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Packages that use ParameterizedTree | |
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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.tree | Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint). |
Uses of ParameterizedTree in pal.coalescent |
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Classes in pal.coalescent that implement ParameterizedTree | |
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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). |
Uses of ParameterizedTree in pal.eval |
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Methods in pal.eval with parameters of type ParameterizedTree | |
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double[] |
ModelParameters.estimateFromTree(ParameterizedTree t)
estimate (approximate) values for the model parameters from the data using a given (parameterized) tree |
static double |
LikelihoodOptimiser.optimiseAlternate(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits)
Optimise parameters to acheive maximum likelihood using an alternating stategy. |
static double |
LikelihoodOptimiser.optimiseAlternate(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor)
Optimise parameters to acheive maximum likelihood using an alternating stategy. |
static double |
LikelihoodOptimiser.optimiseCombined(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits)
Optimise parameters to acheive maximum likelihood using a combined stategy. |
static double |
LikelihoodOptimiser.optimiseCombined(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor)
Optimise parameters to acheive maximum likelihood using a combined stategy. |
static double |
LikelihoodOptimiser.optimiseTree(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits)
Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy. |
static double |
LikelihoodOptimiser.optimiseTree(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor)
Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy. |
Uses of ParameterizedTree in pal.tree |
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Classes in pal.tree that implement ParameterizedTree | |
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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). |
class |
UnconstrainedTree
provides parameter interface to an unconstrained tree (parameters are all available branch lengths) |
Methods in pal.tree that return ParameterizedTree | |
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ParameterizedTree |
ParameterizedTree.Factory.generateNewTree(Tree base)
Generate a new parameterized tree wrapped around base |
Constructors in pal.tree with parameters of type ParameterizedTree | |
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LogParameterizedTree(ParameterizedTree params)
Takes a parameterized object and transforms the parameters logarithmically. |
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