Uses of Interface
pal.misc.Parameterized
Packages that use Parameterized
Package
Description
Classes to model population genetic processes using the coalescent.
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
Classes for the analysis of "measurably evolving populations" (mep).
Classes that don't fit elsewhere ;^)
Classes describing substitution models, i.e.
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
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Uses of Parameterized in pal.coalescent
Classes in pal.coalescent that implement ParameterizedModifier and TypeClassDescriptionclassThis class models coalescent intervals for a constant population (parameter: N0=present-day population size).classThis 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.classThis class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.classProvides 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).classThis abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.classThis class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.classThis 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 ParameterizedModifier and TypeMethodDescriptiondoubleLikelihoodOptimiser.optimiseLogLikelihood(Parameterized parameters, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits) doubleLikelihoodOptimiser.optimiseLogLikelihood(Parameterized parameters, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor) -
Uses of Parameterized in pal.mep
Subinterfaces of Parameterized in pal.mepClasses in pal.mep that implement ParameterizedModifier and TypeClassDescriptionclassThis class models a constant mutation rate (parameter: mu = mutation rate).classThis abstract class contains methods that are of general use for modelling mutation rate changes over time.classThis class models a step-wise mutation rate.classThis class models a windowed mutation rate (parameter: mu = mutation rate). -
Uses of Parameterized in pal.misc
Subinterfaces of Parameterized in pal.miscModifier and TypeInterfaceDescriptioninterfaceinterface for class with (optimizable) named parametersClasses in pal.misc that implement ParameterizedModifier and TypeClassDescriptionclassTitle: MultiParameterizedstatic classNullParameterized Object Can be used by subclasses to implement parameterized without actually having paramtersMethods in pal.misc that return ParameterizedModifier and TypeMethodDescriptionstatic final ParameterizedParameterized.Utils.combine(Parameterized[] bases) Combine multiple parameterized objects into onestatic final ParameterizedParameterized.Utils.combine(Parameterized baseOne, Parameterized baseTwo) Combine multiple parameterized objects into onestatic final ParameterizedParameterized.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 final ParameterizedParameterized.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 ParameterizedModifier and TypeMethodDescriptionstatic final ParameterizedParameterized.Utils.combine(Parameterized[] bases) Combine multiple parameterized objects into onestatic final ParameterizedParameterized.Utils.combine(Parameterized baseOne, Parameterized baseTwo) Combine multiple parameterized objects into onestatic final MultivariateFunctionUtils.combineMultivariateFunction(MultivariateFunction base, Parameterized[] additionalParameters) Creates an interface between a parameterised object to allow it to act as a multivariate minimum.protected static final intMultiParameterized.countParameters(Parameterized[] ps) static final IndividualParameterHandler[]IndividualParameterHandler.Utils.createSimple(Parameterized[] bases) static final IndividualParameterHandlerIndividualParameterHandler.Utils.createSimple(Parameterized base, int parameterIndex) static final IndividualParameterHandlerIndividualParameterHandler.Utils.createSimple(Parameterized base, int parameterIndex, IndividualParameterHandler.Listener listener) final double[]MultiParameterized.getBaseParameters(Parameterized base) protected final intMultiParameterized.getIndex(Parameterized base) Get the index of a base parameterized objectstatic final double[]Parameterized.Utils.getParameters(Parameterized source) static final intParameterized.Utils.getTotalNumberOfParameters(Parameterized[] bases) voidIndividualParameterHandler.Listener.parameterChanged(Parameterized base, int parameterIndex, double value) voidMultiParameterized.ParameterAccessWatcher.parameterSet(Parameterized baseParameterized, double param, int localParameter) protected voidParameterized.ParameterizedUser.setParameterizedBase(Parameterized base) Set's the base parameterized object...protected static final voidMultiParameterized.setup(Parameterized[] ps, int[] baseLookup, int[] baseParameter) static final voidParameterized.Utils.setupLookups(Parameterized[] bases, int[] baseLookup, int[] parameterIndexLookup, int totalNumberOfParameters) Constructors in pal.misc with parameters of type ParameterizedModifierConstructorDescriptionMultiParameterized(Parameterized[] bases) MultiParameterized(Parameterized[] bases, MultiParameterized.ParameterAccessWatcher watcher) protected -
Uses of Parameterized in pal.substmodel
Subinterfaces of Parameterized in pal.substmodelModifier and TypeInterfaceDescriptioninterfaceabstract base class for all rate matricesinterfacemodel of sequence substitution (rate matrix + rate variation).Classes in pal.substmodel that implement ParameterizedModifier and TypeClassDescriptionclassabstract base class for all rate matricesclassbase class of rate matrices for amino acidsclassBLOSUM62 model of amino acid evolutionclassa cached rate matrix.classbase class for nucleotide rate matricesclassCPREV model of amino acid evolution (J.Adachi et al.classDayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.classFelsenstein 1981 model of nucleotide evolutionclassFelsenstein 1984 (PHYLIP) model of nucleotide evolutionclassdiscrete Gamma distribution (Z.classclassGTR (general time reversible) model of nucleotide evolution Lanave, C., G.classHasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H.classinvariable sites model (two-rate model with mean rate = 1.0)classJTT model of amino acid evolution Jones, D.classMTREV24 model of amino acid evolutionclassbase class for nucleotide rate matricesclassabstract base class for models of rate variation over sites employing a discrete rate distributionclassclassclassTamura-Nei model of nucleotide evolution Tamura, K.classimplements the most general reversible rate matrix for two-state dataclassuniform rate distributionclassVT (variable time matrix) model of amino acid evolution Modeling Amino Acid Replacement Mueller, T.classWAG model of amino acid evolution (S.classYang's model of codon evolution More advanced codon Substitution Models (of Neilson and Yang) are now included (the M1, and M2 models).static classA 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 classA 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.treeModifier and TypeInterfaceDescriptioninterfaceabstract base class for a tree with an Parameterized interfaceClasses in pal.tree that implement ParameterizedModifier and TypeClassDescriptionclassprovides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)classThis class logarithmically transforms tree parameters.classProvides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).static classFor parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)classprovides parameter interface to an unconstrained tree (parameters are all available branch lengths)