Package index

Run simulation

Main gen3sis2 functions to run and summarize simulations

gen3sis2-package gen3sis2: gen3sis2: General Engine for Eco-Evolutionary Simulations
run_simulation(): Run a simulation in gen3sis and return a summary object possibly saving outputs and plots to the output folder

User defined simulation functions

Functions defined by the user and called by the simulation

apply_ecology(): Allows the user to define the ecological consequences for species within each site, defining thus species survival and abundance
apply_modifiers(): Allows the user to populate the world at the beginning of a simulation
apply_trait_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
create_ancestor_species(): Allows the user to populate the world at the beginning of a simulation
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_modifiers(): Computed the object used to modify the environmental variables trough the simulation

Functions that are used in the simulation but are not user defined

create_species(): Creates a new species
evolution_mode_none(): No evolution considered

Configuration file

Functions to create and handle configs

create_empty_config(): Creates an empty config object
create_input_config(): Creates either an empty configuration or a pre-filled configuration object from a config file
prepare_directories(): Checks if the necessary directories exist, and otherwise creates them
verify_config(): Verifies if all required config fields are provided
write_config_skeleton(): Writes out a config skeleton

Spaces input

Functions to create and handle spaces input

check_names(): Check names of spaces
check_spaces(): Check gen3sis_spaces
create_spaces(): create empty gen3sis_spaces
create_spaces_raster(): Create an spaces input from a named list of rasters or raster files and user defined cost function
is_geodynamic(): Determine if environmental data is geodynamic

Plotting functions

Functions used to plot gen3sis 2 spaces and species

color_richness(): Define richness color scale which is colour-vision deficient and colour-blind people safe based on scientific colour maps by Fabio Crameri
color_richness_CVDCBP(): Define gen3sis richness color scale for non colour-vision deficient
plot_ranges(): Plot species ranges of the given list of species on a space
plot_richness(): Plot the richness of the given list of species on a space
plot_space(): Plot the environment variable of a given space
plot_space_overview(): Plot the outline of a given space over time
plot_species_abundance(): Plot a species' abundance on a given space
plot_species_presence(): Plot a species' presence on a given space
plot_summary(): Plot simulation default summary object
raster_plot_aesthetics(): Provides the default gen3sis2 plot aesthetics for raster spaces
set_color(): Set the color scale for plots, adding zero_col if zero values are present
sf_plot_aesthetics(): Provides the default gen3sis2 plot aesthetics for H3 and points spaces

Support functions

Functions that can be used to save, get and handle sumation information