sim_thomas_coords: Simulate clumped spatial coordinates
In mobsim: Spatial Simulation and Scale-Dependent Analysis of Biodiversity Changes

Description Usage Arguments Details Value Author(s) References See Also Examples

Add clumped (aggregated) positions to a species abundance distribution. Clumping is simulated using a Thomas cluster process, also known as Poisson cluster process (Morlon et al. 2008, Wiegand & Moloney 2014)

sim_thomas_coords(
  abund_vec,
  sigma = 0.02,
  mother_points = NA,
  cluster_points = NA,
  xrange = c(0, 1),
  yrange = c(0, 1)
)

`abund_vec`	Species abundance vector (integer)
`sigma`	Mean displacement (along each coordinate axes) of a point from its mother point (= cluster centre). `Sigma` correlates with cluster extent. When `length(sigma) == length(abund_vec)`, each species receives a specific cluster extent. Otherwise, the first value of `sigma` is recycled and all species share the same cluster extent. When `sigma` of any species is more than twice as large as the largest plot dimension, a random Poisson distribution is simulated, which is more efficient than a Thomas cluster process. The parameter `sigma` corresponds to the `scale` parameter of the function `rThomas` in the package spatstat.
`mother_points`	Number of mother points (= cluster centres). If this is a single value, all species have the same number of clusters. For example `mother_points = 1` can be used to simulate only one cluster per species, which then represents the complete species range. If `mother_points` is a vector of the same length as `abund_vec`, each species has a specific number of clusters. If no value is provided, the number of clusters is determined from the abundance and the number of points per cluster (`cluster_points`).
`cluster_points`	Mean number of points per cluster. If this is a single value, species have the same average number of points per cluster. If this is a vector of the same length as `abund_vec`, each species has a specific mean number of points per cluster. If no value is provided, the number of points per cluster is determined from the abundance and from `mother_points`. The parameter `cluster_points` corresponds to the `mu` parameter of `spatstat.core::rThomas`.
`xrange`	Extent of the community in x-direction (numeric vector of length 2)
`yrange`	Extent of the community in y-direction (numeric vector of length 2)

To generate a Thomas cluster process of a single species this function uses a C++ re-implementation of the function rThomas in the package spatstat.

There is an inherent link between the parameters abund_vec, mother_points, and cluster_points. For every species the abundance has to be equal to the number of clusters (mother_points) times the number of points per cluster (cluster_points).

abundance = mother_points * cluster_points

Accordingly, if one of the parameters is provided, the other one is directly calculated from the abundance. Values for mother_points override values for cluster_points. If none of the parameters is specified, it is assumed that for every species there is a similar number of clusters and of points per cluster.

mother_points = cluster_points = √(abundance),

In this case rare species have few clusters with few points per cluster, while abundant species have many clusters with many points per cluster.

A community object as defined by community.

Felix May

Morlon et al. 2008. A general framework for the distance-decay of similarity in ecological communities. Ecology Letters 11, 904-917.

Wiegand and Moloney 2014. Handbook of Spatial Point-Pattern Analysis in Ecology. CRC Press

rThomas

abund <- c(10,20,50,100)
sim1 <- sim_thomas_coords(abund, sigma = 0.02)
plot(sim1)

# Simulate species "ranges"
sim2 <- sim_thomas_coords(abund, sigma = 0.02, mother_points = 1)
plot(sim2)

# Equal numbers of points per cluster
sim3 <- sim_thomas_coords(abund, sigma = 0.02, cluster_points = 5)
plot(sim3)

# With large sigma the distribution will be essentially random (see Details)
sim4 <- sim_thomas_coords(abund, sigma = 10)
plot(sim4)