|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
Packages that use Parameterized | |
---|---|
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 | |
---|---|
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 | |
---|---|
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 | |
---|---|
static interface |
DeltaModel.Instance
|
Classes in pal.mep that implement Parameterized | |
---|---|
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 | |
---|---|
interface |
NamedParameterized
interface for class with (optimizable) named parameters |
Classes in pal.misc that implement Parameterized | |
---|---|
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 | |
---|---|
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 | |
---|---|
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 | |
---|---|
MultiParameterized(Parameterized[] bases)
|
|
MultiParameterized(Parameterized[] bases,
MultiParameterized.ParameterAccessWatcher watcher)
|
|
MultiParameterized(Parameterized b1,
Parameterized b2)
|
|
Parameterized.ParameterizedUser(Parameterized base)
|
|
ParameterizedNeoWrapper(Parameterized base)
|
Uses of Parameterized in pal.substmodel |
---|
Subinterfaces of Parameterized in pal.substmodel | |
---|---|
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 | |
---|---|
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 | |
---|---|
interface |
ParameterizedTree
abstract base class for a tree with an Parameterized interface |
Classes in pal.tree that implement Parameterized | |
---|---|
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) |
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |