Calculates the pairwise matching between two alternate paintings of the same phylogenetic tree. This is done by creating a halfmatrix for each hansentree
object indicating whether each pairwise comparison of tip species or branches shows they are in the same regime (coded ‘1’) or different regimes (coded ‘0’). The ‘proportion matching’ value returned is the proportion of elements of the two matrices that are equal; a measure of correspondence between two Hansen models (one of which may be the ‘true’ model if data are simulated)
1  propRegMatch(fit1, fit2, internal = FALSE)

fit1 
First fitted Hansen model; can be the 
fit2 
Second fitted Hansen model; see 
internal 
A logical indicating whether internal branches should be included in the calculation of matching in addition to tip taxa; this is only possible if the two trees have identical topology; defaults to FALSE 
A single value quantifying the proportion of pairwise regime comparisons that are the same between the two models
Travis Ingram
Ingram, T. & Mahler, D.L. (2013) SURFACE: detecting convergent evolution from comparative data by fitting OrnsteinUhlenbeck models with stepwise AIC. Methods in Ecology and Evolution 4: 416425.
surfaceForward
, surfaceBackward
, surfaceSimulate
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