ToleranceSubstitution: The ToleranceSubstitution class
In phylosim: Flexible Simulations of Biological Sequence Evolution

Description Usage Arguments Fields and Methods Author(s) See Also Examples

This a class representing a continuous-time Markov process acting on the state space defined by the symbols stored in the Alphabet object passed to the object constructor.

In contrast to GeneralSubstitution, the ToleranceSubstitution class has a site-specific substitution tolerance parameter ("substitution.tolerance") which determines the probability of accepting the proposed events. As a consequence, the branch lengths inferred from the simulated data will no longer correspond to the neutral expectations unless all tolerance values are equal to 1.

Package:
Class ToleranceSubstitution

Object
~~|
~~+--PSRoot
~~~~~~~|
~~~~~~~+--Process
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ToleranceSubstitution

Directly known subclasses:

public static class ToleranceSubstitution
extends Process

1	ToleranceSubstitution(name="Anonymous", alphabet=NA, rate.list=NA, equ.dist=NA, ...)

`name`	The name of the object.
`alphabet`	The alphabet on which the process acts (Alphabet object).
`rate.list`	A list with the substitution rates. It will be passed to `setRateList` method.
`equ.dist`	The equilibrium distribution (see `setEquDist.ToleranceSubstitution`).
`...`	Not used.

Methods:

	`as.character`	-
	`checkConsistency`	-
	`clone`	-
	`getAlphabet`	-
	`getEquDist`	-
	`getEventRate`	-
	`getEventRateAtSite`	-
	`getEventsAtSite`	-
	`getQMatrix`	-
	`getRate`	-
	`getRateList`	-
	`hasUndefinedRate`	-
	`is`	-
	`plot`	-
	`rescaleQMatrix`	-
	`sampleState`	-
	`setAlphabet`	-
	`setEquDist`	-
	`setQMatrix`	-
	`setRate`	-
	`setRateList`	-
	`summary`	-

Methods inherited from Process:
!=, ==, as.character, checkConsistency, clone, getAlphabet, getEventsAtSite, getId, getName, getParameterAtSite, getSiteSpecificParamIds, getSiteSpecificParamList, getWriteProtected, hasSiteSpecificParameter, hasUndefinedRate, is, setAlphabet, setId, setName, setParameterAtSite, setSiteSpecificParamIds, setSiteSpecificParamList, setWriteProtected, summary

Methods inherited from PSRoot:
checkConsistency, enableVirtual, getComments, getMethodsList, globalConsistencyCheck, intersect.list, is, is.na, ll, my.all.equal, plot, setComments, setMethodsList, summary, virtualAssignmentForbidden

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Botond Sipos, Gregory Jordan

Process QMatrix Event Site GeneralIndel GTR WAG

 # construct a GTR process object, we will use this to fill in the rates
 # for the ToleranceSubstitution process.
 gtr         <- GTR(
       name="MyGTR",
           rate.params=list(
               "a"=1, "b"=2, "c"=3,
                   "d"=1, "e"=2, "f"=3
           ),
           base.freqs=c(2,2,1,1)/6
   )
 rate.list.gtr   <- gtr$rateList

 # Construct the ToleranceSubstitution process.
 p   <- ToleranceSubstitution(
     name        = "MyTolSubst",
     alphabet    = NucleotideAlphabet(),
     rate.list   = rate.list.gtr,
 )

 plot(p)

 # construct root sequence object
 s<-NucleotideSequence(length=20)

 # attach process
 attachProcess(s,p)

 # sample states from the equilibrium
 # distribution of the attached processes
 sampleStates(s)

 ## Set the substitution tolerance parameters for some sites:
 setParameterAtSites(s, p, "substitution.tolerance",c(0,0.05,0.1),1:3)

 ## Plot the substitution tolerance parameters across sites:
 plotParametersAtSites(s,p,"substitution.tolerance")

 # Construct simulation object:
 sim <-PhyloSim(root.seq=s, phylo=rtree(3))

 # Run simulation:
 Simulate(sim)

 # Plot alignment:
 plot(sim)