Пример #1
0
    def test_hard(self):
        # the SLIARD model is considered to be hard because a state can
        # go to multiple state.  This is not as hard as the SEIHFR model
        # below.
        stateList = ['S', 'L', 'I', 'A', 'R', 'D']
        paramList = [
            'beta', 'p', 'kappa', 'alpha', 'f', 'delta', 'epsilon', 'N'
        ]
        odeList = [
            Transition('S', '- beta * S/N * ( I + delta * A)', 'ODE'),
            Transition('L', 'beta * S/N * (I + delta * A) - kappa * L', 'ODE'),
            Transition('I', 'p * kappa * L - alpha * I', 'ODE'),
            Transition('A', '(1-p) * kappa * L - epsilon * A', 'ODE'),
            Transition('R', 'f * alpha * I + epsilon * A', 'ODE'),
            Transition('D', '(1-f) * alpha * I', 'ODE')
        ]

        ode = SimulateOdeModel(stateList, paramList, odeList=odeList)

        ode2 = ode.returnObjWithTransitionsAndBD()
        diffEqZero = map(lambda x: x == 0,
                         sympy.simplify(ode.getOde() - ode2.getOde()))

        if numpy.any(numpy.array(list(diffEqZero)) == False):
            raise Exception("Hard: SLIARD Decomposition failed")
    def test_simple(self):
        ode1 = Transition('S','-beta*S*I', 'ode')
        ode2 = Transition('I','beta*S*I - gamma * I', 'ode')
        ode3 = Transition('R','gamma*I', 'ode')
        stateList = ['S','I','R']
        paramList = ['beta','gamma']
        ode = SimulateOdeModel(stateList, paramList, odeList=[ode1,ode2,ode3])

        ode2 = ode.returnObjWithTransitionsAndBD()
        diffEqZero = map(lambda x: x==0, sympy.simplify(ode.getOde() - ode2.getOde()))

        if numpy.any(numpy.array(diffEqZero) == False):
            raise Exception("Simple: SIR Decomposition failed")
Пример #3
0
    def test_simple(self):
        ode1 = Transition('S', '-beta*S*I', 'ode')
        ode2 = Transition('I', 'beta*S*I - gamma * I', 'ode')
        ode3 = Transition('R', 'gamma*I', 'ode')
        stateList = ['S', 'I', 'R']
        paramList = ['beta', 'gamma']
        ode = SimulateOdeModel(stateList,
                               paramList,
                               odeList=[ode1, ode2, ode3])

        ode2 = ode.returnObjWithTransitionsAndBD()
        diffEqZero = map(lambda x: x == 0,
                         sympy.simplify(ode.getOde() - ode2.getOde()))

        if numpy.any(numpy.array(list(diffEqZero)) == False):
            raise Exception("Simple: SIR Decomposition failed")
Пример #4
0
    def test_derived_param(self):
        # the derived parameters are treated separately when compared to the
        # normal parameters and the odes
        ode = common_models.Legrand_Ebola_SEIHFR()

        odeList = [
            Transition(
                'S',
                '-(beta_I * S * I + beta_H_Time * S * H + beta_F_Time * S * F)'
            ),
            Transition(
                'E',
                '(beta_I * S * I + beta_H_Time * S * H + beta_F_Time * S * F)-alpha * E'
            ),
            Transition(
                'I',
                '-gamma_I * (1 - theta_1) * (1 - delta_1) * I - gamma_D * (1 - theta_1) * delta_1 * I - gamma_H * theta_1 * I + alpha * E'
            ),
            Transition(
                'H',
                'gamma_H * theta_1 * I - gamma_DH * delta_2 * H - gamma_IH * (1 - delta_2) * H'
            ),
            Transition(
                'F',
                '- gamma_F * F + gamma_DH * delta_2 * H + gamma_D * (1 - theta_1) * delta_1 * I'
            ),
            Transition(
                'R',
                'gamma_I * (1 - theta_1) * (1 - delta_1) * I + gamma_F * F + gamma_IH * (1 - delta_2) * H'
            ),
            Transition('tau', '1')
        ]

        ode1 = SimulateOdeModel(ode._stateList,
                                ode._paramList,
                                ode._derivedParamEqn,
                                odeList=odeList)

        ode2 = ode1.returnObjWithTransitionsAndBD()
        diffEqZero = map(lambda x: x == 0,
                         sympy.simplify(ode.getOde() - ode2.getOde()))

        if numpy.any(numpy.array(list(diffEqZero)) == False):
            raise Exception("FAILED!")
    def test_derived_param(self):
        # the derived parameters are treated separately when compared to the
        # normal parametes and the odes
        ode = common_models.Legrand_Ebola_SEIHFR()

        odeList = [
            Transition('S', '-(beta_I * S * I + beta_H_Time * S * H + beta_F_Time * S * F)'),
            Transition('E', '(beta_I * S * I + beta_H_Time * S * H + beta_F_Time * S * F)-alpha * E'),
            Transition('I','-gamma_I * (1 - theta_1) * (1 - delta_1) * I - gamma_D * (1 - theta_1) * delta_1 * I - gamma_H * theta_1 * I + alpha * E'),
            Transition('H', 'gamma_H * theta_1 * I - gamma_DH * delta_2 * H - gamma_IH * (1 - delta_2) * H'),
            Transition('F','- gamma_F * F + gamma_DH * delta_2 * H + gamma_D * (1 - theta_1) * delta_1 * I'),
            Transition('R', 'gamma_I * (1 - theta_1) * (1 - delta_1) * I + gamma_F * F + gamma_IH * (1 - delta_2) * H'),
            Transition('tau', '1')
        ]

        ode1 = SimulateOdeModel(ode._stateList, ode._paramList, ode._derivedParamEqn, odeList=odeList)

        ode2 = ode1.returnObjWithTransitionsAndBD()
        diffEqZero = map(lambda x: x==0, sympy.simplify(ode.getOde() - ode2.getOde()))
        
        if numpy.any(numpy.array(diffEqZero) == False):
            raise Exception("FAILED!")
    def test_hard(self):
        # the SLIARD model is considered to be hard because a state can
        # go to multiple state.  This is not as hard as the SEIHFR model
        # below.
        stateList = ['S', 'L','I','A','R','D']
        paramList = ['beta','p','kappa','alpha','f','delta','epsilon', 'N']
        odeList = [
            Transition('S', '- beta * S/N * ( I + delta * A)', 'ODE'),
            Transition('L', 'beta * S/N * (I + delta * A) - kappa * L', 'ODE'),
            Transition('I', 'p * kappa * L - alpha * I', 'ODE'),
            Transition('A', '(1-p) * kappa * L - epsilon * A', 'ODE'),
            Transition('R', 'f * alpha * I + epsilon * A', 'ODE'),
            Transition('D', '(1-f) * alpha * I', 'ODE') 
            ]

        ode = SimulateOdeModel(stateList, paramList, odeList=odeList)

        ode2 = ode.returnObjWithTransitionsAndBD()
        diffEqZero = map(lambda x: x==0, sympy.simplify(ode.getOde() - ode2.getOde()))

        if numpy.any(numpy.array(diffEqZero) == False):
            raise Exception("Hard: SLIARD Decomposition failed")
    def test_bd(self):
        stateList = ['S', 'I', 'R']
        paramList = ['beta', 'gamma', 'B', 'mu']
        odeList = [
            Transition(origState='S', 
                       equation='-beta * S * I + B - mu * S',
                       transitionType=TransitionType.ODE),
            Transition(origState='I', 
                       equation='beta * S * I - gamma * I - mu * I',
                       transitionType=TransitionType.ODE),
            Transition(origState='R', 
                       destState='R', 
                       equation='gamma * I',
                       transitionType=TransitionType.ODE)
            ]

        ode = SimulateOdeModel(stateList, paramList, odeList=odeList)

        ode2 = ode.returnObjWithTransitionsAndBD()
        diffEqZero = map(lambda x: x==0, sympy.simplify(ode.getOde() - ode2.getOde()))

        if numpy.any(numpy.array(diffEqZero) == False):
            raise Exception("Birth Death: SIR+BD Decomposition failed")
Пример #8
0
    def test_bd(self):
        stateList = ['S', 'I', 'R']
        paramList = ['beta', 'gamma', 'B', 'mu']
        odeList = [
            Transition(origState='S',
                       equation='-beta * S * I + B - mu * S',
                       transitionType=TransitionType.ODE),
            Transition(origState='I',
                       equation='beta * S * I - gamma * I - mu * I',
                       transitionType=TransitionType.ODE),
            Transition(origState='R',
                       destState='R',
                       equation='gamma * I',
                       transitionType=TransitionType.ODE)
        ]

        ode = SimulateOdeModel(stateList, paramList, odeList=odeList)

        ode2 = ode.returnObjWithTransitionsAndBD()
        diffEqZero = map(lambda x: x == 0,
                         sympy.simplify(ode.getOde() - ode2.getOde()))

        if numpy.any(numpy.array(list(diffEqZero)) == False):
            raise Exception("Birth Death: SIR+BD Decomposition failed")