vanderPloeg2024

The vanderPloeg2024 longitudinal multi-omics dataset containing six oral microbiome niches,
as well as salivary metabolomics and oral health measurements.

datasets

Creation and selection of PARAllel FACtor Analysis (PARAFAC)
models of longitudinal microbiome data. You can import your own data with
our import functions or use one of the example datasets to create your own
PARAFAC models. Selection of the optimal number of components can be done
using assessModelQuality() and assessModelStability(). The selected model can
then be plotted using plotPARAFACmodel(). The Parallel Factor
Analysis method was originally described by Caroll and Chang (1970)
<doi:10.1007/BF02310791> and Harshman (1970)
<https://www.psychology.uwo.ca/faculty/harshman/wpppfac0.pdf>.

Geert Roelof van der Ploeg

parafac4microbiome

Parallel Factor Analysis Modelling of Longitudinal Microbiome
Data

Johan Westerhuis

Anna Heintz-Buschart

Age Smilde

University of Amsterdam 

vanderPloeg2024 function

<div class="section" id="vanderploeg-">
<h3><code>vanderPloeg2024</code></h3>
Each measured dataset contains three elements:<dl>
<dt>data</dt>
<dd>Array object of the data cube</dd><dt>mode1</dt>
<dd>Dataframe with all the subject metadata, ordered the same as the rows in the data cube.</dd><dt>mode2</dt>
<dd>Taxonomic classification of the microbiota, ordered the same as the columns in the data cube.</dd><dt>mode3</dt>
<dd>Dataframe with the time metadata, ordered the same as the third dimension in the array.</dd>...</dl></div>

Format

vanderPloeg2024 longitudinal multi-omics dataset — vanderPloeg2024

<div class='section' id='vanderploeg-'>
<h3><code>vanderPloeg2024</code></h3>


Each measured dataset contains three elements:<dl>
<dt>data</dt>
<dd>Array object of the data cube</dd>

<dt>mode1</dt>
<dd>Dataframe with all the subject metadata, ordered the same as the rows in the data cube.</dd>

<dt>mode2</dt>
<dd>Taxonomic classification of the microbiota, ordered the same as the columns in the data cube.</dd>

<dt>mode3</dt>
<dd>Dataframe with the time metadata, ordered the same as the third dimension in the array.</dd>

...

</dl>

</div>

vanderPloeg2024: vanderPloeg2024 longitudinal multi-omics dataset

Description

Usage

Arguments

Format

`vanderPloeg2024`