Getting Started Running a First Simulation

Running Osmose demo

Now that the R package is installed, let's try to run the Osmose demo configuration.

First, launch an R console and load the Osmose library:

library(osmose)
ls("package:osmose")

Now, call the osmose_demo function, which will copy the reference configuration into your working directory:

demo = osmose_demo(path = "original-demo", config="eec_4.3.0")
demo

The demo object contains the location of the configuration file and extra arguments.

If some parameters provided in the default configuration need to be overwritten, an extra_args argument can be provided. It must have the following format:

extra_args = "-Psimulation.time.nyear=15 -Poutput.recordfrequency.ndt=1"

Here, the simulation.time.nyear and output.recordfrequency.ndt have been modified. The updated demo configuration can then be created as follows:

demo2 = osmose_demo(path = "modified-demo", config="eec_4.3.0", extra_args=extra_args)
demo2

Now, you can run the Osmose model as follows:

run_osmose(demo$config_file, parameters=demo$extra_args, force=TRUE)

The first argument is the Osmose configuration file, the parameters argument allows you to overwrite some of the original parameters. The force argument allows you to run the configuration even if the configuration version number is inconsistent with the Osmose version.

Warning

Use the force argument with caution!

If you installed Osmose from sources, as discussed in @sec-install-sources, and you want to use the Jar file compiled with Maven, set the version argument to NULL:

run_osmose(demo$config_file, parameters=demo$extra_args, force=TRUE, version=NULL)

While Osmose is running, an osmose.log file is written in the working directory. This file gives you some information about the simulation. If it has finished properly, you should see:

osmose[info] Simulation 0 completed (time ellapsed: 123 seconds)
osmose[info] *********************************************
osmose[info] OSMOSE Model copyright © IRD
osmose[info] *********************************************

Now that the simulation has been properly completed, you can read the Osmose output files by using the read_osmose function:

output = read_osmose(demo$output_dir)
output

You can now plot some of the available fields using the plot function. For example, to plot the biomass for all the species:

plot(output, what="biomass")

To plot the abundance of a single species:

plot(output, what="abundance", species=c(0, 1, 2))

You can also change the type of the plot as follows:

plot(output, what="abundance", species=c(0, 1), type=3)