Computer code

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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