Nothing
bayesx.construct.mrf.smooth.spec <- bayesx.construct.spatial.smooth.spec <- function(object, dir, prg, data)
{
if(missing(prg))
prg <- " "
if(missing(dir))
dirok <- FALSE
else
dirok <- TRUE
if(is.null(object$xt))
stop("need to supply a map object in argument xt!")
map.name <- help.map.name(deparse(substitute(object, env = .GlobalEnv),
backtick = TRUE, width.cutoff = 500L))
if(!is.null(object$xt$map.name))
map.name <- object$xt$map.name
if(!is.list(object$xt))
object$xt <- list(object$xt)
map.name <- rmf(gsub("\\s", "", paste(map.name, sep = "", collapse = "")))
map <- object$xt$map
if(is.null(map)) {
if(!is.null(object$xt$polys))
map <- object$xt$polys
if(!is.null(object$xt$penalty))
map <- object$xt$penalty
}
if(is.null(map))
map <- object$xt$gra
if(is.null(map)) {
if(!is.list(object$xt[[1L]])) {
if(inherits(object$xt[[1L]], "gra"))
map <- object$xt[[1L]]
else
map <- object$xt
} else map <- object$xt[[1L]]
if(is.null(map)) {
map <- object$xt
if(inherits(map, "SpatialPolygons"))
map <- sp2bnd(map)
if(is.null(map) || (!is.list(map) && !inherits(map, "bnd") || !inherits(map, "gra")))
stop("need to supply a bnd or graph file object in argument xt!")
}
}
if(is(map, "nb"))
map <- nb2gra(map)
if(inherits(map, "SpatialPolygons"))
map <- sp2bnd(map)
if(!inherits(map, "bnd") && !inherits(map, "gra")) {
if(is.list(map))
class(map) <- "bnd"
else
class(map) <- "gra"
}
if(dirok) {
counter <- NULL
ok <- TRUE
files <- list.files(dir)
while(ok) {
classm <- class(map)
if(length(classm) > 1L)
if("list" %in% classm)
class(map) <- classm[classm != "list"]
mapfile <- paste(map.name, counter, ".", class(map), sep = "")[1]
if(any(grepl(mapfile, files))) {
if(is.null(counter))
counter <- 0L
counter <- counter + 1L
} else ok <- FALSE
}
mapfile <- file.path(dir, mapfile)
prgfile <- file.path(dir, prg)
prgok <- file.exists(prgfile)
} else prgok <- FALSE
if(prgok)
cat("map", map.name, "\n", file = prgfile, append = TRUE)
if(dirok) {
if(inherits(map, "bnd")) {
if(!any(is.na(poly.names <- as.integer(names(map))))) {
poly.names <- sort(poly.names)
poly.names <- as.character(poly.names)
} else poly.names <- sort(names(map))
map <- map[poly.names]
class(map) <- "bnd"
write.bnd(map = map, file = mapfile, replace = TRUE)
cmd <- paste(map.name, ".infile using ", mapfile, "\n", sep = "")
} else {
if(!is.character(map)) {
dx <- as.character(unique(data[[object$term]]))
cnm <- colnames(map)
if(!all(dx %in% cnm))
stop(paste("not all regions specified in variable", object$term, "in adjacency matrix!"))
write.gra(map = map, file = mapfile, replace = TRUE)
cmd <- paste(map.name, ".infile, graph using ", mapfile, "\n", sep = "")
} else {
stopifnot(is.character(map))
pos <- regexpr("\\.([[:alnum:]]+)$", map)
fext <- ifelse(pos > -1L, substring(map, pos + 1L), "")
if(fext == "gra")
cmd <- paste(map.name, ".infile, graph using ", path.expand(map), "\n", sep = "")
else
cmd <- paste(map.name, ".infile using ", path.expand(map), "\n", sep = "")
}
}
}
if(prgok)
cat(cmd, file = prgfile, append = TRUE)
term <- object$term
term <- paste(term, "(spatial,map=", map.name, sep = "")
term <- paste(do.xt(term, object, c("map", "polys", "penalty", "map.name")), ")", sep = "")
if(object$by != "NA")
term <- make_by(term, object, data)
return(term)
}
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