paleoTSalt-package {paleoTSalt} | R Documentation |
This package facilitates analysis of paleontological sequences of trait values from an evolving lineage.
Functions are provided to fit, using maximum likelihood, evolutionary models including unbiased random walks,
directional evolution, stasis and OU (Orstein-Uhlenbeck) models. This package has a similar purpose as the
paleoTS
package, but employs a different parameterization of evolutionary models.
Package: | paleoTSalt |
Type: | Package |
Version: | 0.1-1 |
Date: | 2007-10-22 |
License: | GPL 3 or newer |
Gene Hunt, hunte@si.edu
Hunt, G. 2006. Fitting and comparing models of phyletic evolution: random walks and beyond. Paleobiology 32:578–601.
data(dorsal.spines) # get subset of samples from invading lineage (tt>=4.5 Kyr), only those with nn>=5 ok<- dorsal.spines$tt >= 4.5 & dorsal.spines$nn >=5 ds2<- sub.paleoTS(dorsal.spines, ok=ok) # convert time scale to generations (500 gen per Kyr) ds2$tt<- ds2$tt*(1000/2) plot(ds2, pool=TRUE) # compare URW (drift) and OU (adaptive) models m.urw<- opt.alt.URW(ds2, pool=TRUE) m.ou<- opt.alt.OU(ds2, pool=TRUE) cat ("Model","logL", "AICc\n", sep="\t") cat ("URW", round(m.urw$val, 2), round(m.urw$AICc, 2), sep="\t") cat ("\nOU", round(m.ou$val, 2), round(m.ou$AICc, 2), sep="\t") add.OU.curves(m.ou, ds2, col="grey")