ecostatscale (version 1.1)

symdynN: 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
)

Value

a matrix or data.frame with columns for sampling times, abundances, and number of disturbances for each time interval

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

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)