generate_efast_parameter_sets

Directory where the parameter samples should be output to

FILEPATH

The number of 'resamples' to perform (see eFAST
documentation) - recommend using at least 3

NUMCURVES

The number of parameter subsets to generate - should be at
least 65 for eFAST

NUMSAMPLES

Array containing the names of the parameters of which
parameter samples will be generated. For eFAST, remember to add a
parameter named 'Dummy'

PARAMETERS

Array containing the minimum value that should be used for each
parameter and the dummy. Sets a lower bound on sampling space

PMIN

Array containing the maximum value that should be used for each
parameter and the dummy. Sets an upper bound on sampling space

PMAX

Use the eFAST approach to generate parameter sets

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.

generate_efast_parameter_sets: Use the eFAST approach to generate parameter sets

Description

Usage

Arguments