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# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Library General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Library General Public License for more details.
#
# You should have received a copy of the GNU Library General
# Public License along with this library; if not, write to the
# Free Foundation, Inc., 59 Temple Place, Suite 330, Boston,
# MA 02111-1307 USA
################################################################################
# FUNCTION: DESCRIPTION:
# .mst Minimum spanning tree
# .sortIndexMST
# .mstPlot
# .nsca
################################################################################
# Rmetrics:
# Note that covRobust is not available on Debian as of 2009-04-28.
# To run these functions under Debian/Rmetrics we have them
# implemented here as a builtin.
# We also made modifications for tailored usage with Rmetrics.
# Package: ape
# Version: 2.3
# Date: 2009-03-30
# Title: Analyses of Phylogenetics and Evolution
# Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
# Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
# Gangolf Jobb, Christoph Heibl, Daniel Lawson, Vincent Lefort,
# Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander,
# Rainer Opgen-Rhein, Korbinian Strimmer, Damien de Vienne
# Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
# Depends: R (>= 2.6.0)
# Suggests: gee
# Imports: gee, nlme, lattice
# ZipData: no
# Description: ape provides functions for reading, writing, plotting, and
# manipulating phylogenetic trees, analyses of comparative data
# in a phylogenetic framework, analyses of diversification and
# macroevolution, computing distances from allelic and nucleotide
# data, reading nucleotide sequences, and several tools such as
# Mantel's test, computation of minimum spanning tree, the
# population parameter theta based on various approaches,
# nucleotide diversity, generalized skyline plots, estimation of
# absolute evolutionary rates and clock-like trees using mean
# path lengths, non-parametric rate smoothing and penalized
# likelihood, classifying genes in trees using the
# Klastorin-Misawa-Tajima approach. Phylogeny estimation can be
# done with the NJ, BIONJ, and ME methods.
# License: GPL (>= 2)
# URL: http://ape.mpl.ird.fr/
# Packaged: Mon Mar 30 08:46:28 2009; paradis
# Repository: CRAN
# Date/Publication: 2009-03-30 06:56:17
# ------------------------------------------------------------------------------
.mst <-
function(X)
{
# Description:
# The function mst finds the minimum spanning tree between
# a set of observations using a matrix of pairwise distances.
# Authors:
# Original Code: Yvonnick Noel, Julien Claude, and Emmanuel Paradis
# Source:
# Contributed R-packe "ape".
# FUNCTION:
# Minimum Spanning Tree:
if (class(X) == "dist") X = as.matrix(X)
n = dim(X)[1]
N = matrix(0, n, n)
tree = NULL
large.value = max(X) + 1
diag(X) = large.value
index.i = 1
for (i in 1:(n - 1)) {
tree = c(tree, index.i)
# calcul les minimum par colonne
m = apply(as.matrix(X[, tree]), 2, min)
a = .sortIndexMST(X[, tree])[1, ]
b = .sortIndexMST(m)[1]
index.j = tree[b]
index.i = a[b]
N[index.i, index.j] = 1
N[index.j, index.i] = 1
for (j in tree) {
X[index.i, j] = large.value
X[j, index.i] = large.value
}
}
dimnames(N) = dimnames(X)
class(N) = "mst"
# Return Value:
return(N)
}
# ------------------------------------------------------------------------------
.sortIndexMST <-
function(X)
{
# Function returning an index matrix for an increasing sort
if(length(X) == 1) return(1) # sorting a scalar?
if(!is.matrix(X)) X = as.matrix(X) # force vector into matrix
# n = nrow(X)
apply(X, 2, function(v) order(rank(v))) # find the permutation
}
# ------------------------------------------------------------------------------
.mstPlot <-
function (x, graph = "circle", x1 = NULL, x2 = NULL, ...)
{
# Description:
# Plots the minimum spanning tree showing the links
# where the observations are identified by their numbers.
# FUNCTION:
# Plot:
n = nrow(x)
if (is.null(x1) || is.null(x2)) {
if (graph == "circle") {
ang = seq(0, 2 * pi, length = n + 1)
x1 = cos(ang)
x2 = sin(ang)
plot(x1, x2,
type = "n",
xlab = "", ylab = "", xaxt = "n",
yaxt = "n", bty = "n", ...)
}
if (graph == ".nsca") {
XY = .nsca(x)
x1 = XY[, 1]
x2 = XY[, 2]
xLim = c(min(x1) - 0.25 * diff(range(x1)), max(x1))
plot(XY,
type = "n",
xlim = xLim,
xlab = "", # "\".nsca\" -- axis 1",
ylab = "", # "\".nsca\" -- axis 2",
xaxt = "n", yaxt = "n", col = "red",
...)
# Legend:
Names = colnames(x)
legendtext = paste(1:length(Names), Names, sep = "-")
legendtext = substr(legendtext, 1, 8)
legend("topleft", legend = legendtext, bty = "n", cex = 0.8)
}
} else {
plot(x1, x2, type = "n",
xlab = deparse(substitute(x1)),
ylab = deparse(substitute(x2)), ...)
}
for (i in 1:n) {
w1 = which(x[i, ] == 1)
segments(x1[i], x2[i], x1[w1], x2[w1], lwd = 2)
}
points(x1, x2, pch = 21, col = "red", bg = "black", cex = 4)
text(x1, x2, 1:n, col = "white", cex = 0.7)
}
# ------------------------------------------------------------------------------
.nsca <-
function(A)
{
# FUNCTION:
Dr = apply(A, 1, sum)
Dc = apply(A, 2, sum)
eig.res = eigen(diag(1 / sqrt(Dr)) %*% A %*% diag(1 / sqrt(Dc)))
r = diag(1 / Dr) %*% (eig.res$vectors)[, 2:4]
# The next line has been changed by EP (20-02-2003), since
# it does not work if 'r' has no dimnames already defined
# dimnames(r)[[1]] = dimnames(A)[[1]]
rownames(r) = rownames(A)
# Return Value:
r
}
################################################################################
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