mcbrnet: metacommunity simulation in a branching network

Akira Terui
March 09, 2022

Overview

Main functions are the following:

brnet: Function brnet() generates a random branching network with the specified number of patches and probability of branching. The function returns adjacency and distance matrices, hypothetical environmental values at each patch, and the number of patches upstream (akin to the watershed area in river networks). The output may be used in function mcsim() to simulate metacommunity dynamics in a branching network.
mcsim: Function mcsim() simulates metacommunity dynamics. By default, it produces a square-shaped landscape with randomly distributed habitat patches (x- and y-coordinates are drawn from a uniform distribution). If a distance matrix is given, the function simulates metacommunity dynamics in the specified landscape. Function mcsim() follows a general framework proposed by Thompson et al. (2020) with some modifications.
igpsim: Function igpsim() simulates three-species meta-food web dynamics with intraguild predation. By default, it produces a square-shaped landscape with randomly distributed habitat patches (x- and y-coordinates are drawn from a uniform distribution). If a distance matrix is given, the function simulates three-species meta-food web dynamics in the specified landscape.
adjtodist: Function adjtodist() converts an adjacency matrix to a distance matrix.

version 1.2.0
- added a major function igpsim()
- simplified brnet() and mcsim() by introducing internal sub-functions
version 1.1.1
- added a local noise parameter for disturbance values to brnet() (argument sd_disturb_lon)
version 1.1.0
- added disturbance arguments to brnet()
- added function adjtodist()
version 1.0.0: initial release

Thompson et al. (2020) A process-based metacommunity framework linking local and regional scale community ecology. Ecology Letters 23: 1314-1329.