Description Usage Arguments Details Value Author(s) References See Also Examples
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
.
1 2 3 4 5 6 |
x |
an object of class |
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
|
type |
the type of lines. |
xlab, ylab |
the default labels on the axes. |
... |
further arguments passed to other methods. |
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).
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. |
Emmanuel Paradis
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.
1 2 3 | data(woodmouse)
sp <- site.spectrum(woodmouse)
stairway(sp, c(1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2))
|
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"
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