Uses of Interface
pal.misc.Parameterized
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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). -
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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)
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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 parametersClasses in pal.misc that implement Parameterized Modifier and Type Class Description class
MultiParameterized
Title: MultiParameterizedstatic class
Parameterized.Null
NullParameterized Object Can be used by subclasses to implement parameterized without actually having paramtersMethods in pal.misc that return Parameterized Modifier and Type Method Description static Parameterized
Parameterized.Utils. combine(Parameterized[] bases)
Combine multiple parameterized objects into onestatic Parameterized
Parameterized.Utils. combine(Parameterized baseOne, Parameterized baseTwo)
Combine multiple parameterized objects into onestatic 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 onestatic Parameterized
Parameterized.Utils. combine(Parameterized baseOne, Parameterized baseTwo)
Combine multiple parameterized objects into onestatic 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 objectstatic 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)
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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 matricesinterface
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 matricesclass
AminoAcidModel
base class of rate matrices for amino acidsclass
BLOSUM62
BLOSUM62 model of amino acid evolutionclass
CachedRateMatrix
a cached rate matrix.class
CodonModel
base class for nucleotide rate matricesclass
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 evolutionclass
F84
Felsenstein 1984 (PHYLIP) model of nucleotide evolutionclass
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 evolutionclass
NucleotideModel
base class for nucleotide rate matricesclass
RateDistribution
abstract base class for models of rate variation over sites employing a discrete rate distributionclass
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 dataclass
UniformRate
uniform rate distributionclass
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 interfaceClasses 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)
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