com.rubecula.darwin.domain.genetics
Class Mortality_

java.lang.Object
  net.sf.tostring0.AToString
      com.rubecula.darwin.domain.genetics.Mortality_

All Implemented Interfaces:

Mortality, net.sf.tostring0.IToString

Direct Known Subclasses:

Mortality_Reaper, Mortality_TS

public abstract class Mortality_
extends net.sf.tostring0.AToString
implements Mortality

Abstract class which defines the base methods and fields needed to implement the Mortality interface.

Author:

Robin Hillyard

Field Summary

protected static org.apache.commons.logging.Log

LOG The logger for this class.

Fields inherited from interface net.sf.tostring0.IToString

ANGBR_OPEN, ANGBRA_CLSE, BRA_CLSE, BRA_OPEN, BRCE_OPEN, BRCS_CLSE, COLON, LIST_SEPARATOR, MAX_ELEMENTS_DEFAULT, S_MT, S_PERCENT, SEPARATOR, SPACE

Constructor Summary

protected

Mortality_(org.apache.commons.math.random.RandomGenerator random) Protected primary constructor.

Method Summary

protected double	calculateAgeViabilityFactor(int age) Subclasses where viability depends on age must override this method.
double	calculateMortality(int age, double fitness, double saturation) Method to calculate the mortality for an organism as 1 less the simple value of calculateViability(int, double, double), given the age, fitness and saturation.
protected double	calculateViability(int age, double fitness, double saturation)
boolean	equals(java.lang.Object obj)
protected double	getBias()
protected org.apache.commons.math.random.RandomGenerator	getRandom()
int	hashCode()
boolean	isMarked(double mortality)
void	setBias(double bias) Set the value of bias.

Methods inherited from class net.sf.tostring0.AToString

toString, toString, toStringBrief, toStringId

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

LOG

protected static final org.apache.commons.logging.Log LOG

The logger for this class.

Constructor Detail

Mortality_

protected Mortality_(org.apache.commons.math.random.RandomGenerator random)

Protected primary constructor.

Parameters:

random - a random number generator

Method Detail

calculateMortality

public double calculateMortality(int age,
                                 double fitness,
                                 double saturation)

Method to calculate the mortality for an organism as 1 less the simple value of calculateViability(int, double, double), given the age, fitness and saturation. The viability factor (VF) = (1-IM) if age=0 where IM is the infant mortality (20%, by default) otherwise, VF = (1-AF)^(age+1) where AF is the actuarial factor (10%, by default). The sustainabilityIndex (SI) = 1 if saturation less than 1; else SI = (1 - saturation)^2.

Specified by:

calculateMortality in interface Mortality

Parameters:

age - the age of the organism in generations.

fitness - the fitness of the organism for an environment.

saturation - a measure of the current population saturation (1 corresponds to the ideal population supportable by the environment.

Returns:

the probability of death before the next generation (between 0 and 1). TODO consider inlining this into isMarked (ie. pass in age, fitness, saturation, and return boolean)

See Also:

Mortality.calculateMortality(int,double,double)

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

See Also:

Object.equals(java.lang.Object)

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

See Also:

Object.hashCode()

isMarked

public boolean isMarked(double mortality)

Specified by:

isMarked in interface Mortality

Parameters:

mortality - the probability that an organism will die before the next generation (a value between 0 and 1).

Returns:

true if that organism is actually marked for death (i.e. if the mortality value exceeds the current bias, perturbed by a random variation)

setBias

public void setBias(double bias)

Set the value of bias. Typically set by dependency injection.

Parameters:

bias - a value between 0 and 1. If 0 then most organisms will probably die, while if 1 then few organisms are likely to die.

calculateAgeViabilityFactor

protected double calculateAgeViabilityFactor(int age)

Subclasses where viability depends on age must override this method. TEST

Parameters:

age -

Returns:

1.0, that is to say mortality depends only on fitness and saturation -- not age.

calculateViability

protected double calculateViability(int age,
                                    double fitness,
                                    double saturation)

Parameters:

age -

fitness -

saturation -

Returns:

the viability, between 0 and 1

getBias

protected double getBias()

getRandom

protected org.apache.commons.math.random.RandomGenerator getRandom()

Returns:

the random number generator