dcmle (version 0.2-4)

dcmle-package: Hierarchical Models Made Easy with Data Cloning

Description

S4 classes around infrastructure provided by the dclone package to make package development with data cloning for hierarchical models easy as a breeze.

Details

The package defines S4 object classes for plain BUGS models ("gsFit", after BU*GS*/JA*GS*), and BUGS models made ready for data cloning ("dcFit"). It also defines virtual classes for S3 object classes defined in the dclone and coda packages. The S4 class "dcmle" is a fitted model object containing MCMC results as returned by the dcmle function. These object classes are easily extensible to allow inclusion into functions fitting specific models to the data (see Examples). sourceDcExample can be used to get examples from http://dcr.r-forge.r-project.org/examples gathered from various sources (WinBUGS Manual, articles, books, etc.). This under continuous development, and used in the testing suite of the dclone package. Contributions of examples are welcome.

References

http://cran.r-project.org/package=dcmle, http://dcr.r-forge.r-project.org

See Also

Fitting wrapper function: dcmle Object classes: "dcmle", "codaMCMC", "dcCodaMCMC" Creator functions makeGsFit and makeDcFit

Examples

## Data and model taken from Ponciano et al. 2009
## Ecology 90, 356-362.

## Function to create template object for the Beverton-Holt model
## R CMD check will not choke on character representation of model
## the convenient makeDcFit creator function is used here
bevholtFit <- 
function(y) {
makeDcFit(
  data = list(ncl=1, n=length(y), Y=dcdim(data.matrix(y))),
  model = structure(
    c("model {",
      "for (k in 1:ncl) {",
      "for(i in 2:(n+1)) {",
      "Y[(i-1), k] ~ dpois(exp(X[i, k]))",
      "X[i, k] ~ dnorm(mu[i, k], 1 / sigma^2)",
      "mu[i,k] <- X[(i-1),k]+log(lambda)-log(1+beta*exp(X[(i-1),k]))",
      "}",
      "X[1, k] ~ dnorm(mu0, 1 / sigma^2)",
      "}",
      "beta ~ dlnorm(-1, 1)",
      "sigma ~ dlnorm(0, 1)",
      "tmp ~ dlnorm(0, 1)",
      "lambda <- tmp + 1",
      "mu0 <- log(2)  + log(lambda) - log(1 + beta * 2)",
      "}"),
      class = "custommodel"),
  multiply = "ncl",
  unchanged = "n",
  params <- c("lambda","beta","sigma"))
}
## S4 class 'bevholtMle' extends the 'dcMle' class
## it can have additional slots
setClass("bevholtMle", 
    representation(y="numeric", title="character"), 
    contains = "dcmle")
## Function to fit the Beverton-Holt model to data
bevholt <- function(y, n.clones, ...) {
    new("bevholtMle",
        dcmle(bevholtFit(y), n.clones=n.clones, ...),
        y = y,
        title = "Beverton-Holt Model")
}
## Show method with appropriate heading
setMethod("show", "bevholtMle", function(object)
    show(summary(as(object, "dcmle"), object@title)))
paurelia <- c(17,29,39,63,185,258,267,392,510,
    570,650,560,575,650,550,480,520,500)
(m <- bevholt(paurelia, n.clones=2, n.iter=1000))
vcov(m)
m@y