úÎ!´ç¨uÍ      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜™š›œžŸ ¡¢£¤¥¦§¨©ª«¬­®¯°±²³´µ¶· ¸ ¹ º » ¼ ½ ¾ ¿ À Á Â Ã Ä Å Æ Ç È É Ê Ë Ì  Safe «None7­epi-simJType containing values at times. The times are increasing as required by asTimed.epi-sim#Construct a timed list if possible.epi-simHPredicate to check if a list of orderable objects is in ascending order.epi-sim:Evaluate the timed object treating it as a cadlag function epi-sim@Evaluate the timed object treating it as a direct delta function epi-sim:Check if there exists a pair with a particular time index. epi-simNReturn the value of the next time if possible or an exact match if it exists.epi-sim"list of ascending times and values  None7ƒepi-simA list of persons as a peopleepi-sim3Predicate for whether a person is one of the peopleepi-simDPredicate for whether two sets of people have any members in common.epi-sim*Predicate for whether there are any peopleepi-simThe number of peopleepi-sim!Add a person to a group of peopleepi-sim&Remove a person from a group of people epi-sim!A bytestring builder for a person   None76e0epi-sim5Return a representation of the tree in Newick format.1epi-sim„A representation of the events that can be observed in an epidemic but which are not included in the reconstructed tree, i.e. the ? and @ events.3epi-simWA representation of the reconstructed tree which is the phylogeny connecting all the = and > events.6epi-simµA representation of the whole transmission tree in a realisation of an epidemic including the unobserved leaves. Lineages that are still extant are modelled as shoots and contain a $ as their data rather than an event.7epi-sim*Internal node representing infection event8epi-sim(External node representing removal event9epi-sim*External node representing extant lineages:epi-sim>Events that can occur in an epidemic with their absolute time.;epi-sim"infection time, infector, infectee<epi-simremoval without observation=epi-sim"removal and inclusion in phylogeny>epi-simscheduled sampling of lineages?epi-sim(removal and observed by not in phylogeny@epi-sim scheduled occurrence of lineagesAepi-sim$The absolute time an event occurred.Bepi-simJThe events that occurred as a result of the existance of the given person.Íepi-simJThe events that occurred as a result of the existance of a group of peopleCepi-sim-A tree representation of the epidemic events.Depi-sim5A tree representation of the reconstructed phylogeny.Îepi-simPredicate for whether an 60 has a leaf which corresponds to a node in the 3.Eepi-simdExtract the events from an epidemic tree which are observed but not part of the reconstructed tree.Fepi-sim:Epidemic Events are ordered based on which occurred first.Bepi-simordered epidemic eventsÍepi-simordered epidemic eventsCepi-simordered epidemic events/0123456789:;<=>?@ABCDE:;<=>?@6789CA345D12EB/0None79Kª depi-sim2The number of people added or removed in an event.eepi-sim-The first scheduled event after a given time.fepi-simDPredicate for whether there is a scheduled event during an interval.iepi-simMPredicate for whether the first person infected the second in the given eventjepi-sim?The people infected by a particular person in a list of events.kepi-simQPredicate for whether a person or one of their descendents satisfies a predicatemepi-sim>Predicate for whether a person was sampled in the given eventsnepi-sim6Return the sampling event of a person who was sampled.oepi-simBA transmission tree of all the events starting from a given personpepi-simHA predicate for whether there is a sampled leaf in the transmission treeqepi-sim8A transmission tree with all non-sampling leaves removedrepi-sim@Recurse through the tree and extract all birth and death events.sepi-sim#The unique events in a sample tree.eepi-simThe given timeepi-sim*The information about all scheduled eventsfepi-simStart time for intervalepi-simEnd time for intervalepi-sim&Information about all scheduled eventsiepi-simPotential infectorepi-simPotential infecteeepi-sim Given eventjepi-simPotential infectorepi-simEventsmepi-simThe given eventsepi-simThe person of interest TVUWZYX[_^]\`cbadefghijklmnopqrs defghijklmn`cba[_^]\WZYXopTVUqrsNone"#7^“epi-sim·Example run > (Success foo) = parseString newickTree mempty "((foo:1.1,bar:1.2):1.3,baz:1.4);" > (Success bar) = parseString newickTree mempty $ show foo > foo == bar True•epi-sim5Run a simulation described by a configuration object.–epi-simPPredicate for whether an epidemic event is either an occurrence or a disaaster.—epi-simYPredicate for whether an epidemic event will appear as a leaf in the reconstructed tree.™epi-simxRun a simulation described by a configuration object but using a random seed generated by the system rather than a seedšepi-sim2The number of lineages at the end of a simulation.›epi-simKGenerate exponentially distributed random variates with inhomogeneous rate.œepi-simKGenerate exponentially distributed random variates with inhomogeneous rate.•epi-sim<Condition upon at least two leaves in the reconstructed tree™epi-sim<Condition upon at least two leaves in the reconstructed treešepi-simThe events from the simulation›epi-sim Step functionepi-sim Generator.œepi-simTimerepi-sim Step functionepi-sim Generator.'vwxzy{|}~€‚†…„ƒ‡ˆ‰Š‹ŒŽ‘’“”•–—˜™š›œ'‚†…„ƒ‡ˆ‰Š€}~{|xzyvw‹ŒŽ‘’“”•–—˜™š›œNone"#næ¥epi-sim&Return a BDS-process parameters objectYNote that this requires that the rates are all positive, if they are not it will return Nothing.¦epi-simAConfiguration of a inhomogeneous birth-death-sampling simulation._Note that this requires that the timed rates are all positive, if they are not it will return Nothing which can lead to cryptic bugs.Ïepi-sim'A random event and the state afterwards§epi-simVThe state of the simulation at the time of the last event prior to the stopping time.¨epi-simIJust the observable events from a list of all the events in a simulation.¥epi-sim birth rateepi-sim death rateepi-sim sample rate¦epi-simDuration of the simulationepi-simBirth, Death and Sampling ratesÏepi-simmodel parametersepi-simthe current timeepi-simthe populationepi-simcurrent identifierepi-simPRNG§epi-simmodel parametersepi-sim stopping timeepi-simsimulation stateepi-simPRNG¨epi-simAll of the simulation events¥¦§¨¦§¨¥None"#xbÐepi-sim%Return a BD-process parameters object¬epi-sim8Configuration of a inhomogeneous birth-death simulation.Ñepi-sim'A random event and the state afterwards­epi-simVThe state of the simulation at the time of the last event prior to the stopping time.Ðepi-sim birth rateepi-sim death rate¬epi-simDuration of the simulationepi-simBirth and Death ratesÑepi-simmodel parametersepi-simthe current timeepi-simthe populationepi-simcurrent identifierepi-simPRNG­epi-simmodel parametersepi-sim stopping timeepi-simsimulation stateepi-simPRNG¬­¬­None}±epi-sim=Configuration of a birth-death-sampling-occurrence simulation³epi-simIJust the observable events from a list of all the events in a simulation.±epi-simDuration of the simulationepi-sim+Birth, Death, Sampling and Occurrence rates³epi-simAll of the simulation events±²³±²³ None"#‹pÒepi-simSbirth rate, death rate, sampling rate, catastrophe probability and occurrence rate.·epi-sim=Configuration of a birth-death-sampling-occurrence simulationÓepi-simTReturn a random event from the BDSCO-process given the current state of the process.Ôepi-sim+Return a randomly sampled Catastrophe event¹epi-simIJust the observable events from a list of all the events in a simulation.·epi-simDuration of the simulationepi-simDBirth, Death, Sampling, Catastrophe probability and Occurrence ratesÓepi-simParameters of the processepi-sim#The current time within the processepi-sim"The current state of the populaionepi-sim-The current state of the identifier generatorepi-simThe current state of the PRNGÔepi-sim3Time and probability of sampling in the catastropheepi-sim4The state of the population prior to the catastrophe¹epi-simAll of the simulation events·¸¹·¸¹ Noneí½epi-sim3Configuration of a birth-death-sampling simulation.½epi-simDuration of the simulationepi-simBirth, Death and Sampling rates½¾½¾ None"#‘‰Õepi-sim%Return a BD-process parameters objectÂepi-sim*Configuration of a birth-death simulation.Õepi-sim birth rateepi-sim death rateÂepi-simDuration of the simulationepi-simBirth and Death ratesÂÃÂà None"#§úÖepi-simlbirth rate, death rate, sampling rate, catastrophe specification, occurrence rate and disaster specificationÇepi-sim=Configuration of a birth-death-sampling-occurrence simulation×epi-simUReturn a random event from the BDSCOD-process given the current state of the process.Øepi-sim+Return a randomly sampled Catastrophe eventÙepi-sim(Return a randomly sampled Disaster eventÚepi-sim2The events from the nodes of a reconstructed tree not in time sorted order.Éepi-simÿJust the observable events from a list of all the events that occurred in a simulation of the BDSCOD-process. These events are the result of extracting the events from the reconstructed tree and getting the point process events that make up the unsequenced samples (see E# for details on this latter data.)Çepi-simDuration of the simulationepi-simDBirth, Death, Sampling, Catastrophe probability and Occurrence rates×epi-simParameters of the processepi-sim#The current time within the processepi-sim"The current state of the populaionepi-sim-The current state of the identifier generatorepi-simThe current state of the PRNGØepi-sim3Time and probability of sampling in the catastropheepi-sim4The state of the population prior to the catastropheÙepi-sim0Time and probability of sampling in the disasterepi-sim1The state of the population prior to the disasterÉepi-simAll of the simulation eventsÇÈÉÇÈÉSafe¨PÛÜÝÞßàáâã !"##$$%&'()*+,-./0123456789:;<==>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~€‚ƒ„……††‡ˆ‰‰Š‹ŒŽ‘’“”•–—˜™š›œžŸ ¡¢£¤¥¦§¨©ª«¬­®¯°±²­®³´µ­®¯¶·¸ ­ ® ¯ ¹ º » ­ ® ¼ ½ ¾ ­ ® ¿ À Á ­ ® ¯  à ÄÅÆÇÈÇ É Ê Ë Ì Í Ç Ë Î ÏÐÑÒÓÔÕÖ×Ø&epi-sim-0.2.2.0-Ha1De45mQngC03CdEKHswBEpidemic.Types.ParameterEpidemic.Types.PopulationEpidemic.Types.EventsEpidemicEpidemic.UtilityEpidemic.InhomogeneousBDSEpidemic.InhomogeneousBD%Epidemic.BirthDeathSamplingOccurrence0Epidemic.BirthDeathSamplingCatastropheOccurrenceEpidemic.BirthDeathSamplingEpidemic.BirthDeathEpidemic.BDSCODEpidemic.Types.Observations Paths_epi_sim ProbabilityRateTimedTimeasTimed isAscending cadlagValue cadlagValue'diracDeltaValuediracDeltaValue'hasTimehasTime'nextTime nextTime'$fSemigroupTimed $fToJSONTimed$fFromJSONTimed$fGenericTimed $fEqTimed $fShowTimedPeoplePersonasPeopleincludesPersonhaveCommonPeople nullPeople numPeople addPerson removePersonpersonByteString$fFromFieldPerson$fToFieldPerson$fToJSONPerson$fFromJSONPerson$fFromFieldPeople$fToFieldPeople$fToJSONPeople$fFromJSONPeople $fShowPerson$fGenericPerson $fEqPerson $fShowPeople $fEqPeople$fGenericPeopleNewickasNewickStringPointProcessEventsReconstructedTreeRBranchRLeaf EpidemicTreeBranchLeafShoot EpidemicEvent InfectionRemovalSampling Catastrophe OccurrenceDisaster eventTime derivedFrommaybeEpidemicTreemaybeReconstructedTreepointProcessEvents$fOrdEpidemicEvent$fFromRecordEpidemicEvent$fToRecordEpidemicEvent$fToJSONEpidemicEvent$fFromJSONEpidemicEvent$fNewickReconstructedTree$fNewickEpidemicTree$fShowEpidemicEvent$fGenericEpidemicEvent$fEqEpidemicEvent$fShowEpidemicTree$fEqEpidemicTree$fShowReconstructedTree$fEqReconstructedTree SampleTreeSTBirthSTDeathTransmissionTree TTUnresolvedTTDeathTTBirth PopulationsusceptiblePeopleinfectiousPeople removedPeople isInfectedModelParametersrNaught eventRate birthProb eventPopDeltafirstSchedulednoScheduledEventpersonsInEventpeopleInEventsinfected infectedByhasDescendentWhichhasSampledDescendent wasSampled samplingEventtransmissionTreehasSampledLeaf sampleTreesampleTreeEvents'sampleTreeEvents$fShowTransmissionTree$fShowSampleTreeNTreeNSubtreeNLeaf NInternal NBranchSetNBranchNLengthNNameSimulationConfigurationrates population newIdentifier timeLimitinitialIdentifier newPerson selectElem randomPerson newickName newickLeaf newickLength newickBranchnewickBranchSetnewickInternal newickSubtree newickTreesortcount' simulationisNonReconTreeObservationisReconTreeLeaf simulation'simulationWithSystemRandom finalSizeinhomExponential randInhomExp$fShowNSubtree$fShowNBranchSet $fShowNBranch $fShowNTree $fEqNSubtree$fEqNBranchSet $fEqNBranch $fEqNTree inhomBDSRates configuration allEventsobservedEvents$fModelParametersInhomBDSRates$fPopulationInhomBDSPop$fShowInhomBDSPop$fModelParametersInhomBDRates$fPopulationInhomBDPop$fShowInhomBDPop$fModelParametersBDSORates$fPopulationBDSOPopulation$fShowBDSOPopulation $fModelParametersBDSCOParameters$fPopulationBDSCOPopulation$fShowBDSCOPopulation$fModelParametersBDSRates$fPopulationBDSPopulation$fShowBDSPopulation$fModelParametersBDRates$fPopulationBDPopulation$fShowBDPopulation!$fModelParametersBDSCODParameters$fPopulationBDSCODPopulation$fShowBDSCODPopulationderivedFromPeoplehasSequencedLeaf randomEventinhomBirthDeathRatesBDSCOParametersrandomBdscoEventrandomCatastropheEventbirthDeathRatesBDSCODParametersrandomDisasterEventreconstructedTreeEventsversion getBinDir getLibDir getDynLibDir getDataDir getLibexecDir getSysconfDirgetDataFileName