categorical_MARKOV1.xml

<?xml version="1.0" encoding="UTF-8"?>
<PharmML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns="http://www.pharmml.org/pharmml/0.7/PharmML"
    xsi:schemaLocation="http://www.pharmml.org/pharmml/0.7/PharmML http://www.pharmml.org/pharmml/0.7/PharmML"
    xmlns:math="http://www.pharmml.org/pharmml/0.7/Maths"
    xmlns:ct="http://www.pharmml.org/pharmml/0.7/CommonTypes"
    xmlns:ds="http://www.pharmml.org/pharmml/0.7/Dataset"
    xmlns:mstep="http://www.pharmml.org/pharmml/0.7/ModellingSteps"
    implementedBy="MJS" writtenVersion="0.8" id="i1">
    
    <ct:Name>Example 1: Simple Markov Model</ct:Name>
    
    <ct:Description>Simple Markov Model from Sharing Disease Models Paper DRAFT</ct:Description>
    
    <IndependentVariable symbId="t"/>
    
    <!-- SECTION I -->
    <ModelDefinition xmlns="http://www.pharmml.org/pharmml/0.7/ModelDefinition">
        
        <!-- OBSERVATIONS -->
        <ObservationModel blkId="om1">
            <Discrete>
                <CategoricalData>
                    
                    <ListOfCategories> 
                        <Category symbId="Alive"/>
                        <Category symbId="Dead"/>
                    </ListOfCategories>
                    
                    <CategoryVariable symbId="Y"/>

                    <InitialStateVariable symbId="Yinit"/>  <!-- 100 people - see ModellingSteps/SimulationStep -->
                    <PreviousStateVariable symbId="Yp"/>
                    
                    <Dependance type="discreteMarkov"/>
                    
                    <!-- P(Y=Dead|Yp=Alive)=0.05 -->
                    <ProbabilityAssignment>
                        <Probability symbId="p1">
                            <CurrentState>
                                <math:LogicBinop op="eq">
                                    <ct:SymbRef symbIdRef="Y"/>
                                    <ct:SymbRef symbIdRef="Dead"/>
                                </math:LogicBinop>
                            </CurrentState>
                            <PreviousState>
                                <math:LogicBinop op="eq">
                                    <ct:SymbRef symbIdRef="Yp"/>
                                    <ct:SymbRef symbIdRef="Alive"/>
                                </math:LogicBinop>
                            </PreviousState>
                        </Probability>
                        <ct:Assign>
                            <ct:Real>0.05</ct:Real>
                        </ct:Assign>
                    </ProbabilityAssignment>
                    
                    
                </CategoricalData>
            </Discrete>
        </ObservationModel>
    </ModelDefinition>



    <!-- OBSERVATION DEFINITION: Amount of people in each state for years 1-10 -->
    <TrialDesign xmlns="http://www.pharmml.org/pharmml/0.7/TrialDesign">
        <Observations>
            <Observation oid="obsOid">
                <ObservationTimes>
                    <ct:Assign>
                        <ct:Sequence>
                            <ct:Begin>
                                <ct:Real>1</ct:Real>
                            </ct:Begin>
                            <ct:StepSize>
                                <ct:Real>1</ct:Real>
                            </ct:StepSize>
                            <ct:End>
                                <ct:Real>10</ct:Real>
                            </ct:End>
                        </ct:Sequence>
                    </ct:Assign>
                </ObservationTimes>
                <Discrete>
                    <ct:SymbRef blkIdRef="om1" symbIdRef="Y"/>
                </Discrete>
            </Observation>
        </Observations>
    </TrialDesign>
    


    <!-- SIMULATION TASK DESCRIPTION -->
    <mstep:ModellingSteps>
        <mstep:SimulationStep oid="simOid">
            
            <mstep:ObservationsReference>
                <ct:OidRef oidRef="obsOid"/>
            </mstep:ObservationsReference>
            
            <ct:VariableAssignment>
                <ct:SymbRef blkIdRef="om1" symbIdRef="Yinit"/>
                <ct:Assign>
                    <ct:Vector>
                        <ct:VectorElements>
                            <ct:Real>100</ct:Real>
                            <ct:Real>0</ct:Real>
                        </ct:VectorElements>
                    </ct:Vector>
                </ct:Assign>
            </ct:VariableAssignment>
            
            <mstep:Operation order="1" opType="Amount of people in each state for years 1-10"/>
        </mstep:SimulationStep>
    </mstep:ModellingSteps>
</PharmML>