Description Usage Arguments Details Value Author(s) References See Also Examples

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

1 2 3 |

`n` |
numeric; the length of the returned vector of permuted
values. Usually the number of observations under consideration. May
also be any object that |

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

`i` |
integer; row of |

`shuffle`

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.

`permute`

is a higher level utility function for use in a loop
within a function implementing a permutation test. The main purpose of
`permute`

is to return the correct permutation in each iteration
of the loop, either a random permutation from the current design or
the next permutation from `control$all.perms`

if it is not
`NULL`

and `control$complete`

is `TRUE`

.

For `shuffle`

a vector of length `n`

containing a
permutation of the observations 1, ..., n using the permutation
scheme described by argument `control`

.

For `permute`

the `i`

th permutation from the set of all
permutations, or a random permutation from the design.

Gavin Simpson

`shuffle()`

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).

`check`

, a utility function for checking
permutation scheme described by `how`

.

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set.seed(1234)
## unrestricted permutations
shuffle(20)
## observations represent a time series of line transect
CTRL <- how(within = Within(type = "series"))
shuffle(20, control = CTRL)
## observations represent a time series of line transect
## but with mirroring allowed
CTRL <- how(within = Within(type = "series", mirror = TRUE))
shuffle(20, control = CTRL)
## observations represent a spatial grid, 5rx4c
nr <- 5
nc <- 4
CTRL <- how(within = Within(type = "grid", ncol = nc, nrow = nr))
perms <- shuffle(20, control = CTRL)
## view the permutation as a grid
matrix(matrix(1:20, nrow = nr, ncol = nc)[perms],
ncol = nc, nrow = nr)
## random permutations in presence of strata
plots <- Plots(strata = gl(4, 5))
CTRL <- how(plots = plots, within = Within(type = "free"))
shuffle(20, CTRL)
## as above but same random permutation within strata
CTRL <- how(plots = plots, within = Within(type = "free",
constant = TRUE))
shuffle(20, CTRL)
## time series within each level of block
CTRL <- how(plots = plots, within = Within(type = "series"))
shuffle(20, CTRL)
## as above, but with same permutation for each level
CTRL <- how(plots = plots, within = Within(type = "series",
constant = TRUE))
shuffle(20, CTRL)
## spatial grids within each level of block, 4 x (5r x 5c)
nr <- 5
nc <- 5
nb <- 4 ## number of blocks
plots <- Plots(gl(nb, 25))
CTRL <- how(plots = plots,
within = Within(type = "grid", ncol = nc, nrow = nr))
shuffle(100, CTRL)
## as above, but with same permutation for each level
CTRL <- how(plots = plots,
within = Within(type = "grid", ncol = nc, nrow = nr,
constant = TRUE))
shuffle(100, CTRL)
## permuting levels of plots instead of observations
CTRL <- how(plots = Plots(gl(4, 5), type = "free"),
within = Within(type = "none"))
shuffle(20, CTRL)
## permuting levels of plots instead of observations
## but plots represent a time series
CTRL <- how(plots = Plots(gl(4, 5), type = "series"),
within = Within(type = "none"))
shuffle(20, CTRL)
## permuting levels of plots but plots represent a time series
## free permutation within plots
CTRL <- how(plots = Plots(gl(4, 5), type = "series"),
within = Within(type = "free"))
shuffle(20, CTRL)
## permuting within blocks
grp <- gl(2, 10) # 2 groups of 10 samples each
CTRL <- how(blocks = grp)
shuffle(length(grp), control = CTRL)
## Simple function using permute() to assess significance
## of a t.test
pt.test <- function(x, group, control) {
## function to calculate t
t.statistic <- function(x, y) {
m <- length(x)
n <- length(y)
## means and variances, but for speed
xbar <- mean(x)
ybar <- mean(y)
xvar <- var(x)
yvar <- var(y)
pooled <- sqrt(((m-1)*xvar + (n-1)*yvar) / (m+n-2))
(xbar - ybar) / (pooled * sqrt(1/m + 1/n))
}
## check the control object
#control <- check(x, control)$control ## FIXME
## number of observations
Nobs <- nobs(x)
## group names
lev <- names(table(group))
## vector to hold results, +1 because of observed t
t.permu <- numeric(length = control$nperm) + 1
## calculate observed t
t.permu[1] <- t.statistic(x[group == lev[1]], x[group == lev[2]])
## generate randomisation distribution of t
for(i in seq_along(t.permu)) {
## return a permutation
want <- permute(i, Nobs, control)
## calculate permuted t
t.permu[i+1] <- t.statistic(x[want][group == lev[1]],
x[want][group == lev[2]])
}
## pval from permutation test
pval <- sum(abs(t.permu) >= abs(t.permu[1])) / (control$nperm + 1)
## return value
return(list(t.stat = t.permu[1], pval = pval))
}
## generate some data with slightly different means
set.seed(1234)
gr1 <- rnorm(20, mean = 9)
gr2 <- rnorm(20, mean = 10)
dat <- c(gr1, gr2)
## grouping variable
grp <- gl(2, 20, labels = paste("Group", 1:2))
## create the permutation design
control <- how(nperm = 999, within = Within(type = "free"))
## perform permutation t test
perm.val <- pt.test(dat, grp, control)
perm.val
## compare perm.val with the p-value from t.test()
t.test(dat ~ grp, var.equal = TRUE)
``` |

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