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java.lang.Object | +--pal.tree.ParameterizedTree | +--pal.tree.DatedTipsClockTree
provides parameter interface to a clock tree with dated tips, following A. Rambaut. 2000. Bioinformatics 16:395-399. (parameters are the minimal node height differences at each internal node and the evolutionary rate)
Field Summary | |
static int |
NO_PARAMETRIZE
|
static int |
PARAMETERIZE_WITH_DEFAULTS
|
static int |
PARAMETERIZE_WITH_GIVEN
|
Fields inherited from interface pal.misc.Units |
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, YEARS |
Constructor Summary | |
DatedTipsClockTree(Tree t)
Constructor without TimeOrderCharacterData. |
|
DatedTipsClockTree(Tree t,
ParameterizedDouble rate,
TimeOrderCharacterData tocd,
int internalHeightMode,
int rateMode)
take any tree and afford it with an interface suitable for a clock-like tree with dated tips (parameters are the minimal node height differences at each internal node and the rate). |
|
DatedTipsClockTree(Tree t,
TimeOrderCharacterData tocd,
boolean useDefaultParameters)
take any tree and afford it with an interface suitable for a clock-like tree with dated tips (parameters are the minimal node height differences at each internal node and the rate). |
Method Summary | |
double |
getDefaultValue(int n)
get default value of parameter |
double |
getLowerLimit(int n)
get lower parameter limit |
double |
getMaxRate()
find max. rate (for setRate) allowed by current node heights |
int |
getNumParameters()
get number of parameters |
double |
getParameter(int n)
get model parameter |
double |
getParameterSE(int n)
return standard error of parameter |
double |
getRate()
get rate |
TimeOrderCharacterData |
getTimeOrderCharacterData()
Gets the TimeOrderCharacterData |
double |
getUpperLimit(int n)
get upper parameter limit |
void |
parameterChanged(ParameterEvent pe)
The rate was changed externally |
void |
setParameter(double param,
int n)
set model parameter |
void |
setParameterSE(double paramSE,
int n)
set standard errors for model parameter |
void |
setRate(double r)
set rate (and thus node heights and branch lengths of leaves) without changing all other node heights and branch lengths |
void |
setRateSE(double rSE)
set rate SE |
void |
update()
make parameters consistent with branch lengths and rate 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 |
Field Detail |
public static final int PARAMETERIZE_WITH_DEFAULTS
public static final int PARAMETERIZE_WITH_GIVEN
public static final int NO_PARAMETRIZE
Constructor Detail |
public DatedTipsClockTree(Tree t)
public DatedTipsClockTree(Tree t, TimeOrderCharacterData tocd, boolean useDefaultParameters)
This parameterisation of a clock-tree, ensuring that all parameters are independent of each other is due to Andrew Rambaut (personal communication).
public DatedTipsClockTree(Tree t, ParameterizedDouble rate, TimeOrderCharacterData tocd, int internalHeightMode, int rateMode)
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 void parameterChanged(ParameterEvent pe)
parameterChanged
in interface ExternalParameterListener
public void update()
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 void setParameterSE(double paramSE, int n)
Parameterized
pal.misc.Parameterized
paramSE
- standard error of parameter valuen
- parameter numberpublic double getParameterSE(int n)
public double getLowerLimit(int n)
Parameterized
pal.misc.Parameterized
n
- parameter numberpublic double getUpperLimit(int n)
Parameterized
pal.misc.Parameterized
n
- parameter numberpublic double getDefaultValue(int n)
Parameterized
pal.misc.Parameterized
n
- parameter numberpublic void setRate(double r)
public double getRate()
public void setRateSE(double rSE)
public double getMaxRate()
public TimeOrderCharacterData getTimeOrderCharacterData()
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