check: Utility functions for permutation schemes

Description

check provides checking of permutation schemes for validity. permuplot produces a graphical representation of the selected permutation design.

Usage

check(object, control = how(), quietly = FALSE)
# S3 method for check
summary(object, …)

Arguments

object

an R object. See Details for a complete description, especially for numPerms. For summary.check an object of class "check".

control

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

quietly

logical; should messages by suppressed?

…

arguments to other methods.

Value

For check a list containing the maximum number of permutations possible and an object of class "how".

Details

check is a utility functions for working with the new permutation schemes available in shuffle.

check is used to check the current permutation schemes against the object to which it will be applied. It calculates the maximum number of possible permutations for the number of observations in object and the permutation scheme described by control. The returned object contains component control, an object of class "how" suitably modified if check identifies a problem.

The main problem is requesting more permutations than is possible with the number of observations and the permutation design. In such cases, nperm is reduced to equal the number of possible permutations, and complete enumeration of all permutations is turned on (control$complete is set to TRUE).

Alternatively, if the number of possible permutations is low, and less than control$minperm, it is better to enumerate all possible permutations, and as such complete enumeration of all permutations is turned on (control$complete is set to TRUE). This guarantees that permutations are all unique and there are no duplicates.

Examples

Run this code

# NOT RUN {
## only run this example if vegan is available
if (suppressPackageStartupMessages(require("vegan"))) {
    ## use example data from ?pyrifos in package vegan
    example(pyrifos)

    ## Demonstrate the maximum number of permutations for the pyrifos data
    ## under a series of permutation schemes

    ## no restrictions - lots of perms
    CONTROL <- how(within = Within(type = "free"))
    (check1 <- check(pyrifos, CONTROL))
    ## summary(check1)
    
    ## no strata but data are series with no mirroring, so 132 permutations
    CONTROL <- how(within = Within(type = "series", mirror = FALSE))
    check(pyrifos, CONTROL)
    
    ## no strata but data are series with mirroring, so 264 permutations
    CONTROL <- how(within = Within(type = "series", mirror = TRUE))
    check(pyrifos, control = CONTROL)
    
    ## unrestricted within strata
    check(pyrifos, control = how(plots = Plots(strata = ditch),
                   within = Within(type = "free")))
    
    ## time series within strata, no mirroring
    check(pyrifos,
          control = how(plots = Plots(strata = ditch),
          within = Within(type = "series", mirror = FALSE)))
    
    ## time series within strata, with mirroring
    check(pyrifos,
          control = how(plots = Plots(strata = ditch),
          within = Within(type = "series", mirror = TRUE)))
    
    ## time series within strata, no mirroring, same permutation
    ## within strata
    check(pyrifos,
          control = how(plots = Plots(strata = ditch),
          within = Within(type = "series", constant = TRUE)))
    
    ## time series within strata, with mirroring, same permutation
    ## within strata
    check(pyrifos,
          control = how(plots = Plots(strata = ditch),
          within = Within(type = "series", mirror = TRUE,
          constant = TRUE)))
    ## permute strata
    check(pyrifos, how(plots = Plots(strata = ditch, type = "free"),
                       within = Within(type = "none")))
}
    
## this should also also for arbitrary vectors
vec1 <- check(1:100)
vec2 <- check(1:100, how())
all.equal(vec1, vec2)
vec3 <- check(1:100, how(within = Within(type = "series")))
all.equal(100, vec3$n)
vec4 <- check(1:100, how(within = Within(type= "series", mirror = TRUE)))
all.equal(vec4$n, 200)

## enumerate all possible permutations
fac <- gl(2,6)
ctrl <- how(plots = Plots(strata = fac),
            within = Within(type = "grid", mirror = FALSE,
                            constant = TRUE, nrow = 3, ncol = 2))
check(1:12, ctrl)

numPerms(1:12, control = ctrl)
(tmp <- allPerms(12, control = update(ctrl, observed = TRUE)))
(tmp2 <- allPerms(12, control = ctrl))

## turn on mirroring
ctrl <- update(ctrl, within = update(getWithin(ctrl), mirror = TRUE))
numPerms(1:12, control = ctrl)
(tmp3 <- allPerms(12, control = update(ctrl, observed = TRUE)))
(tmp4 <- allPerms(12, control = ctrl))
## prints out details of the permutation scheme as
## well as the matrix of permutations
summary(tmp)
summary(tmp2)

## different numbers of observations per level of strata
fac <- factor(rep(1:3, times = c(3,2,2)))
## free permutations in levels of strata
numPerms(7, how(within = Within(type = "free"),
                plots = Plots(strata = fac, type = "none")))
allPerms(7, how(within = Within(type = "free"),
                plots = Plots(strata = fac)))
## series permutations in levels of strata
ctrl <- how(within = Within(type = "series"), plots = Plots(strata = fac))
numPerms(7, control = ctrl)
allPerms(7, control = ctrl)
# }