README.md

In SimmonsBI/bmotif-release: Motif Analyses of Bipartite Networks

Overview

bmotif is software for motif analyses of bipartite networks. It can count occurrences of motifs in bipartite networks, as well as the number of times each node or link appears in each unique node or link position within motifs (a node or link’s structural role). bmotif was intended for use in ecology but its methods are general and can be applied to any bipartite graph. As well as R, core functionality is also available in MATLAB and Python.

Installation

To install the released version from CRAN:

install.packages("bmotif")

To install the released version from GitHub:

install.packages("devtools") # install the devtools package
devtools::install_github("SimmonsBI/bmotif-release", build_vignettes = TRUE) # install bmotif

Dictionary

bmotif considers all 44 unique bipartite motifs up to six nodes. Within these motifs there are 148 unique node positions. All motifs and node positions considered by bmotif are shown in the Figure below. This is the ‘dictionary’ used by bmotif: the canonical reference for all motif and node position IDs used by the package and returned by the functions.

Large numbers above and to the left of each motif represent the ID of a motif. Small numbers at the end of links represent node position IDs within motifs. Motif IDs and node position IDs can also be found in Simmons, B. I., Sweering, M. J. M., Schillinger, M., Dicks, L. V., Sutherland W. J., Di Clemente, R. bmotif: a package for motif analyses of bipartite networks. Methods in Ecology and Evolution (accepted). Node positions were defined following Baker et al (2015) Appendix 1 Figure A27.

Consider the example of motif 5:

We know this is motif 5 because the large number above and to the left of the motif gives the motif ID as 5. This motif contains four unique node positions, given by the numbers at the ends of each link: 9, 10, 11 and 12.

This dictionary can be accessed inside R by typing vignette("bmotif-dictionary"). If R says the vignette was not found, download the package and run devtools::install(build_vignettes = TRUE)

Use

bmotif considers all 44 unique bipartite motifs up to six nodes. Within these motifs there are 148 unique positions.

bmotif has two functions: mcount and positions. mcount counts occurrences of motifs in a bipartite network. positions counts the number of times each node in a network occurs in each of the positions within the motifs.

License

The code is released under the MIT license (see LICENSE file).

Citation

If you use the package in your work, please cite: Simmons, B. I., Sweering, M. J. M., Schillinger, M., Dicks, L. V., Sutherland W. J., Di Clemente, R. bmotif: a package for motif analyses of bipartite networks. Methods in Ecology and Evolution (accepted)

SimmonsBI/bmotif-release documentation built on May 9, 2019, 3:38 p.m.