--- title: "Simulation of diffusion networks: rdiffnet" author: "Thomas W. Valente and George G. Vega Yon" --- {r setup, echo=FALSE, message=FALSE, warning=FALSE} library(netdiffuseR) knitr::opts_chunk$set(comment = "#")  # Introduction Before we start, a review of the concepts we will be using here 1. Exposure: Proportion/number of neighbors that has adopted an innovation at each point in time. 2. Threshold: The proportion/number of your neighbors who had adopted at or one time period before ego (the focal individual) adopted. 3. Infectiousness: How much$i$'s adoption affects her alters. 4. Susceptibility: How much$i$'s alters' adoption affects her. 5. Structural equivalence: How similar are$i$and$j$in terms of position in the network. # Simulating diffusion networks We will simulate a diffusion network with the following parameters: 1. Will have 1,000 vertices, 2. Will span 20 time periods, 3. The initial adopters (seeds) will be selected random, 4. Seeds will be a 10\% of the network, 5. The graph (network) will be small-world, 6. Will use the WS algorithmwith$p=.2$(probability of rewire). 7. Threshold levels will be uniformly distributed between [0.3, 0.7\] To generate this diffusion network we can use the rdiffnet function included in the package: {r Generating the random graph} # Setting the seed for the RNG set.seed(1213) # Generating a random diffusion network net <- rdiffnet( n = 1e3, # 1. t = 20, # 2. seed.nodes = "random", # 3. seed.p.adopt = .1, # 4. seed.graph = "small-world", # 5. rgraph.args = list(p=.2), # 6. threshold.dist = function(x) runif(1, .3, .7) # 7. )  * The function rdiffnet generates random diffusion networks. Main features: 1. Simulating random graph or using your own, 2. Setting threshold levels per node, 3. Network rewiring throughout the simulation, and 4. Setting the seed nodes. * The simulation algorithm is as follows: 1. If required, a baseline graph is created, 2. Set of initial adopters and threshold distribution are established, 3. The set of t networks is created (if required), and 4. Simulation starts at t=2, assigning adopters based on exposures and thresholds: a. For each$i \in N$, if its exposure at$t-1$is greater than its threshold, then adopts, otherwise continue without change. b. next$i# Rumor spreading {r sim-rumor} library(netdiffuseR) set.seed(09) diffnet_rumor <- rdiffnet( n = 5e2, t = 5, seed.graph = "small-world", rgraph.args = list(k = 4, p = .3), seed.nodes = "random", seed.p.adopt = .05, rewire = TRUE, threshold.dist = function(i) 1L, exposure.args = list(normalized = FALSE) )  {r summary-rumor} summary(diffnet_rumor)  {r plot-rumor, fig.align='center', cache=TRUE} plot_diffnet(diffnet_rumor, slices = c(1, 3, 5)) # We want to use igraph to compute layout igdf <- diffnet_to_igraph(diffnet_rumor, slices=c(1,2))[[1]] pos <- igraph::layout_with_drl(igdf) plot_diffnet2(diffnet_rumor, vertex.size = dgr(diffnet_rumor)[,1], layout=pos)  # Difussion {r sim-complex} set.seed(09) diffnet_complex <- rdiffnet( seed.graph = diffnet_rumorgraph, seed.nodes = which(diffnet_rumor$toa == 1), rewire = FALSE, threshold.dist = function(i) rbeta(1, 3, 10), name = "Diffusion", behavior = "Some social behavior" )  {r plot-complex-and-disease} plot_adopters(diffnet_rumor, what = "cumadopt", include.legend = FALSE) plot_adopters(diffnet_complex, bg="tomato", add=TRUE, what = "cumadopt") legend("topleft", legend = c("Disease", "Complex"), col = c("lightblue", "tomato"), bty = "n", pch=19)  # Mentor Matching {r mentor-match, cache = TRUE} # Finding mentors mentors <- mentor_matching(diffnet_rumor, 25, lead.ties.method = "random") # Simulating diffusion with these mentors set.seed(09) diffnet_mentored <- rdiffnet( seed.graph = diffnet_complex, seed.nodes = which(mentors$1$isleader), rewire = FALSE, threshold.dist = diffnet_complex[["real_threshold"]], name = "Diffusion using Mentors" ) summary(diffnet_mentored)  {r toa_mat-mentors} cumulative_adopt_count(diffnet_complex) cumulative_adopt_count(diffnet_mentored)  # Example by changing threshold {r sim-sim, cache = TRUE, collapse = TRUE} # Simulating a scale-free homophilic network set.seed(1231) X <- rep(c(1,1,1,1,1,0,0,0,0,0), 50) net <- rgraph_ba(t = 499, m=4, eta = X) # Taking a look in igraph ig <- igraph::graph_from_adjacency_matrix(net) plot(ig, vertex.color = c("azure", "tomato")[X+1], vertex.label = NA, vertex.size = sqrt(dgr(net))) # Now, simulating a bunch of diffusion processes nsim <- 500L ans_1and2 <- vector("list", nsim) set.seed(223) for (i in 1:nsim) { # We just want the cum adopt count ans_1and2[[i]] <- cumulative_adopt_count( rdiffnet( seed.graph = net, t = 10, threshold.dist = sample(1:2, 500L, TRUE), seed.nodes = "random", seed.p.adopt = .10, exposure.args = list(outgoing = FALSE, normalized = FALSE), rewire = FALSE ) ) # Are we there yet? if (!(i %% 50)) message("Simulation ", i," of ", nsim, " done.") } # Extracting prop ans_1and2 <- do.call(rbind, lapply(ans_1and2, "[", i="prop", j=)) ans_2and3 <- vector("list", nsim) set.seed(223) for (i in 1:nsim) { # We just want the cum adopt count ans_2and3[[i]] <- cumulative_adopt_count( rdiffnet( seed.graph = net, t = 10, threshold.dist = sample(2:3, 500L, TRUE), seed.nodes = "random", seed.p.adopt = .10, exposure.args = list(outgoing = FALSE, normalized = FALSE), rewire = FALSE ) ) # Are we there yet? if (!(i %% 50)) message("Simulation ", i," of ", nsim, " done.") } ans_2and3 <- do.call(rbind, lapply(ans_2and3, "[", i="prop", j=))  This can actually be simplified by using the function rdiffnet_multiple. The following lines of code accomplish the same as the previous code avoiding the for-loop (from the user's perspective). Besides of the usual parameters passed to rdiffnet, the rdiffnet_multiple function requires R (number of repetitions/simulations), and statistic (a function that returns the statistic of insterst). Optionally, the user may choose to specify the number of clusters to run it in parallel (multiple CPUs): {r rdiffnet-multiple} ans_1and3 <- rdiffnet_multiple( # Num of sim R = nsim, # Statistic statistic = function(d) cumulative_adopt_count(d)["prop",], seed.graph = net, t = 10, threshold.dist = sample(1:3, 500, TRUE), seed.nodes = "random", seed.p.adopt = .1, rewire = FALSE, exposure.args = list(outgoing=FALSE, normalized=FALSE), # Running on 4 cores ncpus = 4L )  {r sim-sim-results} boxplot(ans_1and2, col="ivory", xlab = "Time", ylab = "Threshold") boxplot(ans_2and3, col="tomato", add=TRUE) boxplot(t(ans_1and3), col = "steelblue", add=TRUE) legend( "topleft", fill = c("ivory", "tomato", "steelblue"), legend = c("1/2", "2/3", "1/3"), title = "Threshold range", bty ="n" )  * Example simulating a thousand networks by changing threshold levels. The final prevalence, or hazard as a function of threshold levels. # Problems 1. Given the following types of networks: Small-world, Scale-free, Bernoulli, what set of$n\$ initiators maximizes diffusion? (solution script and solution plot)