Created
April 24, 2020 20:56
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| #' | |
| #' Add outgroup to phylogenetic tree. | |
| #' The tree must be ultrametric. | |
| #' | |
| #' `tree`: a `phylo` object | |
| #' `taxon_name`: name of the taxon to add; should be a single string | |
| #' `divergence` total divergence time between a species inside `tree` and the outgroup, | |
| #' in whatever units branchlengths in `tree` are in | |
| #' | |
| add_outgroup <- function(tree, taxon_name, divergence) { | |
| stopifnot(inherits(tree, "phylo")) | |
| stopifnot(is.ultrametric(tree)) | |
| stopifnot(inherits(taxon_name, "character") && length(taxon_name) == 1) | |
| stopifnot(is.numeric(divergence) && length(divergence) == 1) | |
| tip <- list(edge = matrix(c(2,1),1,2), | |
| tip.label = taxon_name, | |
| edge.length = divergence, | |
| root.edge = 0, | |
| Nnode = 1) | |
| class(tip) <- "phylo" | |
| tree$root.edge <- divergence - max(node.depth.edgelength(tree)) | |
| new_tr <- bind.tree(tree, tip, position = divergence - max(node.depth.edgelength(tree))) | |
| # Remove unnecessary node and its relevant info: | |
| rm_node <- new_tr$edge[new_tr$edge[,2] == length(new_tr$tip.label), 1] | |
| rm_to <- new_tr$edge[,2] == rm_node | |
| rm_from <- new_tr$edge[,1] == rm_node | |
| new_edgelength <- sum(new_tr$edge.length[rm_from | rm_to]) | |
| new_tr$edge.length[rm_to] <- new_edgelength | |
| new_tr$edge[rm_to, 2] <- length(new_tr$tip.label) | |
| new_tr$edge <- new_tr$edge[!rm_from,] | |
| new_tr$edge.length <- new_tr$edge.length[!rm_from] | |
| new_tr$Nnode <- new_tr$Nnode - 1 | |
| if (!is.null(new_tr$node.label)) { | |
| new_tr$node.label <- new_tr$node.label[-(rm_node - length(new_tr$tip.label))] | |
| } | |
| return (new_tr) | |
| } |
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