Date a given tree topology using a given set of congruified calibrations or ages

use_all_calibrations generates one or multiple chronograms (i.e., phylogenetic trees with branch lengths proportional to time) by dating a tree topology given in phy, and secondary calibrations given in calibrations, using the algorithm specified in the argument dating_method.

Usage

use_all_calibrations(
  phy = NULL,
  calibrations = NULL,
  each = FALSE,
  dating_method = "bladj",
  ...
)

Arguments

phy

A phylo object to use as tree topology.

calibrations

A calibrations object, an output of get_all_calibrations().

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.

dating_method

Tree dating algorithm to use. Options are "bladj" or "pathd8" (Webb et al., 2008, doi:10.1093/bioinformatics/btn358 ; Britton et al., 2007, doi:10.1080/10635150701613783 ).

...

Arguments passed on to use_calibrations

type: The type of age to use as calibration. Options are "median", "mean", "min", or "max".

Value

A phylo or multiPhylo object with branch lengths proportional to time.

Details

If phy has no branch lengths, dating_method is ignores, and the function applies secondary calibrations to date the tree with the BLADJ algorithm. See make_bladj_tree() and use_calibrations_bladj(). If phy has branch lengths, the function can use the PATHd8 algorithm. See use_calibrations_pathd8().

The output object stores the used calibrations and dating_method as attributes(output)$datelife_calibrations and attributes(output)$dating_method.

References

Webb, C. O., Ackerly, D. D., & Kembel, S. W. (2008). "Phylocom: software for the analysis of phylogenetic community structure and trait evolution". Bioinformatics, 24(18), doi:10.1093/bioinformatics/btn358 .