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Use congruification to extract secondary calibrations from a datelifeResult object.

Source: R/calibrations_extract.R
extract_calibrations_dateliferesult.Rd

This function extracts node ages for each taxon pair given in input$tip.labels. It applies the congruification method described in Eastman et al. (2013) doi:10.1111/2041-210X.12051 , implemented with the function geiger::congruify.phylo(), to create a data.frame of taxon pair node ages that can be used as secondary calibrations.

Usage

extract_calibrations_dateliferesult(input = NULL, each = FALSE)

Arguments

input

A datelifeResult 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 takes a datelifeResult object and calls summarize_datelife_result() with summary_format = "phylo_all". This goes from a datelifeResultobject to aphyloormultiPhylo` object that is passed to extract_calibrations_phylo().