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```
#' Tree with sampled ancestors represented as zero-length edges
#'
#' @description
#' Converts a phylo object to SAtree, without modification of tip labels.
#'
#' @param tree Phylo object.
#' @param complete Whether the tree is complete. Default TRUE. If the tree is not complete, then all fossil tips correspond to fossil samples, otherwise only sampled ancestors are considered samples.
#'
#' @export
SAtree = function(tree, complete = TRUE) {
if(! "phylo" %in% class(tree)) stop("SAtree must be a valid phylo object")
tree$complete = complete
attr(tree, "class") <- c("SAtree", class(tree))
tree
}
#' Transforms a tree and fossils dataframe to a combined SA tree.
#' Sampled ancestors are represented as tips on zero-length edges to maintain compatibility with the ape format.
#' Tip labels are set to "species id"_"index", where the most recent tip of a given species receives index 1 and indices increase towards the past.
#'
#' @param tree Phylo object.
#' @param fossils Fossils object.
#' @return A tree integrating the fossils.
#' @examples
#' # simulate tree
#' t = ape::rtree(6)
#'
#' # simulate fossils
#' f = sim.fossils.poisson(rate = 2, tree = t)
#'
#' # transform format
#' t2 = SAtree.from.fossils(t,f)
#' plot(t2)
#' @export
SAtree.from.fossils = function(tree, fossils) {
if(length(fossils[,1])==0) {
tree$tip.label = paste0(tree$tip.label, "_", 1)
return(SAtree(tree, TRUE))
}
fossils$h = (fossils$hmin + fossils$hmax)/2
fossils = fossils[order(fossils$sp, -fossils$h),]
ntips = length(tree$tip.label)
totalnodes = ntips + tree$Nnode
depths = ape::node.depth.edgelength(tree)
times = max(depths) - depths
# adding root edge in case fossils appear on it
if(!is.null(tree$root.edge)) {
root = (ntips + length(fossils[,1]))*2
tree$edge = rbind(tree$edge, c(root, ntips +1))
tree$edge.length = c(tree$edge.length, tree$root.edge)
times[root] = max(times) + tree$root.edge
}
#renaming all species not in fossils
for(i in 1:ntips) {
if(!i %in% fossils$sp) {
tree$tip.label[i] = paste0(tree$tip.label[i], "_", 1)
}
}
current_spec = 0
count_spec = 1
for(i in 1:length(fossils[,1])) {
if(fossils$sp[i] != current_spec) {
if(current_spec <= ntips) tree$tip.label[current_spec] = paste0(tree$tip.label[current_spec], "_", count_spec)
current_spec = fossils$sp[i]
count_spec = 1
}
#adding new speciation node
edge = which(tree$edge[,2] == fossils$edge[i])
tree$edge.length[edge] = times[tree$edge[edge,1]]-fossils$h[i]
tree$edge = rbind(tree$edge,c(totalnodes+1,tree$edge[edge,2]))
tree$edge.length = c(tree$edge.length,fossils$h[i]-times[tree$edge[edge,2]])
tree$edge[edge,2]=totalnodes+1
times[totalnodes+1] = fossils$h[i]
totalnodes=totalnodes+1
tree$Nnode=tree$Nnode+1
#adding fossil tip
tree$edge = rbind(tree$edge,c(totalnodes,-i))
tree$edge.length = c(tree$edge.length,0)
if(current_spec <= ntips) tree$tip.label = c(tree$tip.label, paste0(tree$tip.label[current_spec], "_", count_spec))
else tree$tip.label = c(tree$tip.label, paste0("t", current_spec, "_", count_spec))
count_spec = count_spec +1
}
if(current_spec <= ntips) tree$tip.label[current_spec] = paste0(tree$tip.label[current_spec], "_", count_spec)
#handling root edge again, mrca may have been modified by the inclusion of fossils
if(!is.null(tree$root.edge)) {
rootedge = which(tree$edge[,1] == root)
newroot = tree$edge[rootedge,2]
rootidx = which(tree$edge == newroot)
tree$edge[which(tree$edge == ntips + 1)] = newroot
tree$edge[rootidx] = ntips + 1
tree$root.edge = tree$edge.length[rootedge]
tree$edge = tree$edge[-rootedge,]
tree$edge.length = tree$edge.length[-rootedge]
}
#renumbering all nodes to maintain ape format
for(n in totalnodes:(ntips+1)) {
tree$edge[which(tree$edge==n)] = n + length(fossils[,1])
}
for(i in 1:length(fossils[,1])) {
tree$edge[which(tree$edge==-i)] = ntips + i
}
#force reordering for nice plotting
attr(tree,"order")=NULL
tree = ape::reorder.phylo(tree)
SAtree(tree, TRUE)
}
```

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