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Calibration and Validation Install
To run the calibration, the following packages need to be installed manually.
The fks package provides algorithms for fitting free-knot splines for data with one independent variable and one dependent variable. Four free-knot spline algorithms are provided for the case where the number of knots is known in advance. A knot-search algorithm is provided for the case where the number of knots is not known in advance. In addition, methods are available to compute the fitted values, the residuals and the coefficients of the splines, and to plot the results, along with a method to summarise the results. This package is used to estimate a flexible selectivity by the empirical.selectivity package described in the next section.
This package must be installed from Ricardo Oliveros-Ramos's fork:
library("devtools")
install_github("roliveros-ramos/fks")or
library("pak")
pak("roliveros-ramos/fks")The empirical.selectivity (https://github.com/roliveros-ramos/empirical.selectivity/) package contains empirical selectivity fitting and diagnostics functions. This package is used to estimate the fishing selectivity during the OSMOSE initialisation process when catch-at-length is provided.
This package must be installed from Ricardo Oliveros-Ramos's fork:
library("devtools")
install_github("roliveros-ramos/empirical.selectivity")or
library("pak")
pak("roliveros-ramos/empirical.selectivity")The calibrar package (https://github.com/roliveros-ramos/calibrar/) allows the parameter estimation or calibration of complex models, including stochastic ones. It is a generic tool that can be used for fitting any type of models, especially those with non-differentiable objective functions [@oliveros2016calibrar]. It supports multiple phases and constrained optimisation. It implements maximum likelihood estimation methods and automated construction of the objective function from simulated model outputs. This is the package that is currently used for the calibration of OSMOSE.
The calibrar package must be installed from the drat OSMOSE repository (and not it's CRAN version):
library("devtools")
install.packages("calibrar", repo="https://osmose-model.github.io/drat/")
The drat OSMOSE repository will always contain the latest tested functional version for OSMOSE calibration.