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| loop-package | an R package for analyzing and plotting directed networks |
| convertion | this function convert graph matrix form into graph edge form |
| decomp | decompose the weighted graph into directional single connected graphs and a non-connected graph |
| find.ranks | make food trophic ranks for all the species in the matrix for fplot.foodweb function |
| fplot | Another way to plot network structure based on similar vertex will be grouped together, while dissimilar nodes/vertex will depart from each others. |
| fplot.foodweb | a special group graph plot function for food web-style hierarchical structure |
| gplot | make a plot for directional graph from edge matrix graph form |
| gplot1 | plot directed graphs directly from square graph matrix |
| groupplot | A group way to plot network structure based on similar vertex will be grouped together, while dissimilar nodes/vertex will depart from each others. |
| groupplot.foodweb | a special group graph plot function for food web-style hierarchical structure |
| largest.weight | find out the food chain with largest weights among all food chains that are linked to a given species |
| lclw | find the largest weight food chain among the candidate longest food chains for a given node (species) |
| longest.chain | find out the food chain with longest length among all food chains that are linked to a given species |
| loop | an R package for analyzing and plotting directed networks |
| loop.forward | forward method to decompose the weighted graph into single connected graphs |
| loop.random | a random method to decompose the weighted graph into single connected graphs |
| mst.primm | Primm's algorithm to search minimum spanning tree |
| nmds.ordination | perform non-dimensional scaling of the nodes by employing the function 'isoMDS' from package 'MASS' |
| node.similarity | calculate pair similarity of nodes based on the nodes' similarity which have links with the focused pair of nodes |
| pathways | enumerate all food chains that are linked to a given species/node |
| rank.nodes | rank nodes based on the inward links/outward links/both links |
| shortest.chain | find out the food chain with shortest 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 |
| uniquepaths | enumerate all unique food chains that are linked to a given species/node |