## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
-dist.nodes <- function(phy)
+dist.nodes <- function(x)
{
- phy <- reorder(phy)
- n <- Ntip(phy)
- m <- phy$Nnode
+ x <- reorder(x) # required for the C code
+ n <- Ntip(x)
+ m <- x$Nnode
+ nm <- n + m
d <- .C("dist_nodes", as.integer(n), as.integer(m),
- as.integer(phy$edge[, 1] - 1L), as.integer(phy$edge[, 2] - 1L),
- as.double(phy$edge.length), as.integer(Nedge(phy)),
+ as.integer(x$edge[, 1] - 1L), as.integer(x$edge[, 2] - 1L),
+ as.double(x$edge.length), as.integer(Nedge(x)),
double(nm * nm), DUP = FALSE, NAOK = TRUE,
PACKAGE = "ape")[[7]]
- nm <- n + m
dim(d) <- c(nm, nm)
dimnames(d) <- list(1:nm, 1:nm)
d
-## reorder.phylo.R (2012-08-01)
+## reorder.phylo.R (2012-08-17)
## Internal Reordering of Trees
.C("neworder_cladewise", as.integer(nb.tip),
as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
as.integer(nb.edge), integer(nb.edge),
- PACKAGE = "ape")[[5]]
+ DUP = FALSE, NAOK = TRUE, PACKAGE = "ape")[[5]]
} else {
##node.degree <- tabulate(x$edge[, 1])
neworder <-
as.integer(nb.node), as.integer(x$edge[, 1]),
as.integer(x$edge[, 2]), as.integer(nb.edge),
integer(nb.edge), PACKAGE = "ape")[[6]]
- }
+ }
x$edge <- x$edge[neworder, ]
if (!is.null(x$edge.length))
x$edge.length <- x$edge.length[neworder]
-/* reorder_phylo.c 2012-08-01 */
+/* reorder_phylo.c 2012-08-17 */
/* Copyright 2008-2012 Emmanuel Paradis */
#include <R.h>
-void neworder_cladewise(int *n, int *edge1, int *edge2,
- int *N, int *neworder)
-/* n: nb of tips, N: nb of edges */
+static int iii;
+
+void foo_reorder(int node, int n, int m, int *e1, int *e2, int *neworder, int *L, int *pos)
{
- int i, j, k, node, *done, dn, *node_back, eb;
- done = &dn;
- node_back = &eb;
-
- /* done: indicates whether an edge has been collected
- node_back: the series of node from the root to `node'
- node: the current node */
-
- done = (int*)R_alloc(*N, sizeof(int));
- node_back = (int*)R_alloc(*N + 2 - *n, sizeof(int));
- memset(done, 0, *N * sizeof(int));
-
- j = k = 0;
- node = *n + 1;
- while (j < *N) {
- for (i = 0; i < *N; i++) {
- if (done[i] || edge1[i] != node) continue;
- neworder[j] = i + 1;
- j++;
- done[i] = 1;
- if (edge2[i] > *n) {
- node_back[k] = node;
- k++;
- node = edge2[i];
- /* if found a new node, reset the loop */
- i = -1;
- }
+ int i = node - n - 1, j, k;
+
+/* 'i' is the C index corresponding to 'node' */
+
+ for (j = 0; j < pos[i]; j++) {
+ k = L[i + m * j];
+ neworder[iii++] = k + 1;
+ if (e2[k] > n) /* is it an internal edge? */
+ foo_reorder(e2[k], n, m, e1, e2, neworder, L, pos);
}
- /* if arrived at the end of `edge', go down one node */
- k--;
- node = node_back[k];
- }
}
+void neworder_cladewise(int *n, int *e1, int *e2, int *N, int *neworder)
+/* n: nb of tips
+ m: nb of nodes
+ N: nb of edges */
+{
+ int i, j, k, *L, *pos, m = *N - *n + 1, degrmax = *n - m + 1;
+
+/* degrmax is the largest value that a node degree can be */
+
+/* L is a 1-d array storing, for each node, the C indices of the rows of
+ the edge matrix where the node is ancestor (i.e., present in the 1st
+ column). It is used in the same way than a matrix (which is actually
+ a vector) is used in R as a 2-d structure. */
+
+ L = (int*)R_alloc(m * degrmax, sizeof(int));
+
+/* pos gives the position for each 'row' of L, that is the number of elements
+ which have already been stored for that 'row'. */
+
+ pos = (int*)R_alloc(m, sizeof(int));
+ memset(pos, 0, m * sizeof(int));
+
+/* we now go down along the edge matrix */
+
+ for (i = 0; i < *N; i++) {
+ k = e1[i] - *n - 1; /* k is the 'row' index in L corresponding to node e1[i] */
+ j = pos[k]; /* the current 'column' position corresping to k */
+ pos[k]++; /* increment in case the same node is found in another row of the edge matrix */
+ L[k + m * j] = i;
+ }
+
+/* L is now ready: we can start the recursive calls. */
+/* We start with the root 'n + 1': its index will be changed into
+ the corresponding C index inside the recursive function. */
+
+ iii = 0;
+ foo_reorder(*n + 1, *n, m, e1, e2, neworder, L, pos);
+}
+
+
#define DO_NODE_PRUNING\
/* go back down in `edge' to set `neworder' */\
for (j = 0; j <= i; j++) {\
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