efast_process_netlogo_result

Directory where the simulation runs can be found

FILEPATH

Name of the result file generated by
Netlogo, for an eFAST parameter sample.

EFASTSAMPLE_RESULTFILENAME

Array containing the names of the parameters of which
parameter samples will be generated

PARAMETERS

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

NUMCURVES

The number of parameter subsets that were generated
from each curve in the eFAST design

NUMSAMPLES

Array containing the names of the Netlogo output measures
which are used to analyse the simulation.

MEASURES

Name of the result file that will be produced which
summarises all results

RESULTFILENAME

Timestep of the Netlogo simulation being analysed.

TIMESTEP

Takes each parameter value set generated by eFAST in turn, and analyses the
Netlogo simulation results. For each parameter set, there will be n
simulation results. This method goes through these results, producing
a file containing the median of each output measure for each of the n runs.
Thus, if a Netlogo simulation was replicated 10 times, the median file will
contain 10 medians for each simulation output measure. The user should then
run <code>efast_get_overall_medians</code> and
<code>efast_run_Analysis</code> to analyse the results

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.

efast_process_netlogo_result: Analyses Netlogo simulation data for parameter sets generated for eFAST

Description

Usage

Arguments