metacommunity: Create a metacommunity
| metacommunity | R Documentation |
Create a metacommunity
Description
Create a metacommunity
Usage
metacommunity(
nsp = 2,
nr = 1,
niches = niches_uniform,
dispersal = dispersal_custom,
sp_names = paste0("sp", 1:nsp),
r_names = paste0("r", 1:nr),
niche_args = list(),
dispersal_args = list(),
comp_scale = 0.001
)
Arguments
niches |
The niche scenario to use. |
dispersal |
The dispersal scenario to use |
sp_names |
A vector of species names |
r_names |
A vector of resource names |
niche_args |
A list of named arguments to be passed to the niche function |
dispersal_args |
A list of named arguments to be passed to the dispersal function |
comp_scale |
Scale for the strength of competition, see 'details'. |
Details
The metacommunity describes the possible biological space for a flume model. It
consists of a few named elements:
-
species: a list ofspecies()objects, describing the niche and dispersal parameters for each possible species -
competition: A square species interaction matrix describing the effect of each species on each other species; generated using the overlap between species' fundamental niches. -
boundary: A function that returns a site by species matrix giving the colonisation flux from outside the river network; by default returns zero for all sites/species.
The comp_scale is treated as a multiplier, changing the value of the competition matrix.
By default the comp_scale parameter is 0.001. This parameter must be:
a single value, interpreted as the overall strength of competition in the metacommunity,
a vector of length
nsp, interpreted as the competitive strength of each species, ora matrix with
nsprows andnspcolumns, if asymmetric competition or fine control over the strength of each interaction is desired. For asymmetric competition, changing the value ofcomp_scale[i,j]will change the effect of speciesion speciesj, but not the other way around.
Each species' fundamental niche is defined as the difference between a Gaussian colonisation
function and a constant extinction function; a species will be present when c - e > 0.
Niches can be automatically generated (see generate_niches(); alternatively, to specify
the parameters manually, the following can be specified.
Value
A metacommunity object
Examples
# defaults
mc = metacommunity()
# multiple species
mc = metacommunity(nsp = 5)
# multiple resources
nlim = list( location = matrix(c(1, 2, 1, 3, 2, 4), ncol = 2)) # we need to specify the limits manually
mc = metacommunity(nsp = 3, nr=2, niches = niches_custom, niche_args = nlim)
# multiple species and resources with variance covariance matrices
loc = matrix(c(1, 2, 1, 3, 2, 4), ncol = 2) # 3 species, 2 resources
br_sp1 = matrix(c(1, 0.2, 0.2, 1), ncol = 2) # vcv matrix for one species
breadth = list(br_sp1, br_sp1, br_sp1) # assume the same matrix for all species
nopts = list(location = matrix(c(1, 2, 1, 3, 2, 4), ncol = 2), breadth = breadth, scale_c = c(0.5, 0.5, 0.55))
# location of the species along the resource space
# breadth defines the resouce utilisation
# scale competition
mc = metacommunity(nsp = 3, nr = 2, niches = niches_custom, niche_args = nopts)
plot(mc)
