CompartmentalSystem#

class pharmpy.model.CompartmentalSystem(builder, t=t)[source]#

Bases: Statement

System of ODEs descibed as a compartmental system

Examples

>>> from pharmpy.model import Bolus, Compartment, output
>>> from pharmpy.model import CompartmentalSystemBuilder, CompartmentalSystem
>>> cb = CompartmentalSystemBuilder()
>>> dose = Bolus.create("AMT")
>>> central = Compartment.create("CENTRAL", doses=(dose,))
>>> cb.add_compartment(central)
>>> peripheral = Compartment.create("PERIPHERAL")
>>> cb.add_compartment(peripheral)
>>> cb.add_flow(central, peripheral, "K12")
>>> cb.add_flow(peripheral, central, "K21")
>>> cb.add_flow(central, output, "CL / V")
>>> CompartmentalSystem(cb)        
Bolus(AMT)
                 ┌──────────┐
                 │PERIPHERAL│
                 └──────────┘
                  ↑        │
                 K12      K21
                  │        ↓
┌───────┐      ┌──────────┐      ┌──────────┐
│CENTRAL│──K12→│PERIPHERAL│──K21→│ CENTRAL  │──CL/V→
└───────┘      └──────────┘      └──────────┘

Attributes Summary

`amounts`	Column vector of amounts for all compartments
`central_compartment`	The central compartment
`compartment_names`	Names of all compartments
`compartmental_matrix`	Compartmental matrix of the compartmental system
`dosing_compartments`	The dosing compartment(s)
`eqs`	Tuple of equations
`free_symbols`	Get set of all free symbols in the compartmental system
`rhs_symbols`	Get set of all free symbols in the right hand side expressions
`t`	Independent variable of CompartmentalSystem
`zero_order_inputs`	Vector of all zero order inputs to each compartment

Methods Summary

`create`(builder[, t])
`find_compartment`(name)	Find a compartment using its name
`find_compartment_or_raise`(comp)
`find_depot`(statements)	Find the depot compartment
`find_peripheral_compartments`([name])	Find perihperal compartments
`find_transit_compartments`(statements)	Find all transit compartments
`from_dict`(d)
`get_bidirectionals`(compartment)	Get list of all compartments with bidirectional flow from/to a compartment
`get_compartment_inflows`(compartment)	Get list of all flows going in to a compartment
`get_compartment_outflows`(compartment)	Get list of all flows going out from a compartment
`get_flow`(source, destination)	Get the rate of flow between two compartments
`get_n_connected`(comp)	Get the number of compartments connected to a compartment
`replace`(**kwargs)
`subs`(substitutions)	Substitute expressions or symbols in ODE system
`to_dict`()

Attributes Documentation

amounts#

Column vector of amounts for all compartments

Examples

>>> from pharmpy.modeling import load_example_model
>>> import sympy
>>> model = load_example_model("pheno")
>>> sympy.pprint(model.statements.ode_system.amounts)
[A_CENTRAL(t)]

central_compartment#

The central compartment

The central compartment is defined to be the compartment that has an outward flow to the output compartment. Only one central compartment is supported.

Returns:: Compartment – Central compartment

Examples

>>> from pharmpy.modeling import load_example_model
>>> model = load_example_model("pheno")
>>> model.statements.ode_system.central_compartment
Compartment(CENTRAL, amount=A_CENTRAL(t), doses=Bolus(AMT, admid=1))

compartment_names#

Names of all compartments

Examples

>>> from pharmpy.modeling import load_example_model
>>> model = load_example_model("pheno")
>>> model.statements.ode_system.compartment_names
['CENTRAL']

compartmental_matrix#

Compartmental matrix of the compartmental system

Examples

>>> from pharmpy.modeling import load_example_model, set_first_order_absorption
>>> model = load_example_model("pheno")
>>> model.statements.ode_system.compartmental_matrix
⎡-CL ⎤
⎢────⎥
⎣ V  ⎦

dosing_compartments#

The dosing compartment(s)

A dosing compartment is a compartment that receives an input dose. Multiple dose compartments are supported. The order of dose compartments is defined to put the central compartment last.

Returns:: tuple – A tuple of dose compartments

Examples

>>> from pharmpy.modeling import load_example_model
>>> model = load_example_model("pheno")
>>> model.statements.ode_system.dosing_compartments
(Compartment(CENTRAL, amount=A_CENTRAL(t), doses=Bolus(AMT, admid=1)),)

eqs#: Tuple of equations

free_symbols#

Get set of all free symbols in the compartmental system

Returns:: set – Set of symbols

Examples

>>> from pharmpy.modeling import load_example_model
>>> model = load_example_model("pheno")
>>> model.statements.ode_system.free_symbols  
{AMT, CL, V, t}

rhs_symbols#

Get set of all free symbols in the right hand side expressions

Returns:: set – Set of symbols

Examples

>>> from pharmpy.modeling import load_example_model
>>> model = load_example_model("pheno")
>>> model.statements.ode_system.rhs_symbols   
{AMT, CL, V, t}

t#: Independent variable of CompartmentalSystem

zero_order_inputs#

Vector of all zero order inputs to each compartment

Example

>>> from pharmpy.modeling import load_example_model, set_zero_order_absorption
>>> model = load_example_model("pheno")
>>> model.statements.ode_system.zero_order_inputs
[0]

Methods Documentation

classmethod create(builder, t=t)[source]#

find_compartment(name)[source]#

Find a compartment using its name

Parameters:: name (str) – Name of compartment to find
Returns:: Compartment – Compartment named name or None if not found

Examples

>>> from pharmpy.modeling import load_example_model
>>> model = load_example_model("pheno")
>>> central = model.statements.ode_system.find_compartment("CENTRAL")
>>> central
Compartment(CENTRAL, amount=A_CENTRAL(t), doses=Bolus(AMT, admid=1))

find_compartment_or_raise(comp)[source]#

find_depot(statements)[source]#

Find the depot compartment

The depot compartment is defined to be the compartment that only has out flow to the central compartment, but no flow from the central compartment.

For drug metabolite models however, it is possible to have outflow with unidirectional flow to both the central and metabolite compartment. In this case, the central compartment is found based on name.

Returns:: Compartment – Depot compartment

Examples

>>> from pharmpy.modeling import load_example_model, set_first_order_absorption
>>> model = load_example_model("pheno")
>>> model = set_first_order_absorption(model)
>>> model.statements.ode_system.find_depot(model.statements)
Compartment(DEPOT, amount=A_DEPOT(t), doses=Bolus(AMT, admid=1))

find_peripheral_compartments(name=None)[source]#

Find perihperal compartments

A peripheral compartment is defined as having one flow to the central compartment and one flow from the central compartment.

If name is set, peripheral compartments connected to the compartment with the associated name is returned.

Returns:: list of compartments – Peripheral compartments

Examples

>>> from pharmpy.modeling import load_example_model
>>> model = load_example_model("pheno")
>>> model.statements.ode_system.find_peripheral_compartments()
[]

find_transit_compartments(statements)[source]#

Find all transit compartments

Transit compartments are a chain of compartments with the same out rate starting from the dose compartment. Because one single transit compartment cannot be distinguished from one depot compartment such compartment will be defined to be a depot and not a transit compartment.

Returns:: list of compartments – Transit compartments

Examples

>>> from pharmpy.modeling import load_example_model
>>> model = load_example_model("pheno")
>>> model.statements.ode_system.find_transit_compartments(model.statements)
[]

classmethod from_dict(d)[source]#

get_bidirectionals(compartment)[source]#

Get list of all compartments with bidirectional flow from/to a compartment

Parameters:: compartment (Compartment or str) – Compartment of interest
Returns:: list – Compartments with bidirectional flow

Examples

>>> from pharmpy.modeling import load_example_model
>>> model = load_example_model("pheno")
>>> central = model.statements.ode_system.central_compartment
>>> model.statements.ode_system.get_bidirectionals(central)
[]

get_compartment_inflows(compartment)[source]#

Get list of all flows going in to a compartment

Parameters:: compartment (Compartment or str) – Get inflows to this compartment
Returns:: list – Pairs of compartments and symbolic rates

Examples

>>> from pharmpy.modeling import load_example_model
>>> from pharmpy.model import output
>>> model = load_example_model("pheno")
>>> model.statements.ode_system.get_compartment_inflows(output)
[(Compartment(CENTRAL, amount=A_CENTRAL(t), doses=Bolus(AMT, admid=1)), CL/V)]

get_compartment_outflows(compartment)[source]#

Get list of all flows going out from a compartment

Parameters:: compartment (Compartment or str) – Get outflows for this compartment
Returns:: list – Pairs of compartments and symbolic rates

Examples

>>> from pharmpy.modeling import load_example_model
>>> model = load_example_model("pheno")
>>> model.statements.ode_system.get_compartment_outflows("CENTRAL")
[(Output(), CL/V)]

get_flow(source, destination)[source]#

Get the rate of flow between two compartments

Parameters:

source (Compartment) – Source compartment
destination (Compartment) – Destination compartment

Returns:

Expression – Symbolic rate

Examples

>>> from pharmpy.model import Compartment, CompartmentalSystemBuilder
>>> from pharmpy.model import CompartmentalSystem
>>> cb = CompartmentalSystemBuilder()
>>> depot = Compartment.create("DEPOT")
>>> cb.add_compartment(depot)
>>> central = Compartment.create("CENTRAL")
>>> cb.add_compartment(central)
>>> cb.add_flow(depot, central, "KA")
>>> odes = CompartmentalSystem(cb)
>>> odes.get_flow(depot, central)
KA
>>> odes.get_flow(central, depot)
0

get_n_connected(comp)[source]#

Get the number of compartments connected to a compartment

Parameters:: comp (Compartment) – The compartment
Returns:: int – Number of compartments connected to comp

Examples

>>> from pharmpy.modeling import load_example_model
>>> model = load_example_model("pheno")
>>> model.statements.ode_system.get_n_connected("CENTRAL")
0

replace(**kwargs)[source]#

subs(substitutions)[source]#

Substitute expressions or symbols in ODE system

Examples

>>> from pharmpy.modeling import load_example_model
>>> model = load_example_model("pheno")
>>> model.statements.ode_system.subs({'AMT': 'DOSE'})
Bolus(DOSE, admid=1) → CENTRAL
┌───────┐
│CENTRAL│──CL/V→
└───────┘

to_dict()[source]#