The goal of this assignment is evaluate the Watts-Strogatz model (WS) by running Watts & Strogatz’ (1998) key simulation showing the impact of p on clustering and shortest path lengths.

Overview

This assignment contains of 4 steps.

1. Place your model inside a function.
2. Running the simulation.
3. Controlling for the results of a regular lattice.
4. Plotting the results.

Step I - Create function

1. The first step of running the simulation is to put the Watts-Strogatz model into its own function, which is actually easier than it sounds. Functions are created in R using the code below.
function_name <- function(ARGUMENT1, ARGUMENT2, ARGUMENT3){

CODE_HERE

}
1. What you need to do is three things. First, place your Watts & Strogatz model in-between the curly brackets (inplace of CODE_HERE). If you don’t have a running version of the model, use this one:
# get edges
edges = matrix(ncol = 3, nrow = size * max_dist)
ind = 0
for(i in 1:(size-1)){
for(j in (i+1):size){
dist = min(c(abs(j - i),abs((j - size)-i)))
if(i != j & dist <= max_dist){
ind = ind + 1
edges[ind, ] = c(i, j, dist)
}
}
}

# sort edges by distance
edges = edges[order(edges[,3],edges[,1],edges[,2]),]

# fill matrix
network = matrix(0, ncol = size, nrow = size)
network[edges[,1:2]] = network[edges[,2:1]]  = 1

# rewire
for(i in 1:nrow(edges)){
if(runif(1,0,1) < p){
new_end = sample(1:size,1)
if(new_end != edges[i, 1] & network[edges[i,1], new_end] == 0){
network[edges[i,1], edges[i,2]] = network[edges[i,2], edges[i,1]] = 0
network[edges[i,1], new_end]    = network[new_end, edges[i,1]]    = 1
}
}
}
network
}
1. Now, change the names of ARGUMENT1, ARGUMENT2, and ARGUMENT3 to the names of the three objects that control the size of the network, the neighborhood size (i.e., max_dist), and the probability of rewiring (in that order). Finally, change the name of the function to watts_strogatz. That’s it. Run the code and you can use your function like any other.

2. Try running watts_strogatz(10, 2, .2). Does it work? Does the resulting matrix appear correct? If not, try to find the error before you proceed.

Step II - Simulate

1. In their simulation, Watts and Strogatz varied the probability of rewiring edges to evaluate its impact on clustering and average shortest path length. To do the same, we need to find a way to run the same model for different values of the rewiring probability. Solution: a for-loop. We begin by defining values for the rewiring probability using ps <- seq(start, end, step) where start is the smallest value, end the largest, and step the step size of the sequence. Choose start and end to be .00001 and 1, and step to be some number that produces, for now, no more than say 10 or 20 values.

2. Now create a loop that iterates over those ps and another one inside that loop that repeats the simulation for each value in ps exactly n times. Just like the code below. Chose n to be a small number, say 10, for now. Later you can increase it to increase the precision of your simulation. Alright, this is the backbone of our simulation.

n = 10
for(i in 1:length(ps)){
for(j in 1:n){

CODE_HERE

}
}
1. Let’s figure out how to calculate clustering and shortest path lengths. To do this, we want to use the igraph package. Once you installed the package (install.packages('igraph')) and loaded it (library(igraph)), you can use graph_from_adjacency_matrix() to load the matrix produced by your watts_strogatz-function into the igraph format. That is, assume network is an object created from watts_strogatz, use graph_from_adjacency_matrix(network, mode = 'undirected') and assign the result to a new object called igraph_network.

2. Now you can use the igraph functions transitivity() and average.path.length() on the new igraph_network-object to compute clustering and average shortest path length. In using transitivity, make sure to set type to "localaverage" to compute the type of clustering that Watts & Strogatz used.

3. Ok, now you pretty much got all the ingredients. What’s left is storing. Create a 2-column matrix with n * length(ps) rows called result. Also create an index object and set it to 1. Create both before the loops. Then inside the inner loop assign the result of transitivity() to result[index, 1] and the result of average.path.length() to result[index, 2].

4. Now, you are technically ready to run the simulation. Before starting it, however, I recommend placing an print(i) between the inner and outer loop. This will help you keep track of the progress of the loop. Now run the simulation once with network size equal 10 and max_dist equal 2. If it takes to long, reduce the length of ps and/or the value of n. If it runs fine, set the values of size and max_dist to what Watts & Strogatz used in their simualtion.

Step III - Normalization

1. If you pay close attention, you will see that Watts and Strogatz do not show the raw clustering coefficients and average shortest path length, but those normalized for the results of regular lattices. Obtain the necessary normalization constants, by creating networks using watts_strogatz(size, max_dist, p = 0) - remember p = 0 means regular lattice - and evaluating its clustering and shortest path length using the same functions as before. Store the results as C0 and L0, respectively.

2. Now normalize the simulation results using result[, 1] <- result[, 1] / C0 and result[, 2] <- result[, 2] / L0.

Step IV - Aggregate & Plot

1. Ok, you ran the simulation, got results, normalized them, and now its finally time to inspect the results. First, aggregate the results of the repeated simulations. Do this using agg_C <- tapply(res[,1], rep(ps, rep(n, length(ps))), mean) and, respectively, the same for the average shortest path lengths. Now, plot the relationship between ps and agg_C using plot(ps, agg_C, type = 'l', ylim = c(0, 1), log = 'x'). Then run lines(ps, agg_L), which will add a dashed line for the average shortest path lengths. What do you see? Does it look the same as in Watts & Strogatz (1998)?
require(igraph)

watts_strogatz = function(size = 10, max_dist = 2, p = 0, igraph = TRUE){

# get edges
edges = matrix(ncol = 3, nrow = size * max_dist)
ind = 0
for(i in 1:(size-1)){
for(j in (i+1):size){
dist = min(c(abs(j - i),abs((j - size)-i)))
if(i != j & dist <= max_dist){
ind = ind + 1
edges[ind, ] = c(i, j, dist)
}
}
}

# sort edges by distance
edges = edges[order(edges[,3],edges[,1],edges[,2]),]

# fill matrix
network = matrix(0, ncol = size, nrow = size)
network[edges[,1:2]] = network[edges[,2:1]]  = 1

# rewire
for(i in 1:nrow(edges)){
if(runif(1,0,1) < p){
new_end = sample(1:size,1)
if(new_end != edges[i, 1] & network[edges[i,1], new_end] == 0){
network[edges[i,1], edges[i,2]] = network[edges[i,2], edges[i,1]] = 0
network[edges[i,1], new_end]    = network[new_end, edges[i,1]]    = 1
}
}
}
network
}

# simulate
ps <- seq(.00001, 1, length = 20)
n = 10
res = matrix(ncol = 2, nrow = length(ps) * n)
ind = 0
for(i in 1:length(ps)){
print(i)
for(j in 1:n){
ind = ind + 1
network <- watts_strogatz(1000, 10, ps[i])
igraph_network = graph_from_adjacency_matrix(network, mode = "undirected")
res[ind, 1] = transitivity(igraph_network, type = 'localaverage')
res[ind, 2] = average.path.length(igraph_network)
}
}
## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
## [1] 13
## [1] 14
## [1] 15
## [1] 16
## [1] 17
## [1] 18
## [1] 19
## [1] 20
# normalize
network_0 = graph_from_adjacency_matrix(watts_strogatz(1000, 10, 0), mode = "undirected")
res[,1] = res[,1] / transitivity(network_0, type = 'localaverage')
res[,2] = res[,2] / average.path.length(network_0)

# aggregate & plot
agg_C = tapply(res[,1], rep(ps, rep(n, length(ps))), mean)
agg_L = tapply(res[,2], rep(ps, rep(n, length(ps))), mean)

# plot
plot(ps, agg_C, type = 'l', ylim = c(0, 1), log = 'x')
lines(ps, agg_L, lty = 2)