Nothing
make.phy.time.series <-
function (sim.result, time.steps = 100, all.phy = TRUE, phylo.vector = NA)
{
end.time <- max(na.omit(sim.result %v% "time_recovered"))
start.time <- min(na.omit(sim.result %v% "time_infected"))
step.size <- (end.time - start.time)/time.steps
time.sequence <- seq(start.time, end.time, by = step.size)
df <- data.frame(time = time.sequence)
if (!all.phy) {
subset.ids <- which(sim.result %v% "phylo_id" %in%
phylo.vector == TRUE)
for (x in seq(along = time.sequence)) {
t <- time.sequence[x]
nisf <- sum((sim.result %v% "time_infected" < t)[subset.ids])
nrsf <- sum((sim.result %v% "time_recovered" < t)[subset.ids])
nsi <- nisf - nrsf
df[x, 2] <- nsi
}
}
else {
for (x in seq(along = time.sequence)) {
t <- time.sequence[x]
nisf <- sum(na.omit(sim.result %v% "time_infected" <
t))
nrsf <- sum(na.omit(sim.result %v% "time_recovered" <
t))
nsi <- nisf - nrsf
df[x, 2] <- nsi
}
}
if (is.na(phylo.vector) || all.phy != TRUE) {
colnames(df)[2] <- paste("I", phylo.vector, sep = ".")
}
else {
colnames(df)[2] <- "infectious"
}
df
}
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