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Source code modules

The model is individual-based so that information can be stored for each person in the simulated population. It is capable of simulating the entire population of the UK, upwards of sixty-million distinct individuals tracked. Other features of the model include parameter values which depend on age, sex, and birthplace. Realistic demography and the migration of individuals to and from the study population are also incorporated. The model is a discrete-event simulation, which moves through time continuously by processing events in chronological order rather than moving through time by small finite time steps.

The individual-based nature of the model allowed recording genetic strain types for each infection and disease case. The model was intended to reproduce genotype clustering patterns seen in observed, genotyped cases to help reveal how these patterns may have been generated and to compare the level of genotype clustering to the proportion of cases due to recent transmission in the simulation.

Timing tests indicated that IBM version ran faster than finite difference approximations to partial differential equations for the same level of accuracy.

Modules

Description

Module

Date

Formats

Main simulation module  

tb36gen.c  

2012/12/17  

PDF

Text

Secondary service routines  

service.c  

2012/12/16  

Text

Common headers  

common.ch  

2012/12/16  

Text

Parameter fitting  

fit5i.c  

2012/12/16  

Text

Fitting convergence tests  

converge.c  

2012/12/16  

Text

Multiprocessing interface  

mpi.c  

2012/12/16  

Text

Schedule future events  

schedule.c  

2012/12/16  

Text

Random numbers for arbitrary distributions  

randh.c  

2012/12/16  

Text

Centinel file input/output  

fileio.c  

2012/12/16  

Text

Special headers  

fileio.ch  

2012/12/16  

Text

Random numbers on the unit interval  

rand.c  

2012/12/16  

Text

Alphabetic or numeric ordering  

sort.c  

2012/12/16  

Text

Error interface  

error.c  

2012/12/16  

Text