In keepsimpler/perturbEcol: Simulation of ecological dynamic systems under environmental perturbations

This R markdown file tests the fragility of mutualistic ecological communities undergoing gradual (incremental) environmental pressures.

First, we need to initialize the running environment of the simulation

library(perturbEcol)
library(deSolve)
library(rootSolve)
library(plyr)
library(igraph)

extinct_threshold <- .Machine$double.eps * 100  # threshold of species become extinct
s = 5  # number of species

# Initialize an object of cmModel
cm <- new("cmModel")
cm@times <- 1:200  # time steps
cm@perturb <- perturb_growthrate  # perturbation function
cm@perturbNum <- 500  # number of iterated steps
cm@solver <- sim_ode_press # 

Next, we start from a full mutualistic graph, that means all species cooperate with each other.

# mutualistic graph is a full graph
mutual_graph <- matrix(1, nrow = s, ncol = s)
#diag(mutual_graph) <- 0 
# competitive network is a null network
competitive_graph <- matrix(0, nrow = s, ncol = s)
coeff <- c(alpha.mu = 0.2, alpha.sd = 0.1, beta0.mu = 1., beta0.sd = 0.1, beta1.mu = 0.0, beta1.sd = 0.0, gamma.mu = 0.01, gamma.sd = 0.0, h.mu = 0.0, h.sd = 0., delta = 0.)

cm@params <- params_lv2_cm(mutual_graph, competitive_graph, coeff)
cm@init <- init_lv2_cm(cm@params)
cm <- sim(cm, extinct_threshold = extinct_threshold)
plot(cm, main = 'mutual, full graph')

We next evaluate the case of hybrid communities.

keepsimpler/perturbEcol documentation built on May 20, 2019, 8:45 a.m.