Supplement 1. Example R code and models.

File List R files: simulation.r (md5: 282588866b80f0d3318a1446a3251665) bayestest.r (md5: 61c4b9620541b11764e0f8b15885fbd6) interface.r (md5: 7c8d3c8a1dea0653bb13e63898028f65) mutual.r (md5: 36d845acc9de95c5d14ba9a85c04be5f) tree.r (md5: 6c2fdcfa45bd39c90b400018bf928fb3) distance.r (md5: 9fa284893caf861e4c8127b676305269) community.r (md5: 9741154bc2029b4f5c22e93c86609a99) dia.r (md5: 59bddece34b9577c83202b4a845e40e7) tk.r (md5: de75b0f1e80a830d0eecd10a7e86515f) Dia model files: macquarie.dia (md5: 45d926fc48b1bf9a148dc71167bb87a3) mesocosm1.dia (md5: 56f4b10b0ffd15714dc76221740dd2a7) mesocosm2.dia (md5: c8cafd5b4fa2ff319515c995a73e769c) fivevariable1.dia (md5: 77bfb61c147c45bbc6f5dc47aa1ed6c3) fivevariable2.dia (md5: d39313ae9302b7fa7940e44e13734614) fivevariable3.dia (md5: b0d04d241a7d4622a80043f12e982fb6) fivevariable4.dia (md5: 36a4e77580957e9bdeee305af4855258) fivevariable5.dia (md5: b6eb08d1f3cf294df3db469bf19afefa) Description Example R code for analyses presented in the main text is provided in simulation.r, bayestest.r, interface.r, mutual.r, tree.r, distance.r. Comments are provided at the beginning of each of these files describing the application of network analysis algorithms, and comments throughout annotate the steps involved. Dependencies are community.r, dia.r, and tk.r. These analyses require signed directed graphs created in Dia (available from http://live.gnome.org/Dia) as inputs. Example models provided as part of this supplement are macquarie.dia, mesocosm1.dia, mesocosm2.dia, and fivevariable1.dia–fivevariable5.dia.