Nothing
#' @export
glmmBUGS <- function (formula, data, effects, modelFile = "model.txt",
initFile = "getInits.R",
family = c("bernoulli", "binomial", "poisson", "gaussian"),
spatial = NULL, spatialEffect = NULL, reparam = NULL,
prefix=NULL, priors=NULL,
brugs=length(grep("unix|linux",
.Platform$OS.type,
ignore.case=TRUE))
)
{
data = getDesignMatrix(formula, data, effects)
data = stats::na.omit(data)
covariates = attributes(data)$covariates
observations = attributes(data)$response
#if new col created, change it back for ragged
# reparam = paste(prefix, reparam, sep="")
ragged = winBugsRaggedArray(data, effects = effects, covariates = covariates,
observations = observations, prefix= prefix , reparam=reparam)
#ragged$Xreparam = ????
geostat=FALSE
if (!is.null(spatial)) {
# if spatial is a data frame, matrix, or spatialPoints or vector, use a geostatistical model
if(class(spatial) %in% c("SpatialPoints","SpatialPointsDataFrame","complex","data.frame","matrix"))
geostat=TRUE
ragged = addSpatial(spatial, ragged, spatialEffect, prefix= prefix)
}
thepql = glmmPQLstrings(effects = effects, covariates = covariates,
observations = observations, data = data, family = family)
startingValues = getStartingValues(pql = thepql, ragged = ragged, prefix=prefix, reparam = reparam )
startingFunction(startingValues, file=initFile)
spatialEffect = grep("^N[[:graph:]]+Spatial$", names(ragged),
value = T)
spatialEffect = gsub("^N", "", spatialEffect)
spatialEffect = gsub("Spatial$", "", spatialEffect)
effects = paste(prefix, effects, sep="")
writeBugsModel(file=modelFile, effects = effects, covariates = covariates,
observations = observations, family = family, spatial = spatialEffect,
geostat=geostat,
prefix= attributes(ragged)$prefix, reparam =reparam, priors=priors, brugs=brugs)
return(list(ragged = ragged, startingValues = startingValues,
pql = thepql))
}
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