Copy: Recursive copying of nested environments, and other "hard to...

In PredictiveEcology/reproducible: Enhance Reproducibility of R Code

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

Description

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).

Usage

Copy(object, ...)

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

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

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

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

## S4 method for signature '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

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).

Value

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

Author(s)

Eliot McIntire

See Also

.robustDigest(), Filenames()

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)

# 'normal' copy
f <- e
ls(f)
f$one
f$one <- 2L
f$one
e$one ## uh oh, e has changed!

# deep copy
e$one <- 1L
g <- Copy(e)
ls(g)
g$one
g$one <- 3L
g$one
f$one
e$one
## 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
##           })

PredictiveEcology/reproducible documentation built on April 14, 2024, 3:14 p.m.