Recursive copying of nested environments, and other "hard to copy" objects

When copying environments and all the objects contained within them, there are no copies made: it is a pass-by-reference operation. Sometimes, a deep copy is needed, and sometimes, this must be recursive (i.e., environments inside environments).

Copy(object, ...)

# S4 method for class 'ANY'
Copy(
  object,
  filebackedDir,
  drv = getDrv(getOption("reproducible.drv", NULL)),
  conn = getOption("reproducible.conn", NULL),
  verbose = getOption("reproducible.verbose"),
  ...
)

# S4 method for class 'data.table'
Copy(object, ...)

# S4 method for class 'list'
Copy(object, ...)

# S4 method for class 'refClass'
Copy(object, ...)

# S4 method for class 'data.frame'
Copy(object, ...)

Arguments

object

An R object (likely containing environments) or an environment.

...

Only used for custom Methods

filebackedDir

A directory to copy any files that are backing R objects, currently only valid for Raster classes. Defaults to .reproducibleTempPath(), which is unlikely to be very useful. Can be NULL, which means that the file will not be copied and could therefore cause a collision as the pre-copied object and post-copied object would have the same file backing them.

drv

if using a database backend, drv must be an object that inherits from DBIDriver e.g., from package RSQLite, e.g., SQLite

conn

an optional DBIConnection object, as returned by dbConnect().

verbose

Numeric, -1 silent (where possible), 0 being very quiet, 1 showing more messaging, 2 being more messaging, etc. Default is 1. Above 3 will output much more information about the internals of Caching, which may help diagnose Caching challenges. Can set globally with an option, e.g., options('reproducible.verbose' = 0) to reduce to minimal

Value

The same object as object, but with pass-by-reference class elements "deep" copied. reproducible has methods for several classes.

Details

To create a new Copy method for a class that needs its own method, try something like shown in example and put it in your package (or other R structure).

See also

.robustDigest(), Filenames()

Author

Eliot McIntire

Examples

e <- new.env()
e$abc <- letters
e$one <- 1L
e$lst <- list(W = 1:10, X = runif(10), Y = rnorm(10), Z = LETTERS[1:10])
ls(e)
#> [1] "abc" "lst" "one"

# 'normal' copy
f <- e
ls(f)
#> [1] "abc" "lst" "one"
f$one
#> [1] 1
f$one <- 2L
f$one
#> [1] 2
e$one ## uh oh, e has changed!
#> [1] 2

# deep copy
e$one <- 1L
g <- Copy(e)
ls(g)
#> [1] "abc" "lst" "one"
g$one
#> [1] 1
g$one <- 3L
g$one
#> [1] 3
f$one
#> [1] 1
e$one
#> [1] 1
## To create a new deep copy method, use the following template
## setMethod("Copy", signature = "the class", # where = specify here if not in a package,
##           definition = function(object, filebackendDir, ...) {
##           # write deep copy code here
##           })