permute: allPerms – R documentation

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allPerms

Complete enumeration of all possible permutations

Description

allPerms is a utility function to return the set of permutations for a given R object and a specified permutation design.

Usage

allPerms(n, control = how(), check = TRUE)

## S3 method for class 'allPerms'
summary(object, ...)

## S3 method for class 'allPerms'
as.matrix(x, ...)

as.allPerms(object, control)

Arguments

`n`	the number of observations or an 'object' from which the number of observations can be determined via `getNumObs`.
`control`	a list of control values describing properties of the permutation design, as returned by a call to `how`.
`check`	logical; should `allPerms` check the design? The default is to check, but this can be skipped, for example if a function checked the design earlier.
`object`	for `summary.allPerms`, an object of class `"allPerms"`. For `as.allPerms` a matrix or something that can be coerced to a matrix by `as.matrix`.
`...`	arguments to other methods.
`x`	an object of class `"allPerms"`, as returned by `allPerms`.

Details

Function allPerms enumerates all possible permutations for the number of observations and the selected permutation scheme. It has print and summary methods. allPerms returns a matrix containing all possible permutations, possibly containing the observed ordering (if argument observed is TRUE). The rows of this matrix are the various permutations and the columns reflect the number of samples.

With free permutation designs, and restricted permutation schemes with large numbers of observations, there are a potentially huge number of possible permutations of the samples. It would be inefficient, not to mention incredibly time consuming, to enumerate them all. Storing all possible permutations would also become problematic in such cases. To control this and guard against trying to evaluate too large a number of permutations, if the number of possible permutations is larger than getMaxperm(control), allPerms exits with an error.

The as.matrix method sets the control and seed attributes to NULL and removes the "permutationMatrix" class, resulting in a standard matrix object.

Value

For allPerms, and object of class "allPerms", a matrix whose rows are the set of all possible permutations for the supplies number of observations and permutation scheme selected. The matrix has two additional attributes control and observed. Attribute control contains the argument control (possibly updated via check). Attribute observed contains argument observed.

Warning

If permuting the strata themselves, a balanced design is required (the same number of observations in each level of strata. This is common to all functions in the package.

Author(s)

Gavin Simpson

Examples

## allPerms can work with a vector
vec <- c(3,4,5)
allPerms(vec) ## free permutation

## enumerate all possible permutations for a more complicated
## design
fac <- gl(2,6)
ctrl <- how(within = Within(type = "grid", mirror = FALSE,
                            constant = TRUE, nrow = 3, ncol = 2),
            plots = Plots(strata = fac))
Nobs <- length(fac)
numPerms(seq_len(Nobs), control = ctrl) ## 6
(tmp <- allPerms(Nobs, control = update(ctrl, observed = TRUE)))
(tmp2 <- allPerms(Nobs, control = ctrl))

## turn on mirroring
##ctrl$within$mirror <- TRUE
ctrl <- update(ctrl, within = update(getWithin(ctrl), mirror = TRUE))
numPerms(seq_len(Nobs), control = ctrl)
(tmp3 <- allPerms(Nobs, control = update(ctrl, observed = TRUE)))
(tmp4 <- allPerms(Nobs, control = ctrl))

## prints out details of the permutation scheme as
## well as the matrix of permutations
summary(tmp3)
summary(tmp4)

permute

Functions for Generating Restricted Permutations of Data

v0.9-5

GPL-2

Authors

Gavin L. Simpson [aut, cph, cre] (<https://orcid.org/0000-0002-9084-8413>), R Core Team [cph], Douglas M. Bates [ctb], Jari Oksanen [ctb]

Initial release

2019-03-10