bmotif: A package for motif analyses of bipartite networks

• Published in: Methods in Ecology and Evolution
• Main Authors: Simmons, BI, Sweering, MJM, Schillinger, M, Dicks, LV, Sutherland, WJ, Di Clemente, R
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley for British Ecological Society 2019
• Subjects: bipartite networks; food web; MATLAB; motifs; pollination; Python; seed dispersal; Greenland
• Online Access: http://hdl.handle.net/10871/40633; https://doi.org/10.1111/2041-210X.13149

This is the final version. Available on open access from Wiley via the DOI in this record Data accessibility: All networks are available from the Web of Life repository (www.web-of-life.es), with the exception of the Greenland plant–pollinator networks which are available from Data Dryad https://doi.org/10.5061/dryad.3pk73 (Saavedra et al., 2016). To obtain the Web of Life networks go to www.web-of-life.es, click “Pollination”, then click “Download”; next, repeat this process but click “Seed dispersal” rather than “Pollination” in the second step. Network names have the format “M_T_X” where T is the type of interaction (PL for pollination, SD for seed dispersal) and X is the network identity. Where T = PL, remove all networks where X > 071; where T = SD, remove all networks where X > 034. Networks with identity values greater than these were added to the Web of Life repository after our analyses were conducted. Finally, remove “M_PL_057” and “M_PL_062” networks as these were unusually large containing c. 1,000 species or more. Plant origin data for Mauritius networks was from Kaiser‐Bunbury et al. (2009, Appendix II) (paper https://doi.org/10.1016/j.ppees.2009.04.001; Appendix link: https://ars.els-cdn.com/content/image/1-s2.0-S1433831909000183-mmc8.doc). The owners of these data had to deny the request to archive them in a repository that meets the requirements of the BES Data Archiving Policy due to the policies of the journal that they published their article in. Bipartite networks are widely used to represent a diverse range of species interactions, such as pollination, herbivory, parasitism and seed dispersal. The structure of these networks is usually characterised by calculating one or more indices that capture different aspects of network architecture. While these indices capture useful properties of networks, they are relatively insensitive to changes in network structure. Consequently, variation in ecologically-important interactions can be missed. Network motifs are a way to characterise ...