Covarion.MultiFreq
Usage
Covarion.MultiFreq(submodel: Map<String,Double> ->
CTMC<a>, tree: Tree<t>, freqs: DiscreteDist<Map<String,Double>>,
nodeFreqs: IntMap<Map<String,Double>>,
n: Int, rateDist: DiscreteDist<Double>, r: Double, pi1: Double, a: Alphabet) → DiscreteDist<CTMC<a>>
Arguments
Underlined names in default expressions refer to other arguments. A
default beginning with ~ specifies a prior
distribution.
-
submodel: -
The model to use on each branch
-
Default:
|pi:GTR(pi=pi)| -
tree: -
The base model
-
Default: The tree in the current context
-
n: -
The number of frequency components
-
Default:
2 -
rateDist: -
Rates for each category
-
Default:
~DirichletOnDirichlet(4,2,2) -
r: -
s01 + s10
-
Default:
~Gamma(2,1/4) -
pi1: -
Fraction of time spent in the ON state
-
Default:
~Beta(2,2) -
a: -
The alphabet
-
Default: The alphabet in the current context
Original default expressions
-
tree -
get_state(tree) -
freqs -
~DirichletMixture(SymmetricDirichletOn(letters(@a),2),2,@n) -
nodeFreqs -
~IIDMap(nodes(@tree),@freqs) -
a -
get_state(alphabet)
Description
A non-equilibrium model where each node selects from a weighted collection of n frequences.
Examples
|pi:TN93(pi=pi)| +> Covarion.MultiFreq(n=3)