Nothing
`cca.default` <-
function (X, Y = NULL, Z = NULL, ...)
{
## Protect against grave misuse: some people have used
## dissimilarities instead of data
if (inherits(X, "dist") || NCOL(X) == NROW(X) &&
isTRUE(all.equal(X, t(X))))
stop("function cannot be used with (dis)similarities")
X <- as.matrix(X)
if (!is.null(Y)) {
if (is.data.frame(Y) || is.factor(Y))
Y <- model.matrix(~ ., as.data.frame(Y))[,-1,drop=FALSE]
Y <- as.matrix(Y)
}
if (!is.null(Z)) {
if (is.data.frame(Z) || is.factor(Z))
Z <- model.matrix(~ ., as.data.frame(Z))[,-1,drop=FALSE]
Z <- as.matrix(Z)
}
if (any(rowSums(X) <= 0))
stop("all row sums must be >0 in the community data matrix")
if (any(tmp <- colSums(X) <= 0)) {
exclude.spec <- seq(along=tmp)[tmp]
names(exclude.spec) <- colnames(X)[tmp]
class(exclude.spec) <- "exclude"
X <- X[, !tmp, drop = FALSE]
}
sol <- ordConstrained(X, Y, Z, method = "cca")
if (exists("exclude.spec")) {
if (!is.null(sol$CCA$v))
attr(sol$CCA$v, "na.action") <- exclude.spec
if (!is.null(sol$CA$v))
attr(sol$CA$v, "na.action") <- exclude.spec
}
call <- match.call()
call[[1]] <- as.name("cca")
sol <- c(list(call = call,
inertia = "scaled Chi-square"),
sol)
class(sol) <- "cca"
sol
}
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