lhc_generatePRCoEffs_db_link

Set of experiment results from the DB

db_results

parameters

measures

Way to calculate the correlation coefficient: Pearson's
("p"), Spearman's ("s"), and Kendall's ("k"). Default is p

cor_calc_method

For each parameter, and each simulation output measure, calculates the
Partial Rank Correlation Coefficient between the parameter value and the
simulation results, giving a statistical measurement of any effect that
is present. In this case, results are mined from a database, as created by
the spartanDB package, and the statistics returned for adding back to the DB.

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

lhc_generatePRCoEffs_db_link function

Generate Partial Rank Correlation Coefficients for parameter/response pairs for results in database — lhc_generatePRCoEffs_db_link

Generate Partial Rank Correlation Coefficients for parameter/response pairs for results in database

lhc_generatePRCoEffs_db_link: Generate Partial Rank Correlation Coefficients for parameter/response pairs for results in database

Description

Usage

Arguments