Computer code

Bayesian Methods in Health Economics


General/overall files

  • R/JAGS code to run the examples (all files at once here). There’s also an accompanying instruction file
  • Utils.R: script containing some utility functions, for examples to draw traceplots of MCMC chains, or estimating the parameters of suitable distributions to obtain given values for its mean and standard deviation [Needed to run most of the other scripts]

Chapter 2

  • MCMC.R: script to run the Gibbs sampling simulations and check convergence, as in Figure 2.10
  • modelNormal.R: script to run the analysis of the Normal model (pages 69-73)
  • modelNormal.txt: JAGS code for the Bayesian model (pages 69-73)
  • phbirths.dta: Dataset used for the Normal model example - courtesy of German Rodriguez

Chapter 3

  • HEexample.R: script to run the Bayesian model to analyse the health economic problem described in the chapter (chemotherapy) and the several cost-effectiveness analyses presented throughout the chapter. This example is used throughout chapter 4 as well
  • model.txt: JAGS code for the basic cost-effectiveness analysis
  • modelEVPPI_rho.txt: JAGS code for the analysis of the Expected Value of Partial Perfect Information (EVPPI) for the parameter $\rho$
  • modelEVPPI_gamma.txt: JAGS code for the analysis of the Expected Value of Partial Perfect Information (EVPPI) for the parameter $\gamma$

Chapter 4

  • modelNormal.R: script to run the analysis of the Normal model (pages 129-141); continues the analysis from chapter 2
  • modelNormalBlocking.txt: JAGS code to run the model using blocking to improve convergence (page 133)
  • modelNormal2.txt: JAGS code to run the compute the predictive distribution (page 135)

Chapter 5

Example 1: RCT of acupuncture for chronic headache in primary care

  • acupuncture.R: script to run the cost-effectiveness analysis of acupuncture. Based on this paper
  • dataRCTacupuncture.csv: Dataset used for the acupuncture example - courtesy of David Wonderling, Richard Nixon and Richard Grieve
  • actptRCT.txt: JAGS code to run the normal/normal (on the logit/log scale) model
  • actptRCT_gamma.txt: JAGS code to run the normal/gamma (on the logit/natural scale) model
  • actptRCT_logN.txt: JAGS code to run the normal/log-normal (on the logit/natural scale) model

Example 2: Neuraminidase inhibitors to reduce influenza in healthy adults

  • EvSynth.R: script to run the cost-effectiveness analysis based on evidence synthesis for the influenza treatment with neuraminidase
  • EvSynth.txt: JAGS code to run the evidence synthesis model
  • Example 3: Markov model for the treatment of asthma
  • MarkovModel.R: script to run the cost-effectiveness analysis for the treatment of asthma
  • MarkovModel.txt: JAGS code to run the conjugated Markov model

NB: Everything works fine on my computer, originally configured with Linux, R 2.15.1 and JAGS 3.2.0. But if you experience problems with any of the code, drop me an email and I’ll fix it.

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