surface (version 0.6)

propRegMatch: Similarity of Two Hansen Models

Description

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)

Usage

propRegMatch(fit1, fit2, internal = FALSE)

Value

A single value quantifying the proportion of pairwise regime comparisons that are the same between the two models

Arguments

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

Author

Travis Ingram

References

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.

See Also

surfaceForward, surfaceBackward, surfaceSimulate

Examples

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)