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

## Documentation for package ‘SDDE’ version 1.0.1

- DESCRIPTION file.
- Package NEWS.

## Help Pages

SDDE-package | Shortcuts, Detours and Dead Ends (SDDE) Path Types in Genome Similarity Networks
complete_network | compare two given networks (original and augmented, presented as undirected graphs) using a path analysis
complete_restart | compares two given networks (original and augmented, presented as undirected graphs) using a path analysis
complete_trace | return properties of a single path in two given networks (original and augmented, presented as undirected graphs) using a path analysis
Eukaryote_nonphoto | An original and an augmented real genomic networks
Eukaryote_photo | An original and an augmented real genomic networks
g1 | generic name for network X
g2 | generic name for network Y
info_network | returns additional information regarding the networks X and Y (original and augmented).
info_node | returns additional information regarding the nodes of networks X and Y (original and augmented)
load_network | is a helper function to load networks from files
Plasmids | An original and an augmented real genomic networks
plot_network | Helper function to display an illustration of a network.
random_network | creates random augmented networks X and Y
Sample_1 | An original network X with 11 nodes and an augmented network Y of 14 nodes
Sample_2 | An network X of 6 nodes and an augmented network Y with 7 nodes
sample_network | compares two networks using a path analysis of total pathways
sample_path | is a helper function that creates a vector of non-repeating pathways to investigate
save_network | is an helper function to save an illustration of a network into a file
save_network_big | Helper function to save an illustration of a network to file with more than 50 nodes.
SDDE | Shortcuts, Detours and Dead Ends (SDDE) Path Types in Genome Similarity Networks
SDDE.version | Version information.
Viruses | An original and an augmented real genomic networks