R/commonCode.R

In BUGSExamples: Collection of BUGS examples

makeExample <- function(name, parameters, nSample=20000, nBurnin=5000,
                        nThin=1, nChain=1)
{
    return(list("name"=name,
                "parameters"=parameters,
                "nSample"=nSample,
                "nBurnin"=nBurnin,
                "nThin"=nThin,
                "nChain"=nChain))
}

Air <- makeExample("Air", c("X", "theta"), nSample=50000, nBurnin=10000)

Alligators <- makeExample("Alligators", c("b", "beta", "g", "gamma"),
                          nSample=50000, nBurnin=10000)

Asia <- makeExample("Asia",
                    c("bronchitis", "either", "lung.cancer", "smoking",
                      "tuberculosis", "xray"),
                    nSample=10000, nBurnin=1000, nThin=10)

Beetles <- makeExample("Beetles", c("alpha", "beta", "rhat"))

BiRats <- makeExample("BiRats", c("mu.beta", "sigma"))

Biopsies <- makeExample("Biopsies",
                        c("error[2,1:2]", "error[3,1:3]", "error[4,1:4]", "p"))

Blockers <- makeExample("Blockers", c("d", "delta.new", "sigma"))

Bones <- makeExample("Bones", c("theta"))

Camel <- makeExample("Camel", c("Sigma2", "rho", "tau"), nSample=10000,
                     nThin=10)

Cervix <- makeExample("Cervix",
                      c("beta", "beta0C", "gamma1", "gamma2", "phi", "q"))

Dogs <- makeExample("Dogs", c("A", "B", "alpha", "beta"))

Dugongs <- makeExample("Dugongs", c("U3","alpha", "beta", "gamma","sigma"))

Dyes <- makeExample("Dyes", c("sigma2.btw","sigma2.with", "theta"),
                    nSample=10000, nThin=10, nBurnin=2500)

Endo <- makeExample("Endo", "beta", nSample=15000, nBurnin=5000)

Epil <- makeExample("Epil", c("alpha0", "alpha.Age", "alpha.Base", "alpha.BT",
                              "alpha.Trt", "alpha.V4","sigma.b","sigma.b1"),
                    nSample=15000, nBurnin=5000)

Equiv <- makeExample("Equiv", c("equiv", "mu", "phi", "pi", "sigma1", "sigma2",
                                "theta"))

Eyes <- makeExample("Eyes", c("P","lambda", "sigma"))

Eyetracking <- makeExample("Eyetracking", c("K", "deviance", "mu[92]"))

Hearts <- makeExample("Hearts", c("alpha", "beta", "delta", "theta"))

HepatitisME <- makeExample("HepatitisME", c("alpha0", "beta0", "gamma",
                                            "sigma"),
                           nSample=50000, nBurnin=10000)

Hepatitis <- makeExample("Hepatitis", c("alpha0", "beta0", "gamma", "sigma"))

Hips2 <- makeExample("Hips2", c("BL", "BQ", "C", "mean.BL", "mean.BQ","mean.C"))

Hips3 <- makeExample("Hips3", c("BL", "BQ", "C", "mean.BL", "mean.BQ",
                                "mean.C", "var.BL", "var.BQ","var.C"))

Ice <- makeExample("Ice",c("logRR", "sigma"), nSample=10000, nThin=10)

Jama <- makeExample("Jama", c("alpha.desc", "beta.desc"), nSample=15000,
                    nBurnin=5000)

Jaws <- makeExample("Jaws", c("beta0", "beta1", "mu", "Sigma"))

Kidney <- makeExample("Kidney", c("alpha", "beta.sex", "beta.dis", "r",
                                  "sigma"), nSample=50000, nBurnin=10000)

Leukfr <- makeExample("Leukfr", c("beta", "sigma"))

Leuk <- makeExample("Leuk", c("beta", "S.placebo", "S.treat"))

Line <- makeExample("Line", c("alpha", "beta", "sigma"))

Lsat <- makeExample("Lsat", c("a", "beta"))

Magnesium <- makeExample("Magnesium", c("OR", "tau"), nSample=5000)

Mice <- makeExample("Mice", c("median", "pos.control", "r", "test.sub",
                              "veh.control"))

OtreesMVN <- makeExample("OtreesMVN", c("mu", "sigma", "sigmaC"),
                         nSample=50000, nBurnin=5000)

Otrees <- makeExample("Otrees", c("mu", "sigma", "sigmaC"), nSample=30000,
                      nBurnin=10000)

Oxford <- makeExample("Oxford", c("alpha", "beta1", "beta2", "sigma"))

Pigs <- makeExample("Pigs", c("i", "p"), nSample=10000, nThin=10, nBurnin=1000)

Pigweights <- makeExample("Pigweights", "Sm")

Pumps <- makeExample("Pumps", c("alpha", "beta", "theta"))

Rats <- makeExample("Rats", c("alpha0", "beta.c", "sigma"))

Salm <- makeExample("Salm", c("alpha", "beta", "gamma", "sigma"))

Schools <- makeExample("Schools", c("beta", "gamma", "phi", "theta"))

Seeds <- makeExample("Seeds", c("alpha0", "alpha1", "alpha12", "alpha2",
                                "sigma"))

StVeit <- makeExample("StVeit", "within", nSample=50000, nBurnin=10000)

Stacks <- makeExample("Stacks", c("b", "b0", "outlier[21]", "outlier[3]",
                                  "outlier[4]", "sigma"))

Stagnantc <- makeExample("Stagnantc", c("alpha", "beta", "sigma", "x.change"))

Surgical <- makeExample("Surgical", "p")

Surgicalrand <- makeExample("Surgicalrand", c("p", "pop.mean", "sigma"))

tdf <- makeExample("t-df", "d")

Scotland <- makeExample("Scotland", c("RR","alpha0","alpha1","sigma"),
                        nSample=50000, nBurnin=10000)

LHA <- makeExample("LHA", c("RR", "alpha", "beta", "sigma.b", "sigma.h"),
                   nThin=4)

Scotland1 <- makeExample("Scotland1", c("RR", "alpha", "sigma"))

Elevation <- makeExample("Elevation", c("height.pred", "height.pred.multi"))

Forest <- makeExample("Forest",
                      c("theta0", "theta1", "theta2", "spatial.effect"),
                      nSample=20000, nBurnin=10000)

Huddersfield <- makeExample("Huddersfield",
                            c("PC.base", "PC.latent", "PC.no2",
                              "rate.base", "rate.latent", "rate.no2"),
                            nSample=60000, nBurnin=30000)

MVCAR <- makeExample("MVCAR", c("alpha", "corr", "sigma"), nSample=51000,
                     nBurnin=1000)

Shared <- makeExample("Shared", c("RR.ratio", "delta", "frac.shared",
                                  "var.shared","var.specific"),
                      nSample=100000, nBurnin=30000)

Pollution <- makeExample("Pollution", c("beta", "mu", "sigma", "sigma.err"))