chronosCI: Confidence Intervals of Chronograms

In josephwb/chronosCI: Molecular Dating by Penalised Likelihood and Maximum Likelihood

Confidence Intervals of Chronograms

Description

Computes the confidence intervals of a chronogram using different methods.

Usage

chronosCI(
  chronogram,
  pml.output,
  B = 100,
  type = "semiparametric",
  calibration = NULL,
  method = "StraussSadler",
  control = NULL,
  quiet = FALSE,
  trees = FALSE
)

Arguments

chronogram	a chronogram output by ape::chronos().
pml.output	an unrooted tree output by phangorn::optim.pml().
B	the number of replications.
type	the bootstrap method to be used. Can be either a character string among "nonparametric", "semiparametric", or "parametric", or an integer between 1 and 3.
calibration	a data frame with the calibration points of the tree.
method	a character string specifying the method used to assess calibration uncertainty. See qage() for available methods.
control	see ape::chronos(). By default, these are the same than used to estimate the chronogram with chronos().
quiet	a logical value. By default, the progress of the computations is printed.
trees	a logical value specifying whether to return the bootstrap trees produced by phangorn (FALSE, by default).

Details

The details of the methods are presented in the manuscript below.

The labels (or taxa names) of the first argument (chronogram) must be present in the second argument (pml.output), and this second one must also include the outgroup.

Value

a matrix with the 50\ confidence intervals.

Author(s)

Emmanuel Paradis, Santiago Claramunt, Joseph Brown, Klaus Schliep

References

Paradis, E., Claramunt, S., Brown, J., and Schliep, K. Confidence intervals in molecular dating by penalized likelihood. (in preparation)

See Also

qage() drawChronosCI() ape::chronos() phangorn::bootstrap.pml()

Examples

## Not run: 
##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)for the standard data sets.

## End(Not run)

josephwb/chronosCI documentation built on Jan. 30, 2023, 5:34 a.m.