MCMC I for Infectious Diseases
This module is an introduction to Markov chain Monte Carlo (MCMC) methods with some simple applications in infectious disease studies. The course includes an introduction to Bayesian statistics, Monte Carlo, MCMC, some background theory, and convergence diagnostics. Algorithms include Gibbs sampling, Metropolis-Hastings and their combinations. Familiarity with the R statistical package or other computing language would be helpful.
Time: July 18-19, 8:00 am - 2:30 pm, July 20, 8:00 am - 11:00 am
Place: https://uci.zoom.us/j/99078849451 (check Slack for passcode)
Instructors: Kari Auranen, M. Elizabeth Halloran, Vladimir Minin
Schedule:: mcmc_time_table.pdf
R tutorials: R for Beginners, Swirl (Learn R, in R), SISMID/SISG Introduction to R
Course Introduction: intro_video
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mc_mcmc2022.pdf (pages 14-18) | mh-lab.pdf | mh_lab_live | norm_mh_reduced.R |
norm_mh.R | |||
infect_time_gibbs_live | infect_time_reduced.R | ||
infect_time.R |
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mc_mcmc2022.pdf (pages 18-20) | PracticalGibbs.pdf | chainGibbs.R |
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mc_mcmc2022.pdf (pages 20-21) | betabin-lab.pdf | beta_bin_lab_live | beta_bin_reduced.R |
beta_bin.R |
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chain_bin_revisited.pdf | chain-bin-revisit-lab.pdf | model_check_live | checkmodel_reduced.R |
checkmodel.R | |||
chain_hierarchical_reduced.R | |||
chain_hierarchical.R | |||
check_hierarchical.R |
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sir_lecture.pdf | sir-lab.pdf | sir_live | SIRaugmentation_reduced.R |
SIRaugmentation.R | |||
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mc_mcmc2022.pdf (pages 21-22) | diagnostics-lab.pdf | diagnostics_live | diagnostics_reduced.R |
diagnostics.R |
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sis_lecture.pdf | sis-lab.pdf | simulateSIS_N.R | |
MH_SIS.R | |||