summarize_datelife_result {datelife} | R Documentation |
Summarize a datelifeResult
object.
Description
Get different types of summaries from a datelifeResult
object, an output from get_datelife_result()
.
This allows rapid processing of data.
If you need a list of chronograms from your datelifeResult
object, this
is the function you are looking for.
Usage
summarize_datelife_result(
datelife_result = NULL,
datelife_query = NULL,
summary_format = "phylo_all",
na_rm = TRUE,
summary_print = c("citations", "taxa"),
taxon_summary = c("none", "summary", "matrix"),
criterion = "taxa"
)
Arguments
datelife_result |
A datelifeResult object, usually an output of get_datelife_result() .
|
datelife_query |
A datelifeQuery object, usually an output of make_datelife_query() .
|
summary_format |
A character vector of length one, indicating the output
format for results of the DateLife search. Available output formats are:
- "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.
|
na_rm |
If TRUE , it drops rows containing NA s from the datelifeResult
patristic matrix; if FALSE , it returns NA where there are missing entries.
|
summary_print |
A character vector specifying the type of summary information
to be printed to screen. Options are:
- "citations"
Prints references of chronograms where target taxa are found.
- "taxa"
Prints a summary of the number of chronograms where each target
taxon is found.
- "none"
Nothing is printed to screen.
Defaults to c("citations", "taxa") , which displays both.
|
taxon_summary |
A character vector specifying if data on target taxa missing
in source chronograms should be added to the output as a "summary" or as a
presence/absence "matrix" . Default to "none" , no information on taxon_summary
added to the output.
|
criterion |
Defaults to criterion = "taxa" . Used for chronogram summarizing, i.e., obtaining a single
summary chronogram from a group of input chronograms.
For summarizing approaches that return a single summary tree from a group of
phylogenetic trees, it is necessary that the latter form a grove, roughly,
a sufficiently overlapping set of taxa between trees, see Ané et al. (2009) doi:10.1007/s00026-009-0017-x.
In rare cases, a group of trees can have multiple groves. This argument indicates
whether to get the grove with the most trees (criterion = "trees" ) or the
most taxa (criterion = "taxa" ).
|
Value
The output is determined by the argument summary_format
:
- If
summary_format = "citations"
The function returns a character
vector of references.
- If
summary_format = "mrca"
The function returns a named numeric
vector of most recent common ancestor (mrca) ages.
- If
summary_format = "newick_[all, sdm, or median]"
The function
returns output chronograms as newick strings.
- If
summary_format = "phylo_[all, sdm, median, or biggest]"
The
function returns output chronograms as phylo
or multiPhylo
objects.
- If
summary_format = "html" or "data_frame"
The function returns a
4 column table with data on mrca ages, number of taxa, references, and output chronograms as newick strings.
References
Ané, C., Eulenstein, O., Piaggio-Talice, R., & Sanderson, M. J. (2009).
"Groves of phylogenetic trees". Annals of Combinatorics, 13(2), 139-167,
doi:10.1007/s00026-009-0017-x.
[Package
datelife version 0.6.8
Index]