predict,lnm-method

Given an input dataset, predict the output composition. Specifically, this
outputs \(\phi^{-1}(Bx)\), for the inverse log ratio transformation
\(\phi^{-1}\) and fitted covariate matrix \(B\).

Logistic-normal Multinomial (LNM) models are common in problems with multivariate count data. This package gives a simple implementation with a 30 line 'Stan' script. This lightweight implementation makes it an easy starting point for other projects, in particular for downstream tasks that require analysis of "compositional" data. It can be applied whenever a multinomial probability parameter is thought to depend linearly on inputs in a transformed, log ratio space. Additional utilities make it easy to inspect, create predictions, and draw samples using the fitted models. More about the LNM can be found in Xia et al. (2013) "A Logistic Normal Multinomial Regression Model for Microbiome Compositional Data Analysis" <doi:10.1111/biom.12079> and Sankaran and Holmes (2023) "Generative Models: An Interdisciplinary Perspective" <doi:10.1146/annurev-statistics-033121-110134>.

Kris Sankaran

miniLNM

Miniature Logistic-Normal Multinomial Models

predict,lnm-method function

<dl><dt>object</dt>
<dd>An object of class lnm with fitted parameters \(\hat{B}\) and
which we want to use to form predictions on new samples.</dd>
<dt>newdata</dt>
<dd>New samples on which to form predictions. Defaults to NULL, in
which case predictions are made at the same design points as those used
during the original training.</dd>
<dt>...</dt>
<dd>Additional keyword arguments, for consistency with R's predict
generic (never used).</dd></dl>

Arguments

LNM Fitted Probabilities — predict,lnm-method

<dl>

<dt>object</dt>
<dd>An object of class lnm with fitted parameters \(\hat{B}\) and
which we want to use to form predictions on new samples.</dd>


<dt>newdata</dt>
<dd>New samples on which to form predictions. Defaults to NULL, in
which case predictions are made at the same design points as those used
during the original training.</dd>


<dt>...</dt>
<dd>Additional keyword arguments, for consistency with R's predict
generic (never used).</dd>

</dl>

predict,lnm-method: LNM Fitted Probabilities

Description

Usage

Value

Arguments

Examples