NRooted {TreeTools} | R Documentation |
Number of trees
Description
These functions return the number of rooted or unrooted binary trees consistent with a given pattern of splits.
Usage
NRooted(tips)
NUnrooted(tips)
NRooted64(tips)
NUnrooted64(tips)
LnUnrooted(tips)
LnUnrooted.int(tips)
Log2Unrooted(tips)
Log2Unrooted.int(tips)
LnRooted(tips)
LnRooted.int(tips)
Log2Rooted(tips)
Log2Rooted.int(tips)
LnUnrootedSplits(...)
Log2UnrootedSplits(...)
NUnrootedSplits(...)
LnUnrootedMult(...)
Log2UnrootedMult(...)
NUnrootedMult(...)
Arguments
tips |
Integer specifying the number of leaves. |
... |
Integer vector, or series of integers, listing the number of leaves in each split. |
Details
Functions starting N
return the number of rooted or unrooted trees.
Replace this initial N
with Ln
for the natural logarithm of this number;
or Log2
for its base 2 logarithm.
Calculations follow Cavalli-Sforza and Edwards (1967) and Carter et al. (1990), Theorem 2.
Functions
-
NUnrooted()
: Number of unrooted trees -
NRooted64()
: Exact number of rooted trees as 64-bit integer (13 <nTip
< 19) -
NUnrooted64()
: Exact number of unrooted trees as 64-bit integer (14 <nTip
< 20) -
LnUnrooted()
: Log Number of unrooted trees -
LnUnrooted.int()
: Log Number of unrooted trees (as integer) -
LnRooted()
: Log Number of rooted trees -
LnRooted.int()
: Log Number of rooted trees (as integer) -
NUnrootedSplits()
: Number of unrooted trees consistent with a bipartition split. -
NUnrootedMult()
: Number of unrooted trees consistent with a multi-partition split.
Author(s)
Martin R. Smith (martin.smith@durham.ac.uk)
References
Carter M, Hendy M, Penny D, Székely LA, Wormald NC (1990).
“On the distribution of lengths of evolutionary trees.”
SIAM Journal on Discrete Mathematics, 3(1), 38–47.
doi:10.1137/0403005.
Cavalli-Sforza LL, Edwards AWF (1967).
“Phylogenetic analysis: models and estimation procedures.”
Evolution, 21(3), 550–570.
ISSN 00143820, doi:10.1111/j.1558-5646.1967.tb03411.x.
See Also
Other tree information functions:
CladisticInfo()
,
TreesMatchingTree()
Examples
NRooted(10)
NUnrooted(10)
LnRooted(10)
LnUnrooted(10)
Log2Unrooted(10)
# Number of trees consistent with a character whose states are
# 00000 11111 222
NUnrootedMult(c(5,5,3))
NUnrooted64(18)
LnUnrootedSplits(c(2,4))
LnUnrootedSplits(3, 3)
Log2UnrootedSplits(c(2,4))
Log2UnrootedSplits(3, 3)
NUnrootedSplits(c(2,4))
NUnrootedSplits(3, 3)