rSpCommunity | R Documentation |
This function extends rCommunity by spatializing the randomized community.
rSpCommunity(
n,
size = sum(NorP),
NorP = 1,
BootstrapMethod = "Chao2015",
S = 300,
Distribution = "lnorm",
sd = 1,
prob = 0.1,
alpha = 40,
Spatial = "Binomial",
scale = 0.2,
mu = 10,
win = spatstat.geom::owin(),
Species = NULL,
Sizes = "Uniform",
MinSize = 1,
MaxSize = 1,
MeanSize = 20,
Wscale = 20,
shape = 2,
CheckArguments = TRUE
)
n |
The number of communities to draw. |
size |
The number of individuals to draw in each community. |
NorP |
A numeric vector or a two-column matrix. Contains either abundances or probabilities. Two-column matrices should contain the observed abundances (or probabilities) in the first column and the expected ones in the second column, to allow using beta diversity functions. |
BootstrapMethod |
The method used to obtain the probabilities to generate bootstrapped communities
from observed abundances.
If |
S |
The number of species. |
Distribution |
The distribution of species frequencies.
May be |
sd |
The simulated distribution standard deviation. For the log-normal distribution, this is the standard deviation on the log scale. |
prob |
The probability of success in each trial. |
alpha |
Fisher's alpha. |
Spatial |
The spatial distribution of points.
May be "Binomial" (a completely random point pattern except for its fixed number of points) or
"Thomas" for a clustered point pattern with parameters |
scale |
In Thomas point patterns, the standard deviation of random displacement (along each coordinate axis) of a point from its cluster center. |
mu |
In Thomas point patterns, the mean number of points per cluster.
The intensity of the Poisson process of cluster centers is calculated as the number of points ( |
win |
The window containing the point pattern. It is an owin object. |
Species |
A vector of characters or of factors containing the possible species. |
Sizes |
The distribution of point sizes.
May be "Uniform" for a uniform distribution between |
MinSize |
The minimum size in a uniform or Weibull distribution. |
MaxSize |
The maximum size in a uniform distribution. |
MeanSize |
The mean size in an exponential distribution (i.e. the negative of the inverse of the rate). |
Wscale |
The scale parameter in a Weibull distribution. |
shape |
The shape parameter in a Weibull distribution. |
CheckArguments |
If |
A wmppp.object, with PointType
values as species names if n
=1.
An object of class "SpCommunities", which is a list of wmppp.objects, is returned if n
>1.
spCommunity <- rSpCommunity(1, size=30, S=5)
autoplot(spCommunity)
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