pylag.mortality module

MortalityCalculators can be used to determine whether a living particle lives or dies.

Note

mortality is implemented in Cython. Only a small portion of the API is exposed in Python with accompanying documentation.

class pylag.mortality.FixedTimeMortalityCalculator(config)

Bases: MortalityCalculator

Kill particles once they reach a given age

Three different methods are used to initialise the parameter giving the age at which an individual dies. These are: a) A single fixed value in days, 2) 2) A value in days drawn from a uniform distribution with given limits, and 3) A value in days drawn from a gaussian distribution with given mean and standard deviation.

Parameters

config (ConfigParser) – Configuration object

Variables

• age_of_death_parameter_name (str) – The age of death parameter name.

• initialisation_method (str) – The method used for initialising particle parameters.

• age_of_death (float) – The age at which an individual dies.

• minimum_bound (float) – The minimum bound used for the uniform random number initialisation method.

• maximum_bound (float) – The maximum bound used for the uniform random number initialisation method.

• mean (float) – The mean used for the guassian random number initialisation method.

• standard_deviation (float) – The standard deviation used for the guassian random number initialisation method.

class pylag.mortality.MortalityCalculator

Bases: object

Abstract base class for PyLag mortality calculator

apply_wrapper(self, DataReader data_reader, DTYPE_FLOAT_t time, ParticleSmartPtr particle)

Python friendly wrapper for apply()

The apply() method must be implemented in the derived class.

Parameters

• data_reader (pylag.data_reader.DataReader) – A concrete PyLag data reader which inherits from the base class pylag.data_reader.DataReader.

• time (float) – The time the crossing occurred.

• particle (pylag.particle_cpp_wrapper.ParticleSmartPtr) – A ParticleSmartPtr.

set_initial_particle_properties_wrapper(self, ParticleSmartPtr particle)

Python friendly wrapper for apply()

Parameters

particle (C pointer) – C pointer to a Particle struct

class pylag.mortality.ProbabilisticMortalityCalculator(config)

Bases: MortalityCalculator

Kill individuals randomly given a specified death rate

The probability of an individual dying is:

P_{D} = mu_{D} Delta t

where mu_{D} is the death rate and Delta t is the model time step for biological processes.

Parameters

config (ConfigParser) – Configuration object

Variables

• death_rate_parameter_name (str) – The name of the death rate parameter name.

• test_value (float) – The value against which to test the condition, equal to the death rate multiplied by the time step for biological processes.

pylag.mortality.get_mortality_calculator(config)

Factory method for mortality calculators

Parameters

config (ConfigParser) – PyLag configuraton object

Returns

A mortality calculator

Return type

MortalityCalculator