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 TypeClassDescriptionclass
This class models coalescent intervals for a constant population (parameter: N0=present-day population size).class
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
This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.class
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
This abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.class
This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.class
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 ParameterizedModifier and TypeMethodDescriptiondouble
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.mepClasses in pal.mep that implement ParameterizedModifier and TypeClassDescriptionclass
This class models a constant mutation rate (parameter: mu = mutation rate).class
This abstract class contains methods that are of general use for modelling mutation rate changes over time.class
This class models a step-wise mutation rate.class
This class models a windowed mutation rate (parameter: mu = mutation rate). -
Uses of Parameterized in pal.misc
Subinterfaces of Parameterized in pal.miscModifier and TypeInterfaceDescriptioninterface
interface for class with (optimizable) named parametersClasses in pal.misc that implement ParameterizedModifier and TypeClassDescriptionclass
Title: MultiParameterizedstatic class
NullParameterized Object Can be used by subclasses to implement parameterized without actually having paramtersMethods in pal.misc that return ParameterizedModifier and TypeMethodDescriptionstatic final Parameterized
Parameterized.Utils.combine
(Parameterized[] bases) Combine multiple parameterized objects into onestatic final Parameterized
Parameterized.Utils.combine
(Parameterized baseOne, Parameterized baseTwo) Combine multiple parameterized objects into onestatic final 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 final 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 ParameterizedModifier and TypeMethodDescriptionstatic final Parameterized
Parameterized.Utils.combine
(Parameterized[] bases) Combine multiple parameterized objects into onestatic final Parameterized
Parameterized.Utils.combine
(Parameterized baseOne, Parameterized baseTwo) Combine multiple parameterized objects into onestatic final 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 final int
MultiParameterized.countParameters
(Parameterized[] ps) static final IndividualParameterHandler[]
IndividualParameterHandler.Utils.createSimple
(Parameterized[] bases) static final IndividualParameterHandler
IndividualParameterHandler.Utils.createSimple
(Parameterized base, int parameterIndex) static final IndividualParameterHandler
IndividualParameterHandler.Utils.createSimple
(Parameterized base, int parameterIndex, IndividualParameterHandler.Listener listener) final double[]
MultiParameterized.getBaseParameters
(Parameterized base) protected final int
MultiParameterized.getIndex
(Parameterized base) Get the index of a base parameterized objectstatic final double[]
Parameterized.Utils.getParameters
(Parameterized source) static final 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 final void
MultiParameterized.setup
(Parameterized[] ps, int[] baseLookup, int[] baseParameter) static final void
Parameterized.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
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Uses of Parameterized in pal.substmodel
Subinterfaces of Parameterized in pal.substmodelModifier and TypeInterfaceDescriptioninterface
abstract base class for all rate matricesinterface
model of sequence substitution (rate matrix + rate variation).Classes in pal.substmodel that implement ParameterizedModifier and TypeClassDescriptionclass
abstract base class for all rate matricesclass
base class of rate matrices for amino acidsclass
BLOSUM62 model of amino acid evolutionclass
a cached rate matrix.class
base class for nucleotide rate matricesclass
CPREV model of amino acid evolution (J.Adachi et al.class
Dayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.class
Felsenstein 1981 model of nucleotide evolutionclass
Felsenstein 1984 (PHYLIP) model of nucleotide evolutionclass
discrete Gamma distribution (Z.class
class
GTR (general time reversible) model of nucleotide evolution Lanave, C., G.class
Hasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H.class
invariable sites model (two-rate model with mean rate = 1.0)class
JTT model of amino acid evolution Jones, D.class
MTREV24 model of amino acid evolutionclass
base class for nucleotide rate matricesclass
abstract base class for models of rate variation over sites employing a discrete rate distributionclass
class
class
Tamura-Nei model of nucleotide evolution Tamura, K.class
implements the most general reversible rate matrix for two-state dataclass
uniform rate distributionclass
VT (variable time matrix) model of amino acid evolution Modeling Amino Acid Replacement Mueller, T.class
WAG model of amino acid evolution (S.class
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
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
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.treeModifier and TypeInterfaceDescriptioninterface
abstract base class for a tree with an Parameterized interfaceClasses in pal.tree that implement ParameterizedModifier and TypeClassDescriptionclass
provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)class
This class logarithmically transforms tree parameters.class
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
For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)class
provides parameter interface to an unconstrained tree (parameters are all available branch lengths)