View source: R/calibrations_use.R
use_calibrations  R Documentation 
use_calibrations
combines all given calibrations and uses them as
constraints to perform a dating analysis on a given tree topology, using BLADJ
if it has no branch lengths, or PATHd8 if the given tree topology has initial
branch lengths.
use_calibrations(
phy = NULL,
calibrations = NULL,
dating_method = "bladj",
type = "median",
...
)
phy 
A 
calibrations 
A 
dating_method 
Tree dating algorithm to use. Options are "bladj" or "pathd8" (Webb et al., 2008, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bioinformatics/btn358")}; Britton et al., 2007, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1080/10635150701613783")}). 
type 
The type of age to use as calibration. Options are "median", "mean", "min", or "max". 
... 
Arguments passed on to

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()
.
A phylo
object with branch lengths proportional to time.
The output object stores the used calibrations
and dating_method
as
attributes(output)$datelife_calibrations
and attributes(output)$dating_method
.
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