create_incidence_matrix

Create Incidence Matrix for Graph Construction

internal

Implementation of the bootstrapping approach for the estimation of clustering stability and its application in estimating the number of clusters, as introduced by Yu et al (2016)<doi:10.1142/9789814749411_0007>. Implementation of the non-parametric bootstrap approach to assessing the stability of module detection in a graph, the extension for the selection of a parameter set that defines a graph from data in a way that optimizes stability and the corresponding visualization functions, as introduced by Tian et al (2021) <doi:10.1002/sam.11495>. Implemented out-of-bag stability estimation function and k-select Smin-based k-selection function as introduced by Liu et al (2022) <doi:10.1002/sam.11593>. Implemented ensemble clustering method based-on k-means clustering method, spectral clustering method and hierarchical clustering method.

Tianmou Liu

bootcluster

Bootstrapping Estimates of Clustering Stability

Han Yu

Mingmei Tian

create_incidence_matrix function

<dl><dt>results_km</dt>
<dd>K-means results</dd>
<dt>results_hc</dt>
<dd>Hierarchical clustering results</dd>
<dt>results_sc</dt>
<dd>Spectral clustering results</dd>
<dt>k_km</dt>
<dd>Number of k-means clusters</dd>
<dt>k_hc</dt>
<dd>Number of hierarchical clusters</dd>
<dt>k_sc</dt>
<dd>Number of spectral clusters</dd>
<dt>Smin_delta_km</dt>
<dd>K-means stability delta</dd>
<dt>Smin_delta_hc</dt>
<dd>Hierarchical clustering stability delta</dd>
<dt>Smin_delta_sc</dt>
<dd>Spectral clustering stability delta</dd>
<dt>combine_fn</dt>
<dd>Function to combine stability measures</dd>
<dt>n_samples</dt>
<dd>Number of samples</dd></dl>

Arguments

Create Incidence Matrix for Graph Construction — create_incidence_matrix

<dl>

<dt>results_km</dt>
<dd>K-means results</dd>


<dt>results_hc</dt>
<dd>Hierarchical clustering results</dd>


<dt>results_sc</dt>
<dd>Spectral clustering results</dd>


<dt>k_km</dt>
<dd>Number of k-means clusters</dd>


<dt>k_hc</dt>
<dd>Number of hierarchical clusters</dd>


<dt>k_sc</dt>
<dd>Number of spectral clusters</dd>


<dt>Smin_delta_km</dt>
<dd>K-means stability delta</dd>


<dt>Smin_delta_hc</dt>
<dd>Hierarchical clustering stability delta</dd>


<dt>Smin_delta_sc</dt>
<dd>Spectral clustering stability delta</dd>


<dt>combine_fn</dt>
<dd>Function to combine stability measures</dd>


<dt>n_samples</dt>
<dd>Number of samples</dd>

</dl>

create_incidence_matrix: Create Incidence Matrix for Graph Construction

Description

Usage

Value

Arguments