shuffleSet | R Documentation |
shuffleSet
returns a set of nset
permutations from the
specified design. The main purpose of the function is to circumvent
the overhead of repeatedly calling shuffle
to generate a
set of permutations.
shuffleSet(n, nset, control = how(), check = TRUE, quietly = FALSE) ## S3 method for class 'permutationMatrix' as.matrix(x, ...)
n |
numeric; the number of observations in the sample set. May also be
any object that |
nset |
numeric; the number of permutations to generate for the set. Can be
missing, the default, in which case |
control |
an object of class |
check |
logical; should the design be checked for various problems via
function |
quietly |
logical; should messages by suppressed? |
x |
an object of class |
... |
arguments passed to other methods. For the |
shuffleSet
is designed to generate a set of nset
permutation indices over which a function can iterate as part of a
permutation test. It is only slightly more efficient than calling
shuffle
nset
times, but it is far more practical
than the simpler function because a set of permutations can be worked
on by applying a function to the rows of the returned object. This
simplifies the function applied, and facilitates the use of parallel
processing functions, thus enabling a larger number of permutations to
be evaluated in reasonable time.
By default, shuffleSet
will check the permutations design
following a few simple heuristics. See check
for details
of these. Whether some of the heuristics are activiated or not can be
controlled via how
, essentialy via its argument
minperm
. In particular, if there are fewer than minperm
permutations, shuffleSet
will generate and return all
possible permutations, which may differ from the number requested via
argument nset
.
The check
argument to shuffleSet
controls whether
checking is performed in the permutation design. If you set
check = FALSE
then exactly nset
permutations will be
returned. However, do be aware that there is no guarantee that the set
of permutations returned will be unique, especially so for designs and
data sets where there are few possible permutations relative to the
number requested.
The as.matrix
method sets the control
and seed
attributes to NULL
and removes the "permutationMatrix"
class, resulting in a standard matrix object.
Returns a matrix of permutations, where each row is a separate
permutation. As such, the returned matrix has nset
rows and
n
columns.
Gavin L. Simpson
shuffleSet()
is modelled after the permutation schemes of Canoco
3.1 (ter Braak, 1990); see also Besag & Clifford (1989).
Besag, J. and Clifford, P. (1989) Generalized Monte Carlo significance tests. Biometrika 76; 633–642.
ter Braak, C. J. F. (1990). Update notes: CANOCO version 3.1. Wageningen: Agricultural Mathematics Group. (UR).
See shuffle
for generating a single permutation, and
how
for setting up permutation designs.
set.seed(1) ## simple random permutations, 5 permutations in set shuffleSet(n = 10, nset = 5) ## series random permutations, 5 permutations in set shuffleSet(10, 5, how(within = Within(type = "series"))) ## series random permutations, 10 permutations in set, ## with possible mirroring CTRL <- how(within = Within(type = "series", mirror = TRUE)) shuffleSet(10, 10, CTRL) ## Permuting strata ## 4 groups of 5 observations CTRL <- how(within = Within(type = "none"), plots = Plots(strata = gl(4,5), type = "free")) shuffleSet(20, 10, control = CTRL) ## 10 random permutations in presence of Plot-level strata plotStrata <- Plots(strata = gl(4,5)) CTRL <- how(plots = plotStrata, within = Within(type = "free")) numPerms(20, control = CTRL) shuffleSet(20, 10, control = CTRL) ## as above but same random permutation within Plot-level strata CTRL <- how(plots = plotStrata, within = Within(type = "free", constant = TRUE)) numPerms(20, control = CTRL) shuffleSet(20, 10, CTRL) ## check this. ## time series within each level of Plot strata CTRL <- how(plots = plotStrata, within = Within(type = "series")) shuffleSet(20, 10, CTRL) ## as above, but with same permutation for each Plot-level stratum CTRL <- how(plots = plotStrata, within = Within(type = "series", constant = TRUE)) shuffleSet(20, 10, CTRL)
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