patristic_matrix_to_phylo: Convert a patristic matrix to a 'phylo' object.

In phylotastic/datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

Convert a patristic matrix to a phylo object.

Description

Function patristic_matrix_to_phylo is used inside summarize_datelife_result().

Usage

patristic_matrix_to_phylo(
  patristic_matrix,
  clustering_method = "nj",
  fix_negative_brlen = TRUE,
  fixing_method = 0,
  ultrametric = TRUE,
  variance_matrix = NULL
)

Arguments

patristic_matrix	A patristic matrix
clustering_method	A character vector indicating the method to construct the tree. Options are: nj Neighbor-Joining method applied with ape::nj(). upgma Unweighted Pair Group Method with Arithmetic Mean method applied with phangorn::upgma(). bionj An improved version of the Neighbor-Joining method applied with ape::bionj(). triangle Triangles method applied with ape::triangMtd() mvr Minimum Variance Reduction method applied with ape::mvr().
fix_negative_brlen	Boolean indicating whether to fix negative branch lengths in resulting tree or not. Default to TRUE.
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 datelifeResult object, usually an output from datelife_result_variance_matrix(). Only used if clustering_method = "mvr".

Details

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.

Value

A rooted phylo object.

phylotastic/datelife documentation built on Jan. 17, 2024, 11:10 p.m.