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bitrugs (version 0.1)

Bayesian Inference of Transmission Routes Using Genome Sequences

Description

MCMC methods to estimate transmission dynamics and infection routes in hospitals using genomic sampling data.

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Version

Install

install.packages('bitrugs')

Monthly Downloads

11

Version

0.1

License

GPL-3

Maintainer

Colin Worby

Last Published

May 24th, 2016

Functions in bitrugs (0.1)

bitrugs-internal

Internal functions
hospitaldata

Example hospital data
plot_transnetwork

Plot transmission networks
simulate_data

Nosocomial transmission data simulation
bitrugs

Bayesian Inference of Transmission Routes Using Genome Sequences
traceplots

Create MCMC trace plots
translinks

Calculate tree distance
mcmcoutput

Example MCMC output
simulate_data_dates

Nosocomial transmission data simulation with fixed dates.
transmission_analysis

Estimate transmission dynamics and parameters