2016 holiday caRd

Once more, tis the season! Hope you had an excellent year of science and R coding. This card requires the igraph library - it (loosely) relies on an infection (S-I model) moving through a network :-)

To view season's greetings from 2016:
Go to the gist and download the file directly ("download gist") or hit "raw" and copy/paste. Or, copy and paste the code below.

Users of Rstudio will not be able to see the animation, so base R is highly recommended.

For those not able or willing to run the card, you can view it and the past years' cards here!

	#Holiday caRd 2016
	#Caroline M. Tucker
	##install library
	install.packages("igraph")
	library("igraph")
	###Make SI model
	par(bg="aliceblue")
	#Initial set up
	size=50 #number of vertices
	rate <- 0.10 #infection rate
	infnum <- round(seq(from=0, to=size, length.out=10)) #initial infection
	#wreath <- make_ring(size)
	wreath <- graph.ring(size)
	wreathN = connect.neighborhood(wreath, 7)
	V(wreathN)$color <- "yellow3"
	V(wreathN)$size <- runif(size, 2, 7)
	wreathN$AdjList = get.adjlist(wreathN, mode="out")
	L=layout.fruchterman.reingold(wreathN) #layout_with_fr(wreathN)
	#Plot
	plot(wreathN, vertex.label=NA, vertex.size=V(wreathN)$size, edge.width=2, edge.color="green", vertex.color=V(wreathN)$color, vertex.frame.color=NA, edge.curved=0.2, layout=L)
	for(i in 1:25){ #timesteps
	oldinf <- infnum #recovering
	newinf <- sort(unlist(lapply(wreathN$AdjList[infnum], FUN=function(X){sample(X, round(length(X)*rate))})))
	V(wreathN)$color <- "yellow" #all
	V(wreathN)$color[oldinf] <- "orange" #recovering
	V(wreathN)$color[newinf] <- "red" #new infected
	V(wreathN)$size[newinf] <- 5
	plot(delete.edges(wreathN, E(wreathN)), vertex.size=runif(size, 1, 10), vertex.label=NA, edge.width=0, vertex.frame.color=c("lightgrey"), add=TRUE, layout=L)
	}
	text(0, 0, "Happy Holidays! \n2016", cex=2, col=c("darkgreen"), font=2.1, family="serif")
	text(0.5, -1.2, "\n from the EEB & Flow", font=2, col="darkred", cex=1.5, family="serif")

view raw 2016holidaycaRd.r hosted with ❤ by GitHub