evolutionary Simulations
| apply_ecology | Allows the user to define the ecological consequences for... |
| apply_evolution | Allows defining the function that changes the values of... |
| color_richness | Define gen3sis richness color scale which is colour-vision... |
| color_richness_non_CVDCBP | Define gen3sis richness color scale for non colour-vision... |
| create_ancestor_species | Allows the user to populate the world at the beginning of a... |
| create_input_config | Creates either an empty configuration or a pre-filled... |
| create_input_landscape | create an landscape input from a named list of rasters or... |
| 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... |
| get_divergence_factor | Allows the user to define the rate at which geographic... |
| get_divergence_matrix | Returns the full divergence matrix for a given species (site... |
| get_geo_richness | calculate the richness of a list of species over a given... |
| 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... |
| 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... |
| run_simulation | Run a simulation in gen3sis and return a summary object... |
| save_abundance | This function can be called within the observer function to... |
| save_divergence | This function can be called within the observer function to... |
| save_landscape | This function can be called within the observer function to... |
| save_occupancy | This function can be called within the observer function to... |
| save_phylogeny | This function can be called within the observer function to... |
| save_richness | This function can be called within the observer function to... |
| save_species | This function can be called within the observer function to... |
| save_traits | This function can be called within the observer function to... |
| skeleton_config | empty skeleton config |
| verify_config | Verifies if all required config fields are provided |
| write_config_skeleton | Writes out a config skeleton |
