# 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.