mcbrnet 1.4.2

• ggbrnet() has been updated to increase flexibility (some incompatibility with earlier versions). See Articles for details.
• disabled functions findr(), ppm(), extra_prey(), to_alpha(), foodweb(), stability(); these functions were moved to ecotools package at https://github.com/aterui/ecotools

mcbrnet 1.4.1

• disabled functions foodchain(), max_tp()
• disabled disturb argument in sglv()

mcbrnet 1.4.0

• add new major functions sglv(), foodweb(), foodchain(), findr(); full documentation to follow

• full description for igpsim() is now available; see Articles

• moved utility functions to utils.R

mcbrnet 1.3.1

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).

mcbrnet 1.3.0

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() .

• ptsource() is a function to simulate propagation of environmental
  pollutants in a river network. Produced values may be plugged into
  q argument in mcsim().

• 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.1.3.0 (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).

mcbrnet 1.2.3

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).

mcbrnet 1.2.2

mcbrnet: metacommunity simulation in a branching network

Akira Terui
March 24, 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. This function shares many features with mcsim()

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

Change log

• version 1.2.2
  • fix a bug in fun_igp()
• version 1.2.1
  • implement internal functions to mcsim() and brnet().
  • remove argument weighted_distance_matrix from mcsim() and brnet().
  • add argument dispersal_matrix to mcsim().
• 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

References

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

mcbrnet 1.2.1

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. This function shares many features with mcsim()

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

Change log

• version 1.2.1
  • implement internal functions to mcsim() and brnet().
  • remove argument weighted_distance_matrix from mcsim() and brnet().
  • add argument dispersal_matrix to mcsim().
• 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

References

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

mcbrnet 1.2.0

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.

Change log

• 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

References

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

mcbrnet 1.1.1

mcbrnet: metacommunity simulation in a branching network

Akira Terui
November 03, 2021

Overview

The package mcbrnet is composed of two main functions: brnet() and mcsim().

• 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.

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

Change log

• 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

References

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