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Search and extract available secondary calibrations for taxon names in a given datelifeQuery object

Source: R/calibrations_get.R
get_calibrations_datelifequery.Rd

The function searches DateLife's local database of phylogenetic trees with branch lengths proportional to time (chronograms) with datelife_search(), and extracts available node ages for each pair of given taxon names with extract_calibrations_phylo().

Usage

get_calibrations_datelifequery(datelife_query = NULL, each = FALSE)

Arguments

datelife_query

A datelifeQuery object.

each

Boolean, default to FALSE: all calibrations are returned in the same data.frame. If TRUE, calibrations from each chronogram are returned in separate data frames.

Value

An object of class calibrations, which is a data.frame (if each = FALSE) or a list of data.frames (if each = TRUE) of node ages for each pair of taxon names. You can access the input data from which the calibrations were extracted with attributes(output)$chronograms.

Details

The function calls datelife_search() with summary_format = "phylo_all" to get all chronograms in the database containing at least two taxa in input, and generates a phylo or multiPhylo object object that will be passed to extract_calibrations_phylo().