bitrugs: Bayesian Inference of Transmission Routes Using Genome Sequences

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

Author
Colin Worby
Date of publication
2016-05-24 23:30:13
Maintainer
Colin Worby <cworby@hsph.harvard.edu>
License
GPL-3
Version
0.1

View on CRAN

Man pages

bitrugs-internal
Internal functions
bitrugs-package
Bayesian Inference of Transmission Routes Using Genome...
hospitaldata
Example hospital data
mcmcoutput
Example MCMC output
plot_transnetwork
Plot transmission networks
simulate_data
Nosocomial transmission data simulation
simulate_data_dates
Nosocomial transmission data simulation with fixed dates.
traceplots
Create MCMC trace plots
translinks
Calculate tree distance
transmission_analysis
Estimate transmission dynamics and parameters

Files in this package

bitrugs
bitrugs/src
bitrugs/src/wgs_mcmc.c
bitrugs/src/wgsmcmc_head.h
bitrugs/src/wgs_functions.c
bitrugs/NAMESPACE
bitrugs/data
bitrugs/data/hospitaldata.rda
bitrugs/data/mcmcoutput.rda
bitrugs/R
bitrugs/R/networkplots.r
bitrugs/R/transmissionanalysis.r
bitrugs/R/simulatedata.r
bitrugs/MD5
bitrugs/DESCRIPTION
bitrugs/man
bitrugs/man/plot_transnetwork.Rd
bitrugs/man/bitrugs-package.Rd
bitrugs/man/traceplots.Rd
bitrugs/man/simulate_data.Rd
bitrugs/man/hospitaldata.Rd
bitrugs/man/bitrugs-internal.Rd
bitrugs/man/transmission_analysis.Rd
bitrugs/man/simulate_data_dates.Rd
bitrugs/man/translinks.Rd
bitrugs/man/mcmcoutput.Rd