#we want to create a dynamic network with 10 nodes and no edges
dyn <- as.dynamic(network.initialize(10))
#now we add an edge with a time interval 1 to 10, linking nodes 1 and 2
dyn<-add.edge.dynamic(dyn,c(1,10),1,2)
#now we add a bunch more edges with various times
dyn <- add.edge.dynamic(dyn,c(2,10),2,3)
dyn <- add.edge.dynamic(dyn,c(3,10),3,4)
dyn <- add.edge.dynamic(dyn,c(4,10),4,5)
dyn <- add.edge.dynamic(dyn,c(5,10),5,6)
dyn <- add.edge.dynamic(dyn,c(6,10),6,7)
dyn <- add.edge.dynamic(dyn,c(6,10),7,8)
dyn <- add.edge.dynamic(dyn,c(7,10),8,9)
dyn <- add.edge.dynamic(dyn,c(8,10),9,1)
dyn <- add.edge.dynamic(dyn,c(9,10),10,1)
dyn <- add.edge.dynamic(dyn,c(9,20),10,1)
dyn <- add.edge.dynamic(dyn,c(9,20),10,5)
dyn <- add.edge.dynamic(dyn,c(9,20),10,3)
dyn <- add.edge.dynamic(dyn,c(9,20),10,8)
#now add some attributes
#first give vertex ten the color blue at time 8
dyn <- set.dynamic.vertex.attribute(dyn,"color","blue",valid.time=8,v=10)
dyn <- set.dynamic.vertex.attribute(dyn,"color","green",valid.time=9,v=10)
dyn <- set.dynamic.vertex.attribute(dyn,"color","blue",valid.time=10,v=10)

#now plot a series of slices through our example network
#to show it at various times
par(mfrow=c(3,3))
for(p in 5:13){
 slice <-get.slice.network(dyn,p)
 plot(slice,vertex.col=get.vertex.attribute(slice,"color"),vertex.cex=5, main=p)
}

plot.intervals(dyn,pickSlice=TRUE)

plot(dyn)


## Application to faux.mesa.high

#load the faux.mesa.high data
data(faux.mesa.high)
mesa <- faux.mesa.high

#check what attributes are present
list.vertex.attributes(mesa)


#define an exponential random graph model includes various attribute effects

# no dd terms

fauxmodel.01 <- ergm(mesa ~ edges
+nodefactor("Race")
+nodematch("Race",diff=T)
+nodefactor("Grade")
+nodematch("Grade",diff=T)
+nodefactor("Sex")
+nodematch("Sex"))
 
#generate 20 networks using one of every 100 draws so there is enough
#change between networks for us to see something.

fauxsim <- simulate(fauxmodel.01,nsim=20,interval=100)

#load the rSoNIA and dynamicnetwork libraries
library(rSoNIA)

#convert the simulation output to a dynamic network object
fauxdyn <- as.dynamic(fauxsim$networks,check.renewal=FALSE)

#launch sonia with the basic network just to test
launchSonia(fauxdyn)


#NOTE: above does not produce output

#get the sex attribute, convert it to shapes, and save it back
shapes <- get.vertex.attribute(fauxdyn,"Sex")
shapes <- replace(shapes,shapes==1,"square")
shapes <- replace(shapes,shapes==2,"circle")
#now we set the shape property of all the vertices
fauxdyn <- set.vertex.attribute(fauxdyn,"shapes",shapes)

#set vertex colors using results of a function
set.vertex.attribute(fauxdyn,"color",
colorize(get.vertex.attribute(fauxdyn,"Race")))

# NOTE ˆ the output here is entertaining, but only for PH

launchSonia(fauxdyn,
vertex.col="color",
usearrows=FALSE,
displaylabels=FALSE,
vertex.shape="shape",
vertex.cex="Grade" )


## USING SONIA IN BATCH MODE

#need to specify some of the settings so it won‚t use defaults
#set desired spacing between connected nodes
soniaApplySettings$kk.opt.dist[2]<-20
#specify distance between un-connected nodes and components
soniaApplySettings$kk.comp.connect[2] <- 10
#increase height of the movie to 500 pixels
soniaGraphicsSettings$layout.height[2]<-500
#decrease number of interpolated frames to reduce file size
soniaBrowseSettings$num.frames[2]<-10
#generate a flash movie in batch mode
launchSonia(fauxDyn,
max.iter=5000,
interactive=FALSE,
vertex.col="color",
usearrows=FALSE,
displaylabels=FALSE,
vertex.shape="shape",
vertex.cex="Grade",
movie.file="myMovie",
movie.type="swf")

#same command, but change movie.type to "mov" instead of "swf"
launchSonia(fauxDyn,
max.iter=5000,
interactive=FALSE,
vertex.col="color",
usearrows=FALSE,
displaylabels=FALSE,
vertex.shape="shape",
vertex.cex="Grade",
movie.file="myMovie",
movie.type="mov")

source("buildInfectNet.R")

edgeTiming <- read.table("tel.conrsmons.txt", header=TRUE)

edgeTiming[1:3,]

infectStatus <- read.table("infect.conrsmons.b1.10comseed.05.txt",
  header=TRUE, fill=TRUE)

names(infectStatus)

infectNgh<- buildInfectNet(edgeTiming, infectStatus, neighbors=TRUE)

plot(infectNgh,vertex.cex=0.3,edge.lwd=0.1,
  vertex.col=hiliteColor(infectStatus$serostatus[infectNgh%v%"vertex.names"]))

seedNormal <- buildInfectNet(edgeTiming, infectStatus,
  neighbors=FALSE,
  keep.infected=FALSE,
  color.mode="seed")

soniaApplySettings$kk.opt.dist[2] <- 5
soniaApplySettings$kk.comp.connect[2] <- 60
soniaGraphicsSettings$layout.height[2] <- 600
soniaGraphicsSettings$layout.width[2] <- 600
soniaGraphicsSettings$arc.width.fact[2] <- 2
soniaGraphicsSettings$node.trans[2] <- 1
soniaGraphicsSettings$node.trans[2] <- 1
soniaLayoutSettings$slice.duration[2] <- 60
soniaLayoutSettings$slice.delta[2] <- 30;  

soniaBrowseSettings$num.frames[2] <- 5
soniaBrowseSettings$render.dur[2] <- 60
launchSonia(seedNormal,
  vertex.col="color", 
  arc.col="color", 
  vertex.shape="shape", 
  vertex.cex="size", 
  usearrows=FALSE,
  displaylabels=FALSE,
  max.iter=5000,
  interactive=FALSE,
  movie.file=file.path(getwd(),"simSeedNormal"));       

soniaLayoutSettings$slice.duration[2] <- 3650
soniaLayoutSettings$slice.delta[2] <- 3650

soniaApplySettings$rescale.layout[2] <- "rescale layout to fit window"
launchSonia(seedNormal, vertex.col="color",  arc.col="color",
 vertex.shape="shape", vertex.cex="size",  usearrows=FALSE,
 displaylabels=FALSE, max.iter=5000, interactive=TRUE)

seedSustain  <- buildInfectNet(edgeTiming, infectStatus, neighbors=FALSE,
  keep.infected=TRUE, color.mode="seed")
soniaLayoutSettings$slice.duration[2] <- 60; 
soniaLayoutSettings$slice.delta[2] <- 30
soniaApplySettings$rescale.layout[2] <- "none"

launchSonia(seedSustain, vertex.col="color",  arc.col="color",
 vertex.shape="shape",  vertex.cex="size", usearrows=FALSE, 
 displaylabels=FALSE, max.iter=5000, interactive=FALSE, 
 movie.file=file.path(getwd(),"simSeedSustain"))

raceSustain <- buildInfectNet(edgeTiming, infectStatus, 
 neighbors=FALSE, keep.infected=TRUE,  color.mode="race"); 
launchSonia(raceSustain, vertex.col="color", arc.col="color", 
 vertex.shape="shape",vertex.cex="size", usearrows=FALSE,  
 displaylabels=FALSE, max.iter=5000, interactive=FALSE, 
 movie.file=file.path(getwd(),"simRaceSustain"))
ageSustain <- buildInfectNet(edgeTiming, infectStatus, neighbors=FALSE, 
 keep.infected=TRUE,  color.mode="age"); 
launchSonia(ageSustain, vertex.col="color",  arc.col="color", 
 vertex.shape="shape", vertex.cex="size", usearrows=FALSE,
 displaylabels=FALSE, max.iter=5000, interactive=FALSE, 
 movie.file=file.path(getwd(),"simAgeSustain"))
launchSonia(concurSustain, vertex.col="color",  arc.col="color", 
 vertex.shape="shape", vertex.cex="size", usearrows=FALSE,
 displaylabels=FALSE, max.iter=5000, interactive=FALSE, 
 movie.file=file.path(getwd(),"simConcurSustain"))