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scenarioIRS30.xml
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<?xml version='1.0' encoding='UTF-8'?>
<om:scenario xmlns:om="http://openmalaria.org/schema/scenario_47" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" analysisNo="0" name="Rachuonyo 5-day Intervention cohort" schemaVersion="47" wuID="0" xsi:schemaLocation="http://openmalaria.org/schema/scenario_47 scenario_current.xsd">
<demography maximumAgeYrs="90" name="Rachuonyo" popSize="979">
<ageGroup lowerbound="0">
<group poppercent="2.6" upperbound="1"/>
<group poppercent="13.1" upperbound="5"/>
<group poppercent="15.2" upperbound="10"/>
<group poppercent="13.8" upperbound="15"/>
<group poppercent="10" upperbound="20"/>
<group poppercent="8.6" upperbound="25"/>
<group poppercent="7.2" upperbound="30"/>
<group poppercent="6" upperbound="35"/>
<group poppercent="4.7" upperbound="40"/>
<group poppercent="4.1" upperbound="45"/>
<group poppercent="3.5" upperbound="50"/>
<group poppercent="2.9" upperbound="55"/>
<group poppercent="2.2" upperbound="60"/>
<group poppercent="1.9" upperbound="65"/>
<group poppercent="1.3" upperbound="70"/>
<group poppercent="1.1" upperbound="75"/>
<group poppercent="0.6" upperbound="80"/>
<group poppercent="1" upperbound="85"/>
<group poppercent="0.1" upperbound="90"/>
</ageGroup>
</demography>
<monitoring name="Monthly Surveys" startDate="2100-01-01">
<continuous duringInit="false" period="5d">
<option name="input EIR" value="true"/>
<option name="simulated EIR" value="true"/>
<option name="human infectiousness" value="true"/>
<option name="immunity h" value="true"/>
<option name="immunity Y" value="true"/>
<option name="recent births" value="true"/>
<!--<option name="IRS insecticide content" value="true"/>
<option name="IRS effects" value="true"/>-->
</continuous>
<SurveyOptions>
<option name="nHost" value="true"/>
<option name="nPatent" value="true"/>
<option name="sumlogDens" value="true"/>
<option name="nTreatments1" value="true"/>
<option name="nTreatments2" value="true"/>
<option name="nTreatments3" value="true"/>
<option name="annAvgK" value="true"/>
<option name="nMassIRS" value="true"/>
<option name="nMDAs" value="true"/>
</SurveyOptions>
<surveys detectionLimit="200">
<surveyTime reported="false" repeatStep="18t" repeatEnd="150t">0</surveyTime>
<surveyTime reported="true">1t</surveyTime>
<surveyTime reported="true" repeatStep="6t" repeatEnd="150t">6t</surveyTime>
</surveys>
<ageGroup lowerbound="0">
<group upperbound="1"/>
<group upperbound="5"/>
<group upperbound="10"/>
<group upperbound="15"/>
<group upperbound="20"/>
<group upperbound="99"/>
</ageGroup>
</monitoring>
<interventions name="Full Set">
<human>
<component id="MDA">
<treatSimple durationBlood="1t" durationLiver="0"/>
</component>
<component id="ITN" name="LLIN test">
<ITN>
<usage value="0.8"/>
<holeRate mean="0.9" CV="0.946826741968" distr="lognormal"/>
<ripRate mean="0.7" CV="0.946826741968" distr="lognormal"/>
<ripFactor value="0.4"/>
<initialInsecticide mean="70" SD="20" distr="normal"/>
<insecticideDecay L="2.2y" function="exponential" CV="0.946826741968"/>
<attritionOfNets L="12y" function="smooth-compact" k="2"/>
<anophelesParams mosquito="gambiae_ss">
<deterrency holeFactor="0.5" holeScalingFactor="0.1" insecticideFactor="0.67" insecticideScalingFactor="0.1" interactionFactor="1.492537"/>
<preprandialKillingEffect baseFactor="0.09" holeFactor="0.57" holeScalingFactor="0.1" insecticideFactor="0.604" insecticideScalingFactor="1" interactionFactor="-0.424"/>
<postprandialKillingEffect baseFactor="0.10" holeFactor="0" holeScalingFactor="0.1" insecticideFactor="0.55" insecticideScalingFactor="0.1" interactionFactor="0"/>
</anophelesParams>
</ITN>
</component>
<component id="IRS" name="new param">
<IRS>
<!-- Initial insecticide: units are μg/cm²; no variance here -->
<initialInsecticide mean="118"/>
<insecticideDecay L="0.15y" function="exponential"/>
<anophelesParams mosquito="gambiae_ss">
<deterrency insecticideFactor="0.12" insecticideScalingFactor="0.05"/>
<preprandialKillingEffect baseFactor="0.01" insecticideFactor="0.25" insecticideScalingFactor="0.008"/>
<postprandialKillingEffect baseFactor="0.01" insecticideFactor="0.5" insecticideScalingFactor="0.006"/>
</anophelesParams>
</IRS>
<subPopRemoval afterYears="0.5"/>
</component>
<component id="vectorDeterrent" name="hypothetical deterrency">
<GVI>
<decay L="4y" function="exponential"/>
<anophelesParams mosquito="gambiae_ss">
<deterrency value="0"/>
</anophelesParams>
</GVI>
</component>
<component id="mdaPop">
<recruitmentOnly/>
</component>
<deployment>
<component id="MDA"/>
<timed>
<restrictToSubPop id="mdaPop"/>
<deploy coverage="1" time="2100-06-01"/>
</timed>
</deployment>
<deployment name="LLIN test">
<component id="ITN"/>
<continuous>
<deploy coverage=".677" targetAgeYrs="0.0833"/>
</continuous>
</deployment>
<deployment name="new param">
<component id="IRS"/>
<timed>
<cumulativeCoverage component="IRS"/>
<deploy coverage="0.05775" time="18t"/>
<deploy coverage="0.1155" time="19t"/>
<deploy coverage="0.17325" time="20t"/>
<deploy coverage="0.231" time="21t"/>
<deploy coverage="0.28875" time="22t"/>
<deploy coverage="0.3465" time="23t"/>
<deploy coverage="0.40425" time="24t"/>
<deploy coverage="0.462" time="25t"/>
<deploy coverage="0.51975" time="26t"/>
<deploy coverage="0.5775" time="27t"/>
<deploy coverage="0.63525" time="28t"/>
<deploy coverage="0.693" time="29t"/>
<deploy coverage="0.05775" time="103t"/>
<deploy coverage="0.1155" time="104t"/>
<deploy coverage="0.17325" time="105t"/>
<deploy coverage="0.231" time="106t"/>
<deploy coverage="0.28875" time="107t"/>
<deploy coverage="0.3465" time="108t"/>
<deploy coverage="0.40425" time="109t"/>
<deploy coverage="0.462" time="110t"/>
<deploy coverage="0.51975" time="111t"/>
<deploy coverage="0.5775" time="112t"/>
<deploy coverage="0.63525" time="113t"/>
<deploy coverage="0.693" time="114t"/>
</timed>
</deployment>
<deployment>
<component id="mdaPop"/>
<timed>
<deploy coverage="0.018696" maxAge="5" minAge="1" time="2100-01-01"/>
<deploy coverage="0.249757" maxAge="10" minAge="5" time="2100-01-06"/>
<deploy coverage="0.195228" maxAge="15" minAge="10" time="2100-01-11"/>
<deploy coverage="0.207164" maxAge="20" minAge="15" time="2100-01-16"/>
<deploy coverage="0.157818" maxAge="90" minAge="20" time="2100-01-21"/>
</timed>
</deployment>
</human>
</interventions>
<healthSystem>
<ImmediateOutcomes name="Kenya ACT">
<drugRegimen firstLine="ACT" inpatient="QN" secondLine="QN"/>
<initialACR>
<ACT value="0.96"/>
<QN value="0.998"/>
<selfTreatment value="0.63"/>
</initialACR>
<compliance>
<ACT value="0.892"/>
<selfTreatment value="0.85"/>
</compliance>
<nonCompliersEffective>
<ACT value="0.8544"/>
<selfTreatment value="0"/>
</nonCompliersEffective>
<treatmentActions>
<ACT name="legacy (emulate pre-32 treatment)">
<clearInfections stage="both" timesteps="-1t"/>
</ACT>
<QN name="legacy (emulate pre-32 treatment)">
<clearInfections stage="both" timesteps="-1t"/>
</QN>
</treatmentActions>
<pSeekOfficialCareUncomplicated1 value="0.04"/>
<pSelfTreatUncomplicated value="0.0212"/>
<pSeekOfficialCareUncomplicated2 value="0.04"/>
<pSeekOfficialCareSevere value="0.48"/>
</ImmediateOutcomes>
<CFR>
<group lowerbound="0" value="0.09189"/>
<group lowerbound="0.25" value="0.0810811"/>
<group lowerbound="0.75" value="0.0648649"/>
<group lowerbound="1.5" value="0.0689189"/>
<group lowerbound="2.5" value="0.0675676"/>
<group lowerbound="3.5" value="0.0297297"/>
<group lowerbound="4.5" value="0.0459459"/>
<group lowerbound="7.5" value="0.0945946"/>
<group lowerbound="12.5" value="0.1243243"/>
<group lowerbound="15" value="0.1378378"/>
</CFR>
<pSequelaeInpatient interpolation="none">
<group lowerbound="0.0" value="0.0132"/>
<group lowerbound="5.0" value="0.005"/>
</pSequelaeInpatient>
</healthSystem>
<entomology mode="dynamic" name="Nyanza">
<vector>
<anopheles mosquito="gambiae_ss" propInfected="0.078" propInfectious="0.015">
<seasonality annualEIR=".6" input="EIR">
<monthlyValues smoothing="fourier">
<value>0.076</value>
<value>0.368</value>
<value>0.164</value>
<value>0</value>
<value>0.101</value>
<value>0.118</value>
<value>0.328</value>
<value>0.053</value>
<value>0.021</value>
<value>0.048</value>
<value>0</value>
<value>0.01</value>
</monthlyValues>
</seasonality>
<mosq minInfectedThreshold="0.001">
<mosqRestDuration value="3"/>
<extrinsicIncubationPeriod value="14"/>
<mosqLaidEggsSameDayProportion value="0.313"/>
<mosqSeekingDuration value="0.33"/>
<mosqSurvivalFeedingCycleProbability value="0.623"/>
<mosqProbBiting mean="0.95" variance="0"/>
<availability/>
<mosqProbFindRestSite mean="0.95" variance="0"/>
<mosqProbResting mean="0.99" variance="0"/>
<mosqProbOvipositing value="0.88"/>
<mosqHumanBloodIndex value="0.8"/>
</mosq>
<nonHumanHosts name="unprotectedAnimals">
<mosqRelativeEntoAvailability value="1.0"/>
<mosqProbBiting value="0.95"/>
<mosqProbFindRestSite value="0.95"/>
<mosqProbResting value="0.99"/>
</nonHumanHosts>
</anopheles>
<nonHumanHosts name="unprotectedAnimals" number="1.0"/>
</vector>
</entomology>
<model>
<ModelOptions>
<option name="LOGNORMAL_MASS_ACTION" value="true"/>
<option name="NO_PRE_ERYTHROCYTIC" value="true"/>
<option name="INNATE_MAX_DENS" value="false"/>
<option name="INDIRECT_MORTALITY_FIX" value="false"/>
</ModelOptions>
<clinical healthSystemMemory="28d"/>
<human>
<availabilityToMosquitoes>
<group lowerbound="0.0" value="0.225940909648"/>
<group lowerbound="1.0" value="0.286173633441"/>
<group lowerbound="2.0" value="0.336898395722"/>
<group lowerbound="3.0" value="0.370989854675"/>
<group lowerbound="4.0" value="0.403114915112"/>
<group lowerbound="5.0" value="0.442585112522"/>
<group lowerbound="6.0" value="0.473839351511"/>
<group lowerbound="7.0" value="0.512630464378"/>
<group lowerbound="8.0" value="0.54487872702"/>
<group lowerbound="9.0" value="0.581527755812"/>
<group lowerbound="10.0" value="0.630257580698"/>
<group lowerbound="11.0" value="0.663063362714"/>
<group lowerbound="12.0" value="0.702417432755"/>
<group lowerbound="13.0" value="0.734605377277"/>
<group lowerbound="14.0" value="0.788908765653"/>
<group lowerbound="15.0" value="0.839587932303"/>
<group lowerbound="20.0" value="1.0"/>
<group lowerbound="20.0" value="1.0"/>
</availabilityToMosquitoes>
</human>
<parameters interval="5" iseed="2" latentp="15d">
<parameter include="false" name="'-ln(1-Sinf)'" number="1" value="0.050736"/>
<parameter include="false" name="Estar" number="2" value="0.03247"/>
<parameter include="false" name="Simm" number="3" value="0.138161050830301"/>
<parameter include="false" name="Xstar_p" number="4" value="1514.385853233699891"/>
<parameter include="false" name="gamma_p" number="5" value="2.03692533424484"/>
<parameter include="false" name="sigma2i" number="6" value="10.173598698525799"/>
<parameter include="false" name="CumulativeYstar" number="7" value="35158523.31132510304451"/>
<parameter include="false" name="CumulativeHstar" number="8" value="97.334652723897705"/>
<parameter include="false" name="'-ln(1-alpha_m)'" number="9" value="2.33031045876193"/>
<parameter include="false" name="decay_m" number="10" value="2.53106547375805"/>
<parameter include="false" name="sigma2_0" number="11" value="0.655747311168152"/>
<parameter include="false" name="Xstar_v" number="12" value="0.916181104713054"/>
<parameter include="false" name="Ystar2" number="13" value="6502.26335600001039"/>
<parameter include="false" name="alpha" number="14" value="142601.912520000012591"/>
<parameter include="false" name="Density bias (non Garki)" number="15" value="0.177378570987455"/>
<parameter include="false" name=" sigma2 " number="16" value="0.05"/>
<parameter include="false" name="log oddsr CF community" number="17" value="0.736202"/>
<parameter include="false" name="Indirect risk cofactor" number="18" value="0.018777338"/>
<parameter include="false" name="Non-malaria infant mortality" number="19" value="49.539046599999999"/>
<parameter include="false" name="Density bias (Garki)" number="20" value="4.79610772546704"/>
<parameter include="false" name="Severe Malaria Threshhold" number="21" value="784455.599999999976717"/>
<parameter include="false" name="Immunity Penalty" number="22" value="1"/>
<parameter include="false" name="Immune effector decay" number="23" value="0"/>
<parameter include="false" name="comorbidity intercept" number="24" value="0.0968"/>
<parameter include="false" name="Ystar half life" number="25" value="0.275437402"/>
<parameter include="false" name="Ystar1" number="26" value="0.596539864"/>
<parameter include="false" name="Asexual immunity decay" number="27" value="0"/>
<parameter include="false" name="Ystar0" number="28" value="296.302437899999973"/>
<parameter include="false" name="Idete multiplier" number="29" value="2.797523626"/>
<parameter include="false" name="critical age for comorbidity" number="30" value="0.117383"/>
</parameters>
</model>
</om:scenario>