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mcbrnet 1.2.3
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@aterui aterui released this 13 Apr 13:13
· 197 commits to master since this release
1.2.3
4232f71

mcbrnet

Overview

mcbrnet is a collection of functions to perform metacommunity simulation in branching networks. Main functions include:

  • 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/disturbance 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() 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). However, it has several unique features that are detailed in Terui et al (2021).

  • igpsim() simulates three-species meta-food web dynamics with intraguild predation. This function shares many features with mcsim(). Currently under development.

  • ggbrnet() is a wrapper of ggraph functions for easy visualization of a network produced by brnet() .

  • adjtodist() converts an adjacency matrix to a distance matrix.

See Articles for instruction.

Citation

Current best citation for this package is:

Terui A, Kim S, Dolph CL, Kadoya T, Miyazaki Y. (2021) Emergent dual scaling of riverine biodiversity. Proceedings of the National Academy
of Sciences 118: e2105574118

Installation

The mcbrnet package can be installed with the following script:

#install.packages("remotes")
remotes::install_github("aterui/mcbrnet")
library(mcbrnet)

Change-log

v.1.2.3 (04/13/22)

  • fix a bug in fun_disp_mat()

  • add ggbrnet()

  • add disturbance arguments to mcsim() (p_disturb & m_disturb)

v.1.2.2 (03/24/22)

  • fix a bug in fun_igp()

v.1.2.1 (03/09/22)

  • implement internal functions to mcsim() and brnet()

  • remove argument weighted_distance_matrix from mcsim() and
    brnet()

  • add argument dispersal_matrix to mcsim()

v.1.2.0 (03/09/22)

  • add a major function igpsim()

  • simplified brnet() and mcsim() by introducing internal
    sub-functions

v.1.1.1 (12/07/21)

  • add a local noise parameter for disturbance values to brnet()
    (argument sd_disturb_lon)

v.1.1.0 (08/02/21)

  • add disturbance arguments to brnet() added function adjtodist()

v.1.0.0 (05/03/21)

  • initial release

Funding

This material is based upon work supported by the National Science Foundation through the Division of Environmental Biology (DEB 2015634).

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