feat_sample

Creates a feature that represents the sampling from one population

internal

Coalescent simulators can rapidly simulate biological sequences
evolving according to a given model of evolution.
You can use this package to specify such models, to conduct the simulations
and to calculate additional statistics from the results (Staab, Metzler,
2016 <doi:10.1093/bioinformatics/btw098>).
It relies on existing simulators for doing the simulation, and currently
supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites
mutation models by combining the simulators with the program 'seq-gen'.
Coala provides functions for calculating certain summary statistics, which
can also be applied to actual biological data.
One possibility to import data is through the 'PopGenome' package
(<https://github.com/pievos101/PopGenome>).

Dirk Metzler

coala

A Framework for Coalescent Simulation

Paul Staab

Jorge E. Amaya Romero

feat_sample function

<dl><dt>individuals</dt>
<dd>The number of individuals that are sampled per population,
given as a numeric vector.</dd>
<dt>ploidy</dt>
<dd>The number of chromosomes that will be simulated per
individual.</dd>
<dt>time</dt>
<dd>The time at which the sample is taken.</dd>
<dt>locus_group</dt>
<dd>The loci for which this features is used. Can either be
<code>"all"</code> (default), in which case the feature is used for simulating
all loci, or a numeric vector. In the latter case, the feature is only
used for the loci added in <code>locus_</code> commands with the corresponding
index starting from 1 in order in which the commands where added to the
model. For example, if a model has
<code>locus_single(10) + locus_averaged(10, 11) + locus_single(12)</code> and
this argument is <code>c(2, 3)</code>, than the feature is used for all but
the first locus (that is locus 2 - 12).</dd></dl>

Arguments

Creates a feature that represents the sampling from one population — feat_sample

<dl>

<dt>individuals</dt>
<dd>The number of individuals that are sampled per population,
given as a numeric vector.</dd>


<dt>ploidy</dt>
<dd>The number of chromosomes that will be simulated per
individual.</dd>


<dt>time</dt>
<dd>The time at which the sample is taken.</dd>


<dt>locus_group</dt>
<dd>The loci for which this features is used. Can either be
<code>"all"</code> (default), in which case the feature is used for simulating
all loci, or a numeric vector. In the latter case, the feature is only
used for the loci added in <code>locus_</code> commands with the corresponding
index starting from 1 in order in which the commands where added to the
model. For example, if a model has
<code>locus_single(10) + locus_averaged(10, 11) + locus_single(12)</code> and
this argument is <code>c(2, 3)</code>, than the feature is used for all but
the first locus (that is locus 2 - 12).</dd>

</dl>

feat_sample: Creates a feature that represents the sampling from one population

Description

Usage

Value

Arguments

See Also