This function simulates a community with a certain abundance distribution and with intraspecific aggregation, i.e. individuals of the same species are distributed in clusters.
sim_thomas_community(
s_pool,
n_sim,
sad_type = "lnorm",
sad_coef = list(cv_abund = 1),
fix_s_sim = FALSE,
sigma = 0.02,
cluster_points = NA,
mother_points = NA,
xmother = NA,
ymother = NA,
xrange = c(0, 1),
yrange = c(0, 1),
seed = NULL
)A community object as defined by community
Number of species in the pool (integer)
Number of individuals in the simulated community (integer)
Root name of the species abundance distribution model of the
species pool (character) - e.g., "lnorm" for the lognormal distribution
(rlnorm); "geom" for the geometric distribution
(rgeom), or "ls" for Fisher's log-series distribution
(rls).
See the table in Details below, or rsad
for all SAD model options.
List with named arguments to be passed to the distribution
function defined by the argument sad_type. An overview of parameter
names is given in the table below.
In mobsim the log-normal and the Poisson log-normal distributions
can alternatively be parameterized by the coefficient of variation (cv)
of the relative abundances in the species pool. Accordingly, cv_abund
is the standard deviation of abundances divided by the mean abundance
(no. of individuals / no. of species). cv_abund is thus negatively
correlated with the evenness of the species abundance distribution.
Please note that the parameters mu and sigma are not equal to the mean and standard deviation of the log-normal distribution.
Should the simulation constrain the number of species in the simulated local community? (logical)
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.random.
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. If mother_points and cluster_points are given OR
xmother and ymother, and cluster points are given, cluster_points is overridden.
If mother_points=0, there will be no clustering even if cluster_points=400 (high clustering) because
cluster_points is overridden.
The parameter cluster_points corresponds to the
mu parameter of spatstat.random::rThomas.
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 mother_points equals 0
there is no clustering and the distribution is homogeneous. If no value is provided,
the number of clusters is determined from the abundance and the number of points
per cluster (cluster_points).
List of length equal to the number of species. Each list element is a vector of x coordinates for every mother points. If one element is NA, the the corresponding species is not clustered.
List of length equal to the number of species. Each list element is a vector of y coordinates for every mother points. If one element is NA, the the corresponding species is not clustered.
Extent of the community in x-direction. If this a numeric vector
of length 2, all species share the same range. To specify different x ranges for
all species, xrange should be a data.frame with 2 columns, min and max.
Extent of the community in y-direction. If this a numeric vector
of length 2, all species share the same range. To specify different y ranges for
all species, xrange should be a data.frame with 2 columns, min and max.
Integer. Any integer passed to set.seed for reproducibility.
Felix May
This function consecutively calls sim_sad and
sim_thomas_coords
See the documentations of sim_sad and
sim_thomas_coords for details.
com1 <- sim_thomas_community(s_pool = 20, n_sim = 500, sad_type = "lnorm",
sad_coef = list("meanlog" = 2, "sdlog" = 1),
sigma = 0.01)
plot(com1)
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