patristic_matrix_to_phylo | R Documentation |
phylo
object.Function patristic_matrix_to_phylo
is used inside summarize_datelife_result()
.
patristic_matrix_to_phylo(
patristic_matrix,
clustering_method = "nj",
fix_negative_brlen = TRUE,
fixing_method = 0,
ultrametric = TRUE,
variance_matrix = NULL
)
patristic_matrix |
A patristic matrix |
clustering_method |
A character vector indicating the method to construct the tree. Options are:
|
fix_negative_brlen |
Boolean indicating whether to fix negative branch
lengths in resulting tree or not. Default to |
fixing_method |
A character vector specifying the method to fix branch lengths: "bladj", "mrbayes" or a number to be assigned to all branches meeting fixing_criterion |
ultrametric |
Boolean indicating whether to force ultrametric or not. |
variance_matrix |
A variance matrix from a |
We might add the option to insert a function as clustering_method
in the future.
Before, we had hard-coded the function to try Neighbor-Joining (NJ) first; if it
errors, it will try UPGMA.
Now, it uses NJ for a "phylo_all" summary, and we are using our own algorithm to
get a tree from a summary matrix.
A rooted phylo
object.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.