datelifeResult object.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.
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"
)The output is determined by the argument summary_format:
summary_format = "citations"The function returns a character vector of references.
summary_format = "mrca"The function returns a named numeric vector of most recent common ancestor (mrca) ages.
summary_format = "newick_[all, sdm, or median]"The function returns output chronograms as newick strings.
summary_format = "phylo_[all, sdm, median, or biggest]"The
function returns output chronograms as phylo or multiPhylo objects.
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.
A datelifeResult object, usually an output of get_datelife_result().
A datelifeQuery object, usually an output of make_datelife_query().
A character vector of length one, indicating the output format for results of the DateLife search. Available output formats are:
A character vector of references where chronograms with some or all of the target taxa are published (source chronograms).
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.
A named character vector of newick strings corresponding to target chronograms derived from source chronograms. Names of newick_all vector are equal to citations.
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).
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.
Only if multiple source chronograms are available. A phylo object with a single target chronogram obtained with SDM supertree method (Criscuolo et al. 2006).
Only if multiple source chronograms are available. A phylo object with a single target chronogram obtained from source chronograms with median method.
A named list of phylo objects corresponding to each target chronogram obtained from available source chronograms. Names of phylo_all list correspond to citations.
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.
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.
A 4 column data.frame with data on target taxa: mrca, number of
taxa, citations of source chronograms and newick string.
If TRUE, it drops rows containing NAs from the datelifeResult
patristic matrix; if FALSE, it returns NA where there are missing entries.
A character vector specifying the type of summary information to be printed to screen. Options are:
Prints references of chronograms where target taxa are found.
Prints a summary of the number of chronograms where each target taxon is found.
Nothing is printed to screen.
Defaults to c("citations", "taxa"), which displays both.
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.
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) tools:::Rd_expr_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").
Ané, C., Eulenstein, O., Piaggio-Talice, R., & Sanderson, M. J. (2009). "Groves of phylogenetic trees". Annals of Combinatorics, 13(2), 139-167, tools:::Rd_expr_doi("10.1007/s00026-009-0017-x").