R: Go from a summary matrix to an ultrametric 'phylo' object.

summary_matrix_to_phylo {datelife}

R Documentation

Go from a summary matrix to an ultrametric `phylo` object.

Go from a summary matrix to an ultrametric phylo object.

summary_matrix_to_phylo(
  summ_matrix,
  datelife_query = NULL,
  target_tree = NULL,
  total_distance = TRUE,
  use = "mean",
  ...
)

`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.
`use`	A character vector indicating what type of age to use for summary tree. One of the following: "mean" It will use the `mean()` of the node ages in `summ_matrix`. "median" It uses the `stats::median()` age of node ages in `summ_matrix`. "min" It will use the `min()` age from node ages in `summ_matrix`. "max" Choose this if you wanna be conservative; it will use the `max()` age from node ages in `summ_matrix`. "midpoint" It will use the mean of minimum age and maximum age.
`...`	Arguments passed on to `summary_matrix_to_phylo_all`

It can take a regular patristic distance matrix, but there are simpler methods for that implemented in patristic_matrix_to_phylo().

An ultrametric phylo object.

[Package datelife version 0.6.8 Index]