Created
April 4, 2017 18:29
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| # 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) | |
| # remove edges from graph | |
| gnoe <- g - edges(1:ecount(g)) | |
| # make list of graphs | |
| graph_list <- list(gnoe, | |
| gnoe + edge(ends(g, es = E(g), names = FALSE)[1,]), | |
| gnoe + edge(ends(g, es = E(g), names = FALSE)[1,]) + edge(ends(g, es = E(g), names = FALSE)[2,]), | |
| gnoe + edge(ends(g, es = E(g), names = FALSE)[1,]) + edge(ends(g, es = E(g), names = FALSE)[2,]) + edge(ends(g, es = E(g), names = FALSE)[3,]), | |
| gnoe + edge(ends(g, es = E(g), names = FALSE)[1,]) + edge(ends(g, es = E(g), names = FALSE)[2,]) + edge(ends(g, es = E(g), names = FALSE)[3,]) + edge(ends(g, es = E(g), names = FALSE)[4,]), | |
| gnoe + edge(ends(g, es = E(g), names = FALSE)[1,]) + edge(ends(g, es = E(g), names = FALSE)[2,]) + edge(ends(g, es = E(g), names = FALSE)[3,]) + edge(ends(g, es = E(g), names = FALSE)[4,]) + edge(ends(g, es = E(g), names = FALSE)[5,]), | |
| gnoe + edge(ends(g, es = E(g), names = FALSE)[1,]) + edge(ends(g, es = E(g), names = FALSE)[2,]) + edge(ends(g, es = E(g), names = FALSE)[3,]) + edge(ends(g, es = E(g), names = FALSE)[4,]) + edge(ends(g, es = E(g), names = FALSE)[5,]) + edge(ends(g, es = E(g), names = FALSE)[6,]), | |
| gnoe + edge(ends(g, es = E(g), names = FALSE)[1,]) + edge(ends(g, es = E(g), names = FALSE)[2,]) + edge(ends(g, es = E(g), names = FALSE)[3,]) + edge(ends(g, es = E(g), names = FALSE)[4,]) + edge(ends(g, es = E(g), names = FALSE)[5,]) + edge(ends(g, es = E(g), names = FALSE)[6,]) + edge(ends(g, es = E(g), names = FALSE)[7,]), | |
| gnoe + edge(ends(g, es = E(g), names = FALSE)[1,]) + edge(ends(g, es = E(g), names = FALSE)[2,]) + edge(ends(g, es = E(g), names = FALSE)[3,]) + edge(ends(g, es = E(g), names = FALSE)[4,]) + edge(ends(g, es = E(g), names = FALSE)[5,]) + edge(ends(g, es = E(g), names = FALSE)[6,]) + edge(ends(g, es = E(g), names = FALSE)[7,]) + edge(ends(g, es = E(g), names = FALSE)[8,]), | |
| gnoe + edge(ends(g, es = E(g), names = FALSE)[1,]) + edge(ends(g, es = E(g), names = FALSE)[2,]) + edge(ends(g, es = E(g), names = FALSE)[3,]) + edge(ends(g, es = E(g), names = FALSE)[4,]) + edge(ends(g, es = E(g), names = FALSE)[5,]) + edge(ends(g, es = E(g), names = FALSE)[6,]) + edge(ends(g, es = E(g), names = FALSE)[7,]) + edge(ends(g, es = E(g), names = FALSE)[8,]) + edge(ends(g, es = E(g), names = FALSE)[9,]), | |
| gnoe + edge(ends(g, es = E(g), names = FALSE)[1,]) + edge(ends(g, es = E(g), names = FALSE)[2,]) + edge(ends(g, es = E(g), names = FALSE)[3,]) + edge(ends(g, es = E(g), names = FALSE)[4,]) + edge(ends(g, es = E(g), names = FALSE)[5,]) + edge(ends(g, es = E(g), names = FALSE)[6,]) + edge(ends(g, es = E(g), names = FALSE)[7,]) + edge(ends(g, es = E(g), names = FALSE)[8,]) + edge(ends(g, es = E(g), names = FALSE)[9,]) + edge(ends(g, es = E(g), names = FALSE)[10,]), | |
| gnoe + edge(ends(g, es = E(g), names = FALSE)[1,]) + edge(ends(g, es = E(g), names = FALSE)[2,]) + edge(ends(g, es = E(g), names = FALSE)[3,]) + edge(ends(g, es = E(g), names = FALSE)[4,]) + edge(ends(g, es = E(g), names = FALSE)[5,]) + edge(ends(g, es = E(g), names = FALSE)[6,]) + edge(ends(g, es = E(g), names = FALSE)[7,]) + edge(ends(g, es = E(g), names = FALSE)[8,]) + edge(ends(g, es = E(g), names = FALSE)[9,]) + edge(ends(g, es = E(g), names = FALSE)[10,]) + edge(ends(g, es = E(g), names = FALSE)[11,]), | |
| gnoe + edge(ends(g, es = E(g), names = FALSE)[1,]) + edge(ends(g, es = E(g), names = FALSE)[2,]) + edge(ends(g, es = E(g), names = FALSE)[3,]) + edge(ends(g, es = E(g), names = FALSE)[4,]) + edge(ends(g, es = E(g), names = FALSE)[5,]) + edge(ends(g, es = E(g), names = FALSE)[6,]) + edge(ends(g, es = E(g), names = FALSE)[7,]) + edge(ends(g, es = E(g), names = FALSE)[8,]) + edge(ends(g, es = E(g), names = FALSE)[9,]) + edge(ends(g, es = E(g), names = FALSE)[10,]) + edge(ends(g, es = E(g), names = FALSE)[11,]) + edge(ends(g, es = E(g), names = FALSE)[12,]) | |
| ) | |
| # plot graphs | |
| graphjs(graph_list, | |
| vertex.shape="sphere", | |
| vertex.label = names(V(gnoe)), | |
| edge.width=3) |
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