species: Creates species

In flee-group/flume: A Model For Fluvial Meta-Ecosystems

Creates species

Description

Creates species

Usage

species(
  location,
  breadth,
  scale_c,
  scale_e,
  alpha,
  beta,
  r_use,
  r_trans = identity
)

Arguments

location	Location of the niche optimum; one per niche axis
breadth	Niche breadth, or variance-covariance matrix for multivariate
scale_c	Scale of the colonisation portion of the niche
scale_e	Scale of the extinction portion of the niche
alpha	Active dispersal ability
beta	Passive dispersal ability
r_use	Resource use scaling parameter, one per resource axis
r_trans	A transformation function for converting resources into niche dimensions

Details

Creates a species, which is defined by its niche parameters and its colonisation/extinction functions.

Note that for gaussian functions in multiple variables, scale is always a scalar, but location must be a location vector of length nx, and width must be a variance covariance matrix with dim = c(nx, nx).

The resource use function is set automatically by default, but can be set to an arbitrary function; see resource use functions for details on how this function should behave.

Value

An S3 object of class 'species', which contains the following named elements:

• col: The colonisation function, takes a state matrix R and returns a vector of colonisation rates

• ext: The extinction function

• par_c: colonisation niche parameters

• par_e: extinction niche parameters

• alpha: Active dispersal ability

• beta: Passive dispersal ability

• r_use: Resource use rate per niche axis

• r_trans: Resource-to-niche transformation function

Additionally, the following attributes:

• niche_max: the maximum possible value of the fundamental niche

Examples

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flee-group/flume documentation built on Jan. 29, 2024, 6:44 p.m.