plot_map

Plots objects of the three <code>slendr</code> spatial classes (<code>slendr_map</code>,
<code>slendr_region</code>, and <code>slendr_pop</code>).

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

plot_map function

<dl><dt>...</dt>
<dd>Objects of classes <code>slendr_map</code>, <code>slendr_region</code>, or
<code>slendr_pop</code></dd>
<dt>time</dt>
<dd>Plot a concrete time point</dd>
<dt>gene_flow</dt>
<dd>Indicate geneflow events with an arrow</dd>
<dt>labels</dt>
<dd>Should the (starting) polygons of each populations be labeled with
a respective population label (default <code>FALSE</code>)?</dd>
<dt>graticules</dt>
<dd>Plot graticules in the original Coordinate Reference System
(such as longitude-latitude), or in the internal CRS (such as meters)?</dd>
<dt>intersect</dt>
<dd>Intersect the population boundaries against landscape and
other geographic boundaries (default <code>TRUE</code>)?</dd>
<dt>show_map</dt>
<dd>Show the underlying world map</dd>
<dt>title</dt>
<dd>Title of the plot</dd>
<dt>interpolated_maps</dt>
<dd>Interpolated spatial boundaries for all populations
in all time points (this is only used for plotting using the <code>explore</code>
shiny app)</dd></dl>

Arguments

Plot slendr geographic features on a map — plot_map

<dl>

<dt>...</dt>
<dd>Objects of classes <code>slendr_map</code>, <code>slendr_region</code>, or
<code>slendr_pop</code></dd>


<dt>time</dt>
<dd>Plot a concrete time point</dd>


<dt>gene_flow</dt>
<dd>Indicate geneflow events with an arrow</dd>


<dt>labels</dt>
<dd>Should the (starting) polygons of each populations be labeled with
a respective population label (default <code>FALSE</code>)?</dd>


<dt>graticules</dt>
<dd>Plot graticules in the original Coordinate Reference System
(such as longitude-latitude), or in the internal CRS (such as meters)?</dd>


<dt>intersect</dt>
<dd>Intersect the population boundaries against landscape and
other geographic boundaries (default <code>TRUE</code>)?</dd>


<dt>show_map</dt>
<dd>Show the underlying world map</dd>


<dt>title</dt>
<dd>Title of the plot</dd>


<dt>interpolated_maps</dt>
<dd>Interpolated spatial boundaries for all populations
in all time points (this is only used for plotting using the <code>explore</code>
shiny app)</dd>

</dl>

plot_map: Plot `slendr` geographic features on a map

Description

Usage

Value

Arguments