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
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
|
## collapsed.intervals.R (2002-09-12)
## Collapsed coalescent intervals (e.g. for the skyline plot)
## Copyright 2002 Korbinian Strimmer
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
# construct collapsed intervals from coalescent intervals
collapsed.intervals <- function(ci, epsilon=0.0)
{
if (!inherits(ci, "coalescentIntervals"))
stop("object \"ci\" is not of class \"coalescentIntervals\"")
sz <- ci$interval.length
lsz <- length(sz)
idx <- c <- 1:lsz
p <- 1
w <- 0
# starting from tips collapes intervals
# until total size is >= epsilon
for (i in 1:lsz)
{
idx[[i]] <- p
w <- w + sz[[i]]
if (w >= epsilon)
{
p <- p+1
w <- 0
}
}
# if last interval is smaller than epsilon merge
# with second last interval
lastInterval <- idx==p
if ( sum(sz[lastInterval]) < epsilon )
{
p <- p-1
idx[lastInterval] <- p
}
obj <- list(
lineages=ci$lineages,
interval.length=ci$interval.length,
collapsed.interval=idx, # collapsed intervals (via reference)
interval.count=ci$interval.count,
collapsed.interval.count = idx[[ci$interval.count]],
total.depth =ci$total.depth,
epsilon = epsilon
)
class(obj) <- "collapsedIntervals"
return(obj)
}
|
