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loop (version 1.1)

loop decomposition of weighted directed graphs for life cycle analysis, providing flexbile network plotting methods, and analyzing food chain properties in ecology

Description

The program can perform loop analysis and plot network structure (especially for food webs),including minimum spanning tree, loop decomposition of weighted directed graphs, and other network properties which may be related to food chain properties in ecology.

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Version

Install

install.packages('loop')

Monthly Downloads

17

Version

1.1

License

GPL-2

Maintainer

Youhua Chen

Last Published

October 1st, 2012

Functions in loop (1.1)

find the largest weight food chain among the candidate longest food chains for a given node (species)

decompose the weighted graph into directional single connected graphs and a non-connected graph

forward method to decompose the weighted graph into single connected graphs

a random method to decompose the weighted graph into single connected graphs

a special group graph plot function for food web-style hierarchical structure

enumerate all unique food chains that are linked to a given species/node

Another way to plot network structure based on similar vertex will be grouped together, while dissimilar nodes/vertex will depart from each others.

find out the food chain with shortest length among all food chains that are linked to a given species

an R package for analyzing and plotting directed networks

A group way to plot network structure based on similar vertex will be grouped together, while dissimilar nodes/vertex will depart from each others.

rank nodes based on the inward links/outward links/both links

plot directed graphs directly from square graph matrix

enumerate all food chains that are linked to a given species/node

nmds.ordination

perform non-dimensional scaling of the nodes by employing the function 'isoMDS' from package 'MASS'

this function convert graph matrix form into graph edge form

find out the food chain with longest length among all food chains that are linked to a given species

smallest.weight

find out the food chain with shortest weight among all food chains that are linked to a given species

make a plot for directional graph from edge matrix graph form

node.similarity

calculate pair similarity of nodes based on the nodes' similarity which have links with the focused pair of nodes

find out the food chain with largest weights among all food chains that are linked to a given species

make food trophic ranks for all the species in the matrix for fplot.foodweb function

groupplot.foodweb

a special group graph plot function for food web-style hierarchical structure

Primm's algorithm to search minimum spanning tree