|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--pal.tree.ParameterizedTree | +--pal.tree.MutationRateModelTree
Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node). Any mutation rate model can be used.
MutationRateModel
, Serialized FormFields inherited from interface pal.misc.Units |
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, YEARS |
Constructor Summary | |
MutationRateModelTree(Tree t,
TimeOrderCharacterData tocd,
MutationRateModel model)
take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node). |
Method Summary | |
double |
getDefaultValue(int n)
get default value of parameter |
double |
getLnL()
|
double |
getLowerLimit(int n)
Returns lower limit of parameter estimate. |
MutationRateModel |
getMutationRateModel()
returns mu |
int |
getNumParameters()
get number of parameters |
double |
getParameter(int n)
get model parameter |
double |
getUpperLimit(int n)
get upper parameter limit |
protected void |
heights2parameters()
|
protected void |
parameters2Heights()
|
void |
setLnL(double lnL)
|
void |
setParameter(double param,
int n)
set model parameter |
void |
setParameterSE(double paramSE,
int n)
set standard errors for model parameter |
Methods inherited from class pal.tree.ParameterizedTree |
createNodeList, getAttribute, getBaseTree, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setBaseTree, setRoot, setUnits, toString |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
public MutationRateModelTree(Tree t, TimeOrderCharacterData tocd, MutationRateModel model) throws java.lang.RuntimeException
This parameterisation of a clock-tree, ensuring that all parameters are independent of each other is due to Andrew Rambaut (personal communication).
Method Detail |
public int getNumParameters()
Parameterized
pal.misc.Parameterized
public void setParameter(double param, int n)
Parameterized
pal.misc.Parameterized
param
- parameter valuen
- parameter numberpublic double getParameter(int n)
Parameterized
pal.misc.Parameterized
n
- parameter numberpublic double getLowerLimit(int n)
pal.misc.Parameterized
n
- parameter numberpublic double getDefaultValue(int n)
Parameterized
pal.misc.Parameterized
n
- parameter numberpublic void setParameterSE(double paramSE, int n)
Parameterized
pal.misc.Parameterized
paramSE
- standard error of parameter valuen
- parameter numberpublic double getUpperLimit(int n)
Parameterized
pal.misc.Parameterized
n
- parameter numberpublic MutationRateModel getMutationRateModel()
protected void parameters2Heights()
protected void heights2parameters()
public void setLnL(double lnL)
public double getLnL()
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |