Index

A

acquirePathogen() (opqua.internal.host.Host method) (opqua.internal.vector.Vector method) addCustomConditionTracker() (opqua.model.Model method), [1] addHosts() (opqua.internal.population.Population method) (opqua.model.Model method), [1] addPathogensToHosts() (opqua.internal.population.Population method) (opqua.model.Model method), [1]

addPathogensToVectors() (opqua.internal.population.Population method) (opqua.model.Model method), [1] addVectors() (opqua.internal.population.Population method) (opqua.model.Model method), [1] applyTreatment() (opqua.internal.host.Host method) (opqua.internal.vector.Vector method) args (opqua.internal.intervention.Intervention attribute)

B

birth() (opqua.internal.host.Host method) (opqua.internal.vector.Vector method) BIRTH_HOST (opqua.internal.gillespie.Gillespie attribute) birth_rate_host (opqua.internal.setup.Setup attribute)

birth_rate_vector (opqua.internal.setup.Setup attribute) BIRTH_VECTOR (opqua.internal.gillespie.Gillespie attribute) birthHost() (opqua.internal.population.Population method) birthVector() (opqua.internal.population.Population method)

C

CB_PALETTE (opqua.model.Model attribute) CHROMOSOME_SEPARATOR (opqua.internal.population.Population attribute) clustermap() (in module opqua.internal.plot) (opqua.model.Model method), [1] compartmentDf() (in module opqua.internal.data) compartmentPlot() (in module opqua.internal.plot) (opqua.model.Model method), [1] compositionDf() (in module opqua.internal.data) compositionPlot() (in module opqua.internal.plot) (opqua.model.Model method), [1] CONTACT (opqua.internal.population.Population attribute) CONTACT_HOST_HOST (opqua.internal.gillespie.Gillespie attribute) CONTACT_HOST_VECTOR (opqua.internal.gillespie.Gillespie attribute)

contact_rate_host_host (opqua.internal.setup.Setup attribute) contact_rate_host_vector (opqua.internal.setup.Setup attribute) CONTACT_VECTOR_HOST (opqua.internal.gillespie.Gillespie attribute) contactHost (opqua.internal.setup.Setup attribute) contactHostHost() (opqua.internal.population.Population method) contactHostVector() (opqua.internal.population.Population method) contactVector (opqua.internal.setup.Setup attribute) contactVectorHost() (opqua.internal.population.Population method) copyState() (opqua.internal.host.Host method) (opqua.internal.population.Population method) (opqua.internal.vector.Vector method) (opqua.model.Model method), [1] createInterconnectedPopulations() (opqua.model.Model method), [1] customModelFunction() (opqua.model.Model method), [1]

D

death_rate_host (opqua.internal.setup.Setup attribute) death_rate_vector (opqua.internal.setup.Setup attribute) deepCopy() (opqua.model.Model method), [1] DEF_CMAP (opqua.model.Model attribute) die() (opqua.internal.host.Host method) (opqua.internal.vector.Vector method)

DIE_HOST (opqua.internal.gillespie.Gillespie attribute) DIE_VECTOR (opqua.internal.gillespie.Gillespie attribute) dieHost() (opqua.internal.population.Population method) dieVector() (opqua.internal.population.Population method) doAction() (opqua.internal.gillespie.Gillespie method) doIntervention() (opqua.internal.intervention.Intervention method)

E

EVENT_IDS (opqua.internal.gillespie.Gillespie attribute)

F

fitnessHost (opqua.internal.setup.Setup attribute)

fitnessVector (opqua.internal.setup.Setup attribute)

G

getCompositionData() (opqua.model.Model method), [1] getGenomeTimes() (opqua.model.Model method), [1] getGenomeTimesDf() (in module opqua.internal.data) getPathogenDistanceHistoryDf() (in module opqua.internal.data) getPathogens() (in module opqua.internal.data) (opqua.model.Model method), [1] getProtections() (in module opqua.internal.data) (opqua.model.Model method), [1]

getRates() (opqua.internal.gillespie.Gillespie method) getWeightedRandom() (opqua.internal.population.Population method) getWeightedRandomGenome() (opqua.internal.host.Host method) (opqua.internal.vector.Vector method) Gillespie (class in opqua.internal.gillespie) groups (opqua.model.Model attribute), [1]

H

healthyCoefficientRow() (opqua.internal.population.Population method)

history (opqua.model.Model attribute), [1] Host (class in opqua.internal.host)

I

id (opqua.internal.host.Host attribute) (opqua.internal.population.Population attribute) (opqua.internal.setup.Setup attribute) (opqua.internal.vector.Vector attribute) INFECTED (opqua.internal.population.Population attribute) infectHost() (opqua.internal.host.Host method) (opqua.internal.vector.Vector method)

infectVector() (opqua.internal.host.Host method) (opqua.internal.vector.Vector method) inherit_protection_host (opqua.internal.setup.Setup attribute) inherit_protection_vector (opqua.internal.setup.Setup attribute) Intervention (class in opqua.internal.intervention) interventions (opqua.model.Model attribute), [1]

K

KILL_HOST (opqua.internal.gillespie.Gillespie attribute) KILL_VECTOR (opqua.internal.gillespie.Gillespie attribute)

killHost() (opqua.internal.population.Population method) killVector() (opqua.internal.population.Population method)

L

LETHALITY (opqua.internal.population.Population attribute) linkPopulationsHostHostContact() (opqua.model.Model method), [1] linkPopulationsHostMigration() (opqua.model.Model method), [1]

linkPopulationsHostVectorContact() (opqua.model.Model method), [1] linkPopulationsVectorHostContact() (opqua.model.Model method), [1] linkPopulationsVectorMigration() (opqua.model.Model method), [1]

M

mean_inoculum_host (opqua.internal.setup.Setup attribute) mean_inoculum_vector (opqua.internal.setup.Setup attribute) method_name (opqua.internal.intervention.Intervention attribute) migrate() (opqua.internal.population.Population method) MIGRATE_HOST (opqua.internal.gillespie.Gillespie attribute) MIGRATE_VECTOR (opqua.internal.gillespie.Gillespie attribute) MIGRATION (opqua.internal.population.Population attribute) migrationHost (opqua.internal.setup.Setup attribute) migrationVector (opqua.internal.setup.Setup attribute) Model (class in opqua.model), [1] model (opqua.internal.gillespie.Gillespie attribute) (opqua.internal.intervention.Intervention attribute) (opqua.internal.population.Population attribute) module opqua opqua.internal opqua.internal.data opqua.internal.gillespie opqua.internal.host opqua.internal.intervention opqua.internal.plot opqua.internal.population opqua.internal.setup opqua.internal.vector opqua.model

mortality_rate_host (opqua.internal.setup.Setup attribute) mortality_rate_vector (opqua.internal.setup.Setup attribute) mortalityHost (opqua.internal.setup.Setup attribute) mortalityVector (opqua.internal.setup.Setup attribute) mutate() (opqua.internal.host.Host method) (opqua.internal.vector.Vector method) MUTATE_HOST (opqua.internal.gillespie.Gillespie attribute) mutate_in_host (opqua.internal.setup.Setup attribute) mutate_in_vector (opqua.internal.setup.Setup attribute) MUTATE_VECTOR (opqua.internal.gillespie.Gillespie attribute) mutateHost() (opqua.internal.population.Population method) mutateVector() (opqua.internal.population.Population method) MUTATION (opqua.internal.population.Population attribute) mutationHost (opqua.internal.setup.Setup attribute) mutationVector (opqua.internal.setup.Setup attribute)

N

NATALITY (opqua.internal.population.Population attribute) natalityHost (opqua.internal.setup.Setup attribute) natalityVector (opqua.internal.setup.Setup attribute) newHostGroup() (opqua.internal.population.Population method) (opqua.model.Model method), [1] newIntervention() (opqua.model.Model method), [1] newPopulation() (opqua.model.Model method), [1] newSetup() (opqua.model.Model method), [1]

newVectorGroup() (opqua.internal.population.Population method) (opqua.model.Model method), [1] NUM_COEFFICIENTS (opqua.internal.population.Population attribute) num_crossover_host (opqua.internal.setup.Setup attribute) num_crossover_vector (opqua.internal.setup.Setup attribute) num_hosts (opqua.internal.population.Population attribute) num_loci (opqua.internal.setup.Setup attribute) num_vectors (opqua.internal.population.Population attribute)

O

opqua module opqua.internal module opqua.internal.data module opqua.internal.gillespie module opqua.internal.host module opqua.internal.intervention module

opqua.internal.plot module opqua.internal.population module opqua.internal.setup module opqua.internal.vector module opqua.model module

P

pathogenDistanceDf() (in module opqua.internal.data) pathogenDistanceHistory() (opqua.model.Model method), [1] peakLandscape() (opqua.model.Model static method), [1] Population (class in opqua.internal.population) population (opqua.internal.host.Host attribute) (opqua.internal.vector.Vector attribute) POPULATION_CONTACT (opqua.internal.population.Population attribute) POPULATION_CONTACT_HOST_HOST (opqua.internal.gillespie.Gillespie attribute) POPULATION_CONTACT_HOST_VECTOR (opqua.internal.gillespie.Gillespie attribute) POPULATION_CONTACT_VECTOR_HOST (opqua.internal.gillespie.Gillespie attribute) populationContact() (opqua.internal.population.Population method) populationContactHost (opqua.internal.setup.Setup attribute)

populationContactVector (opqua.internal.setup.Setup attribute) populations (opqua.model.Model attribute), [1] populationsDf() (in module opqua.internal.data) populationsPlot() (in module opqua.internal.plot) (opqua.model.Model method), [1] possible_alleles (opqua.internal.setup.Setup attribute) protectHosts() (opqua.internal.population.Population method) (opqua.model.Model method), [1] protection_upon_recovery_host (opqua.internal.setup.Setup attribute) protection_upon_recovery_vector (opqua.internal.setup.Setup attribute) protectVectors() (opqua.internal.population.Population method) (opqua.model.Model method), [1]

R

RECEIVE_CONTACT (opqua.internal.population.Population attribute) RECEIVE_POPULATION_CONTACT (opqua.internal.population.Population attribute) receiveContactHost (opqua.internal.setup.Setup attribute) receiveContactVector (opqua.internal.setup.Setup attribute) RECOMBINATION (opqua.internal.population.Population attribute) recombinationHost (opqua.internal.setup.Setup attribute) recombinationVector (opqua.internal.setup.Setup attribute) recombine() (opqua.internal.host.Host method) (opqua.internal.vector.Vector method) RECOMBINE_HOST (opqua.internal.gillespie.Gillespie attribute) recombine_in_host (opqua.internal.setup.Setup attribute) recombine_in_vector (opqua.internal.setup.Setup attribute) RECOMBINE_VECTOR (opqua.internal.gillespie.Gillespie attribute) recombineHost() (opqua.internal.population.Population method) recombineVector() (opqua.internal.population.Population method) recover() (opqua.internal.host.Host method) (opqua.internal.vector.Vector method)

RECOVER_HOST (opqua.internal.gillespie.Gillespie attribute) RECOVER_VECTOR (opqua.internal.gillespie.Gillespie attribute) recoverHost() (opqua.internal.population.Population method) recoverVector() (opqua.internal.population.Population method) RECOVERY (opqua.internal.population.Population attribute) recovery_rate_host (opqua.internal.setup.Setup attribute) recovery_rate_vector (opqua.internal.setup.Setup attribute), [1] recoveryHost (opqua.internal.setup.Setup attribute) recoveryVector (opqua.internal.setup.Setup attribute) removeHosts() (opqua.internal.population.Population method) (opqua.model.Model method), [1] removeVectors() (opqua.internal.population.Population method) (opqua.model.Model method), [1] run() (opqua.internal.gillespie.Gillespie method) (opqua.model.Model method), [1] runParamSweep() (opqua.model.Model method), [1] runReplicates() (opqua.model.Model method), [1]

S

saveToDataFrame() (opqua.model.Model method), [1] saveToDf() (in module opqua.internal.data) setHostHostPopulationContactNeighbor() (opqua.internal.population.Population method) setHostMigrationNeighbor() (opqua.internal.population.Population method) setHostVectorPopulationContactNeighbor() (opqua.internal.population.Population method) setRandomSeed() (opqua.model.Model method), [1] setSetup() (opqua.internal.population.Population method) (opqua.model.Model method), [1]

Setup (class in opqua.internal.setup) setup (opqua.internal.population.Population attribute) setups (opqua.model.Model attribute), [1] setVectorHostPopulationContactNeighbor() (opqua.internal.population.Population method) setVectorMigrationNeighbor() (opqua.internal.population.Population method) slim (opqua.internal.host.Host attribute) (opqua.internal.population.Population attribute) (opqua.internal.vector.Vector attribute)

T

t_var (opqua.model.Model attribute), [1] time (opqua.internal.intervention.Intervention attribute) transmission_efficiency_host_host (opqua.internal.setup.Setup attribute) transmission_efficiency_host_vector (opqua.internal.setup.Setup attribute)

transmission_efficiency_vector_host (opqua.internal.setup.Setup attribute) treatHosts() (opqua.internal.population.Population method) (opqua.model.Model method), [1] treatVectors() (opqua.internal.population.Population method) (opqua.model.Model method), [1]

U

updateHostCoefficients() (opqua.internal.population.Population method)

updateVectorCoefficients() (opqua.internal.population.Population method)

V

valleyLandscape() (opqua.model.Model static method), [1] Vector (class in opqua.internal.vector)

vertical_transmission_host (opqua.internal.setup.Setup attribute) vertical_transmission_vector (opqua.internal.setup.Setup attribute)

W

wipeProtectionHosts() (opqua.internal.population.Population method) (opqua.model.Model method), [1]

wipeProtectionVectors() (opqua.internal.population.Population method) (opqua.model.Model method), [1]