# multiphyDat2pmlPart

##### Partition model.

Model to estimate phylogenies for partitioned data.

- Keywords
- cluster

##### Usage

`multiphyDat2pmlPart(x, rooted = FALSE, ...)`pmlPart2multiPhylo(x)

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

##### Arguments

- x
an object of class

`pmlPart`

- rooted
Are the gene trees rooted (ultrametric) or unrooted.

- …
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.

##### 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"`

and `"nni"`

are 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.

##### Value

`kcluster`

returns a list with elements

log-likelihood of the fit

a list of all trees during the optimization.

an object of class `"pml"`

or
`"pmlPart"`

##### See Also

##### Examples

```
# NOT RUN {
data(yeast)
dm <- dist.logDet(yeast)
tree <- NJ(dm)
fit <- pml(tree,yeast)
fits <- optim.pml(fit)
weight=xtabs(~ index+genes,attr(yeast, "index"))[,1:10]
sp <- pmlPart(edge ~ rate + inv, fits, weight=weight)
sp
# }
# NOT RUN {
sp2 <- pmlPart(~ edge + inv, fits, weight=weight)
sp2
AIC(sp2)
sp3 <- pmlPen(sp2, lambda = 2)
AIC(sp3)
# }
# NOT RUN {
# }
```

*Documentation reproduced from package phangorn, version 2.5.5, License: GPL (>= 2)*