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`allPerms` <- function(n, control = how(), check = TRUE) {
## start
v <- n
## expand n if a numeric or integer vector of length 1
if((is.numeric(n) || is.integer(n)) && (length(n) == 1))
v <- seq_len(n)
## number of observations in data
n <- nobs(v)
## check permutation scheme and update control
make <- getMake(control)
if (check) {
control2 <- control
setMake(control2) <- FALSE
pcheck <- check(v, control = control2, quietly = TRUE)
}
## ctrl <- pcheck$control
## if we do copy the new updated control, we need to update to
## reset make
## ctrl <- update(ctrl, make = make)
## get max number of permutations
nperms <- numPerms(v, control = control)
## sanity check - don't let this run away to infinity
## esp with type = "free"
if(nperms > getMaxperm(control))
stop("Number of possible permutations too large (> 'maxperm')")
WI <- getWithin(control)
strataP <- getStrata(control, which = "plots")
typeW <- getType(control, which = "within")
typeP <- getType(control, which = "plot")
BLOCKS <- getBlocks(control)
dimW <- getDim(control, which = "within")
dimP <- getDim(control, which = "plots")
mirrorW <- getMirror(control, which = "within")
mirrorP <- getMirror(control, which = "plots")
constantW <- getConstant(control)
## give a BLOCKS if non supplied - i.e. one block
if(is.null(BLOCKS))
BLOCKS <- factor(rep(1, n))
## split v by blocks
spl <- split(seq_len(n), BLOCKS)
nb <- length(spl) # number of blocks
## result object
out <- vector(mode = "list", length = nb)
## null-out Blocks in control
control2 <- control
setBlocks(control2) <- NULL
## loop over blocks and return allPerms on each block
for (i in seq_along(spl)) {
out[[i]] <-
doAllPerms(spl[[i]], strataP, typeW, typeP, mirrorW,
mirrorP, constantW, dimW, dimP, control2,
nperms = nperms)
}
## bind all blocks together, repeating them as required
out <- cbindAllPerms(out)
## bind all the blocks together
## out <- do.call(cbind, out) ## hmm are any of these the same shape?
out[, unlist(spl)] <- out ## is this being done at the doAllPerms level?
if(!(observed <- getObserved(control))) {
obs.v <- seq_len(n)
obs.row <- apply(out, 1, function(x, obs.v) all(x == obs.v), obs.v)
out <- out[!obs.row, ]
## reduce the number of permutations to get rid of the
## observed ordering
setNperm(control) <- getNperm(control) - 1
}
class(out) <- c("allPerms", "matrix")
attr(out, "control") <- control
attr(out, "observed") <- observed
out
}
`doAllPerms` <- function(obs, strataP, typeW, typeP, mirrorW, mirrorP,
constantW, dimW, dimP, control, nperms) {
n <- length(obs)
## subset strataP to take only the obs indices and drop the unused
## levels
if (!is.null(strataP)) {
strataP <- droplevels(strataP[obs])
}
## also need to update the $strata component of control
## FIXME: this really should have a toplevel function to set/update
## sub-components of control
## Pl <- getPlots(control)
## setStrata(Pl) <- strataP
## setPlots(control) <- Pl
control$plots$strata <- strataP
## permuting within?
if (typeW != "none") {
if(is.null(strataP)) {
## no plot-level permutations
res <- switch(typeW,
free = allFree(n),
series = allSeries(n, nperms, mirrorW),
grid = allGrid(n, nperms, dimW[1],
dimW[2], mirrorW, constantW))
## use res to index original observation indices in this group
res[] <- obs[res]
} else {
## permuting within plots
tab <- table(strataP)
pg <- unique(tab)
ng <- length(tab)
if(constantW) {
## same permutation in each plot
controlW <- how(within = getWithin(control))
nperms <- numPerms(pg, controlW)
ord <- switch(typeW,
free = allFree(pg),
series = allSeries(pg, nperms, mirrorW),
grid = allGrid(pg, nperms, dimW[1],
dimW[2], mirrorW, constantW))
res <- vector(mode = "list", length = ng)
ss <- seq(0, to = prod(pg, ng-1), by = pg)
for (i in seq_len(ng)) {
res[[i]] <- ord + ss[i]
}
## same permutation within plots, so just cbind rather than
## cbindAllPerms as we don't need all combns of rows
res <- do.call(cbind, res)
res[] <- obs[res] ## index into the observations in this block
} else {
## different permutations within plots
nperms <- numPerms(sum(tab), control)
if(length(pg) > 1) {
## different number of observations per level of strata
if(typeW == "grid")
## FIXME: this should not be needed once all checks are
## in place in check()
stop("Unbalanced grid designs are not supported")
controlW <- how(within = getWithin(control))
res <- vector(mode = "list", length = ng)
add <- c(0, cumsum(tab)[1:(ng-1)])
for(j in seq_along(tab)) {
np <- numPerms(tab[j], controlW)
ord <- switch(typeW,
free = allFree(tab[j]),
series = allSeries(tab[j], np, mirrorW))
res[[j]] <- ord + add[j]
}
res <- cbindAllPerms(res)
res[] <- obs[res]
} else {
## same number of observations per level of strata
controlW <- how(within = getWithin(control))
np <- numPerms(pg, controlW)
ord <-
switch(typeW,
free = allFree(pg),
series = allSeries(pg, np, mirrorW),
grid = allGrid(pg, np, dimW[1],
dimW[2], mirrorW, constantW))
res <- vector(mode = "list", length = ng)
ss <- seq(0, to = prod(pg, ng-1), by = pg)
for(i in seq_len(ng)) {
res[[i]] <- ord + ss[i]
}
res <- cbindAllPerms(res)
res[] <- obs[res]
}
}
}
}
## Do we need to permute plots?
if (!is.null(strataP) && !isTRUE(all.equal(typeP, "none"))) {
## permuting plots ONLY
if(typeW == "none") {
res <- allStrata(n, control = control)
} else {
## FIXME - this need updating to work with the new code
## permuting blocks AND within blocks
## need a local CONTROL that just permutes blocks
controlP <- how(plots = Plots(strata = strataP, type = typeP),
within = Within(type = "none"))
## FIXME - the above should really only need to update
## within as shown, not fiddle with Plots
## number of permutations for just the block level
permP <- numPerms(n, control = controlP)
## get all permutations for the block level
shuffP <- allStrata(n, control = controlP)
## copy the set of permutations for within blocks
## permP times - results is a list
resP <- rep(list(res), permP)
resP <- lapply(seq_along(resP),
function(i, wi, bl) {
t(apply(wi[[i]], 1,
function(x, bl, i) {
x[bl[i,]]
}, bl = bl, i = i))
},
wi = resP, bl = shuffP)
res <- do.call(rbind, resP)
}
}
## some times storage.mode of res is numeric, sometimes
## it is integer, set to "integer" for comparisons using
## identical to match the observed ordering
storage.mode(res) <- "integer"
## return
res
}
## enumerate all possible permutations for a more complicated
## design
## fac <- gl(2,6)
##ctrl <- how(type = "grid", mirror = FALSE, strata = fac,
## constant = TRUE, nrow = 3, ncol = 2)
## ctrl <- how(strata = fac,
## within = Within(type = "grid", mirror = FALSE,
## constant = TRUE, nrow = 3, ncol = 2),
## blocks = Blocks(type = "free"))
## Nobs <- length(fac)
## numPerms(seq_len(Nobs), control = ctrl)
## numPerms(Nobs, control = ctrl) ## works just as well
## (tmp <- allPerms(Nobs, control = ctrl, observed = TRUE))
## (tmp2 <- allPerms(Nobs, control = ctrl))
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