R: Get minimum, median, mean, midpoint, and maximum summary...

summary_matrix_to_phylo_all {datelife}

R Documentation

Get minimum, median, mean, midpoint, and maximum summary chronograms from a summary matrix of a `datelifeResult` object.

Description

Get minimum, median, mean, midpoint, and maximum summary chronograms from a summary matrix of a datelifeResult object.

Usage

summary_matrix_to_phylo_all(
  summ_matrix,
  datelife_query = NULL,
  target_tree = NULL,
  total_distance = TRUE,
  ...
)

Arguments

`summ_matrix`	Any summary patristic distance matrix, such as the ones obtained with `datelife_result_sdm_matrix()` or `datelife_result_median_matrix()`.
`datelife_query`	A `datelifeQuery` object, usually an output of `make_datelife_query()`.
`target_tree`	A `phylo` object. Use this in case you want a specific backbone for the output tree.
`total_distance`	Whether the input `summ_matrix` stores total age distance (from tip to tip) or distance from node to tip. Default to `TRUE`, divides the matrix in half, if `FALSE` it will take it as is.
`...`	Arguments passed on to `get_otol_synthetic_tree` `otol_version` Version of Open Tree of Life to use `resolve` Defaults to `TRUE`. Whether to resolve the tree at random or not. `input` Optional. A character vector of names or a `datelifeQuery` object. `ott_ids` If not NULL, it takes this argument and ignores input. A numeric vector of ott ids obtained with `rotl::taxonomy_taxon_info()` or `rotl::tnrs_match_names()` or `tnrs_match()`.

Details

With this function users can choose the minimum, mean or maximum ages from the summary matrix as calibration points to get a single summary chronogram. Users get all three summary chronograms in a multiPhylo object.

Value

A multiPhylo object of length 5. It contains min, mean, median, midpoint, and max summary chronograms.