trials.needed

<code>trials.needed</code> estimates the number of monte carlo trials needed to estimate edgewise p-values

internal

An implementation of methods for extracting an unweighted unipartite
graph (i.e. a backbone) from an unweighted unipartite graph, a weighted unipartite
graph, the projection of an unweighted bipartite graph, or the projection
of a weighted bipartite graph (Neal, 2022 <doi:10.1371/journal.pone.0269137>).

Zachary Neal

backbone

Extracts the Backbone from Graphs

Rachel Domagalski

Bruce Sagan

Karl Godard

trials.needed function

<dl><dt>M</dt>
<dd>matrix: An adjacency matrix representing a network from which a backbone is is being extracted</dd>
<dt>alpha</dt>
<dd>real: significance level of hypothesis test(s)</dd>
<dt>signed</dt>
<dd>boolean: TRUE for a signed backbone, FALSE for a binary backbone</dd>
<dt>missing.as.zero</dt>
<dd>boolean: should missing edges be treated as edges with zero weight and tested for significance</dd>
<dt>mtc</dt>
<dd>string: type of Multiple Test Correction to be applied; can be any method allowed by <code><a href="/link/p.adjust?package=backbone&version=2.1.4" data-mini-rdoc="backbone::p.adjust">p.adjust</a></code>.</dd>
<dt>how.close</dt>
<dd>real: How close can the empirical p-value be to alpha and still be distinguishable, expressed as a proportion</dd></dl>

Arguments

Estimate number of monte carlo trials needed to estimate p-value — trials.needed

<dl>

<dt>M</dt>
<dd>matrix: An adjacency matrix representing a network from which a backbone is is being extracted</dd>


<dt>alpha</dt>
<dd>real: significance level of hypothesis test(s)</dd>


<dt>signed</dt>
<dd>boolean: TRUE for a signed backbone, FALSE for a binary backbone</dd>


<dt>missing.as.zero</dt>
<dd>boolean: should missing edges be treated as edges with zero weight and tested for significance</dd>


<dt>mtc</dt>
<dd>string: type of Multiple Test Correction to be applied; can be any method allowed by <code><a href='https://rdrr.io/r/stats/p.adjust.html'>p.adjust</a></code>.</dd>


<dt>how.close</dt>
<dd>real: How close can the empirical p-value be to alpha and still be distinguishable, expressed as a proportion</dd>

</dl>

trials.needed: Estimate number of monte carlo trials needed to estimate p-value

Description

Usage

Value

Arguments