paleoTS (version 0.5-1)

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 = NULL, 
           start.age = NULL, oldest=c("first", "last"), reset.time=TRUE)
read.paleoTS(file = NULL, oldest = "first", reset.time=TRUE, ...)

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

oldest

by default, samples are listed from oldest to youngest. If file is in reverse order, use oldest = "last"

reset.time

logical; if TRUE, then change time scale to start at t=0 and adjust start.age accordingly.

…

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)

Warning

Some functions do assume that reset.time=TRUE, that is that time (tt) starts at zero and increases from there. Do not change this argument unless you know what you are doing.

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 more convenient for getting the relevant data from text files.

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. Generally, setting reset.time = TRUE is good practice.

References

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

See Also

plot.paleoTS

Examples

# NOT RUN {
## 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)
# }