interactionPlot

Visually compare two interaction (adjacency) matrices and return accuracy statistics

Model fitting and species biotic interaction network topology selection for explicit
interaction community models. Explicit interaction community models are an extension of binomial
linear models for joint modelling of species communities, that incorporate both the effects of
species biotic interactions and the effects of missing covariates. Species interactions are modelled
as direct effects of each species on each of the others, and are estimated alongside the effects of
missing covariates, modelled as latent factors. The package includes a penalized maximum likelihood
fitting function, and a genetic algorithm for selecting the most parsimonious species interaction
network topology.

Miguel Porto

eicm

Explicit Interaction Community Models

Pedro Beja

interactionPlot function

<dl><dt>estimated.adjacency.matrix</dt>
<dd>the interaction matrix of the model of interest.</dd>
<dt>true.adjacency.matrix</dt>
<dd>the interaction matrix of the model to compare with (usually, the one used for simulating the data).</dd>
<dt>excluded.interactions</dt>
<dd>a binary species x species matrix telling which interactions were excluded a priori.</dd>
<dt>labels</dt>
<dd>logical. Add default axis labels and title?</dd>
<dt>noplot</dt>
<dd>logical. Do plots? If TRUE, it will return the accuracy statistics only.</dd>
<dt>legend</dt>
<dd>logical. Plot legend?</dd>
<dt>...</dt>
<dd>further arguments to pass to <code>plot</code>.</dd></dl>

Arguments

Compare two interaction matrices — interactionPlot

<dl>

<dt>estimated.adjacency.matrix</dt>
<dd>the interaction matrix of the model of interest.</dd>


<dt>true.adjacency.matrix</dt>
<dd>the interaction matrix of the model to compare with (usually, the one used for simulating the data).</dd>


<dt>excluded.interactions</dt>
<dd>a binary species x species matrix telling which interactions were excluded a priori.</dd>


<dt>labels</dt>
<dd>logical. Add default axis labels and title?</dd>


<dt>noplot</dt>
<dd>logical. Do plots? If TRUE, it will return the accuracy statistics only.</dd>


<dt>legend</dt>
<dd>logical. Plot legend?</dd>


<dt>...</dt>
<dd>further arguments to pass to <code>plot</code>.</dd>

</dl>

interactionPlot: Compare two interaction matrices

Description

Usage

Value

Arguments