paleoTS (version 0.3-1)

add.OU.curves: Adds curves to an existing plot indicating best-fit OU model

Description

This function takes the results of fitting the Orstein-Uhlenbeck (OU) model and plots the expected value (mean) and 95 percent probability interval of the best-fitting OU parameters.

Usage

add.OU.curves(w, x, what = c("lines", "polygon"), tt.offset = 0, ...)

Arguments

w

output from the function opt.alt.OU

x

a paleoTS pbject

what

whether to draw lines or polygon for the model fit

tt.offset

difference between starting age in w and x

...

additional arguments to graphing functions

Value

• None, the function is evoked to add graphics to an existing plot.

Details

Note that tt.offset is only used in the relatively rare instances in which the model fit is not applied to the entire sequence.

See Also

plot.paleoTS, opt.joint.OU

Examples

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)

# fit OU model
m.ou<- opt.joint.OU(ds2, pool=TRUE)
add.OU.curves(m.ou, ds2, what="lines", col="darkgrey")