nsga2_set_user_params

Ensemble object that will be used in the NSGA-2
algorithm to generate predictions

built_ensemble

Names of simulation parameters for which values are input
to the ensemble

parameters

Names of the simulation measures for which the ensemble
predicts

measures

Vector of desired responses for the simulation
measures, used by the fitness function to determine goodness of fit for
evolved parameter sets

desiredResponses

Minimum value of the range of each parameter to be used
in evolving parameter sets

sampleMins

Maximum value of the range of each parameter to be used
in evolving parameter sets

sampleMaxes

Creates an object of the analysis parameters that will be used to evolve
parameter sets or screen parameters for NSGA-2. The user should ensure this
is calle first, establishing this object such that it can be passed in to
the relevant method

Computer simulations are becoming a popular technique to use in attempts to further our understanding of complex systems. 'spartan', first described in our 2013 publication in PLoS Computational Biology, provided code for four techniques described in available literature which aid the analysis of simulation results, at both single and multiple timepoints in the simulation run. The first technique addresses aleatory uncertainty in the system caused through inherent stochasticity, and determines the number of replicate runs necessary to generate a representative result. The second examines how robust a simulation is to parameter perturbation, through the use of a one-at-a-time parameter analysis technique. Thirdly, a latin hypercube based sensitivity analysis technique is included which can elucidate non-linear effects between parameters and indicate implications of epistemic uncertainty with reference to the system being modelled. Finally, a further sensitivity analysis technique, the extended Fourier Amplitude Sampling Test (eFAST) has been included to partition the variance in simulation results between input parameters, to determine the parameters which have a significant effect on simulation behaviour. Version 1.3 added support for Netlogo simulations, aiding simulation developers who use Netlogo to build their simulations perform the same analyses. Version 2.0 added the ability to read all simulations in from a single CSV file in addition to the prescribed folder structure in previous versions. Version 3.0 offers significant additional functionality that permits the creation of emulations of simulation results, derived using the same sampling techniques in the global sensitivity analysis techniques, and the generation of combinations of these machine learning algorithms to one create one predictive tool, more commonly known as an ensemble model. Version 3.0 also improved the standard of the graphs produced in the original sensitivity analysis techniques, and introduced a polar plot to examine parameter sensitivity.

nsga2_set_user_params: Initialise analysis specific parameters for NSGA-2

Description

Usage

Arguments

Value