How would a person dput()
an S4 object? I tried this
require(sp)
require(splancs)
plot(0, 0, xlim = c(-100, 100), ylim = c(-100, 100))
poly.d <- getpoly() #draw a pretty polygon - PRETTY!
poly.d <- rbind(poly.d, poly.d[1,]) # close the polygon because of Polygons() and its kin
poly.d <- SpatialPolygons(list(Polygons(list(Polygon(poly.d)), ID = 1)))
poly.d
dput(poly.d)
Notice that if I dput()
an S4 object, I cannot reconstruct it again. Your thoughts?
The S4 system in R is a system for object oriented programing. Confusingly, R has support for at least 3 different systems for object oriented programming: S3, S4 and S5 (also known as reference classes).
We can check if an object is an S4 object through the function isS4() . The function setClass() returns a generator function. This generator function (usually having same name as the class) can be used to create new objects. It acts as a constructor.
As it currently stands, you cannot dput
this object. The code of dput
contains the following loop:
if (isS4(x)) {
cat("new(\"", class(x), "\"\n", file = file, sep = "")
for (n in slotNames(x)) {
cat(" ,", n, "= ", file = file)
dput(slot(x, n), file = file, control = control)
}
cat(")\n", file = file)
invisible()
}
This handles S4 objects recursively, but it relies on the assumption an S3 object will not contain an S4 object, which in your example does not hold:
> isS4(slot(poly.d,'polygons'))
[1] FALSE
> isS4(slot(poly.d,'polygons')[[1]])
[1] TRUE
Edit: Here is a work-around the limitations of dput
. It works for the example you provided, but I don't think that it will work in general (e.g. it does not handle attributes).
dput2 <- function (x,
file = "",
control = c("keepNA", "keepInteger", "showAttributes")){
if (is.character(file))
if (nzchar(file)) {
file <- file(file, "wt")
on.exit(close(file))
}
else file <- stdout()
opts <- .deparseOpts(control)
if (isS4(x)) {
cat("new(\"", class(x), "\"\n", file = file, sep = "")
for (n in slotNames(x)) {
cat(" ,", n, "= ", file = file)
dput2(slot(x, n), file = file, control = control)
}
cat(")\n", file = file)
invisible()
} else if(length(grep('@',capture.output(str(x)))) > 0){
if(is.list(x)){
cat("list(\n", file = file, sep = "")
for (i in 1:length(x)) {
if(!is.null(names(x))){
n <- names(x)[i]
if(n != ''){
cat(" ,", n, "= ", file = file)
}
}
dput2(x[[i]], file = file, control = control)
}
cat(")\n", file = file)
invisible()
} else {
stop('S4 objects are only handled if they are contained within an S4 object or a list object')
}
}
else .Internal(dput(x, file, opts))
}
And here it is in action:
> dput2(poly.d,file=(tempFile <- tempfile()))
> poly.d2 <- dget(tempFile)
> all.equal(poly.d,poly.d2)
[1] TRUE
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