NutMEG.culture.colony package¶

Submodules¶

class NutMEG.culture.colony.colony.colony(name, collection=[])¶

Bases: object

Class for a colony of base_organism like objects, which monitors its size and structure.

collection¶

List of all active organisms in the colony

inactive¶

List of all inactive organisms in the colony

name¶

Name of the colony, used for output management

base¶

The base organism in the colony, used for general parameters and reproduction.

output¶

Helper attribute for output to terminal and database management.

add_organism(o, n=1)¶

Add an organism or list of organisms o to the colony.

If n is passed, it is the number of random instances of org to generate.

getCHNOPSut()¶: Return the rate of uptake of each CHNOPS element for the whole colony.

get_average_maintenance_fraction()¶: Return the average maintenance fraction of energetic input of the alive population.

get_mass(inactive=False)¶: Return the total mass of the colony. Pass inactive as True to include inactive organisms.

get_population(inactive=False)¶: Return the number of organisms in the colony. Pass inactive as True to include inactive organisms.

get_volume(inactive=False)¶: Return the total volume of the colony. Pass inactive as True to include inactive organisms.

select_timestep(factorup=1.01)¶: Return a timestep which will increase the population factorup times given the current model parameters

take_step(t)¶

Advance the colony by time t.

We calculate the local environment only once to save doing it for every organsim.

class NutMEG.culture.colony.colony_output.colony_output(hostcolony)¶

Bases: object

helper class for managing the output of a colony, either to terminal or to a database.

refreshparams()¶

reset the parameter dictionary to have empty numpy arrays.

Inherit and adjust this method for saved organisms which have specific parameters you want to monitor.