Source code for pkpd.protocols.protocol_pkpd_twocompartments_both_pd

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import pyworkflow.protocol.params as params
from .protocol_pkpd_ode_base import ProtPKPDODEBase
from pkpd.models.pk_models import PK_TwocompartmentsBothPD

[docs]class ProtPKPDTwoCompartmentsBothPD(ProtPKPDODEBase): """ Fit a mono-compartment model to a set of plasma and effect measurements (any arbitrary dosing regimen is allowed)\n The differential equation is dC/dt = -Cl * C/V -Clp *(C-Cp)/V + 1/V * dD/dt, dCp/dt=Cl*C/Vp+Clp*(C-Cp)/Vp and E=E0+a*C^b/(Cm^b+C^b)\n where C is the concentration, Cl the total clearance (metabolic and excretion), V the distribution volume, Clp is the Clearance \n to the peripheric compartment, Vp is the volume of the peripheric compartment, and D the input dosing regime. E is the measured effect, E0 a baseline effect, a and b fitting constants and Cm the biophase concentration at which\n half the maximum effect is attained. This protocol assumes that you have measures of both the central and peripheral compartments. 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\n""" _label = 'two-compartments both pd' #--------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): self._defineParams1(form) form.addParam('predictor', params.StringParam, label="Time variable", default="t") form.addParam('predicted', params.StringParam, label="Plasma concentration", default="Cp") form.addParam('Cperipheral', params.StringParam, label="Peripheral concentration", default="Cper") form.addParam('E', params.StringParam, label="Effect", default="E") form.addParam('bounds', params.StringParam, label="Parameter bounds ([tlag], Cl, V, E0, a, b, Cm)", default="", help="Bounds for the tlag (if it must be estimated), clearance, volume, and effect constants."\ 'Make sure that the bounds are expressed in the expected units (estimated from the sample itself).'\ 'If tlag must be estimated, its bounds must always be specified')
[docs] def getXYvars(self): self.varNameX=self.predictor.get() self.varNameY=[self.predicted.get(),self.Cperipheral.get(),self.E.get()]
[docs] def createModel(self): return PK_TwocompartmentsBothPD()