stairway: The Stairway Plot

In pegas: Population and Evolutionary Genetics Analysis System

Description

This function fits a model of population change using the site frequency spectrum (SFS). The default assumes THETA = 1. A model of population change estimates the temporal changes in THETA with respect to the value of this parameter at present time. The model is specified by the user with the option epoch.

Usage

stairway(x, epoch = NULL, step.min = 1e-6, step.max = 1e-3)
## S3 method for class 'stairway'
plot(x, type = "S", xlab = "Coalescent intervals",
             ylab = expression(Theta), ...)
## S3 method for class 'stairway'
lines(x, type = "S", ...)

Arguments

x	an object of class site.spectrum or of class stairway.
epoch	an optional vector of integers giving the periods of time (or epochs) with distinct THETA.
step.min	a single numeric value giving the smallest step size used during optimization.
step.max	id. for the largest step size (see nlminb).
type	the type of lines.
xlab, ylab	the default labels on the axes.
...	further arguments passed to other methods.

Details

The basic method implemented in this function is similar to Polanski and Kimmel (2003). The temporal model with “epochs” is from Liu and Fu (2015).

Value

By default, a single numeric value with the null deviance. If epoch is used, a list with the following components:

estimates	the maximum likelihood estimates.
deviance	the deviance of the fitted model.
null.deviance	the deviance of the null model.
LRT	the likelihood-ratio test comparing the null and the fitted models.
AIC	the Akaike information criterion of the fitted model.

Author(s)

Emmanuel Paradis

References

Liu, X. M. and Fu, Y. X. (2015) Exploring population size changes using SNP frequency spectra. Nature Genetics, 47, 555–559.

Polanski, A. and Kimmel, M. (2003) New explicit expressions for relative frequencies of single-nucleotide polymorphisms with application to statistical inference on population growth. Genetics, 165, 427–436.

See Also

site.spectrum, nlminb

Examples

data(woodmouse)
sp <- site.spectrum(woodmouse)
stairway(sp, c(1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2))

Example output

Loading required package: ape
Loading required package: adegenet
Loading required package: ade4
Registered S3 method overwritten by 'spdep':
  method   from
  plot.mst ape 

   /// adegenet 2.1.3 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()


Registered S3 method overwritten by 'pegas':
  method      from
  print.amova ade4

Attaching package: ‘pegas’

The following object is masked from ‘package:ade4’:

    amova

The following object is masked from ‘package:ape’:

    mst

Warning message:
In site.spectrum.DNAbin(woodmouse) :
  2 sites with more than two states were ignored
$estimates
[1] 0.299081

$deviance
[1] 151.5061

$null.deviance
[1] 157.1032

$LRT
      chi2         df      P.val 
5.59709274 1.00000000 0.01799031 

$AIC
[1] 153.5061

$epoch
 [1] 1 1 1 1 1 1 1 1 2 2 2 2 2 2

attr(,"class")
[1] "stairway"

pegas documentation built on Dec. 16, 2021, 5:09 p.m.