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# *
# * Authors: Carlos Oscar Sorzano (info@kinestat.com)
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# * Kinestat Pharma
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import pyworkflow.protocol.params as params
from .protocol_pkpd_ode_base import ProtPKPDODEBase
from pkpd.models.pk_models import PK_Threecompartments
# TESTED in test_workflow_gabrielsson_pk08.py
[docs]class ProtPKPDThreeCompartments(ProtPKPDODEBase):
""" Fit a three-compartments model to a set of measurements (any arbitrary dosing regimen is allowed)\n
The central compartment is referred to as C, while the peripheral compartments as Cpa and Cpb.
A and B peripheral compartments are both connected to the central compartment.
The differential equation is V dC/dt = -(Cl+Clpa+Clpb) * C + Clpa * Cpa + Clpb * Cpb + dD/dt, Vpa dCpa/dt = Clpa * C - Clpa * Cpa\n
Vpb dCpb/dt = Clpb * C - Clpb * Cpb\n
where C is the concentration of the central compartment, Cl the clearance, V and Vpa, Vpb the distribution volume of the central and peripheral compartments,
Clpa and Clpb are the distribution rates between the central and the peripheral compartments, and D the input dosing regime.
Confidence intervals calculated by this fitting may be pessimistic because it assumes that all model parameters
are independent, which are not. Use Bootstrap estimates instead.\n
Protocol created by http://www.kinestatpharma.com\n"""
_label = 'pk three-compartments'
def __init__(self,**kwargs):
ProtPKPDODEBase.__init__(self,**kwargs)
#--------------------------- DEFINE param functions --------------------------------------------
def _defineParams(self, form):
self._defineParams1(form, True, "t", "Cp")
form.addParam('bounds', params.StringParam, label="Parameter bounds ([tlag], sourceParameters, Cl, V, Clpa, Vpa, Clpb, Vpb)", default="",
help="Bounds for time delay, central clearance and volume and peripheral clearance and volume. "\
'Make sure that the bounds are expressed in the expected units (estimated from the sample itself).'\
'Be careful that Cl bounds must be given here. If you have an estimate of the elimination rate, this is Ke=Cl/V. Consequently, Cl=Ke*V ')
[docs] def createModel(self):
return PK_Threecompartments()