R/vegan-defunct.R

In vegan: Community Ecology Package

## as.mlm: deprecated in 2.5-0, defunct in 2.6-0

`as.mlm` <-
    function(x)
{
    .Defunct("see ?hatvalues.cca for new alternatives")
    if (is.null(x$CCA))
        stop("'as.mlm' can be used only for constrained ordination")
    UseMethod("as.mlm")
}
`as.mlm.cca` <-
    function (x)
{
    w <- x$rowsum
    WA <- x$CCA$wa
    X <- qr.X(x$CCA$QR)
    ## shall use weighted regression: deweight X
    X <- (1/sqrt(w)) * X
    X <- as.data.frame(X)
    lm(WA ~ ., data = X, weights = w)
}

`as.mlm.rda` <-
    function (x)
{
    X <- as.data.frame(qr.X(x$CCA$QR))
    WA <- x$CCA$wa
    lm(WA ~ . , data = X)
}
### commsimulator was deprecated in 2.4-0, defunct in 2.6-0

"commsimulator" <-
function (x, method, thin = 1)
{
    .Defunct("simulate(nullmodel(x, method))", package="vegan")
    method <- match.arg(method,
                        c("r0","r1","r2","r00","c0","swap", "tswap",
                          "backtrack", "quasiswap"))
    ## r0_old is also removed from vegan 2.6-0, but needed for <2.2-0
    ## compatibility
    ##if (method == "r0")
    ##    method <- "r0_old"
    x <- as.matrix(x)
    out <- simulate(nullmodel(x, method), nsim = 1, thin = thin)
    out <- out[,,1]
    attributes(out) <- attributes(x)
    out
}

### deprecated in 2.2-0, but forgotten and never exported from the NAMESPACE. Make finally defunct for 2.6-0.

"permuted.index" <-
    function (n, strata)
{
    .Defunct("permute package (shuffle or shuffleSet)")
    if (missing(strata) || is.null(strata))
        out <- sample.int(n, n)
    else {
        out <- 1:n
        inds <- names(table(strata))
        for (is in inds) {
            gr <- out[strata == is]
            if (length(gr) > 1)
                out[gr] <- sample(gr, length(gr))
        }
    }
    out
}