setup_env

This function will automatically download a Python miniconda distribution
dedicated to an R-Python interface. It will also create a slendr-specific
Python environment with all the required Python dependencies.

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

setup_env function

<dl><dt>quiet</dt>
<dd>Should informative messages be printed to the console? Default
is <code>FALSE</code>.</dd>
<dt>agree</dt>
<dd>Automatically agree to all questions?</dd>
<dt>pip</dt>
<dd>Should pip be used instead of conda for installing slendr's Python
dependencies?</dd></dl>

Arguments

Setup a dedicated Python virtual environment for slendr — setup_env

<dl>

<dt>quiet</dt>
<dd>Should informative messages be printed to the console? Default
is <code>FALSE</code>.</dd>


<dt>agree</dt>
<dd>Automatically agree to all questions?</dd>


<dt>pip</dt>
<dd>Should pip be used instead of conda for installing slendr's Python
dependencies?</dd>

</dl>

setup_env: Setup a dedicated Python virtual environment for slendr

Description

Usage

Value

Arguments