# 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`

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