PLNmodels

PLNmodels-package

<img src="figures/logo.png?package=PLNmodels&version=1.3.2" style="float: right" alt="logo" width="120">
The Poisson-lognormal model and variants (Chiquet, Mariadassou and Robin, 2021 tools:::Rd_expr_doi("10.3389/fevo.2021.588292")) can be used for a variety of multivariate problems when count data are at play, including principal component analysis for count data, discriminant analysis, model-based clustering and network inference. Implements variational algorithms to fit such models accompanied with a set of functions for visualization and diagnostic.

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The Poisson-lognormal model and variants (Chiquet,
Mariadassou and Robin, 2021 <doi:10.3389/fevo.2021.588292>) can be
used for a variety of multivariate problems when count data are at
play, including principal component analysis for count data,
discriminant analysis, model-based clustering and network inference.
Implements variational algorithms to fit such models accompanied with
a set of functions for visualization and diagnostic.

Julien Chiquet

Poisson Lognormal Models

Mahendra Mariadassou

Stéphane Robin

François Gindraud

Julie Aubert

Bastien Batardière

Giovanni Poggiato

Cole Trapnell

Maddy Duran

Ryan Friedman

PLNmodels-package function

Maintainer: Julien Chiquet <a href="/link/julien.chiquet%40inrae.fr?package=PLNmodels&version=1.3.2" data-mini-rdoc="PLNmodels::julien.chiquet@inrae.fr">julien.chiquet@inrae.fr</a> (<a href="https://orcid.org/0000-0002-3629-3429">ORCID</a>)
Authors:<ul>
<li>Julien Chiquet <a href="/link/julien.chiquet%40inrae.fr?package=PLNmodels&version=1.3.2" data-mini-rdoc="PLNmodels::julien.chiquet@inrae.fr">julien.chiquet@inrae.fr</a> (<a href="https://orcid.org/0000-0002-3629-3429">ORCID</a>)</li>
<li>Mahendra Mariadassou <a href="/link/mahendra.mariadassou%40inrae.fr?package=PLNmodels&version=1.3.2" data-mini-rdoc="PLNmodels::mahendra.mariadassou@inrae.fr">mahendra.mariadassou@inrae.fr</a> (<a href="https://orcid.org/0000-0003-2986-354X">ORCID</a>)</li>
<li>Stéphane Robin <a href="/link/stephane.robin%40inrae.fr?package=PLNmodels&version=1.3.2" data-mini-rdoc="PLNmodels::stephane.robin@inrae.fr">stephane.robin@inrae.fr</a></li>
</ul>Other contributors:<ul>
<li>François Gindraud <a href="/link/francois.gindraud%40gmail.com?package=PLNmodels&version=1.3.2" data-mini-rdoc="PLNmodels::francois.gindraud@gmail.com">francois.gindraud@gmail.com</a> [contributor]</li>
<li>Julie Aubert <a href="/link/julie.aubert%40inrae.fr?package=PLNmodels&version=1.3.2" data-mini-rdoc="PLNmodels::julie.aubert@inrae.fr">julie.aubert@inrae.fr</a> [contributor]</li>
<li>Bastien Batardière <a href="/link/bastien.batardiere%40inrae.fr?package=PLNmodels&version=1.3.2" data-mini-rdoc="PLNmodels::bastien.batardiere@inrae.fr">bastien.batardiere@inrae.fr</a> [contributor]</li>
<li>Giovanni Poggiato <a href="/link/giov.poggiato%40gmail.com?package=PLNmodels&version=1.3.2" data-mini-rdoc="PLNmodels::giov.poggiato@gmail.com">giov.poggiato@gmail.com</a> [contributor]</li>
<li>Cole Trapnell <a href="/link/coletrap%40uw.edu?package=PLNmodels&version=1.3.2" data-mini-rdoc="PLNmodels::coletrap@uw.edu">coletrap@uw.edu</a> [contributor]</li>
<li>Maddy Duran <a href="/link/duran%40uw.edu?package=PLNmodels&version=1.3.2" data-mini-rdoc="PLNmodels::duran@uw.edu">duran@uw.edu</a> [contributor]</li>
<li>Ryan Friedman <a href="/link/ryanfriedman22%40gmail.com?package=PLNmodels&version=1.3.2" data-mini-rdoc="PLNmodels::ryanfriedman22@gmail.com">ryanfriedman22@gmail.com</a> [contributor]</li>
</ul>

Author

<img src='figures/logo.png' style='float: right' alt='logo' width='120' />
The Poisson-lognormal model and variants (Chiquet, Mariadassou and Robin, 2021 tools:::Rd_expr_doi("10.3389/fevo.2021.588292")) can be used for a variety of multivariate problems when count data are at play, including principal component analysis for count data, discriminant analysis, model-based clustering and network inference. Implements variational algorithms to fit such models accompanied with a set of functions for visualization and diagnostic.

PLNmodels: Poisson Lognormal Models — PLNmodels-package

Maintainer: Julien Chiquet <a href='mailto:julien.chiquet@inrae.fr'>julien.chiquet@inrae.fr</a> (<a href='https://orcid.org/0000-0002-3629-3429'>ORCID</a>)
Authors:<ul>
<li>Julien Chiquet <a href='mailto:julien.chiquet@inrae.fr'>julien.chiquet@inrae.fr</a> (<a href='https://orcid.org/0000-0002-3629-3429'>ORCID</a>)</li>
<li>Mahendra Mariadassou <a href='mailto:mahendra.mariadassou@inrae.fr'>mahendra.mariadassou@inrae.fr</a> (<a href='https://orcid.org/0000-0003-2986-354X'>ORCID</a>)</li>
<li>Stéphane Robin <a href='mailto:stephane.robin@inrae.fr'>stephane.robin@inrae.fr</a></li>
</ul>

Other contributors:<ul>
<li>François Gindraud <a href='mailto:francois.gindraud@gmail.com'>francois.gindraud@gmail.com</a> [contributor]</li>
<li>Julie Aubert <a href='mailto:julie.aubert@inrae.fr'>julie.aubert@inrae.fr</a> [contributor]</li>
<li>Bastien Batardière <a href='mailto:bastien.batardiere@inrae.fr'>bastien.batardiere@inrae.fr</a> [contributor]</li>
<li>Giovanni Poggiato <a href='mailto:giov.poggiato@gmail.com'>giov.poggiato@gmail.com</a> [contributor]</li>
<li>Cole Trapnell <a href='mailto:coletrap@uw.edu'>coletrap@uw.edu</a> [contributor]</li>
<li>Maddy Duran <a href='mailto:duran@uw.edu'>duran@uw.edu</a> [contributor]</li>
<li>Ryan Friedman <a href='mailto:ryanfriedman22@gmail.com'>ryanfriedman22@gmail.com</a> [contributor]</li>
</ul>

PLNmodels-package: PLNmodels: Poisson Lognormal Models

Description

Arguments

Author

See Also