permuted.index2: Unrestricted and restricted permutations

Description

Unrestricted and restricted permutation designs for time series, line transects, spatial grids and blocking factors.

Usage

permuted.index2(n, control = permControl())
permControl(strata = NULL, nperm = 199, complete = FALSE,
            type = c("free", "series", "grid", "strata"),
            maxperm = 9999, minperm = 99,
            mirror = FALSE, constant = FALSE,
            ncol = NULL, nrow = NULL)

Arguments

numeric; the length of the returned vector of permuted values. Usually the number of observations under consideration.

control

a list of control values describing properties of the permutation design, as returned by a call to permControl.

strata

An integer vector or factor specifying the strata for permutation. If supplied, observations are permuted only within the specified strata.

nperm

the number of permutations.

complete

logical; should complete enumeration of all permutations be performed?

type

the type of permutations required. One of "free", "series", "grid" or "strata". See Details.

maxperm

the maximum number of permutations to perform. Currently unused.

minperm

the lower limit to the number of possible permutations at which complete enumeration is performed. See argument complete and Details, below.

mirror

logical; should mirroring of sequences be allowed?

constant

logical; should the same permutation be used within each level of strata? If FALSE a separate, possibly restricted, permutation is produced for each level of strata.

ncol, nrow

numeric; the number of columns and rows of samples in the spatial grid respectiavly.

Value

For permuted.index2 a vector of length n containing a permutation of the observations 1, ..., n using the permutation scheme described by argument control. For permControl a list with components for each of the possible arguments.

Details

permuted.index2 can generate permutations for a wide range of restricted permutation schemes. A small selection of the available combinations of options is provided in the Examples section below.

Argument mirror determines whether grid or series permutations can be mirrored. Consider the sequence 1,2,3,4. The relationship between consecutive observations is preserved if we reverse the sequence to 4,3,2,1. If there is no inherent direction in your experimental design, mirrored permutations can be considered part of the Null model, and as such increase the number of possible permutations. The default is to not use mirroring so you must explicitly turn this on using mirror = TRUE in permControl.

To permute strata rather than the observations within the levels of strata, use type = "strata". However, note that the number of observations within each level of strata must be equal!

For some experiments, such as BACI designs, one might wish to use the same permutation within each level of strata. This is controlled by argument constant. If constant = TRUE then the same permutation will be generated for each level of strata. The default is constant = FALSE.

Examples

Run this code

set.seed(1234)

## unrestricted permutations
permuted.index2(20)

## observations represent a time series of line transect
permuted.index2(20, control = permControl(type = "series"))

## observations represent a time series of line transect
## but with mirroring allowed
permuted.index2(20, control = permControl(type = "series", mirror = TRUE))

## observations represent a spatial grid
perms <- permuted.index2(20, permControl(type = "grid",
                                         ncol = 4, nrow = 5))
## view the permutation as a grid
matrix(matrix(1:20, nrow = 5, ncol = 4)[perms], ncol = 4, nrow = 5)

## random permutations in presence of strata
block <- gl(4, 5)
permuted.index2(20, permControl(strata = block, type = "free"))
## as above but same random permutation within strata
permuted.index2(20, permControl(strata = block, type = "free",
                                constant = TRUE))

## time series within each level of block
permuted.index2(20, permControl(strata = block, type = "series"))
## as above, but  with same permutation for each level
permuted.index2(20, permControl(strata = block, type = "series",
                                constant = TRUE))

## spatial grids within each level of block
permuted.index2(100, permControl(strata = block, type = "grid",
                                 ncol = 5, nrow = 5))
## as above, but with same permutation for each level
permuted.index2(100, permControl(strata = block, type = "grid",
                                 ncol = 5, nrow = 5, constant = TRUE))

## permuting levels of block instead of observations
permuted.index2(20, permControl(strata = block, type = "strata"))