paleoTS (version 0.3-1)

as.paleoTS: 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

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)

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.

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)