Nothing
sim2.gsa<-function (treelist, n, sampling)
{
treearray <- list()
numbsvector <- list()
timesvector <- list()
timeperiodvector <- list()
timeoverallvector <- vector()
sumtimes <- 0
k <- 0
for (j in 1:length(treelist)) {
if (class(treelist[[j]]) == "phylo") {
numbs <- getnumbs(treelist[[j]])
temp <- gettimelength(numbs, n)
numbsvector <- c(numbsvector, list(numbs))
timesvector <- c(timesvector, list(temp))
timeperiodvector <- c(timeperiodvector, list(gettimeperiod(numbs,
n)))
timeoverallvector <- c(timeoverallvector, sum(temp))
sumtimes <- sumtimes + sum(temp)
k <- k + 1
}
}
timemax <- sumtimes/k * sampling
j <- 0
for (k in 1:length(treelist)) {
if (class(treelist[[k]]) == "phylo") {
j <- j + 1
timeperiods <- timeperiodvector[[j]]
if (length(timeperiods) > 0) {
tree <- treelist[[j]]
timelength <- timesvector[[j]]
timeoverall <- timeoverallvector[[j]]
numbs <- numbsvector[[j]]
rsamp <- runif(1, min = 0, max = 1)
if (rsamp <= (timeoverall/timemax)) {
r <- runif(1, min = 0, max = timeoverall)
timepassed <- 0
jtest <- 0
while (r > timepassed) {
jtest <- jtest + 1
timepassed <- timepassed + timelength[jtest]
}
cutinterval <- timeperiods[jtest]
cuttime <- numbs[cutinterval, 2] - runif(1,
min = 0, max = timelength[jtest])
if (cuttime > max(branching.times.complete(tree))) {
stop("error")
}
treecut <- cuttree(tree, cuttime)
treearray <- c(treearray, list(reorder(treecut)))
}
}
}
}
treearray
}
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