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Last data update: 2014.03.03

R: Periodogram Power Spectral Density

periodogram

R Documentation

Periodogram Power Spectral Density

Description

periodogram is a wrapper function for spectrum with some special options set. It returns the power spectral density, i.e. the squared modulus of the Fourier coefficient divided by the length of the series, for multiple time series as well as the corresponding Fourier frequencies. The frequencies range between 0 and the Nyquist critical frequency fc = frequency(x)/2.

periodogram is used by the functions avgp and fisher.g.test. For general periodogram functions please refer to spectrum.

Usage

periodogram(x, method = "builtin")

Arguments

`x`	vector or matrix containing the time series data (one time series per column)
`method`	a string that specifies which method should be used to compute the spectral density: "builtin" employs the function `spectrum` with the options taper=0, plot=FALSE, fast=FALSE, detrend=FALSE, and demean=TRUE; "clone" employs directly the Fourier transform function `fft` (with sames results as "builtin"); and "smooth" uses the function `spectrum` with options as above plus span=3.

Value

A list object with the following components:

`spec`	A vector or matrix with the estimated power spectral densities (one column per time series).
`freq`	A vector with frequencies f ranging from 0 to fc (if the sampling rate `frequency`(x)) equals 1 then fc = 0.5). Angular frequencies may be obtained by multiplication with 2pi (i.e. omega = 2pi*f).

Author(s)

Konstantinos Fokianos (http://www.ucy.ac.cy/~fokianos/) and Korbinian Strimmer (http://strimmerlab.org).

Examples

# load GeneCycle library
library("GeneCycle")

# load data set
data(caulobacter)

# how many genes and how many samples?
dim(caulobacter)

# periodograms of the first 10 genes
periodogram(caulobacter[,1:10])

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GeneCycle)
Loading required package: MASS
Loading required package: longitudinal
Loading required package: corpcor
Loading required package: fdrtool
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GeneCycle/periodogram.Rd_%03d_medium.png", width=480, height=480)
> ### Name: periodogram
> ### Title: Periodogram Power Spectral Density
> ### Aliases: periodogram
> ### Keywords: ts
> 
> ### ** Examples
> 
> # load GeneCycle library
> library("GeneCycle")
> 
> # load data set
> data(caulobacter)
> 
> # how many genes and how many samples?
> dim(caulobacter)
[1]   11 1444
> 
> # periodograms of the first 10 genes
> periodogram(caulobacter[,1:10])
$spec
           [,1]        [,2]        [,3]        [,4]       [,5]        [,6]
[1,] 0.44284739 1.130357356 1.068349960 1.419206295 2.27775109 1.639187395
[2,] 0.17385272 0.115400249 0.104251846 0.130276223 0.20037570 0.274096460
[3,] 0.29355408 0.003969141 0.001325152 0.002410588 0.09710114 0.052439716
[4,] 0.23226646 0.005259707 0.001714942 0.006475784 0.09488164 0.001921288
[5,] 0.01466026 0.010919571 0.003348493 0.002697767 0.06143642 0.006730472
             [,7]        [,8]        [,9]     [,10]
[1,] 0.0023735707 2.019760704 0.075547591 0.9021377
[2,] 0.0078230143 0.134738578 0.018713563 0.5507906
[3,] 0.0199583163 0.017368141 0.029188321 0.2945531
[4,] 0.2256001470 0.003061959 0.002084201 0.3577172
[5,] 0.0005818419 0.014593731 0.029949666 0.2678070

$freq
[1] 0.09090909 0.18181818 0.27272727 0.36363636 0.45454545

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>