script to demonstrate outbreak animation with a subset of mers_korea_2015 data

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)