# 4. Running a calibration¶

In this section, the methodology of OSMOSE calibration using the sequential approach described in [ORVES17] is provided. This calibration uses the calibrar and osmose R libraries (see Section 1 for installation instructions). For a detailed description of the calibrar package, the user is referred to [ORS17].

The philosophy of the method is to assess unknown or poorly described parameters (for instance larval mortality or plankton accessibility) by fitting model outputs to observed datasets (biomass, etc.).

The calibration of the reference calibration, which is explained in details in the following, can be tested by typing in R:

rm(list=ls())

library("osmose")

# copy all that is needed for the calibration
demo = osmose_calib_demo(path = "calib/_static/")

# move to the calibration folder
setwd(demo$path) # run the calibration script #source(demo$file)

In [1]: import os

In [2]: import subprocess

In [3]: cwd = os.getcwd()

In [4]: fpath = "calib/_static/democalib.R"

In [5]: with open(fpath) as f:
...:     with open(os.devnull, "w") as DEVNULL:
...:         subprocess.call(["Rscript", fpath])
...: