as.paleoTS {paleoTS}

Paleontological time-series class

Package:

paleoTS

Version:

0.4-4

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

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.

Values

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.

References

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

Note

The analysis estimates the contribution of sampling noise to the observed differences between samples. It does this assuming that one is analyzing sample means, which have sampling variances equal to variance divided by sample size, vv/nn. If one is interested in analyzing statistics other than the sample mean (medians, quantiles, or other statistics), use the the following procedure: set the statistic in question as the mm values, replace vv with a vector of the squared standard errors for each estimate, and set all values of nn to one.

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)

Author(s)

Gene Hunt

Documentation reproduced from package paleoTS, version 0.4-4. License: GPL (>= 2)