This is a generic function intended to randomly break tied data in a
way similar to what jitter does: tie-breaking is
performed by shifting all data points by a random amount.
The surveillance package defines methods for matrices,
"epidataCS", and a default method for numeric vectors.
untie(x, amount, ...)# S3 method for epidataCS
untie(x, amount = list(t=NULL, s=NULL),
minsep = list(t=0, s=0), direction = "left", keep.sources = FALSE,
..., verbose = FALSE)
# S3 method for matrix
untie(x, amount = NULL, minsep = 0,
constraint = NULL, giveup = 1000, ...)
# S3 method for default
untie(x, amount = NULL, minsep = 0,
direction = c("symmetric", "left", "right"), sort = NULL,
giveup = 1000, ...)
the untied (jittered) data.
the data to be untied.
upper bound for the random amount by which data are shifted.
NULL means to use a data-driven default, which equals
the minimum separation of the data points for the non-symmetric
default method and its half for the symmetric default method and the
matrix method.
minimum separation of jittered points. Can only be
obeyed if much smaller than amount (also depending on the
number of points). minsep>0 is currently only implemented for
the spatial (matrix) method.
logical (FALSE). If TRUE, the original list of
possible event sources in x$events$.sources will be
preserved. For instance, events observed at the same time did by
definition not trigger each other; however, after random
tie-breaking one event will precede the other and considered as a
potential source of infection for the latter, although it could just
as well be the other way round. Enabling keep.sources will
use the .sources list from the original (tied)
"epidataCS" object. Note, however, that an update is forced
within twinstim if a subset of the data is selected
for model fitting or if a different qmatrix is supplied.
an object of class "SpatialPolygons"
representing the domain which the points of the matrix should belong
to -- before and after jittering.
number of attempts after which the algorithm should stop trying to generate new points.
one of "symmetric" (default), "left", or
"right", indicating in which direction vector elements should
be shifted.
logical indicating if the jittered vector should be sorted. Defaults to doing so if the original vector was already sorted.
For the "epidataCS"-method: arguments passed to the
matrix- or default-method (giveup).
Unused in other methods.
logical passed to as.epidataCS.
Sebastian Meyer
For numeric vectors (default method), the jittered version is the
same as for jitter(x, amount=amount), if
direction="symmetric" (and amount is non-NULL),
and otherwise uses
x “+-” runif(length(x), 0, amount).
For matrices, a vector uniformly drawn from the disc with radius
amount is added to each point (row).
For "epidataCS", amount is a list stating the amounts
for the temporal and/or spatial dimension, respectively. It then
uses the specific methods with arguments constraint=x$W,
direction, and sort=TRUE. Note that this implements a
simplistic approach of tie-breaking where all events are assumed to be
subject to the same amounts of censoring, and the default amounts may
not be sensible choices.
# vector example
set.seed(123)
untie(c(rep(1,3), rep(1.2, 4), rep(3,3)), direction="left", sort=FALSE)
# spatial example
data(imdepi)
coords <- coordinates(imdepi$events)
table(duplicated(coords))
plot(coords, cex=sqrt(multiplicity(coords)))
set.seed(1)
coords_untied <- untie(coords)
stopifnot(!anyDuplicated(coords_untied))
points(coords_untied, col=2) # shifted by very small amount in this case
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