tutorial-plant-pollinator.html

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    <p class="crumbs"><a href="index.html">MiRA</a> › Tutorials › Plant–pollinator</p>

    <h1>How do I visualize a plant–pollinator network in MiRA?</h1>
    <p class="lead">
      Plant–pollinator networks are <strong>bipartite</strong>: links run between two groups
      (pollinators and plants), never within a group. When the same interaction is recorded at
      several sites or times, it becomes a <strong>bipartite multilayer network</strong>. This
      walkthrough uses a bundled empirical example so you can follow along in the browser with no
      installation and no code.
    </p>

    <h2>The dataset</h2>
    <p>
      The <strong>Canary Islands pollination network</strong>
      (<a href="https://doi.org/10.1111/1365-2656.14174">Vitali et al. 2024</a>) has 5 layers,
      235 nodes, and 651 within-layer plus 154 between-layer links. Each layer is an island;
      nodes are pollinators and plants; interlayer links connect the same species appearing on
      more than one island. It is undirected, bipartite, and geographically explicit.
    </p>

    <h2>Walkthrough</h2>
    <ol class="steps">
      <li>Open <a href="index.html">MiRA</a>, click <strong>Load Example Data</strong>, and choose
        <em>Canary Islands pollination network</em>. It loads directly into Network Mode.</li>
      <li>Because the dataset declares bipartite layers, MiRA draws each layer as two rows —
        pollinators on one side, plants on the other. This is the layout that makes bipartite
        structure legible; a single-row layout would hide it.</li>
      <li>In the <strong>Nodes</strong> panel, color nodes by <code>node_type</code> to separate
        pollinators from plants at a glance, and size them by degree to spot generalist species.</li>
      <li>Use the <strong>Intralayer Links</strong> threshold slider to hide weak interactions and
        reveal the backbone of strong, frequent visits.</li>
      <li>Switch to <strong>Grid View</strong> to see all five islands side by side as small
        multiples — ideal for comparing which islands share structure and which are distinct.</li>
      <li>Type a pollinator's name in <strong>Search</strong> to highlight every copy of it across
        all islands at once, showing how a single species links the layers.</li>
      <li>Open <strong>Dashboard Mode</strong> for the bipartite set-size ratios, degree
        distributions, and layer-similarity (Jaccard) heatmaps.</li>
    </ol>

    <div class="callout">
      <strong>Why bipartite matters.</strong> MiRA is one of the few multilayer visualization
      tools with a dedicated bipartite layout. If your data are bipartite, declare it (see the
      <a href="data-format.html">data format</a> page) so the two node sets are laid out and
      colored correctly.
    </div>

    <h2>Use your own data</h2>
    <p>
      Export your network to MiRA's <a href="data-format.html">JSON or CSV format</a> — from the
      <a href="https://emln.ecomplab.com">emln</a> R package,
      <code>multilayer_to_json(net, bipartite = TRUE)</code> does this directly — then use
      <strong>Load Data</strong> instead of the example loader. Everything above applies unchanged.
    </p>

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