run.ord: ~~function to do ... ~~

In jservadio/TrialistNof1: Bayesian N-of-1 calculations

Usage

run.ord(Y, Treat, Covs, ncat, model = "cumlogit", nChains = 3, conv.limit = 1.05, niters = 50000, nruns = 5000, setsize = 4000, betaprior, dcprior, c1prior, path)

Arguments

Y
Treat
Covs
ncat
model
nChains
conv.limit
niters
nruns
setsize
betaprior
dcprior
c1prior
path

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (Y, Treat, Covs, ncat, model = "cumlogit", nChains = 3, 
    conv.limit = 1.05, niters = 50000, nruns = 5000, setsize = 4000, 
    betaprior, dcprior, c1prior, path) 
{
    nobs = length(Y)
    if (!is.null(Covs)) 
        Covs = as.matrix(Covs)
    prior = prior.ord(Covs, betaprior, dcprior, c1prior, slopeprior = list("norm", 
        0, 0.1))
    inInits = inits.ord(Y, Covs, Treat, ncat)
    inData <- data.ord(Y, Covs, ncat, prior, Treat)
    model.ord(Covs, prior, path)
    pars.to.save <- c("beta", "or", "c", "p")
    if (!is.null(Covs)) 
        pars.to.save = c(pars.to.save, "slope")
    jags.out <- jags.fit(inData, inInits, pars.to.save, model, 
        "model.txt", nChains, niters, conv.limit, setsize, nruns, 
        Covs)
    burn.in <- jags.out[[1]]
    no.runs <- jags.out[[2]]
    samples <- jags.out[[3]]
    varnames <- dimnames(samples)[[3]]
    nvars <- dim(samples)[3]
    beta.vars <- grep("beta", varnames)
    beta <- as.vector(samples[, , beta.vars])
    or.vars <- grep("or", varnames)
    or <- as.vector(samples[, , or.vars])
    c.vars <- grep("c", varnames)
    c <- matrix(samples[, , c.vars], c(no.runs * nChains, length(c.vars)))
    p.vars <- grep("p", varnames)
    p <- array(matrix(samples[, , p.vars], c(no.runs * nChains, 
        length(p.vars))), c(no.runs * nChains, nobs, ncat))
    if (!is.null(Covs)) {
        slope.vars <- grep("slope", varnames)
        slope <- samples[, , slope.vars]
    }
    if (is.null(Covs)) {
        out <- list(burn.in, no.runs, Y, beta, or, c, p)
        names(out) <- c("Burn In", "Number runs per chain", "Y", 
            "beta", "or", "c", "p")
    }
    else {
        out <- list(burn.in, no.runs, Y, beta, or, p, slope)
        names(out) <- c("Burn In", "Number runs per chain", "Y", 
            "beta", "or", "p", "Slopes")
    }
    return(out)
  }

jservadio/TrialistNof1 documentation built on May 20, 2019, 2:08 a.m.