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<title>The clm residue manual</title>
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<p style="text-align:right">
16 May 2014&nbsp;&nbsp;&nbsp;
<a class="local" href="clmresidue.ps"><b>clm residue</b></a>
14-137
</p>
<div class=" itemize " style="margin-top:1em; font-size:100%">
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#name">NAME</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#synopsis">SYNOPSIS</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#description">DESCRIPTION</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#options">OPTIONS</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#author">AUTHOR</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#seealso">SEE ALSO</a>
</div>
</div>

<a name="name"></a>
<h2>NAME</h2>
<p style="margin-bottom:0" class="asd_par">
clm residue &mdash; extend clustering of subgraph to clustering of graph.</p>
<p style="margin-bottom:0" class="asd_par">clmresidue is not in actual fact a program. This manual
page documents the behaviour and options of the clm program when
invoked in mode <i>residue</i>. The options <b>-h</b>, <b>--apropos</b>,
<b>--version</b>, <b>-set</b>, <b>--nop</b> are accessible
in all <b>clm</b> modes. They are described
in the <a class="local sibling" href="clm.html">clm</a> manual page.</p>

<a name="synopsis"></a>
<h2>SYNOPSIS</h2>
<p style="margin-bottom:0" class="asd_par">
<b>clm residue</b>
<a class="intern" href="#opt-icl"><b>-icl</b> fname (<i>input clustering</i>)</a>
<a class="intern" href="#opt-imx"><b>-imx</b> fname (<i>input graph</i>)</a>
<a class="intern" href="#opt-rpm"><b>[-rpm</b> fname (<i>residue projection matrix</i>)<b>]</b></a>
<a class="intern" href="#opt-o"><b>[-o</b> fname (<i>output clustering file</i>)<b>]</b></a>
</p>

<a name="description"></a>
<h2>DESCRIPTION</h2>
<p style="margin-bottom:0" class="asd_par">
The cluster file presumably contains a clustering of a subgraph of the
graph&nbsp;<tt>G</tt> contained by the matrix file, implying that the row domain of
that clustering is a subset of the node domain of the graph. <b>clm residue</b> will
compute a simple upwards projection of that clustering, resulting in a
clustering of&nbsp;<tt>G</tt>.
</p>

<a name="options"></a>
<h2>OPTIONS</h2>
<div class=" itemize " style="margin-top:1em; font-size:100%">
<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> fname (<i>input graph</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
</div>
<div style="margin-top:0em">&nbsp;</div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-icl"></a><b>-icl</b> fname (<i>input clustering</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
</div>
<div style="margin-top:0em">&nbsp;</div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-rpm"></a><b>-rpm</b> fname (<i>residue projection matrix</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
The name for the file in which the residue projection matrix is stored.
It contains for each node and for each cluster in the input clustering
the combined weight of the (edges to the) neighbours of that node
in that cluster.
</p>
<p style="margin-top:0em; margin-bottom:0em">
The default output file name is <tt>out.rpm</tt>.
</p>
</div>
<div style="margin-top:0em">&nbsp;</div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> fname (<i>output clustering file</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
The name for the file in which the majority vote projection clustering
is stored. Aka the majority vote projection clustering storage file name.
</p>
<p style="margin-bottom:0" class="asd_par">
This embodies a very crude approach to distributing the missing nodes in the
input clustering onto that same cluster. For each node, the cluster is
taken for which the residue projection is the largest (see above). The
residue (i.e. the set of missing nodes) is initially viewed as a cluster;
the set of nodes for which the projection is largest for the residue itself
will form a new cluster, if it is not empty.
</p>
<p style="margin-bottom:0" class="asd_par">
By default output is sent to STDOUT.
</p>
</div>
</div>

<a name="author"></a>
<h2>AUTHOR</h2>
<p style="margin-bottom:0" class="asd_par">
Stijn van Dongen.
</p>

<a name="seealso"></a>
<h2>SEE ALSO</h2>
<p style="margin-bottom:0" class="asd_par">
<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
and the utilities in the mcl family.
</p>
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