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@aterui aterui released this 10 Jul 23:42
· 124 commits to master since this release
1.3.1
e39271a

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).

  • mcsim() simulates metacommunity dynamics. This function 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() .

  • ptsource() is a function to simulate propagation of environmental
    pollutants in a river network.

  • frgm() is a function to simulate fragmentation in a river network.

  • 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.1.3.1 (07/10/23)

  • add a new function frgm()

  • update igpsim(): full description coming soon

v.1.3.0 (06/15/22)

  • add a new function ptsource()

  • add new arguments to mcsim()

  • update ggbrnet() to be compatible with piping

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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