Package | Description |
---|---|
pal.coalescent |
Classes to model population genetic processes using the coalescent.
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pal.mep |
Classes for the analysis of "measurably evolving populations" (mep).
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pal.misc |
Classes that don't fit elsewhere ;^)
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Modifier and Type | Class | Description |
---|---|---|
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 |
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).
|
Modifier and Type | Class | Description |
---|---|---|
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.
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class |
SteppedMutationRate |
This class models a step-wise mutation rate.
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class |
WindowedMutationRate |
This class models a windowed mutation rate
(parameter: mu = mutation rate).
|
Modifier and Type | Class | Description |
---|---|---|
class |
SimpleSummarizable |
Constructor | Description |
---|---|
SimpleSummarizable(Summarizable toImitate) |
The Imitation constructor - for immitating another Summarizable object with
minimum memory requirements
|