analyze: function to do ...
In jservadio/TrialistNof1: Bayesian N-of-1 calculations

Usage Arguments Examples

analyze(Pain, Fatigue, Drowsy, Sleep, Thinking, Constipation, Treat, Neuropain, score.range = c(30, 4, 5, 4, 4, 4, 30), Covs, slopeprior, nChains = 3, conv.limit = 1.05, niters = 50000, nruns = 5000, setsize = 4000, alphaprior, beta.norm.prior, beta.ord.prior, c1prior, dcprior, varprior, varprior.params, path = "")

`Pain`
`Fatigue`
`Drowsy`
`Sleep`
`Thinking`
`Constipation`
`Treat`
`Neuropain`
`score.range`
`Covs`
`slopeprior`
`nChains`
`conv.limit`
`niters`
`nruns`
`setsize`
`alphaprior`
`beta.norm.prior`
`beta.ord.prior`
`c1prior`
`dcprior`
`varprior`
`varprior.params`
`path`

##---- 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 (Pain, Fatigue, Drowsy, Sleep, Thinking, Constipation, 
    Treat, Neuropain, score.range = c(30, 4, 5, 4, 4, 4, 30), 
    Covs, slopeprior, nChains = 3, conv.limit = 1.05, niters = 50000, 
    nruns = 5000, setsize = 4000, alphaprior, beta.norm.prior, 
    beta.ord.prior, c1prior, dcprior, varprior, varprior.params, 
    path = "") 
{
    nobs = length(Pain)
    stopifnot(length(Pain) == nobs, length(Fatigue) == nobs, 
        length(Drowsy) == nobs, length(Sleep) == nobs, length(Thinking) == 
            nobs, length(Constipation) == nobs, length(Neuropain) == 
            nobs, length(Treat) == nobs)
    stopifnot(length(varprior) == 2)
    stopifnot(length(alphaprior) == 3, length(beta.norm.prior) == 
        3, length(beta.ord.prior) == 3)
    stopifnot(length(dcprior) == 3, length(c1prior) == 3, length(varprior.params) == 
        2)
    varprior = as.list(varprior)
    alphaprior = as.list(alphaprior)
    beta.norm.prior = as.list(beta.norm.prior)
    beta.ord.prior = as.list(beta.ord.prior)
    dcprior = as.list(dcprior)
    outnames = c("Pain", "Fatigue", "Drowsy", "Sleep", "Thinking", 
        "Constipation", "Neuropathic Pain")
    names(score.range) = outnames
    Pain.out = run.norm(Pain, Treat, Covs, "normal", "hom", nChains, 
        conv.limit, niters, nruns, setsize, slopeprior, alphaprior, 
        beta.norm.prior, varprior, varprior.params, path = "")
    Fatigue.out = run.ord(Fatigue, Treat, Covs, score.range[2] + 
        1, "cumlogit", nChains, conv.limit, niters, nruns, setsize, 
        beta.ord.prior, dcprior, c1prior, path)
    Drowsy.out = run.ord(Drowsy, Treat, Covs, score.range[3] + 
        1, "cumlogit", nChains, conv.limit, niters, nruns, setsize, 
        beta.ord.prior, dcprior, c1prior, path)
    Sleep.out = run.ord(Sleep, Treat, Covs, score.range[4] + 
        1, "cumlogit", nChains, conv.limit, niters, nruns, setsize, 
        beta.ord.prior, dcprior, c1prior, path)
    Thinking.out = run.ord(Thinking, Treat, Covs, score.range[5] + 
        1, "cumlogit", nChains, conv.limit, niters, nruns, setsize, 
        beta.ord.prior, dcprior, c1prior, path)
    Constipation.out = run.ord(Constipation, Treat, Covs, score.range[6] + 
        1, "cumlogit", nChains, conv.limit, niters, nruns, setsize, 
        beta.ord.prior, dcprior, c1prior, path)
    Neuropain.out = run.norm(Neuropain, Treat, Covs, "normal", 
        "hom", nChains, conv.limit, niters, nruns, setsize, slopeprior, 
        alphaprior, beta.norm.prior, varprior, varprior.params, 
        path = "")
    Pain.treat.diff = Pain.out[["beta"]]
    Fatigue.treat.diff = treat.diffs(Fatigue.out[["p"]], Treat)
    Drowsy.treat.diff = treat.diffs(Drowsy.out[["p"]], Treat)
    Sleep.treat.diff = treat.diffs(Sleep.out[["p"]], Treat)
    Thinking.treat.diff = treat.diffs(Thinking.out[["p"]], Treat)
    Constipation.treat.diff = treat.diffs(Constipation.out[["p"]], 
        Treat)
    Neuropain.treat.diff = Neuropain.out[["beta"]]
    Pain.treat.diff.change = treat.diff.change(Pain.treat.diff, 
        score.range[1])
    Fatigue.treat.diff.change = treat.diff.change(Fatigue.treat.diff, 
        score.range[2])
    Drowsy.treat.diff.change = treat.diff.change(Drowsy.treat.diff, 
        score.range[3])
    Sleep.treat.diff.change = treat.diff.change(Sleep.treat.diff, 
        score.range[4])
    Thinking.treat.diff.change = treat.diff.change(Thinking.treat.diff, 
        score.range[5])
    Constipation.treat.diff.change = treat.diff.change(Constipation.treat.diff, 
        score.range[6])
    Neuropain.treat.diff.change = treat.diff.change(Neuropain.treat.diff, 
        score.range[1])
    change.interval = round(rbind(Pain.treat.diff.change[[1]], 
        Fatigue.treat.diff.change[[1]], Drowsy.treat.diff.change[[1]], 
        Sleep.treat.diff.change[[1]], Thinking.treat.diff.change[[1]], 
        Constipation.treat.diff.change[[1]], Neuropain.treat.diff.change[[1]]), 
        3)
    change.probs = round(rbind(Pain.treat.diff.change[[2]], Fatigue.treat.diff.change[[2]], 
        Drowsy.treat.diff.change[[2]], Sleep.treat.diff.change[[2]], 
        Thinking.treat.diff.change[[2]], Constipation.treat.diff.change[[2]], 
        Neuropain.treat.diff.change[[2]]), 3)
    output <- list()
    for (i in 1:nrow(change.interval)) {
        output[[i]] = list(interval = structure(as.list(change.interval[i, 
            ]), names = c("P025", "Median", "P975")), probs = structure(as.list(change.probs[i, 
            ]), names = paste("Proportion", c("< -0.2", "-0.2 - 0", 
            "0 - 0.2", "> 0.2"))))
    }
    names(output) = outnames
    return(output)
  }