format.lassie

Formats a <code>lassie</code> object for printing to console
(see <code>print.lassie</code>) and for writing to a file
(see <code>write.lassie</code>). Melts probability or local association
measure arrays into a data.frame.

Implements the estimation of local (and global) association measures: Lewontin's D, Ducher's Z, pointwise mutual information, normalized pointwise mutual information and chi-squared residuals. The significance of local (and global) association is accessed using p-values estimated by permutations.

Olivier M. F. Martin

zebu

Local Association Measures

Michel Ducher

format.lassie function

<dl><dt>x</dt>
<dd><code>lassie</code> S3 object.</dd>
<dt>what_x</dt>
<dd>vector specifying values to be returned:<ul>
<li>'local': local association measure values (default).</li>
<li>'obs': observed probabilities.</li>
<li>'exp': expected probabilities.</li>
<li>'local_p': p-value of local association (after running <code>permtest</code> or <code>chisqtest</code>).</li>
</ul></dd>
<dt>range</dt>
<dd>range of values to be retained (vector of two numeric values).</dd>
<dt>what_range</dt>
<dd>character specifying what value <code>range</code> refers to
(same options as <code>what_x</code>).
By default, takes the first value in <code>what_x</code>.</dd>
<dt>what_sort</dt>
<dd>character specifying according to which values should <code>x</code> be sorted
(same options as <code>what_x</code>).
By default, takes the first value in <code>what_x</code>.</dd>
<dt>decreasing</dt>
<dd>logical value specifying sort order.</dd>
<dt>na.rm</dt>
<dd>logical value indicating whether NA values should be stripped.</dd>
<dt>...</dt>
<dd>other arguments passed on to methods. Not currently used.</dd></dl>

Arguments

Format a lassie object — format.lassie

<dl>

<dt>x</dt>
<dd><code>lassie</code> S3 object.</dd>


<dt>what_x</dt>
<dd>vector specifying values to be returned:<ul>
<li>'local': local association measure values (default).</li>
<li>'obs': observed probabilities.</li>
<li>'exp': expected probabilities.</li>
<li>'local_p': p-value of local association (after running <code>permtest</code> or <code>chisqtest</code>).</li>
</ul></dd>


<dt>range</dt>
<dd>range of values to be retained (vector of two numeric values).</dd>


<dt>what_range</dt>
<dd>character specifying what value <code>range</code> refers to
(same options as <code>what_x</code>).
By default, takes the first value in <code>what_x</code>.</dd>


<dt>what_sort</dt>
<dd>character specifying according to which values should <code>x</code> be sorted
(same options as <code>what_x</code>).
By default, takes the first value in <code>what_x</code>.</dd>


<dt>decreasing</dt>
<dd>logical value specifying sort order.</dd>


<dt>na.rm</dt>
<dd>logical value indicating whether NA values should be stripped.</dd>


<dt>...</dt>
<dd>other arguments passed on to methods. Not currently used.</dd>

</dl>

format.lassie: Format a lassie object

Description

Usage

Arguments

See Also