Cloning R objects
Makes clones of R objects, that is values in the object are repeated n times, leaving the original structure of the object intact (in most of the cases).
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dclone(x, n.clones=1, ...) ## Default S3 method: dclone(x, n.clones = 1, attrib=TRUE, ...) ## S3 method for class 'dcdim' dclone(x, n.clones = 1, attrib=TRUE, ...) ## S3 method for class 'dciid' dclone(x, n.clones = 1, attrib=TRUE, ...) ## S3 method for class 'dctr' dclone(x, n.clones = 1, attrib=TRUE, ...) ## S3 method for class 'list' dclone(x, n.clones = 1, multiply = NULL, unchanged = NULL, attrib=TRUE, ...) ## S3 method for class 'environment' dclone(x, n.clones = 1, multiply = NULL, unchanged = NULL, attrib=TRUE, ...) dcdim(x, drop = TRUE, perm = NULL) dciid(x, iid=character(0)) dctr(x)
An R object to be cloned, or a cloned object to print.
Number of clones.
Numeric or character index for list element(s) to be multiplied by
Numeric or character index for list element(s) to be left unchanged.
The subscript permutation value, if the cloning dimension is not the last.
Character (or optionally numeric or logical).
Column(s) to be treated as i.i.d. observations.
Other arguments passed to function.
dclone is a generic function for cloning objects.
It is separate from
because there are different ways of cloning, depending on the
BUGS code implementation:
(1) Unchanged: no cloning at all (fo e.g. constants).
(2) Repeat: this is the most often used cloning method,
repeating the observations row-wise as if there
were more samples. The
dctr option allows repeating
the data column-wise.
(3) Multiply: sometimes it is enough to multiply the numbers (e.g. for Binomial distribution).
(4) Add dimension: under specific circumstances, it is easier to
add another dimension for clones,
but otherwise repeat the observations (e.g. in case of time series,
or for addressing special
indexing conventions in the
BUGS code, see examples
(5) Repeat pattern (i.i.d.): this is useful for example when
a grouping variable is considered, and more i.i.d. groups are to be
added to the data set. E.g.
c(1, 1, 2, 2) is to be cloned as
c(1, 1, 2, 2, 3, 3, 4, 4) instead of
c(1, 1, 2, 2, 1, 1, 2, 2).
An object with class attributes
"dclone" plus the original
one(s). Dimensions of the original object might change according to
n.clones. The function tries to take care of names, sometimes
replacing those with the combination of the original names and an
integer for number of clones.
dcdim sets the class attribute of an object to
dclone will clone the object by adding an extra dimension
for the clones.
dciid sets the class attribute of an object to
dclone will clone the object by treating columns
defined by the
iid argument as i.i.d. observations.
These columns must be numeric.
This aims to facilitates working with the INLA
package to generate approximate marginals based on DC.
Columns specified by
iid will be replaced by an increasing
sequence of values respecting possible grouping structure (see
Lists (i.e. BUGS data objects) are handled differently to enable element
specific determination of the mode of cloning. This can be done via the
multiply arguments, or by setting the
behaviour by the
Environments are coerced into a list, and return value is identical to
Peter Solymos, email@example.com, implementation is based on many discussions with Khurram Nadeem and Subhash Lele.
Lele, S.R., B. Dennis and F. Lutscher, 2007. Data cloning: easy maximum likelihood estimation for complex ecological models using Bayesian Markov chain Monte Carlo methods. Ecology Letters 10, 551–563.
Lele, S. R., K. Nadeem and B. Schmuland, 2010. Estimability and likelihood inference for generalized linear mixed models using data cloning. Journal of the American Statistical Association 105, 1617–1625.
Solymos, P., 2010. dclone: Data Cloning in R. The R Journal 2(2), 29–37. URL: http://journal.r-project.org/archive/2010-2/RJournal_2010-2_Solymos.pdf
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## scalar dclone(4, 2) ## vector (x <- 1:6) dclone(x, 2) ## matrix (m <- matrix(x, 2, 3)) dclone(m, 2) ## data frame (dfr <- as.data.frame(t(m))) dclone(dfr, 2) ## list (l <- list(n = 10, y = 1:10, x = 1:10, p = 1)) dclone(l, 2) dclone(as.environment(l), 2) dclone(l, 2, attrib = FALSE) dclone(l, 2, multiply = "n", unchanged = "p") ## effect of dcdim l$y <- dcdim(l$y) dclone(l, 2, multiply = "n", unchanged = "p") ## time series like usage of dcdim z <- data.matrix(rnorm(10)) dclone(dcdim(z), 2) ## usage if dciid ll <- dciid(data.frame(x=1:10, y=1:10), iid="y") dclone(ll, 2) ## respecting grouping structure in iid ll$y <- rep(1:5, each=2) (dci <- dclone(ll, 2)) nclones(dci) ## repeating the data column-wise dclone(dctr(m), 2)
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