propRegMatch: Similarity of Two Hansen Models
In surface: Fitting Hansen Models to Investigate Convergent Evolution

Description Usage Arguments Value Author(s) References See Also Examples

Calculates the pairwise matching between two alternate paintings of the same phylogenetic tree. This is done by creating a half-matrix 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 `$fit` component of the list returned by either one iteration of an analyis with `surfaceForward` or `surfaceBackward`, or the list returned by `surfaceSimulate`
`fit2`	Second fitted Hansen model; see `fit1`
`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 Ornstein-Uhlenbeck models with stepwise AIC. Methods in Ecology and Evolution 4: 416-425.

surfaceForward, surfaceBackward, surfaceSimulate

data(surfaceDemo)
tree<-surfaceDemo$tree
dat<-surfaceDemo$sim$dat
olist<-convertTreeData(tree,dat)
otree<-olist[[1]]; odata<-olist[[2]]
startmod<-startingModel(otree, odata, shifts = c("6"="b")) 
startmod2<-startingModel(otree, odata, shifts = c("6"="b","17"="c")) 
propRegMatch(startmod[[1]]$fit, startmod2[[1]]$fit)