Simulations

Class Simulate

java.lang.Object

Simulations.Simulate

public class Simulate
extends java.lang.Object

Class for constructing simulated data

Version:

2.0

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	Simulate.SimulationException Exception for when there is a problem with the simulation

Constructor Summary

Constructors

Constructor and Description
Simulate(java.util.Map<java.lang.String,Model> m, java.util.Map<java.lang.String,Tree> t, Parameters p) Creates an object to simulate data for a given set of models and trees, parameters and unobserved states.
Simulate(java.util.Map<java.lang.String,Model> m, java.util.Map<java.lang.String,Tree> t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given set of models and trees, parameters and unobserved states.
Simulate(java.util.Map<java.lang.String,Model> m, Tree t, Parameters p) Creates an object to simulate data for a given set of models, a tree and parameters.
Simulate(java.util.Map<java.lang.String,Model> m, Tree t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given set of models, a tree, parameters and unobserved states.
Simulate(Model m, java.util.Map<java.lang.String,Tree> t, Parameters p) Creates an object to simulate data for a given model, set of trees, parameters and unobserved states.
Simulate(Model m, java.util.Map<java.lang.String,Tree> t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given model, set of trees, parameters and unobserved states.
Simulate(Model m, Tree t, Parameters p) Creates an object to simulate data for a given model, tree and parameters.
Simulate(Model m, Tree t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given model, tree, parameters and unobserved states.

Method Summary

Methods

Modifier and Type	Method and Description
Alignment	getAlignment(int length) Gets a simulated alignment, not returning the state of internal nodes
Alignment	getAlignment(int length, boolean internal) Gets a simulated alignment
Alignment	getAlignment(int length, boolean internal, java.util.Map<java.lang.String,java.lang.String> recode) Gets a simulated alignment.
Alignment	getAlignment(int length, java.util.Map<java.lang.String,java.lang.String> recode) Gets a simulated alignment, not returning the state of internal nodes.
Alignment	getAlignment(java.util.List<java.lang.String> siteClasses) Gets a simulated alignment, not returning the state of the internal nodes.
Alignment	getAlignment(java.util.List<java.lang.String> siteClasses, boolean internal) Gets a simulated alignment.
Alignment	getAlignment(java.util.List<java.lang.String> siteClasses, boolean internal, java.util.Map<java.lang.String,java.lang.String> recode) Gets a simulated alignment.
Alignment	getAlignment(java.util.List<java.lang.String> siteClasses, java.util.Map<java.lang.String,java.lang.String> recode) Gets a simulated alignment, not returning the state of the internal nodes.
Site	getSite() Gets a simulated site without returning the state of the internal nodes
Site	getSite(boolean internal) Gets a simulated site
Site	getSite(boolean internal, java.util.Map<java.lang.String,java.lang.String> recode) Gets a simulated site.
Site	getSite(boolean internal, java.util.Map<java.lang.String,java.lang.String> recode, java.lang.String siteClass) Gets a simulated site.
Site	getSite(boolean internal, java.lang.String siteClass) Gets a simulated site
Site	getSite(java.util.Map<java.lang.String,java.lang.String> recode) Gets a simulated site without returning the state of the internal nodes.
Site	getSite(java.util.Map<java.lang.String,java.lang.String> recode, java.lang.String siteClass) Gets a simulated site without returning the state of the internal nodes.
Site	getSite(java.lang.String siteClass) Gets a simulated site without returning the state of the internal nodes
void	setSeed(long seed) Seeds the random number generator with the give seed.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Simulate

public Simulate(Model m,
        Tree t,
        Parameters p)
         throws RateCategory.RateException,
                Model.ModelException,
                TreeException,
                Parameters.ParameterException

Creates an object to simulate data for a given model, tree and parameters. Has no unobserved states.

Parameters:

m - The model

t - The tree

p - The parameters

Throws:

RateCategory.RateException - Thrown if there is an issue with a rate category in the model (e.g. a badly formatted rate).

Model.ModelException - Thrown if there is a problem with the model (e.g. the rate categories differ in their states)

TreeException - Thrown if there is a problem with the tree.

Parameters.ParameterException - Thrown if there is a problem with the parameters (e.g. a required parameter is not present)

Simulate

public Simulate(Model m,
        Tree t,
        Parameters p,
        Alignment unobserved)
         throws RateCategory.RateException,
                Model.ModelException,
                TreeException,
                Parameters.ParameterException

Creates an object to simulate data for a given model, tree, parameters and unobserved states.

Parameters:

m - The model

t - The tree

p - The parameters

unobserved - The unobserved states

Throws:

RateCategory.RateException - Thrown if there is an issue with a rate category in the model (e.g. a badly formatted rate).

Model.ModelException - Thrown if there is a problem with the model (e.g. the rate categories differ in their states)

TreeException - Thrown if there is a problem with the tree.

Parameters.ParameterException - Thrown if there is a problem with the parameters (e.g. a required parameter is not present)

Simulate

public Simulate(java.util.Map<java.lang.String,Model> m,
        Tree t,
        Parameters p)
         throws RateCategory.RateException,
                Model.ModelException,
                TreeException,
                Parameters.ParameterException

Creates an object to simulate data for a given set of models, a tree and parameters. Has no unobserved states. A different model can be given for each rate class.

Parameters:

m - Map from site class to model

t - The tree

p - The parameters

Throws:

RateCategory.RateException - Thrown if there is an issue with a rate category in the model (e.g. a badly formatted rate).

Model.ModelException - Thrown if there is a problem with the model (e.g. the rate categories differ in their states)

TreeException - Thrown if there is a problem with the tree.

Parameters.ParameterException - Thrown if there is a problem with the parameters (e.g. a required parameter is not present)

Simulate

public Simulate(java.util.Map<java.lang.String,Model> m,
        Tree t,
        Parameters p,
        Alignment unobserved)
         throws RateCategory.RateException,
                Model.ModelException,
                TreeException,
                Parameters.ParameterException

Creates an object to simulate data for a given set of models, a tree, parameters and unobserved states. A different model can be given for each rate class.

Parameters:

m - Map from site class to model

t - The tree

p - The parameters

unobserved - The unobserved states

Throws:

RateCategory.RateException - Thrown if there is an issue with a rate category in the model (e.g. a badly formatted rate).

Model.ModelException - Thrown if there is a problem with the model (e.g. the rate categories differ in their states)

TreeException - Thrown if there is a problem with the tree.

Parameters.ParameterException - Thrown if there is a problem with the parameters (e.g. a required parameter is not present)

Simulate

public Simulate(Model m,
        java.util.Map<java.lang.String,Tree> t,
        Parameters p)
         throws RateCategory.RateException,
                Model.ModelException,
                TreeException,
                Parameters.ParameterException

Creates an object to simulate data for a given model, set of trees, parameters and unobserved states. A different model can be given for each rate class.

Parameters:

m - The model

t - Map from site class to tree

p - The parameters

Throws:

RateCategory.RateException - Thrown if there is an issue with a rate category in the model (e.g. a badly formatted rate).

Model.ModelException - Thrown if there is a problem with the model (e.g. the rate categories differ in their states)

TreeException - Thrown if there is a problem with the tree.

Parameters.ParameterException - Thrown if there is a problem with the parameters (e.g. a required parameter is not present)

Simulate

public Simulate(Model m,
        java.util.Map<java.lang.String,Tree> t,
        Parameters p,
        Alignment unobserved)
         throws RateCategory.RateException,
                Model.ModelException,
                TreeException,
                Parameters.ParameterException

Creates an object to simulate data for a given model, set of trees, parameters and unobserved states. A different model can be given for each rate class.

Parameters:

m - The model

t - Map from site class to tree

p - The parameters

unobserved - The unobserved states

Throws:

RateCategory.RateException - Thrown if there is an issue with a rate category in the model (e.g. a badly formatted rate).

Model.ModelException - Thrown if there is a problem with the model (e.g. the rate categories differ in their states)

TreeException - Thrown if there is a problem with the tree.

Parameters.ParameterException - Thrown if there is a problem with the parameters (e.g. a required parameter is not present)

Simulate

public Simulate(java.util.Map<java.lang.String,Model> m,
        java.util.Map<java.lang.String,Tree> t,
        Parameters p)
         throws RateCategory.RateException,
                Model.ModelException,
                TreeException,
                Parameters.ParameterException

Creates an object to simulate data for a given set of models and trees, parameters and unobserved states. A different model can be given for each rate class.

Parameters:

m - Map from site class to model

t - Map from site class to tree

p - The parameters

Throws:

RateCategory.RateException - Thrown if there is an issue with a rate category in the model (e.g. a badly formatted rate).

Model.ModelException - Thrown if there is a problem with the model (e.g. the rate categories differ in their states)

TreeException - Thrown if there is a problem with the tree.

Parameters.ParameterException - Thrown if there is a problem with the parameters (e.g. a required parameter is not present)

Simulate

public Simulate(java.util.Map<java.lang.String,Model> m,
        java.util.Map<java.lang.String,Tree> t,
        Parameters p,
        Alignment unobserved)
         throws RateCategory.RateException,
                Model.ModelException,
                TreeException,
                Parameters.ParameterException

Creates an object to simulate data for a given set of models and trees, parameters and unobserved states. A different model can be given for each rate class.

Parameters:

m - Map from site class to model

t - Map from site class to tree

p - The parameters

unobserved - The unobserved states

Throws:

RateCategory.RateException - Thrown if there is an issue with a rate category in the model (e.g. a badly formatted rate).

Model.ModelException - Thrown if there is a problem with the model (e.g. the rate categories differ in their states)

TreeException - Thrown if there is a problem with the tree.

Parameters.ParameterException - Thrown if there is a problem with the parameters (e.g. a required parameter is not present)

Method Detail

getSite

public Site getSite()
             throws Simulate.SimulationException,
                    RateCategory.RateException

Gets a simulated site without returning the state of the internal nodes

Returns:

The simulated site

Throws:

Simulate.SimulationException - Thrown if there is a problem with the simulation (currently only if attempting to simulate for a site class we don't have a model)

RateCategory.RateException - if a rate category uses the FitzJohn method at the root as this method requires likelihoods to calculate the frequency and we don't have the likelihoods when simulating.

getSite

public Site getSite(java.lang.String siteClass)
             throws Simulate.SimulationException,
                    RateCategory.RateException

Gets a simulated site without returning the state of the internal nodes

Parameters:

siteClass - The site class to simulate for

Returns:

The simulated site

Throws:

Simulate.SimulationException - Thrown if there is a problem with the simulation (currently only if attempting to simulate for a site class we don't have a model for)

RateCategory.RateException - if a rate category uses the FitzJohn method at the root as this method requires likelihoods to calculate the frequency and we don't have the likelihoods when simulating.

getSite

public Site getSite(java.util.Map<java.lang.String,java.lang.String> recode)
             throws Simulate.SimulationException,
                    RateCategory.RateException

Gets a simulated site without returning the state of the internal nodes. Recodes the simulated data before returning. For example if both "A" and "B" are unobserved states representing an observed state of "0" then this can be used to change "A" and "B" to zero. This is necessary as the simulator generates unobserved states by default. The returned site will have ambiguous data set as appropriate.

Parameters:

recode - Map of recodings

Returns:

The simulated site

Throws:

Simulate.SimulationException - Thrown if there is a problem with the simulation (currently only if attempting to simulate for a site class we don't have a model for)

RateCategory.RateException - if a rate category uses the FitzJohn method at the root as this method requires likelihoods to calculate the frequency and we don't have the likelihoods when simulating.

getSite

public Site getSite(java.util.Map<java.lang.String,java.lang.String> recode,
           java.lang.String siteClass)
             throws Simulate.SimulationException,
                    RateCategory.RateException

Gets a simulated site without returning the state of the internal nodes. Recodes the simulated data before returning. For example if both "A" and "B" are unobserved states representing an observed state of "0" then this can be used to change "A" and "B" to zero. This is necessary as the simulator generates unobserved states by default. The returned site will have ambiguous data set as appropriate.

Parameters:

recode - Map of recodings

siteClass - The site class to simulate for

Returns:

The simulated site

Throws:

Simulate.SimulationException - Thrown if there is a problem with the simulation (currently only if attempting to simulate for a site class we don't have a model for)

RateCategory.RateException - if a rate category uses the FitzJohn method at the root as this method requires likelihoods to calculate the frequency and we don't have the likelihoods when simulating.

getSite

public Site getSite(boolean internal)
             throws Simulate.SimulationException,
                    RateCategory.RateException

Gets a simulated site

Parameters:

internal - Whether to return the state of the internal nodes

Returns:

The simulated site

Throws:

Simulate.SimulationException - Thrown if there is a problem with the simulation (currently only if attempting to simulate for a site class we don't have a model for)

RateCategory.RateException - if a rate category uses the FitzJohn method at the root as this method requires likelihoods to calculate the frequency and we don't have the likelihoods when simulating.

getSite

public Site getSite(boolean internal,
           java.lang.String siteClass)
             throws Simulate.SimulationException,
                    RateCategory.RateException

Gets a simulated site

Parameters:

internal - Whether to return the state of the internal nodes

siteClass - The site class to simulate for

Returns:

The simulated site

Throws:

Simulate.SimulationException - Thrown if there is a problem with the simulation (currently only if attempting to simulate for a site class we don't have a model for)

RateCategory.RateException - if a rate category uses the FitzJohn method at the root as this method requires likelihoods to calculate the frequency and we don't have the likelihoods when simulating.

getSite

public Site getSite(boolean internal,
           java.util.Map<java.lang.String,java.lang.String> recode)
             throws Simulate.SimulationException,
                    RateCategory.RateException

Gets a simulated site. Recodes the simulated data before returning. For example if both "A" and "B" are unobserved states representing an observed state of "0" then this can be used to change "A" and "B" to zero. This is necessary as the simulator generates unobserved states by default. The returned site will have ambiguous data set as appropriate.

Parameters:

recode - Map of recodings

internal - Whether to return the state of the internal nodes

Returns:

The simulated site

Throws:

Simulate.SimulationException - Thrown if there is a problem with the simulation (currently only if attempting to simulate for a site class we don't have a model for)

RateCategory.RateException - if a rate category uses the FitzJohn method at the root as this method requires likelihoods to calculate the frequency and we don't have the likelihoods when simulating.

getSite

public Site getSite(boolean internal,
           java.util.Map<java.lang.String,java.lang.String> recode,
           java.lang.String siteClass)
             throws Simulate.SimulationException,
                    RateCategory.RateException

Gets a simulated site. Recodes the simulated data before returning. For example if both "A" and "B" are unobserved states representing an observed state of "0" then this can be used to change "A" and "B" to zero. This is necessary as the simulator generates unobserved states by default. The returned site will have ambiguous data set as appropriate.

Parameters:

recode - Map of recodings

internal - Whether to return the state of the internal nodes

siteClass - The site class to simulate for

Returns:

The simulated site

Throws:

Simulate.SimulationException - Thrown if there is a problem with the simulation (currently only if attempting to simulate for a site class we don't have a model for)

RateCategory.RateException - if a rate category uses the FitzJohn method at the root as this method requires likelihoods to calculate the frequency and we don't have the likelihoods when simulating.

getAlignment

public Alignment getAlignment(int length)
                       throws AlignmentException,
                              Simulate.SimulationException,
                              RateCategory.RateException

Gets a simulated alignment, not returning the state of internal nodes

Parameters:

length - The length of the alignment

Returns:

The simulated alignment

Throws:

AlignmentException - Thrown if there is a problem with the alignment

Simulate.SimulationException - Thrown if there is a problem with the simulation (currently only if attempting to simulate for a site class we don't have a model for)

RateCategory.RateException - if a rate category uses the FitzJohn method at the root as this method requires likelihoods to calculate the frequency and we don't have the likelihoods when simulating.

getAlignment

public Alignment getAlignment(int length,
                     boolean internal)
                       throws AlignmentException,
                              Simulate.SimulationException,
                              RateCategory.RateException

Gets a simulated alignment

Parameters:

length - The length of the alignment

internal - Whether to return the state of the internal nodes

Returns:

The simulated alignment

Throws:

AlignmentException - Thrown if there is a problem with the alignment

Simulate.SimulationException - Thrown if there is a problem with the simulation (currently only if attempting to simulate for a site class we don't have a model for)

RateCategory.RateException - if a rate category uses the FitzJohn method at the root as this method requires likelihoods to calculate the frequency and we don't have the likelihoods when simulating.

getAlignment

public Alignment getAlignment(int length,
                     java.util.Map<java.lang.String,java.lang.String> recode)
                       throws AlignmentException,
                              Simulate.SimulationException,
                              RateCategory.RateException

Gets a simulated alignment, not returning the state of internal nodes. Recodes the simulated data before returning. For example if both "A" and "B" are unobserved states representing an observed state of "0" then this can be used to change "A" and "B" to zero. This is necessary as the simulator generates unobserved states by default. The returned site will have ambiguous data set as appropriate.

Parameters:

length - The length of the alignment

recode - Map of recodings

Returns:

The simulated alignment

Throws:

AlignmentException - Thrown if there is a problem with the alignment

Simulate.SimulationException - Thrown if there is a problem with the simulation (currently only if attempting to simulate for a site class we don't have a model for)

RateCategory.RateException - if a rate category uses the FitzJohn method at the root as this method requires likelihoods to calculate the frequency and we don't have the likelihoods when simulating.

getAlignment

public Alignment getAlignment(int length,
                     boolean internal,
                     java.util.Map<java.lang.String,java.lang.String> recode)
                       throws AlignmentException,
                              Simulate.SimulationException,
                              RateCategory.RateException

Gets a simulated alignment. Recodes the simulated data before returning. For example if both "A" and "B" are unobserved states representing an observed state of "0" then this can be used to change "A" and "B" to zero. This is necessary as the simulator generates unobserved states by default. The returned site will have ambiguous data set as appropriate.

Parameters:

length - The length of the alignment

internal - Whether to return the state of the internal nodes

recode - Map of recodings

Returns:

The simulated alignment

Throws:

AlignmentException - Thrown if there is a problem with the alignment

Simulate.SimulationException - Thrown if there is a problem with the simulation (currently only if attempting to simulate for a site class we don't have a model for)

RateCategory.RateException - if a rate category uses the FitzJohn method at the root as this method requires likelihoods to calculate the frequency and we don't have the likelihoods when simulating.

getAlignment

public Alignment getAlignment(java.util.List<java.lang.String> siteClasses)
                       throws AlignmentException,
                              Simulate.SimulationException,
                              RateCategory.RateException

Gets a simulated alignment, not returning the state of the internal nodes. The simulated alignment will be the same length as siteClasses and each site will have been simulated according to the corresponding class in siteClasses.

Parameters:

siteClasses - List of site classes used to generate the alignment

Returns:

The simulated alignment

Throws:

AlignmentException - Thrown if there is a problem with the alignment

Simulate.SimulationException - Thrown if there is a problem with the simulation (currently only if attempting to simulate for a site class we don't have a model for)

RateCategory.RateException - if a rate category uses the FitzJohn method at the root as this method requires likelihoods to calculate the frequency and we don't have the likelihoods when simulating.

getAlignment

public Alignment getAlignment(java.util.List<java.lang.String> siteClasses,
                     boolean internal)
                       throws AlignmentException,
                              Simulate.SimulationException,
                              RateCategory.RateException

Gets a simulated alignment. The simulated alignment will be the same length as siteClasses and each site will have been simulated according to the corresponding class in siteClasses.

Parameters:

siteClasses - List of site classes used to generate the alignment

internal - Whether to return the state of the internal nodes

Returns:

The simulated alignment

Throws:

AlignmentException - Thrown if there is a problem with the alignment

Simulate.SimulationException - Thrown if there is a problem with the simulation (currently only if attempting to simulate for a site class we don't have a model for)

RateCategory.RateException - if a rate category uses the FitzJohn method at the root as this method requires likelihoods to calculate the frequency and we don't have the likelihoods when simulating.

getAlignment

public Alignment getAlignment(java.util.List<java.lang.String> siteClasses,
                     java.util.Map<java.lang.String,java.lang.String> recode)
                       throws AlignmentException,
                              Simulate.SimulationException,
                              RateCategory.RateException

Gets a simulated alignment, not returning the state of the internal nodes. The simulated alignment will be the same length as siteClasses and each site will have been simulated according to the corresponding class in siteClasses. Recodes the simulated data before returning. For example if both "A" and "B" are unobserved states representing an observed state of "0" then this can be used to change "A" and "B" to zero. This is necessary as the simulator generates unobserved states by default. The returned site will have ambiguous data set as appropriate.

Parameters:

siteClasses - List of site classes used to generate the alignment

recode - Map of recodings

Returns:

The simulated alignment

Throws:

AlignmentException - Thrown if there is a problem with the alignment

Simulate.SimulationException - Thrown if there is a problem with the simulation (currently only if attempting to simulate for a site class we don't have a model for)

RateCategory.RateException - if a rate category uses the FitzJohn method at the root as this method requires likelihoods to calculate the frequency and we don't have the likelihoods when simulating.

getAlignment

public Alignment getAlignment(java.util.List<java.lang.String> siteClasses,
                     boolean internal,
                     java.util.Map<java.lang.String,java.lang.String> recode)
                       throws AlignmentException,
                              Simulate.SimulationException,
                              RateCategory.RateException

Gets a simulated alignment. The simulated alignment will be the same length as siteClasses and each site will have been simulated according to the corresponding class in siteClasses. Recodes the simulated data before returning. For example if both "A" and "B" are unobserved states representing an observed state of "0" then this can be used to change "A" and "B" to zero. This is necessary as the simulator generates unobserved states by default. The returned site will have ambiguous data set as appropriate.

Parameters:

siteClasses - List of site classes used to generate the alignment

internal - Whether to return the state of the internal nodes

recode - Map of recodings

Returns:

The simulated alignment

Throws:

AlignmentException - Thrown if there is a problem with the alignment

Simulate.SimulationException - Thrown if there is a problem with the simulation (currently only if attempting to simulate for a site class we don't have a model for)

RateCategory.RateException - if a rate category uses the FitzJohn method at the root as this method requires likelihoods to calculate the frequency and we don't have the likelihoods when simulating.

setSeed

public void setSeed(long seed)

Seeds the random number generator with the give seed. Useful for testing or in the rare cases where repeatable results are required.

Parameters:

seed - The seed to be used