summary.datelifeResult: Summarize a 'datelifeResult' object.

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

Summarize a datelifeResult object.

Description

Summarize a datelifeResult object.

Usage

## S3 method for class 'datelifeResult'
summary(object, datelife_query, na_rm = TRUE, ...)

Arguments

object	An object of class datelifeResult, usually an output of get_datelife_result().
datelife_query	A datelifeQuery object, usually an output of make_datelife_query().
na_rm	Default to TRUE, whether to include partial matches or not.
...	Further arguments passed to or from other methods.

Value

A named list of 11 elements:

"citations"

A character vector of references where chronograms with some or all of the target taxa are published (source chronograms).

"mrca"

A named numeric vector of most recent common ancestor (mrca) ages of target taxa defined in input, obtained from the source chronograms. Names of mrca vector are equal to citations.

"newick_all"

A named character vector of newick strings corresponding to target chronograms derived from source chronograms. Names of newick_all vector are equal to citations.

"newick_sdm"

Only if multiple source chronograms are available. A character vector with a single newick string corresponding to a target chronogram obtained with SDM supertree method (Criscuolo et al. 2006).

"newick_median"

Only if multiple source chronograms are available. A character vector with a single newick string corresponding to a target chronogram from the median of all source chronograms.

"phylo_sdm"

Only if multiple source chronograms are available. A phylo object with a single target chronogram obtained with SDM supertree method (Criscuolo et al. 2006).

"phylo_median"

Only if multiple source chronograms are available. A phylo object with a single target chronogram obtained from source chronograms with median method.

"phylo_all"

A named list of phylo objects corresponding to each target chronogram obtained from available source chronograms. Names of phylo_all list correspond to citations.

"phylo_biggest"

The chronogram with the most taxa. In the case of a tie, the chronogram with clade age closest to the median age of the equally large trees is returned.

"html"

A character vector with an html string that can be saved and then opened in any web browser. It contains a 4 column table with data on target taxa: mrca, number of taxa, citations of source chronogram and newick target chronogram.

"data_frame"

A 4 column data.frame with data on target taxa: mrca, number of taxa, citations of source chronograms and newick string.

datelife documentation built on July 10, 2023, 2:02 a.m.