summary.datelifeResult {datelife} | R Documentation |
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 |
datelife_query |
A |
na_rm |
Default to |
... |
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.