check | R Documentation |
check
provides checking of permutation schemes for
validity. permuplot
produces a graphical representation of the
selected permutation design.
check(object, control = how(), quietly = FALSE) ## S3 method for class 'check' summary(object, ...)
object |
an R object. See Details for a complete description,
especially for |
control |
a list of control values describing properties of the
permutation design, as returned by a call to |
quietly |
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"
.
Gavin L. Simpson
shuffle
and 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"))) } ## 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)
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