Updating an existing Rdata file
I have found myself in the position of needing to update one or two data objects in an Rdata file previously created using save . If I'm not careful to load the file I can forget to re-save some objects in the file. As an example, I'm working on a package with some objects stored in sysdata.rda (look-up tables for internal use which I do not want to export) and only want to worry about updating individual objects.
I haven't managed to work out if there is a standard way to do this, so created my own function.
resave <- function (..., list = character(), file = stop("'file' must be specified")) {
# create a staging environment to load the existing R objects
stage <- new.env()
load(file, envir=stage)
# get the list of objects to be "resaved"
names <- as.character(substitute(list(...)))[-1L]
list <- c(list, names)
# copy the objects to the staging environment
lapply(list, function(obj) assign(obj, get(obj), stage))
# save everything in the staging environment
save(list=ls(stage, all.names=TRUE), file=file)
}
It does seem like overkill though. Is there a better/easier way to do this?
As an aside, am I right in assuming that a new environment created in the scope of a function is destroyed after the function call?
Here is a slightly shorter version:
resave <- function(..., list = character(), file) {
previous <- load(file)
var.names <- c(list, as.character(substitute(list(...)))[-1L])
for (var in var.names) assign(var, get(var, envir = parent.frame()))
save(list = unique(c(previous, var.names)), file = file)
}
I took advantage of the fact the load function returns the name of the loaded variables, so I could use the function's environment instead of creating one. And when using get , I was careful to only look in the environment from which the function is called, ie parent.frame() .
Here is a simulation:
x1 <- 1
x2 <- 2
x3 <- 3
save(x1, x2, x3, file = "abc.RData")
x1 <- 10
x2 <- 20
x3 <- 30
resave(x1, x3, file = "abc.RData")
load("abc.RData")
x1
# [1] 10
x2
# [1] 2
x3
# [1] 30
I have added a refactored version of @flodel's answer in the stackoverflow package. It uses environments explicitly to be a bit more defensive.
resave <- function(..., list = character(), file) {
e <- new.env()
load(file, e)
list <- union(list, as.character(substitute((...)))[-1L])
copyEnv(parent.frame(), e, list)
save(list = ls(e, all.names=TRUE), envir = e, file = file)
}
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