@@ -1270,17 +1270,30 @@ layoutApe <- function(model, branch.length="branch.length") {

         all.nodes <- setdiff(all.nodes, treeio::rootnode(tree))

     }

     tip.nodes <- .nodeId(tree, type = "tips")

-    .internal_anc <- switch(type, all = treeio::ancestor, parent = treeio::parent)

-    ancestor <- lapply(tip.nodes, .internal_anc, .data = tree)

-    if (include.self) {

-        ancestor <- mapply(append, tip.nodes, ancestor, SIMPLIFY = FALSE)

-    }

-    sbp <- lapply(ancestor, function(i) all.nodes %in% i) %>%

-        stats::setNames(tip.nodes) %>% do.call(rbind, .) 

+    sbp <- lapply(tip.nodes, 

+                       .internal_ancestor, 

+                       .data = tree, 

+                       all.nodes = all.nodes,

+                       type = type, 

+                       include.self = include.self

+                ) %>%

+           stats::setNames(tip.nodes) %>% 

+           do.call(rbind, .) 

     colnames(sbp) <- all.nodes

     return(sbp)

 }

+.internal_ancestor <- function(.data, .node, all.nodes, type = 'all', include.self=TRUE){

+    .internal_anc <- switch(type, all = treeio::ancestor, parent = treeio::parent)

+    x <- .internal_anc(.data=.data, .node=.node)

+    if (include.self){

+        x <- c(x, .node)

+    }

+    x <- all.nodes %in% x

+    return (x)

+}

+

+

 getXcoord_no_length_slanted <- function(x){

     x <- -colSums(x)

     x <- unname(x[order(as.numeric(names(x)))])