SDDE-package: 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
ll{
Package: SDDE
Type: Package
Version: 1.0
Date: 2015-02-22
License: GPL-2
Maintainer: Etienne Lord ,
François-Joseph Lapointe
}
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 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.