run_simulation {gen3sis}

Run a simulation in gen3sis and return a summary object possibly saving outputs and plots to the output folder

Description

Run a simulation in gen3sis and return a summary object possibly saving outputs and plots to the output folder

Usage

run_simulation(
  config = NA,
  landscape = NA,
  output_directory = NA,
  timestep_restart = NA,
  save_state = NA,
  call_observer = "all",
  enable_gc = FALSE,
  verbose = 1
)

Arguments

config

configuration file for the simulation or configuration object derived from a config file

landscape

directory where the all_geo_hab and distance_matrices reside

output_directory

directory for the simulation output

timestep_restart

set the start time time-step. If timestep_restart=NA (default), start at the oldest available landscape. If timestep_restart="ti", start from the last available time-step. If a number "x", start at time-step x (e.g. timestep_restartstart=6)

save_state

save the internal state of the simulation for restarts. If save_state=NA (default), do not save any internal state of the simulation. If save_state="all", save all time-step. If save_state="last", saves only last time-step. If a vector, saves the desired time-steps (e.g. save_state=c(1,3,5))

call_observer

call observer functions. If call_observer="all" (default), call all time-steps. If call_observer=NA, calls the start and end times. If a number "X", call call_observer at x time-steps equally spaced between start and end steps. For example, on a simulation with start time of 1 and end time of 20, call_observer=1 calls the observer function at time-steps 1, 11 and 20.

enable_gc

enable gc in case of memory shortages

verbose

integer value (i.e. 0, 1 ,2 or 3). If verbose=0, no printed statement. If verbose=1 (default), print time-step progress. If verbose=2, enable additional progress outputs regarding current time-step. If verbose=3, enable additional information from within modules

Details

This function runs a simulation with defined landscape and config objects. Possibly plot and save specified outputs as defined in the end_of_timestep_observer function inside the config object

Value

a summary object containing a minimal summary on simulation and dynamics progress (alive, speciations, extinctions) as well as useful simulation data

See Also

plot_summary create_input_config create_input_landscape

Examples

# get path or correct input objects
datapath <- system.file(file.path("extdata", "CaseStudy1"), package="gen3sis")

# run simulation and store summary obejct to sim
sim <- run_simulation(config = file.path(datapath,"config/config_fast.R"), 
                landscape = file.path(datapath,"landscape"),
                output_directory = tempdir())

# plot summary object
plot_summary(sim)