Uses of Interface pal.misc.Parameterized

Packages that use Parameterized
Package	Description
pal.coalescent	Classes to model population genetic processes using the coalescent.
pal.eval	Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.
pal.mep	Classes for the analysis of "measurably evolving populations" (mep).
pal.misc	Classes that don't fit elsewhere ;^)
pal.substmodel	Classes describing substitution models, i.e.
pal.tree	Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).

Uses of Parameterized in pal.coalescent

Classes in pal.coalescent that implement Parameterized
Modifier and Type	Class	Description
`class`	`ConstantPopulation`	This class models coalescent intervals for a constant population (parameter: N0=present-day population size).
`class`	`ConstExpConst`	This class models a population that grows exponentially from an initial population size alpha N0 at time y to a size N0 at time x until the present-day.
`class`	`ConstExpGrowth`	This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.
`class`	`DemographicClockTree`	Provides parameter interface to a clock-like genealogy which is assumed to have some demographic pattern of theta (diversity) as well as branch parameters (the minimal node height differences at each internal node).
`class`	`DemographicModel`	This abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.
`class`	`ExpandingPopulation`	This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.
`class`	`ExponentialGrowth`	This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).

Uses of Parameterized in pal.eval

Methods in pal.eval with parameters of type Parameterized
Modifier and Type	Method	Description
`double`	LikelihoodOptimiser.`optimiseLogLikelihood(Parameterized parameters, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits)`
`double`	LikelihoodOptimiser.`optimiseLogLikelihood(Parameterized parameters, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)`

Uses of Parameterized in pal.mep

Subinterfaces of Parameterized in pal.mep
Modifier and Type	Interface	Description
`static interface`	`DeltaModel.Instance`

Classes in pal.mep that implement Parameterized
Modifier and Type	Class	Description
`class`	`ConstantMutationRate`	This class models a constant mutation rate (parameter: mu = mutation rate).
`class`	`MutationRateModel`	This abstract class contains methods that are of general use for modelling mutation rate changes over time.
`class`	`SteppedMutationRate`	This class models a step-wise mutation rate.
`class`	`WindowedMutationRate`	This class models a windowed mutation rate (parameter: mu = mutation rate).

Uses of Parameterized in pal.misc

Subinterfaces of Parameterized in pal.misc
Modifier and Type	Interface	Description
`interface`	`NamedParameterized`	interface for class with (optimizable) named parameters

Classes in pal.misc that implement Parameterized
Modifier and Type	Class	Description
`class`	`MultiParameterized`	Title: MultiParameterized
`static class`	`Parameterized.Null`	NullParameterized Object Can be used by subclasses to implement parameterized without actually having paramters

Methods in pal.misc that return Parameterized
Modifier and Type	Method	Description
`static Parameterized`	Parameterized.Utils.`combine(Parameterized[] bases)`	Combine multiple parameterized objects into one
`static Parameterized`	Parameterized.Utils.`combine(Parameterized baseOne, Parameterized baseTwo)`	Combine multiple parameterized objects into one
`static Parameterized`	Parameterized.Utils.`createParametizedWrapper(double[] parameters, double[] lowerLimits, double[] upperLimits, double[] defaultValues)`	Create a wrapper around a set of double arrays to create a parameterized object (changes to parameterized object change given arrays)
`static Parameterized`	Parameterized.Utils.`createParametizedWrapper(double[] parameters, double[] lowerLimits, double[] upperLimits, double[] defaultValues, double[] parametersSE)`	Create a wrapper around a set of double arrays to create a parameterized object (changes to parameterized object change given arrays)

Methods in pal.misc with parameters of type Parameterized
Modifier and Type	Method	Description
`static Parameterized`	Parameterized.Utils.`combine(Parameterized[] bases)`	Combine multiple parameterized objects into one
`static Parameterized`	Parameterized.Utils.`combine(Parameterized baseOne, Parameterized baseTwo)`	Combine multiple parameterized objects into one
`static MultivariateFunction`	Utils.`combineMultivariateFunction(MultivariateFunction base, Parameterized[] additionalParameters)`	Creates an interface between a parameterised object to allow it to act as a multivariate minimum.
`protected static int`	MultiParameterized.`countParameters(Parameterized[] ps)`
`static IndividualParameterHandler[]`	IndividualParameterHandler.Utils.`createSimple(Parameterized[] bases)`
`static IndividualParameterHandler`	IndividualParameterHandler.Utils.`createSimple(Parameterized base, int parameterIndex)`
`static IndividualParameterHandler`	IndividualParameterHandler.Utils.`createSimple(Parameterized base, int parameterIndex, IndividualParameterHandler.Listener listener)`
`double[]`	MultiParameterized.`getBaseParameters(Parameterized base)`
`protected int`	MultiParameterized.`getIndex(Parameterized base)`	Get the index of a base parameterized object
`static double[]`	Parameterized.Utils.`getParameters(Parameterized source)`
`static int`	Parameterized.Utils.`getTotalNumberOfParameters(Parameterized[] bases)`
`void`	IndividualParameterHandler.Listener.`parameterChanged(Parameterized base, int parameterIndex, double value)`
`void`	MultiParameterized.ParameterAccessWatcher.`parameterSet(Parameterized baseParameterized, double param, int localParameter)`
`protected void`	Parameterized.ParameterizedUser.`setParameterizedBase(Parameterized base)`	Set's the base parameterized object...
`protected static void`	MultiParameterized.`setup(Parameterized[] ps, int[] baseLookup, int[] baseParameter)`
`static void`	Parameterized.Utils.`setupLookups(Parameterized[] bases, int[] baseLookup, int[] parameterIndexLookup, int totalNumberOfParameters)`

Constructors in pal.misc with parameters of type Parameterized
Constructor	Description
`MultiParameterized(Parameterized[] bases)`
`MultiParameterized(Parameterized[] bases, MultiParameterized.ParameterAccessWatcher watcher)`
`MultiParameterized(Parameterized b1, Parameterized b2)`
`ParameterizedNeoWrapper(Parameterized base)`
`ParameterizedUser(Parameterized base)`

Uses of Parameterized in pal.substmodel

Subinterfaces of Parameterized in pal.substmodel
Modifier and Type	Interface	Description
`interface`	`RateMatrix`	abstract base class for all rate matrices
`interface`	`SubstitutionModel`	model of sequence substitution (rate matrix + rate variation).

Classes in pal.substmodel that implement Parameterized
Modifier and Type	Class	Description
`class`	`AbstractRateMatrix`	abstract base class for all rate matrices
`class`	`AminoAcidModel`	base class of rate matrices for amino acids
`class`	`BLOSUM62`	BLOSUM62 model of amino acid evolution
`class`	`CachedRateMatrix`	a cached rate matrix.
`class`	`CodonModel`	base class for nucleotide rate matrices
`class`	`CPREV`	CPREV model of amino acid evolution (J.Adachi et al.
`class`	`Dayhoff`	Dayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.
`class`	`F81`	Felsenstein 1981 model of nucleotide evolution
`class`	`F84`	Felsenstein 1984 (PHYLIP) model of nucleotide evolution
`class`	`GammaRates`	discrete Gamma distribution (Z.
`class`	`GeneralRateDistributionSubstitutionModel`
`class`	`GTR`	GTR (general time reversible) model of nucleotide evolution Lanave, C., G.
`class`	`HKY`	Hasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H.
`class`	`InvariableSites`	invariable sites model (two-rate model with mean rate = 1.0)
`class`	`JTT`	JTT model of amino acid evolution Jones, D.
`class`	`MTREV24`	MTREV24 model of amino acid evolution
`class`	`NucleotideModel`	base class for nucleotide rate matrices
`class`	`RateDistribution`	abstract base class for models of rate variation over sites employing a discrete rate distribution
`class`	`RateMatrixHandler`
`class`	`SingleClassSubstitutionModel`
`class`	`TN`	Tamura-Nei model of nucleotide evolution Tamura, K.
`class`	`TwoStateModel`	implements the most general reversible rate matrix for two-state data
`class`	`UniformRate`	uniform rate distribution
`class`	`VT`	VT (variable time matrix) model of amino acid evolution Modeling Amino Acid Replacement Mueller, T.
`class`	`WAG`	WAG model of amino acid evolution (S.
`class`	`YangCodonModel`	Yang's model of codon evolution More advanced codon Substitution Models (of Neilson and Yang) are now included (the M1, and M2 models).
`static class`	`YangCodonModel.SimpleNeutralSelection`	A Substitution Model which can be used to implment the Neutral Model (with out continuous rate stuff) Codon model of [1] which uses the weighted sum of trwo base YangCodon models where omega=0, omega=1 repectively [1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene.
`static class`	`YangCodonModel.SimplePositiveSelection`	A Substitution Model which can be used to implment the Postitive Selection (with out continuous rate stuff) Codon model of [1] which uses the weighted sum of a three base Codon model where omega=0, omega=1 and omega=free [1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene.

Uses of Parameterized in pal.tree

Subinterfaces of Parameterized in pal.tree
Modifier and Type	Interface	Description
`interface`	`ParameterizedTree`	abstract base class for a tree with an Parameterized interface

Classes in pal.tree that implement Parameterized
Modifier and Type	Class	Description
`class`	`ClockTree`	provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)
`class`	`LogParameterizedTree`	This class logarithmically transforms tree parameters.
`class`	`MutationRateModelTree`	Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).
`static class`	`ParameterizedTree.ParameterizedTreeBase`	For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)
`class`	`UnconstrainedTree`	provides parameter interface to an unconstrained tree (parameters are all available branch lengths)

Uses of Interfacepal.misc.Parameterized

Uses of Parameterized in pal.coalescent

Uses of Parameterized in pal.eval

Uses of Parameterized in pal.mep

Uses of Parameterized in pal.misc

Uses of Parameterized in pal.substmodel

Uses of Parameterized in pal.tree

Uses of Interface
pal.misc.Parameterized