vpnagraj · June 16, 2017 17:04
diff --git a/outbreak_animation_list.R b/outbreak_animation_list.R
 # script to demonstrate outbreak animation with a subset of mers_korea_2015 data

 # must install github release of threejs package

 # devtools::install_github("bwlewis/rthreejs")
 library(threejs)
 library(outbreaks)
 library(dplyr)

 # use dplyr to subset results to only include hospital visit exposure

 # prep edge attributes
 hospvisit <- 
  mers_korea_2015$contacts %>%
  filter(exposure == "Visit hospital") %>%
  select(from,to)

 # prep node attributes
 hospvisitll <-
  mers_korea_2015$linelist %>%
  filter(id %in% hospvisit$from | id %in% hospvisit$to) %>%
  select(id)

 # create graph object from data frame
 g <- graph_from_data_frame(hospvisit, vertices = hospvisitll)

 # all data
 g <- graph_from_data_frame(mers_korea_2015$contacts, vertices = mers_korea_2015$linelist)


 # remove edges from graph
 gnoe <- g - edges(1:ecount(g))

 buildexp <- function(x) {
  
  foo <- paste0(expression(ends(g, es = E(g), names = FALSE)), "[", x,",]", collapse = "")
  
  foo <- paste0(expression(edge), "(", foo, ")")
  foo
  # edge(eval(parse(text = foo)))
 }

 l <- lapply(1:ecount(g), buildexp)

 graphlist <- list(gnoe)

 for (i in 1:length(l)) {
  
  graphlist[[i + 1]] <- eval(parse(text = paste(expression(gnoe), paste(l[1:i], collapse = " + "), sep = " + ")))
  
 }

 graphjs(graphlist,
        vertex.shape="sphere", 
        vertex.label = names(V(gnoe)),
        edge.width=3,
        fpl = 100,
        cumulative = T)
	# script to demonstrate outbreak animation with a subset of mers_korea_2015 data

	# must install github release of threejs package

	# devtools::install_github("bwlewis/rthreejs")
	library(threejs)
	library(outbreaks)
	library(dplyr)

	# use dplyr to subset results to only include hospital visit exposure

	# prep edge attributes
	hospvisit <-
	mers_korea_2015$contacts %>%
	filter(exposure == "Visit hospital") %>%
	select(from,to)

	# prep node attributes
	hospvisitll <-
	mers_korea_2015$linelist %>%
	filter(id %in% hospvisit$from \| id %in% hospvisit$to) %>%
	select(id)

	# create graph object from data frame
	g <- graph_from_data_frame(hospvisit, vertices = hospvisitll)

	# all data
	g <- graph_from_data_frame(mers_korea_2015$contacts, vertices = mers_korea_2015$linelist)


	# remove edges from graph
	gnoe <- g - edges(1:ecount(g))

	buildexp <- function(x) {

	foo <- paste0(expression(ends(g, es = E(g), names = FALSE)), "[", x,",]", collapse = "")

	foo <- paste0(expression(edge), "(", foo, ")")
	foo
	# edge(eval(parse(text = foo)))
	}

	l <- lapply(1:ecount(g), buildexp)

	graphlist <- list(gnoe)

	for (i in 1:length(l)) {

	graphlist[[i + 1]] <- eval(parse(text = paste(expression(gnoe), paste(l[1:i], collapse = " + "), sep = " + ")))

	}

	graphjs(graphlist,
	vertex.shape="sphere",
	vertex.label = names(V(gnoe)),
	edge.width=3,
	fpl = 100,
	cumulative = T)