patristic_matrix_to_phylo: Convert a patristic matrix to a 'phylo' object.
In datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

patristic_matrix_to_phylo

R Documentation

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.