View source: R/calibrations_use.R
use_all_calibrations | R Documentation |
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
.
use_all_calibrations(
phy = NULL,
calibrations = NULL,
each = FALSE,
dating_method = "bladj",
...
)
phy |
A |
calibrations |
A |
each |
Boolean, default to |
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")}). |
... |
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
or multiPhylo
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
.
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), \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bioinformatics/btn358")}.
Britton, T., Anderson, C. L., Jacquet, D., Lundqvist, S., & Bremer, K. (2007). "Estimating divergence times in large phylogenetic trees". Systematic biology, 56(5), 741-752. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1080/10635150701613783")}.
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