Partition model.

Model to estimate phylogenies for partitioned data.

Usage

multiphyDat2pmlPart(x, method = "unrooted", tip.dates = NULL, ...)

pmlPart2multiPhylo(x)

pmlPart(formula, object, control = pml.control(epsilon = 1e-08, maxit = 10,
  trace = 1), model = NULL, method = "unrooted", ...)

Arguments

x: an object of class pmlPart
method: One of "unrooted", "ultrametric" or "tiplabeled". Only unrooted is properly supported right now.
tip.dates: A named vector of sampling times associated to the tips/sequences. Leave empty if not estimating tip dated phylogenies.
...: Further arguments passed to or from other methods.
formula: a formula object (see details).
object: an object of class pml or a list of objects of class pml .
control: A list of parameters for controlling the fitting process.
model: A vector containing the models containing a model for each partition.

Value

kcluster returns a list with elements

logLik: log-likelihood of the fit
trees: a list of all trees during the optimization.
object: an object of class "pml" or "pmlPart"

Details

The formula object allows to specify which parameter get optimized. The formula is generally of the form edge + bf + Q ~ rate + shape + ...{}, on the left side are the parameters which get optimized over all partitions, on the right the parameter which are optimized specific to each partition. The parameters available are "nni", "bf", "Q", "inv", "shape", "edge", "rate". Each parameters can be used only once in the formula. "rate" is only available for the right side of the formula.

For partitions with different edge weights, but same topology, pmlPen can try to find more parsimonious models (see example).

pmlPart2multiPhylo is a convenience function to extract the trees out of a pmlPart object.

Author

Klaus Schliep klaus.schliep@gmail.com

Examples


data(yeast)
dm <- dist.logDet(yeast)
tree <- NJ(dm)
fit <- pml(tree,yeast)
fits <- optim.pml(fit)
#> optimize edge weights:  -737063 --> -734615.7 
#> optimize edge weights:  -734615.7 --> -734615.7 
#> optimize edge weights:  -734615.7 --> -734615.7 

weight=xtabs(~ index+genes,attr(yeast, "index"))[,1:10]

sp <- pmlPart(edge ~ rate + inv, fits, weight=weight)
#> loglik: -61530.38 --> -59834.29 
#> loglik: -59834.29 --> -59833.25 
#> loglik: -59833.25 --> -59833.25 
#> loglik: -59833.25 --> -59833.25 
sp
#> 
#> loglikelihood: -59833.25 
#> 
#> loglikelihood of partitions:
#>   -9827.497 -8159.024 -8056.932 -5237.677 -3809.733 -5503.277 -2752.2 -7200.052 -4632.422 -4654.434 
#> AIC:  119730.5  BIC:  119963.5 
#> 
#> Proportion of invariant sites: 0.400014 0.3179422 0.4746719 0.44901 0.412222 0.2912371 0.2419212 0.3097902 0.4794213 0.3884183 
#> 
#> Rates:
#> 1.108054 0.9656349 0.8692647 0.8928479 0.8097379 1.266643 1.296063 1.212791 0.842597 0.8275076 
#> 
#> Base frequencies:  
#>      [,1] [,2] [,3] [,4]
#> [1,] 0.25 0.25 0.25 0.25
#> 
#> Rate matrix:
#>      [,1] [,2] [,3] [,4] [,5] [,6]
#> [1,]    1    1    1    1    1    1

if (FALSE) { # \dontrun{
sp2 <- pmlPart(~ edge + inv, fits, weight=weight)
sp2
AIC(sp2)

sp3 <- pmlPen(sp2, lambda = 2)
AIC(sp3)
} # }