paleoTS (version 0.5-1)

opt.joint.GRW: Optimize evolutionary models (joint parameterization)

Description

Functions to find maximum likelihood solutions to general random walk (opt.joint.GRW), unbiased random walk (opt.joint.URW), stasis (opt.joint.Stasis), strict stasis (opt.joint.StrictStasis) and OU models (opt.joint.OU).

Usage

opt.joint.GRW(y, pool = TRUE, cl = list(fnscale = -1), meth = "L-BFGS-B", hess = FALSE)
opt.joint.URW(y, pool = TRUE, cl = list(fnscale = -1), meth = "L-BFGS-B", hess = FALSE)
opt.joint.Stasis(y, pool = TRUE, cl = list(fnscale = -1), meth = "L-BFGS-B", hess = FALSE)
opt.joint.StrictStasis(y, pool = TRUE, cl = list(fnscale = -1), hess = FALSE) 
opt.joint.OU(y, pool = TRUE, cl = list(fnscale = -1), meth = "L-BFGS-B", hess = FALSE)

Arguments

y

a paleoTS object

pool

logical indicating whether to pool variances across samples

cl

control list, passed to function optim

meth

optimization method, passed to function optim

hess

logical, indicating whether to calculate standard errors from the Hessian matrix

Value

An object of class paleoTSfit

Warning

Measures of model fit (log-likelihoods, AIC scores, etc) are not comparable between the two parameterizations.

Details

These functions numerically search a log-likelihood surface for its optimum--they are a convenient wrapper to optim. Arguments meth, cl, and hess are passed to optim; see the help for that function for details. These are included to allow sophisticated users greater control over the optimization; the defaults seem to work well for most, but not all sequences. For meth="L-BFGS-B", some parameters are constrained to be non-negative, which is useful parameters which cannot truly be negative, such as vstep (random walk) and omega (stasis model).

Initial estimates to start the optimization come in part from analytical solutions based on assuming equal sampling error across samples and evenly spaced samples in time (functions mle.GRW, mle.URW and mle.Stasis).

References

Hunt, G. 2006. Fitting and comparing models of phyletic evolution: random walks and beyond. Paleobiology 32:578--601. Hunt, G., M. Bell & M. Travis. 2008. Evolution towards a new adaptive optimum: phenotypic evolution in a fossil stickleback lineage. Evolution 62:700-710. Hunt, G. 2008. Evolutionary patterns within fossil lineages: model-based assessment of modes, rates, punctuations and process.. In R.K. Bambach and P.H. Kelley, eds. From Evolution to Geobiology: Research Questions Driving Paleontology at the Start of a New Century:578--601.

See Also

logL.joint.GRW, opt.GRW, as.paleoTSfit

Examples

# NOT RUN {
 x<- sim.GRW(ns=30, ms=1, vs=1)
 plot(x)
 
 # easier to use  fit3models(, method='Joint') 
 m.urw<- opt.joint.URW(x)
 m.grw<- opt.joint.GRW(x)
 m.sta<- opt.joint.Stasis(x)
 cat(m.urw$AICc, m.grw$AICc, m.sta$AICc, "\n")	# print AICc scores

# }