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

knitr::opts_chunk$set(
  collapse = TRUE,
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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.

knitr::include_graphics("../man/figures/dictionary.png")

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., Dicks, L. V., Sutherland, W. J. and Di Clemente, R. bmotif: a package for counting motifs in bipartite networks. bioRxiv. doi: 10.1101/302356. Node positions were defined following Baker et al (2015) Appendix 1 Figure A27.

Consider the example of motif 5:

knitr::include_graphics("../man/figures/motif5.png")

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.

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