check.Rdcheck provides checking of permutation schemes for
validity. permuplot produces a graphical representation of the
selected permutation design.
an R object. See Details for a complete description,
especially for numPerms. For
summary.check an object of class "check".
a list of control values describing properties of the
permutation design, as returned by a call to how.
logical; should messages by suppressed?
arguments to other methods.
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.
For check a list containing the maximum number of
permutations possible and an object of class "how".
## 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")))
}
#>
#> pyrifs> data(pyrifos)
#>
#> pyrifs> ditch <- gl(12, 1, length=132)
#>
#> pyrifs> week <- gl(11, 12, labels=c(-4, -1, 0.1, 1, 2, 4, 8, 12, 15, 19, 24))
#>
#> pyrifs> dose <- factor(rep(c(0.1, 0, 0, 0.9, 0, 44, 6, 0.1, 44, 0.9, 0, 6), 11))
#> 'nperm' >= set of all permutations: complete enumeration.
#> Set of permutations < 'minperm'. Generating entire set.
#> Set of permutations < 'minperm'. Generating entire set.
#> 'nperm' >= set of all permutations: complete enumeration.
#> Set of permutations < 'minperm'. Generating entire set.
#> 'nperm' >= set of all permutations: complete enumeration.
#> Set of permutations < 'minperm'. Generating entire set.
#> [1] 479001600
## this should also also for arbitrary vectors
vec1 <- check(1:100)
vec2 <- check(1:100, how())
all.equal(vec1, vec2)
#> [1] TRUE
vec3 <- check(1:100, how(within = Within(type = "series")))
#> 'nperm' >= set of all permutations: complete enumeration.
#> Set of permutations < 'minperm'. Generating entire set.
all.equal(100, vec3$n)
#> [1] TRUE
vec4 <- check(1:100, how(within = Within(type= "series", mirror = TRUE)))
#> 'nperm' >= set of all permutations: complete enumeration.
#> Set of permutations < 'minperm'. Generating entire set.
all.equal(vec4$n, 200)
#> [1] TRUE
## 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)
#> 'nperm' >= set of all permutations: complete enumeration.
#> Set of permutations < 'minperm'. Generating entire set.
#> [1] 6
numPerms(1:12, control = ctrl)
#> [1] 6
(tmp <- allPerms(12, control = update(ctrl, observed = TRUE)))
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
#> [1,] 2 3 4 5 6 1 8 9 10 11 12 7
#> [2,] 3 4 5 6 1 2 9 10 11 12 7 8
#> [3,] 4 5 6 1 2 3 10 11 12 7 8 9
#> [4,] 5 6 1 2 3 4 11 12 7 8 9 10
#> [5,] 6 1 2 3 4 5 12 7 8 9 10 11
#> [6,] 1 2 3 4 5 6 7 8 9 10 11 12
(tmp2 <- allPerms(12, control = ctrl))
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
#> [1,] 2 3 4 5 6 1 8 9 10 11 12 7
#> [2,] 3 4 5 6 1 2 9 10 11 12 7 8
#> [3,] 4 5 6 1 2 3 10 11 12 7 8 9
#> [4,] 5 6 1 2 3 4 11 12 7 8 9 10
#> [5,] 6 1 2 3 4 5 12 7 8 9 10 11
## turn on mirroring
ctrl <- update(ctrl, within = update(getWithin(ctrl), mirror = TRUE))
numPerms(1:12, control = ctrl)
#> [1] 12
(tmp3 <- allPerms(12, control = update(ctrl, observed = TRUE)))
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
#> [1,] 2 3 4 5 6 1 8 9 10 11 12 7
#> [2,] 3 4 5 6 1 2 9 10 11 12 7 8
#> [3,] 4 5 6 1 2 3 10 11 12 7 8 9
#> [4,] 5 6 1 2 3 4 11 12 7 8 9 10
#> [5,] 6 1 2 3 4 5 12 7 8 9 10 11
#> [6,] 1 2 3 4 5 6 7 8 9 10 11 12
#> [7,] 1 6 5 4 3 2 7 12 11 10 9 8
#> [8,] 2 1 6 5 4 3 8 7 12 11 10 9
#> [9,] 3 2 1 6 5 4 9 8 7 12 11 10
#> [10,] 4 3 2 1 6 5 10 9 8 7 12 11
#> [11,] 5 4 3 2 1 6 11 10 9 8 7 12
#> [12,] 6 5 4 3 2 1 12 11 10 9 8 7
(tmp4 <- allPerms(12, control = ctrl))
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
#> [1,] 2 3 4 5 6 1 8 9 10 11 12 7
#> [2,] 3 4 5 6 1 2 9 10 11 12 7 8
#> [3,] 4 5 6 1 2 3 10 11 12 7 8 9
#> [4,] 5 6 1 2 3 4 11 12 7 8 9 10
#> [5,] 6 1 2 3 4 5 12 7 8 9 10 11
#> [6,] 1 6 5 4 3 2 7 12 11 10 9 8
#> [7,] 2 1 6 5 4 3 8 7 12 11 10 9
#> [8,] 3 2 1 6 5 4 9 8 7 12 11 10
#> [9,] 4 3 2 1 6 5 10 9 8 7 12 11
#> [10,] 5 4 3 2 1 6 11 10 9 8 7 12
#> [11,] 6 5 4 3 2 1 12 11 10 9 8 7
## prints out details of the permutation scheme as
## well as the matrix of permutations
summary(tmp)
#>
#> Complete enumeration of permutations
#>
#> Permutation Design:
#>
#> Blocks:
#> Defined by: none
#>
#> Plots:
#> Plots: fac
#> Permutation type: none
#> Mirrored?: No
#>
#> Within Plots:
#> Permutation type: grid
#> Mirrored?: No
#> Different permutation within each Plot?: No
#> Grid dimensions: 3 rows 2 cols
#>
#> Permutation details:
#> Number of permutations: 199
#> Max. number of permutations allowed: 9999
#> Evaluate all permutations?: No. Activation limit: 5040
#>
#> All permutations:
#> Contains observed ordering?: Yes
#>
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
#> [1,] 2 3 4 5 6 1 8 9 10 11 12 7
#> [2,] 3 4 5 6 1 2 9 10 11 12 7 8
#> [3,] 4 5 6 1 2 3 10 11 12 7 8 9
#> [4,] 5 6 1 2 3 4 11 12 7 8 9 10
#> [5,] 6 1 2 3 4 5 12 7 8 9 10 11
#> [6,] 1 2 3 4 5 6 7 8 9 10 11 12
summary(tmp2)
#>
#> Complete enumeration of permutations
#>
#> Permutation Design:
#>
#> Blocks:
#> Defined by: none
#>
#> Plots:
#> Plots: fac
#> Permutation type: none
#> Mirrored?: No
#>
#> Within Plots:
#> Permutation type: grid
#> Mirrored?: No
#> Different permutation within each Plot?: No
#> Grid dimensions: 3 rows 2 cols
#>
#> Permutation details:
#> Number of permutations: 198
#> Max. number of permutations allowed: 9999
#> Evaluate all permutations?: No. Activation limit: 5040
#>
#> All permutations:
#> Contains observed ordering?: No
#>
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
#> [1,] 2 3 4 5 6 1 8 9 10 11 12 7
#> [2,] 3 4 5 6 1 2 9 10 11 12 7 8
#> [3,] 4 5 6 1 2 3 10 11 12 7 8 9
#> [4,] 5 6 1 2 3 4 11 12 7 8 9 10
#> [5,] 6 1 2 3 4 5 12 7 8 9 10 11
## 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")))
#> [1] 24
allPerms(7, how(within = Within(type = "free"),
plots = Plots(strata = fac)))
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7]
#> [1,] 1 2 3 4 5 7 6
#> [2,] 1 2 3 5 4 6 7
#> [3,] 1 2 3 5 4 7 6
#> [4,] 1 3 2 4 5 6 7
#> [5,] 1 3 2 4 5 7 6
#> [6,] 1 3 2 5 4 6 7
#> [7,] 1 3 2 5 4 7 6
#> [8,] 2 1 3 4 5 6 7
#> [9,] 2 1 3 4 5 7 6
#> [10,] 2 1 3 5 4 6 7
#> [11,] 2 1 3 5 4 7 6
#> [12,] 2 3 1 4 5 6 7
#> [13,] 2 3 1 4 5 7 6
#> [14,] 2 3 1 5 4 6 7
#> [15,] 2 3 1 5 4 7 6
#> [16,] 3 1 2 4 5 6 7
#> [17,] 3 1 2 4 5 7 6
#> [18,] 3 1 2 5 4 6 7
#> [19,] 3 1 2 5 4 7 6
#> [20,] 3 2 1 4 5 6 7
#> [21,] 3 2 1 4 5 7 6
#> [22,] 3 2 1 5 4 6 7
#> [23,] 3 2 1 5 4 7 6
## series permutations in levels of strata
ctrl <- how(within = Within(type = "series"), plots = Plots(strata = fac))
numPerms(7, control = ctrl)
#> [1] 12
allPerms(7, control = ctrl)
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7]
#> [1,] 2 3 1 5 4 7 6
#> [2,] 2 3 1 5 4 6 7
#> [3,] 2 3 1 4 5 7 6
#> [4,] 2 3 1 4 5 6 7
#> [5,] 3 1 2 5 4 7 6
#> [6,] 3 1 2 5 4 6 7
#> [7,] 3 1 2 4 5 7 6
#> [8,] 3 1 2 4 5 6 7
#> [9,] 1 2 3 5 4 7 6
#> [10,] 1 2 3 5 4 6 7
#> [11,] 1 2 3 4 5 7 6