1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
|
## treePop.R (2011-10-11)
## Tree Reconstruction With the Triangles Method
## Copyright 2011 Andrei-Alin Popescu
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
triangMtd <- function(X)
{
if (is.matrix(X)) X <- as.dist(X)
if (any(is.na(X)))
stop("missing values are not allowed in the distance matrix")
N <- attr(X, "Size")
labels <- attr(X, "Labels")
if (is.null(labels)) labels <- as.character(1:N)
ans <- .C(C_triangMtd, as.double(X), as.integer(N), integer(2*N - 3),
integer(2*N - 3), double(2*N - 3), NAOK = TRUE)
obj <- list(edge = cbind(ans[[3]], ans[[4]]), edge.length = ans[[5]],
tip.label = labels, Nnode = N - 2L)
class(obj) <- "phylo"
reorder(obj)
}
triangMtds <- function(X)
{
if (is.matrix(X)) X <- as.dist(X)
X[is.na(X)] <- -1
X[X < 0] <- -1
N <- attr(X, "Size")
labels <- attr(X, "Labels")
if (is.null(labels)) labels <- as.character(1:N)
ans <- .C(C_triangMtds, as.double(X), as.integer(N), integer(2*N - 3),
integer(2*N - 3), double(2*N - 3), NAOK = TRUE)
obj <- list(edge = cbind(ans[[3]], ans[[4]]), edge.length = ans[[5]],
tip.label = labels, Nnode = N - 2L)
class(obj) <- "phylo"
reorder(obj)
}
|
