Multipartite_EcologicalNetwork.R
In sbm: Stochastic Blockmodels

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

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

## ----loading dataset, eval=TRUE-----------------------------------------------
data(multipartiteEcologicalNetwork)
str(multipartiteEcologicalNetwork)
names(multipartiteEcologicalNetwork)

## ----transform dataset,  eval=TRUE--------------------------------------------
Net <- multipartiteEcologicalNetwork
type = "bipartite"
model = "bernoulli"
directed = FALSE
PlantFlovis <- defineSBM(Net$Inc_plant_flovis, model, type, directed, dimLabels = c("Plants",
    "Flovis"))
PlantAnt <- defineSBM(Net$Inc_plant_ant, model, type, directed, dimLabels = c("Plants",
    "Ants"))
PlantBird <- defineSBM(Net$Inc_plant_bird, model, type, directed, dimLabels = c("Plants",
    "Birds"))

## ----example of dataset, eval=TRUE--------------------------------------------
PlantFlovis$netMatrix[1:2, 1:2]

## ----plot data----------------------------------------------------------------
plotMyMultipartiteMatrix(list(PlantFlovis, PlantAnt, PlantBird))

## ----load result, echo = FALSE, eval = TRUE-----------------------------------
load('resMultipartiteEcological.rda')

## ----MBM, echo = TRUE, eval = FALSE-------------------------------------------
#  estimOptions = list(initBM = FALSE)
#  listSBM <- list(PlantFlovis, PlantAnt, PlantBird)
#  myMSBM <- estimateMultipartiteSBM(listSBM, estimOptions)

## ----MBM what-----------------------------------------------------------------
myMSBM

## ----MBM v_K------------------------------------------------------------------
myMSBM$nbBlocks

## ----MBM param----------------------------------------------------------------
myMSBM$blockProp
myMSBM$connectParam

## ----MBM Z--------------------------------------------------------------------
table(myMSBM$memberships$Plants)
table(myMSBM$memberships$Ants)      

## ----storedmodels-------------------------------------------------------------
myMSBM$storedModels

## ----plot, eval = TRUE--------------------------------------------------------
plot(myMSBM) 

## ----plot meso, eval = TRUE---------------------------------------------------
plotOptions = list(vertex.size = c(12, 6, 4, 4))
plotOptions$vertex.shape = rep("circle", 4)
plotOptions$vertex.color = c("darkolivegreen3", "darkgoldenrod2", "salmon2",
    "cadetblue2")
plotOptions$edge.curved = 0.1
plot(myMSBM, type = "meso", plotOptions = plotOptions)