propRegMatch {surface}

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)

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

Value

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

Author(s)

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)