ca_library {chouca}

Library of stochastic cellular automata

Description

Get one of the SCA models included in chouca

Usage

ca_library(model, parms = NULL, neighbors = NULL, wrap = TRUE)

Arguments

model

The model to return, as a string. See Details for the full list of models included with chouca.

parms

The model parameters to use, as a named list. If unset, the model default parameters will be used.

neighbors

The number of neighbors to use in the cellular automaton (4 for 4-way or von-Neumann neghborhood, or 8 for a Moore neighborhood). If unset, the model default neighborhood will be used.

wrap

Whether the 2D grid should wrap around at the edges. Default it to wrap around the edges of the landscape.

Details

This function gives access to different stochastic cellular automata models. You can provide a named list of parameters, or set the number of neighbor or wrapping options, but default are chosen if left unspecified. This function provides the following models (the string represents the name of the model, as passed using the 'model' argument):

1. "forestgap" Kubo's forest gap model (1996), which describes how gaps form in a forest and expand through disturbances.

2. "musselbed" A model of mussel beds, in which disturbance by waves occurs at the edge of mussel patches (Guichard et al. 2003)

3. "aridvege" A model of arid vegetation, in which facilitation between neighboring plants occur, along with grazing. The original model is to be found in Kéfi et al. (2007), with extensions in Schneider et al. (2016)

4. "aridvege-danet" An extension of the previous model to two species with assymetric facilitation (Danet et al. 2021)

5. "coralreef" A model of coral reef with local feedbacks of corals and macroalgae (Génin, in prep)

6. "gameoflife" The famous Game of Life by Conway, a deterministic model.

7. "rockpaperscissor" A rock-paper-scissor model with three states, in which a cell changes state depending on its neighbors according the game rules (e.g. "rock beats scissors"). This deterministic model produces nice spirals.

Value

This function returns a list object with class ca_model, with the following named components. Please note that most are for internal use and may change with package updates.

transitions

the list of transitions of the model, as returned by transition

nstates

the number of states of the model

parms

the parameter values used for the model

beta_0,beta_q, beta_pp, beta_pq, beta_qq

internal tables used to represent probabilities of transitions when running simulations, these tables are for internal use and probably not interesting for end users, but more information is provided in the package source code

wrap

Whether the model uses a toric space that wraps around the edge

neighbors

The type of neighborhood (4 or 8)

epsilon

The epsilon values used in the model definition, below which transition probabilities are assumed to be zero

xpoints

(for internal use only) The number of values used to represent the proportion of neighbors of a cell in each state

max_error, max_rel_error

vector of numeric values containing the maximum error and maximum relative error on each transition probability

fixed_neighborhood

flag equal to TRUE when cells have a fixed number of neighbors

References

Danet, Alain, Florian Dirk Schneider, Fabien Anthelme, and Sonia Kéfi. 2021. "Indirect Facilitation Drives Species Composition and Stability in Drylands." Theoretical Ecology 14 (2): 189–203. doi:10.1007/s12080-020-00489-0.

Genin, A., S. A. Navarrete, A. Garcia-Mayor, and E. A. Wieters. in press (2023). Emergent spatial patterns can indicate upcoming regime shifts in a realistic model of coral community. The American Naturalist.

Guichard, F., Halpin, P.M., Allison, G.W., Lubchenco, J. & Menge, B.A. (2003). Mussel disturbance dynamics: signatures of oceanographic forcing from local interactions. The American Naturalist, 161, 889–904. doi:10.1086/375300

Kefi, Sonia, Max Rietkerk, Concepción L. Alados, Yolanda Pueyo, Vasilios P. Papanastasis, Ahmed ElAich, and Peter C. de Ruiter. 2007. "Spatial Vegetation Patterns and Imminent Desertification in Mediterranean Arid Ecosystems." Nature 449 (7159): 213–17. doi:10.1038/nature06111.

Kubo, Takuya, Yoh Iwasa, and Naoki Furumoto. 1996. "Forest Spatial Dynamics with Gap Expansion: Total Gap Area and Gap Size Distribution." Journal of Theoretical Biology 180 (3): 229–46.

Schneider, Florian D., and Sonia Kefi. 2016. "Spatially Heterogeneous Pressure Raises Risk of Catastrophic Shifts." Theoretical Ecology 9 (2): 207-17. doi:10.1007/s12080-015-0289-1.

Examples

# Import a model, create an initial landscape and run it for ten iterations
forestgap_model <- ca_library("forestgap")
im <- generate_initmat(forestgap_model, c(0.5, 0.5), nrow = 64, ncol = 100)
run_camodel(forestgap_model, im, times = seq(0,100))