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

## ----setup, message=FALSE, warning=FALSE--------------------------------------
library(sbm)
library(igraph)
library(aricode)

## ----load-data-set------------------------------------------------------------
data("war")

## ----manipulation-------------------------------------------------------------
A <- as.matrix(get.adjacency(war$alliance))
A <- A[1:83, 1:83]
B <- as.matrix(get.adjacency(war$belligerent))

## -----------------------------------------------------------------------------
netA <- defineSBM(A, model = "bernoulli", dimLabels = "country")
netB <- defineSBM(B, model = "bernoulli", dimLabels = "country")
plotMyMultiplexMatrix(list(netA, netB))

## ----echo = FALSE, results='hide'---------------------------------------------
MultiplexFitIndep <- readRDS("Multiplex_allianceNwar_case_study.rds")

## ----eval = FALSE-------------------------------------------------------------
#  MultiplexFitIndep <- estimateMultiplexSBM(list(netA, netB), dependent = FALSE,
#      estimOptions = list(verbosity = 0))

## -----------------------------------------------------------------------------
clust_country_indep <- MultiplexFitIndep$memberships[[1]]
sort(clust_country_indep)

## -----------------------------------------------------------------------------
plot(MultiplexFitIndep)
plot(MultiplexFitIndep, type = "expected")

## -----------------------------------------------------------------------------
MultiplexFitdep <- estimateMultiplexSBM(list(netA, netB), dependent = TRUE,
    estimOptions = list(verbosity = 0))

## -----------------------------------------------------------------------------
clust_country_dep <- MultiplexFitdep$memberships[[1]]
sort(clust_country_indep)
aricode::ARI(clust_country_indep, clust_country_dep)

## -----------------------------------------------------------------------------
MultiplexFitdep$ICL
MultiplexFitIndep$ICL

## -----------------------------------------------------------------------------
plot(MultiplexFitdep)
plot(MultiplexFitdep, type = "expected")

## -----------------------------------------------------------------------------
p11 <- MultiplexFitdep$connectParam$prob11
p01 <- MultiplexFitdep$connectParam$prob01
p10 <- MultiplexFitdep$connectParam$prob10
# conditional probabilities of being at war while having been or will
# be allied
round(p11/(p11 + p10), 2)
# marginal probabilities of being at war
round(p11 + p01, 2)