SDDE-package {SDDE} | R Documentation

## Shortcuts, Detours and Dead Ends (SDDE) Path Types in Genome Similarity Networks

### Description

SDDE compares the evolution of an original network X to an augmented network Y by counting the number of shortcuts, detours, dead ends, equal paths and disconnected nodes.
Four different types of paths in Y that pass by at least one augmented node (i.e. a node that exists in Y but not in X) can be defined as follows:
1) Shortcut is a path between two nodes, originally present in X, that is shorter in Y than in X.
2) Detour is a path such that it connects two nodes originally present in X and is longer in Y than in X.
3) Dead End is a path that exists in X, but is impossible in Y.
4) Equal is a path that has the same length in X an Y.
The numbers of disconnected nodes is also reported.

### Details

Package: | SDDE
Type: | Package
Version: | 1.0.1
Date: | 2015-08-20
License: | GPL-2
Maintainer: | Etienne Lord <m.etienne.lord@gmail.com>,
| François-Joseph Lapointe <francois-joseph.lapointe@umontreal.ca>

Function `complete_network` computes the number of paths in each category.

Function `complete_restart` is similar to the `complete_network` function but it identifies the paths in a predefined order.

Function `complete_trace` is similar to the `complete_network` function but allow the enumeration of nodes and taxa in a path.

Function `sample_network` computes the number of paths in each category for a given set of nodes of the original network X.

Function `random_network` creates a random network X and an augmented network Y using Erdos-Renyi or Barabási–Albert models.

Function `save_network` and codeplot_network creates rendering of network X and network Y in various file formats (svg, png and eps).

Function `load_network` loads a network from a list of edges (tab-separated) which is compatible with the `complete_network`, `complete_restart` and `sample_network` function.

### Author(s)

Etienne Lord, Margaux Le Cam, Éric Bapteste, Vladimir Makarenkov and François-Joseph Lapointe

### See Also

`complete_network`, `complete_restart`, `complete_trace`, `sample_network`, `load_network`, `save_network` `plot_network`

[Package SDDE version 1.0.1 Index]