loop (version 1.1)

loop-package: an R package for analyzing and plotting directed networks

Description

The package can (1) perform loop analysis (van Groenendael et al., 1994) in demographic analysis in ecology, which employed the decomposition algorithm of directed weighted graphs persented in Su and Wang (2007); (2) find food web patterns, including longest food chain, largest-weighted food chain, enumeration of all food chains linked to the proposed species in the food network; (3) plot directed/undirected network structure using flexible methods; (4) other statistics, like minimum spanning tree etc. Next version will include more statistics on food web structure

Details

Package:

loop

Type:

Package

Version:

1.0

Date:

2012-06-22

License:

GPL-2

LazyLoad:

yes

References

van Groenendael J, de Kroon H, Kalisz S, Tuljapurkar S (1994) Loop analysis: evaluating life history pathways in population projection matrices. Ecology, 75, 2410-2415.

Sun L, Wang M (2007) An algorithm for a decomposition of weighted digraphs: with applications to life cycle analysis in Ecology. Journal of Mathematical Biology, 54, 199-226.

Wang HY, Huang Q, Li CZ,Zhu BZ (2010) Graph algorithms and Matlab applications. BUAA Press, Beijing.

Chen Y (2012) loop: an R package for performing decomposition of weighted directed graphs, food web analysis and flexible network plotting. Submitted.

Examples

gemat=matrix(c(13,26,0,11,18,15,15,0,2),nrow=3,ncol=3)
gemat=matrix(c(13,26,0,12,18,15,15,0,2),nrow=3,ncol=3)
#search out all loops
decomp(gemat)
#make plots
mat<-matrix(c(1,2,1,3,2,4,3,5,4,5,6,7,8,9,1,9,9,8),nrow=9,ncol=2)
w<-c(3,10,30,50,20,22,9,15,33)
mat<-cbind(mat,w)
gplot(mat)