README.md

In wdelva/MABC: Approximate Bayesian Computation with MICE

MABC

Model calibration as a missing data problem: Approximate Bayesian Computation with MICE (Multivariate Imputation by Chained Equations)

MABC is an R package for calibrating stochastic simulation models to data. It implements a sequential Approximate Bayesian Computation method that employs MICE (Multivariate Imputation by Chained Equations) as an emulator to link model inputs to model outputs.

CONTENTS

This repository holds the source code for the MABC package:

• Code files
• System and software requirements
• Copyright and licensing information
• Contact information

CODE FILES

All code is written in R. R is a statistical programming language and software package that is distributed under a GNU General Public License. R documentation and software is available for free download through the R Project for Statistical Computing website at http://www.r-project.org. The software is available as an executable file for a wide variety of operating systems and computer architectures, and a compilable binary is also available should you need it.

MABC.R -- The core function to run MABC.

mice.parallel, model.mpi.run.R, model.parallelrun.R -- Helper functions used by the above two functions.

SYSTEM AND SOFTWARE REQUIREMENTS

Operating system

We have only tested this code on personal computers (OS X Version 10.11.6) and the golett cluster of the Flemish Supercomputer Centre (VSC).

Required software

Open MPI or Microsoft MPI Redistributable Package, and Rmpi. For installation instructions, see http://fisher.stats.uwo.ca/faculty/yu/Rmpi/.

R version >= 3.4.0

In addition, a long list of auxiliary R packages is required to run the functions in this package. All of these dependencies will get installed automatically when installing the software.

install.packages("devtools")

library(devtools)

install_github("wdelva/MABC")

COPYRIGHT AND LICENSING INFORMATION

All files are copyright protected and are made available under the GPL 3.0 License https://www.gnu.org/licenses/gpl-3.0.en.html. This means that this work is suitable for commercial use, that licensees can modify the work, that they must release the source alongside with Derivative Work, and that Derivative Work must be released under the same terms.

CONTACT INFORMATION

Please contact Prof Wim Delva with questions regarding the files provided and their authorized usage:

Wim Delva Email: [e-mail]

wdelva/MABC documentation built on May 27, 2019, 9:56 a.m.