as.paleoTS {paleoTS}R Documentation

Paleontological time-series class

Description

A class for storing information on evolutionary time-series data.

Usage

as.paleoTS(mm, vv, nn, tt, MM = NULL, genpars = NULL, label = "", start.age = NULL)
read.paleoTS(file = NULL, hh = FALSE, oldest = "first", ...)

Arguments

mm vector of sample means
vv vector of sample variances
nn vector of sample sizes
tt vector of sample ages
MM vector of true population means (for simulated time series)
genpars generating parameters (for simulated time series)
label optional label describing time series data
start.age optional, indicating age of oldest sample (e.g., in millions of years ago)
file file with paleoTS data; if NULL, then opens file.choose dialog
hh logical; if TRUE, file with paleoTS data has a header
oldest by default, samples are listed from oldest to youngest. If file is in reverse order, use oldest = "last"
... further arguments passed to read.table

Details

Function as.paleoTS() combines time series data into an object of class paleoTS. This function will usually not be used directly; read.paleoTS() is used to get the relevant data from text files, and sim.GRW() and sim.Stasis() are used to simulate paleontological time-series from generating parameters.
If no file name is given for read.paleoTS, the user will be prompted to select a file using the file.choose() interactive prompt. Samples are assumed to be ordered from oldest to youngest (if not, use oldest="last"), with ages indicating time elapsed from the beginning of the sequence, rather than geological age before the present. If sample ages decrease through the sequence, as if given in millions of years ago, tt will automatically be converted to time elapsed from the beginning of the sequence.

Value

mm vector of sample means
vv vector of sample variances
nn vector of sample sizes
tt vector of sample ages
MM vector of true population means (for simulated time series)
genpars generating parameters (for simulated time series)
label optional label describing time series data
start.age optional, indicating age of oldest sample (e.g., in millions of years ago)

Author(s)

Gene Hunt

References

Hunt, G. 2006. Fitting and comparing models of phyletic evolution: random walks and beyond. Paleobiology 32:578–601.

See Also

plot.paleoTS

Examples

## create paleoTS object
 y <- as.paleoTS(mm=rnorm(10), vv=rep(1,10), nn=rep(25,10), tt=1:10, label="white noise time series")
 plot(y)

[Package paleoTS version 0.3-1 Index]