add.OU.curves {paleoTS} | R Documentation |
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.
add.OU.curves(w, x, what = c("lines", "polygon"), tt.offset = 0, ...)
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 |
Note that tt.offset
is only used in the relatively rare instances in which the model fit
is not applied to the entire sequence.
None, the function is evoked to add graphics to an existing plot.
Gene Hunt
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")