ensemble_abc_wrapper

<p>Set of parameter values generated by an EasyABC method</p>

<p>Provides a means of running the ensemble within the EasyABC methods. This
method should be stated as the "model" argument of EasyABC methods such as
ABC_sequential. Note that as arguments cannot be passed to the model
function, these must be created before calling any EasyABC method (see
code description for <code>create_abc_settings_object</code>. The created object
most contain the simulation parameters, output measures, an ensemble object
to be run, declared as built_ensemble, and whether or not the prior
(and generated predictions) should be normalised (normalise). Should this
object not exist an error message will be produced.</p>

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.

Kieran Alden

spartan

Simulation Parameter Analysis R Toolkit ApplicatioN: 'spartan'

Mark Read

Paul Andrews

Jason Cosgrove

Mark Coles

Jon Timmis

ensemble_abc_wrapper function

Wrapper to allow EasyABC functions to run using Ensemble — ensemble_abc_wrapper

Wrapper to allow EasyABC functions to run using Ensemble

ensemble_abc_wrapper: Wrapper to allow EasyABC functions to run using Ensemble

Description

Usage

Arguments

Value