initialise_netlogo_xml_file

Test for the experiment tag of the file (e.g. LHC, eFAST, etc)

EXPERIMENT

Number of the sample being processed

SAMPLE

The number of times Netlogo should repeat the experiment for each set of parameter values.

EXPERIMENT_REPETITIONS

Boolean stating whether Netlogo should produce output for each timestep.

RUN_METRICS_EVERYSTEP

The name of the function in Netlogo that sets up the simulation. Commonly is named setup.

NETLOGO_SETUP_FUNCTION

The name of the function in Netlogo that starts the simulation. Commonly named go.

NETLOGO_RUN_FUNCTION

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

MEASURES

Initialises the Netlogo setup file for this experiment

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.

initialise_netlogo_xml_file: Initialises the Netlogo setup file for this experiment

Description

Usage

Arguments

Value