In hoenlab/SBIC: Structural Bayesian Information Criterion for Graphical Models

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(SBICgraph)
library(network) # for visualization 

# to reset par
resetPar <- function() {
    dev.new()
    op <- par(no.readonly = TRUE)
    dev.off()
    op
}

The function comparison allows for comparison between the true network and the estimated network from the SBIC method.

First we create a simulated data set using the embedded simulate function within SBIC. The function simulate generates a data frame, a real network adjacency matrix and a prior network adjacency matrix.

p <- 200
m1 <- 100
m2 <- 30
d <- simulate(n=100, p=p, m1=m1, m2=m2)
data<- d$data
real<- d$realnetwork
priori<- d$priornetwork

We can visualize the networks

prior_net <- network(priori)
real_net <- network(real)
par(mfrow = c(1,2))
plot(prior_net, main = "Prior network")
plot(real_net, main = "Real network")
par(resetPar())

We examine some features of both the prior network and the real network

sum(priori[lower.tri(priori)])
sum(priori[lower.tri(priori)])/(p*(p-1)/2)
sum(real[lower.tri(real)])
sum(real[lower.tri(real)])/(p*(p-1)/2)

Then we can fit SBIC using one function

lambda<- exp(seq(-10,10, length=30))
# calculating the error rate from the number of edges in the true graph and the number of discordant pairs 
r1 <- m2/m1
r2 <-m2/(p*(p-1)/2-m1)
r <- (r1+r2)/2
model<- sggm(data = data, lambda = lambda, M=priori, prob = r)

Comparing the estimated network to the true and prior network. Our comparison function above calcualtes the Positive selection rate (PSR) and the False positive rate (FDR)

print("Comparing estimated model with the real network")
comparison(real = real, estimate = model$networkhat)
print("Comparing the prior network with the real network")
comparison(real = real, estimate = priori)

We can also compare visualizations

estimated_net <- network(model$networkhat)
par(mfrow = c(1,3))
plot(prior_net, main = "Prior Network")
plot(real_net, main = "Real Network")
plot(estimated_net, main = "Estimated Network")
par(resetPar())