symdynN {ecostatscale} | R Documentation |
Simulate time series for N species or patches
Description
Function for simulating dynamics from Eq.2-3 in the main text.
Usage
symdynN(
r,
amu,
asd,
f,
d,
d_sd,
d_cov,
N,
sf,
tmax,
stochd = TRUE,
stocht = TRUE,
as.matrix = FALSE,
amax = 0,
amin = -Inf,
Ifrac = NULL,
Iloss = NULL,
dffun = df0,
fullout = FALSE,
xstart = NULL,
Ksim = 1
)
Arguments
r |
per-capita growth rate (r in Eq.2-3) |
amu |
the mean interaction strength |
asd |
standard deviation used to generate interaction strengths |
f |
the waiting time (or average waiting time) between disturbance events (equal to 1/lambda in Eq.2-3) |
d |
mean size of disturbance function (mu in Eq.2-3) |
d_sd |
standard deviation of disturbance function (sigma in Eq.5) |
d_cov |
the covariance for generating disturbances |
N |
number of species or patches |
sf |
waiting time between sampling events |
tmax |
the time series length to be simulated |
stochd |
a logical variable, indicating whether disturbance size should be stochastic - otherwise, all disturbances are of magnitude d - defaults to TRUE |
stocht |
a logical variable, indicating whether waiting time between disturbance events should be stochastic - otherwise, waiting time is always f - defaults to TRUE |
as.matrix |
indicates whether results should be returned as matrix (potentially faster for some applications) - defaults to FALSE |
amax |
the maximum value allowed for interaction coefficients - defaults to zero |
amin |
the minimum value allowed for interaction coefficients - defaults to -Inf |
Ifrac |
dispersal rate (D in Eq. 2) - defaults to NULL (i.e. no dispersal) |
Iloss |
loss rate from dispersal that falls outside of the patch - defaults to NULL |
dffun |
the function handed to the ODE solver - should be df_col for spatial simulations, and df0 for multi-species simulations - defaults to df0 |
fullout |
a logical, determining whether the full output or just a summary is returned - defaults to fullout |
xstart |
optional vector of starting abundances - defaults to NULL (i.e. no values) |
Ksim |
carrying capacities - defaults to 1 |
Value
a matrix or data.frame with columns for sampling times, abundances, and number of disturbances for each time interval
Examples
### Example 1: 10 patches
r<-1 #rate of recovery
d<-(0) #mean size of disturbance (mu in text)
d_sd<-sqrt(0.1) #SD of disturbances (sigma in text)
f<-1 #average time between disturbances (1/lambda in text)
sf<-0.1 #sampling interval
tmax<-120 #maximum time for simulation
d_cov<-d_cov0<-(d_sd)^2/2 #covariance in disturbance size among patches
xtNpatches<-symdynN(r = r, amu=0, asd=0, f=f, d=d,
d_sd=d_sd, d_cov=d_cov, N=10,
sf=sf, tmax=tmax, Ifrac=0, dffun = df_col)
### Example 2: 30 species
r<-1 #rate of recovery
d<-(0) #mean size of disturbance (mu in text)
d_sd<-sqrt(0.1) #SD of disturbances (sigma in text)
f<-1 #average time between disturbances (1/lambda in text)
sf<-0.1 #sampling interval
tmax<-120 #maximum time for simulation
d_cov<-0 #covariance in disturbances among species
amu<-(-r/2) #average interaction coefficient
asd<-0.1 #standard deviation of interaction coefficient
xtNsp<-symdynN(r = r, amu=amu, asd=asd, f=f, d=d,
d_sd=d_sd, d_cov=d_cov, N=30,
sf=sf, tmax=tmax)