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Get secondary calibrations from a chronogram database for a set of given taxon names

Source: R/calibrations_get.R, R/datelife_calibrations.R
get_all_calibrations.Rd

get_all_calibrations performs a datelife_search() and gets divergence times (i.e., secondary calibrations) from a chronogram database for each taxon name pair given as input.

get_all_calibrations performs a datelife_search() and gets divergence times (i.e., secondary calibrations) from a chronogram database for each taxon name pair given as input.

Usage

get_all_calibrations(input = NULL, each = FALSE)

get_all_calibrations(input = NULL, each = FALSE)

Arguments

input

One of the following:

A character vector

With taxon names as a single comma separated starting or concatenated with c().

A phylogenetic tree with taxon names as tip labels

As a phylo or multiPhylo object, OR as a newick character string.

A datelifeQuery object

An output from make_datelife_query().

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.