ts_ancestors

Extract (spatio-)temporal ancestral history for given nodes/individuals

A framework for simulating spatially explicit genomic data which
leverages real cartographic information for programmatic and visual encoding
of spatiotemporal population dynamics on real geographic landscapes. Population
genetic models are then automatically executed by the 'SLiM' software by Haller
et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom
built-in simulation 'SLiM' script. Additionally, fully abstract spatial models
not tied to a specific geographic location are supported, and users can also
simulate data from standard, non-spatial, random-mating models. These can be
simulated either with the 'SLiM' built-in back-end script, or using an efficient
coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022)
<doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the
R package. Simulated genomic data is saved in a tree-sequence format and can be
loaded, manipulated, and summarised using tree-sequence functionality via an R
interface to the 'Python' module 'tskit' by Kelleher et al. (2019)
<doi:10.1038/s41588-019-0483-y>. Complete model configuration, simulation and
analysis pipelines can be therefore constructed without a need to leave the R
environment, eliminating friction between disparate tools for population genetic
simulations and data analysis.

Martin Petr

slendr

A Simulation Framework for Spatiotemporal Population Genetics

ts_ancestors function

<dl><dt>ts</dt>
<dd>Tree sequence object of the class <code>slendr_ts</code></dd>
<dt>x</dt>
<dd>Either an individual name or an integer node ID</dd>
<dt>verbose</dt>
<dd>Report on the progress of ancestry path generation?</dd>
<dt>complete</dt>
<dd>Does every individual in the tree sequence need to have
complete metadata recorded? If <code>TRUE</code>, only individuals/nodes with
complete metadata will be included in the reconstruction of ancestral
relationships. For instance, nodes added during the coalescent recapitation
phase will not be included because they don't have spatial information
associated with them.</dd></dl>

Arguments

Extract (spatio-)temporal ancestral history for given nodes/individuals — ts_ancestors

<dl>

<dt>ts</dt>
<dd>Tree sequence object of the class <code>slendr_ts</code></dd>


<dt>x</dt>
<dd>Either an individual name or an integer node ID</dd>


<dt>verbose</dt>
<dd>Report on the progress of ancestry path generation?</dd>


<dt>complete</dt>
<dd>Does every individual in the tree sequence need to have
complete metadata recorded? If <code>TRUE</code>, only individuals/nodes with
complete metadata will be included in the reconstruction of ancestral
relationships. For instance, nodes added during the coalescent recapitation
phase will not be included because they don't have spatial information
associated with them.</dd>

</dl>

ts_ancestors: Extract (spatio-)temporal ancestral history for given nodes/individuals

Description

Usage

Value

Arguments

Examples