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## mvr.R (2012-03-30)
## Minimum Variance Reduction
## Copyright 2011 Andrei-Alin Popescu
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
mvr <- function(X, V)
{
if (is.matrix(X)) X <- as.dist(X)
if (is.matrix(V)) V <- as.dist(V)
if (any(is.na(X)))
stop("missing values are not allowed in the distance matrix")
if (any(is.na(V)))
stop("missing values are not allowed in the variance matrix")
N <- attr(X, "Size")
labels <- attr(X, "Labels")
if (is.null(labels)) labels <- as.character(1:N)
ans <- .C(C_mvr, as.double(X), as.double(V), as.integer(N),
integer(2*N - 3), integer(2*N - 3), double(2*N - 3),
NAOK = TRUE)
obj <- list(edge = cbind(ans[[4]], ans[[5]]), edge.length = ans[[6]],
tip.label = labels, Nnode = N - 2L)
class(obj) <- "phylo"
reorder(obj)
}
mvrs <- function(X, V, fs = 15)
{
if (fs < 1)
stop("argument 'fs' must be a non-zero positive integer")
if (is.matrix(X)) X <- as.dist(X)
if (is.matrix(V)) V <- as.dist(V)
X[is.na(X)] <- -1
X[X < 0] <- -1
X[is.nan(X)] <- -1
N <- attr(X, "Size")
labels <- attr(X, "Labels")
if (is.null(labels)) labels <- as.character(1:N)
ans <- .C(C_mvrs, as.double(X), as.double(V), as.integer(N),
integer(2*N - 3), integer(2*N - 3), double(2*N - 3),
as.integer(fs), NAOK = TRUE)
obj <- list(edge = cbind(ans[[4]], ans[[5]]), edge.length = ans[[6]],
tip.label = labels, Nnode = N - 2L)
class(obj) <- "phylo"
reorder(obj)
}
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