Nothing
## ----init, include=F----------------------------------------------------------
library(knitr)
opts_chunk$set(message=FALSE, warning=FALSE, eval=TRUE, echo=TRUE)
## -----------------------------------------------------------------------------
library(outbreaks)
library(epicontacts)
## -----------------------------------------------------------------------------
str(mers_korea_2015)
## -----------------------------------------------------------------------------
colnames((mers_korea_2015$linelist))
## -----------------------------------------------------------------------------
colnames((mers_korea_2015$contacts))
## -----------------------------------------------------------------------------
merskor15 <- make_epicontacts(linelist = mers_korea_2015$linelist,
contacts = mers_korea_2015$contacts,
directed = FALSE)
class(merskor15)
summary(merskor15)
## -----------------------------------------------------------------------------
contacts_ids <- get_id(merskor15, "contacts")
head(contacts_ids, n = 10)
## -----------------------------------------------------------------------------
length(get_id(merskor15, "common"))
## -----------------------------------------------------------------------------
subset(merskor15, node_attribute = list("outcome" = "Dead", "sex" = "M"),
edge_attribute = list("exposure" = "Emergency room"))
## -----------------------------------------------------------------------------
nodes <- c("SK_14","SK_145")
subset(merskor15, cluster_id = nodes)
## -----------------------------------------------------------------------------
subset(merskor15, cs = 3)
subset(merskor15, cs_min = 10, cs_max = 100)
## -----------------------------------------------------------------------------
plot(merskor15)
## -----------------------------------------------------------------------------
plot(merskor15, "place_infect", node_shape = "sex",
shapes = c(M = "male", F = "female"))
## -----------------------------------------------------------------------------
graph3D(merskor15, node_color = "sex", g_title = "MERS Korea 2014")
## -----------------------------------------------------------------------------
si <- get_pairwise(merskor15, "dt_onset")
summary(si)
hist(si, col="grey", border="white", xlab="Days after symptoms",
main="MERS Korea 2014\nSerial Interval")
## -----------------------------------------------------------------------------
head(get_pairwise(merskor15, "sex"), n = 10)
get_pairwise(merskor15, "sex", f=table)
fisher.test(get_pairwise(merskor15, "sex", f=table))
## ----get_clusters-------------------------------------------------------------
x <- make_epicontacts(ebola_sim$linelist, ebola_sim$contacts,
id = "case_id", to = "case_id", from = "infector",
directed = TRUE)
x
clust <- get_clusters(x, output = "data.frame")
class(clust)
dim(clust)
table(clust$cluster_size)
barplot(table(clust$cluster_size),
main = "Cluster size distribution",
xlab = "Cluster size",
ylab = "Frequency")
## ----get_clusters2------------------------------------------------------------
x <- get_clusters(x)
x_14 <- subset(x, cs = 14)
plot(x_14, "cluster_member")
## -----------------------------------------------------------------------------
deg_both <- get_degree(merskor15, "both", only_linelist = TRUE)
## -----------------------------------------------------------------------------
head(sort(deg_both, decreasing = TRUE), 10)
## -----------------------------------------------------------------------------
mean(deg_both)
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