map.overlap | R Documentation |
Calculates the similarity of two different stochastically mapped character histories.
map.overlap(tree1, tree2, tol=1e-6, ...)
Map.Overlap(tree1, tree2, tol=1e-06, standardize=TRUE, ...)
tree1 |
an object of class |
tree2 |
an object of class |
tol |
an optional tolerance value. |
standardize |
for |
... |
optional arguments, such as |
map.overlap
computes a single quantity giving the overall similarity of the maps, consequently this measure only makes sense of some or all of the states are shared between the two mapped tress.
In Map.Overlap
what is computed instead is a matrix in which the rows correspond to the states observed in tree1
and the columns give the states for tree2
, with the numerical values of the matrix showing the total overlap between each pair of mapped states on the two trees.
A numerical value on the interval (0, 1), for map.overlap
; or a matrix whose elements should sum to 1.0 (Map.Overlap
).
Liam Revell liam.revell@umb.edu
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
make.simmap
, read.simmap
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