sumstats

This data set contains a set of 14 summary statistics computed
from data simulated under an isolation with migration model of two
populations.

datasets

Provides functions to simulate Pool-seq data under models of
demographic formation and to import Pool-seq data from real populations.
Implements two ABC algorithms for performing parameter estimation and
model selection using Pool-seq data. Cross-validation can also be
performed to assess the accuracy of ABC estimates and model choice.
Carvalho et al., (2022) <doi:10.1111/1755-0998.13834>.

João Carvalho

poolABC

Approximate Bayesian Computation with Pooled Sequencing Data

Vítor Sousa

sumstats function

a matrix with 10000 rows and 14 columns:
<dl><dt>Sf</dt>
<dd>fraction of sites fixed between populations.</dd>
<dt>Sx1</dt>
<dd>fraction of exclusive sites for the first population.</dd>
<dt>Sx2</dt>
<dd>fraction of exclusive sites for the second population.</dd>
<dt>SS</dt>
<dd>fraction of sites shared between the two populations.</dd>
<dt>Mean_Het1</dt>
<dd>mean expected heterozygosity of the first population.</dd>
<dt>Mean_Het2</dt>
<dd>mean expected heterozygosity of the second population.</dd>
<dt>SD_Het1</dt>
<dd>standard deviation across loci of the mean expected
heterozygosity of the first population.</dd>
<dt>SD_Het2</dt>
<dd>standard deviation across loci of the mean expected
heterozygosity of the second population.</dd>
<dt>Mean_HetBet</dt>
<dd>mean heterozygosity between the two populations.</dd>
<dt>SD_HetBet</dt>
<dd>standard deviation across loci of the mean heterozygosity
between the two populations.</dd>
<dt>Mean_FST</dt>
<dd>mean pairwise FST between the two populations.</dd>
<dt>SD_FST</dt>
<dd>standard deviation across loci of the mean pairwise FST
between the two populations.</dd>
<dt>FSTQ1</dt>
<dd>5% quantile of the mean pairwise FST distribution.</dd>
<dt>FSTQ2</dt>
<dd>95% quantile of the mean pairwise FST distribution.</dd>
 
</dl>

Format

Matrix of summary statistics computed from simulated data — sumstats

a matrix with 10000 rows and 14 columns:
<dl>

<dt>Sf</dt>
<dd>fraction of sites fixed between populations.</dd>


<dt>Sx1</dt>
<dd>fraction of exclusive sites for the first population.</dd>


<dt>Sx2</dt>
<dd>fraction of exclusive sites for the second population.</dd>


<dt>SS</dt>
<dd>fraction of sites shared between the two populations.</dd>


<dt>Mean_Het1</dt>
<dd>mean expected heterozygosity of the first population.</dd>


<dt>Mean_Het2</dt>
<dd>mean expected heterozygosity of the second population.</dd>


<dt>SD_Het1</dt>
<dd>standard deviation across loci of the mean expected
heterozygosity of the first population.</dd>


<dt>SD_Het2</dt>
<dd>standard deviation across loci of the mean expected
heterozygosity of the second population.</dd>


<dt>Mean_HetBet</dt>
<dd>mean heterozygosity between the two populations.</dd>


<dt>SD_HetBet</dt>
<dd>standard deviation across loci of the mean heterozygosity
between the two populations.</dd>


<dt>Mean_FST</dt>
<dd>mean pairwise FST between the two populations.</dd>


<dt>SD_FST</dt>
<dd>standard deviation across loci of the mean pairwise FST
between the two populations.</dd>


<dt>FSTQ1</dt>
<dd>5% quantile of the mean pairwise FST distribution.</dd>


<dt>FSTQ2</dt>
<dd>95% quantile of the mean pairwise FST distribution.</dd>
 
</dl>

sumstats: Matrix of summary statistics computed from simulated data

Description

Usage

Arguments

Format