Nothing
# Write tree in Newick format into a string or to a file
# The tree does not need to be rooted. In that case, it is rooted temporarily at the first node.
write_tree = function( tree,
file = "",
append = FALSE,
digits = 10,
quoting = 0, # whether and how to quote tip & node & edge names. 0:no quoting, 1:single quoting always, 2:double quoting always, -1:quote only when needed and prefer single quotes if possible, -2:quote only when needed and prefer double quotes if possible
include_edge_labels = FALSE,
include_edge_numbers = FALSE){
Ntips = length(tree$tip.label)
Nnodes = tree$Nnode;
result = tree_to_Newick_string_CPP( Ntips,
Nnodes,
Nedges = nrow(tree$edge),
tree_edge = as.vector(t(tree$edge)) - 1, # flatten in row-major format and adjust clade indices to 0-based
edge_length = (if(is.null(tree$edge.length)) numeric() else tree$edge.length),
tip_labels = (if(is.null(tree$tip.label)) character() else tree$tip.label),
node_labels = (if(is.null(tree$node.label)) character() else tree$node.label),
edge_labels = (if(is.null(tree$edge.label) || (!include_edge_labels)) character() else tree$edge.label),
edge_numbers = (if(is.null(tree$edge.number) || (!include_edge_numbers)) numeric() else tree$edge.number),
digits = digits,
root_edge_length = (if(is.null(tree$root.edge)) -1 else tree$root.edge),
quoting = quoting);
if(file!=""){
parent_dir = dirname(file)
if(!file.exists(parent_dir)) dir.create(parent_dir, showWarnings = FALSE, recursive=TRUE)
cat(result, file=file, append=append)
}else{
return(result)
}
}
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