h$/*      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~                                                                    None 8 epi-sim!A type to represent a population.epi-sim2A type to represent a single person in a group of epi-sim2A type to hold an integer which is unique to each .epi-simClass of types that can represent populations in an epidemic simulation. epi-simA list of persons as a people epi-sim3Predicate for whether a person is one of the people epi-simPredicate 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 peopleepi-sim!A bytestring builder for a person   None8 "epi-simType containing values at times. The times are increasing as required by asTimed.$epi-sim,Duration of time between two absolute times.&epi-simAbsolute time.(epi-sim/The duration of time between two absolute times-timeDelta (AbsoluteTime 1) (AbsoluteTime 2.5) TimeDelta 1.5)epi-simThe time after a given delay/timeAfterDelta (AbsoluteTime 1) (TimeDelta 2.5)AbsoluteTime 3.5*epi-sim#Construct a timed list if possible.+epi-simPredicate to check if a list of orderable objects is in ascending order.,epi-sim:Evaluate the timed object treating it as a cadlag function-epi-simEvaluate the timed object treating it as a direct delta function.epi-sim:Check if there exists a pair with a particular time index./epi-simReturn the value of the next time if possible or an exact match if it exists.0epi-simReturn a list of the (finite) absolute times that the step function changes value.let demoMaybeTimed = asTimed [(AbsoluteTime 1,2),(AbsoluteTime 1.5,1)]liftM allTimes demoMaybeTimed(Just [AbsoluteTime 1.0,AbsoluteTime 1.5](epi-simstartepi-simfinish*epi-sim"list of ascending times and values"#$%&'()*+,-./0&'$%"#(-)/,+.0*None8 ]Eepi-simClass of types that can be considered parameterisations of a epidemic model.CDEHGFEHGFDCNone #$8 Iepi-simThe whole transmission tree including the unobserved leaves. Lineages that are still extant are modelled as shoots and contain a % as their data rather than an event.Mepi-sim>Events that can occur in an epidemic with their absolute time.Nepi-sim!absolute time; infector; infecteeRepi-simepidemic went extinct time time can be recovered from the preceeding removalSepi-sim(the simulation reached the stopping timeZepi-simPredicate for whether an  EpidemicEvent is one of the terminal events of extinction or the stopping time having been reached.[epi-sim$The absolute time an event occurred.\epi-simThe events that occurred as a result of the existance of the given person.]epi-simIf possible return an I describing the sorted list of M.^epi-simEpidemic Events are ordered based on which occurred first. Since R and S events are there as placeholders they are placed as the end of the order.\epi-simordered epidemic events]epi-simordered epidemic eventsIJKLMNOPQSRTVUWXYZ[\]MNOPQSRXYWUVTIJKL]Z[\None'(9hepi-simEither there is a valid simulation state which contains a sequence of epidemic events of there is a terminated simulation which indicates that the simulation has been rejected.mepi-simThe event ratesnepi-simThe populationoepi-simA new identifierpepi-sim0The absolute time at which the simulation startsqepi-sim-The duration of the simulation until it stopsrepi-sim (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 Trueepi-simRun a simulation described by a configuration object with the provided PRNG.epi-simRun a simulation described by a configuration object using the fixed PRNG that is hardcoded in the  mwc-random package.epi-simPredicate for whether an epidemic event will appear as a leaf in the reconstructed tree.epi-simSimulation conditioned upon there being at least two sequenced samples. NOTE This function is deprecated and will be removed in future versions.epi-simRun a simulation described by a configuration object but using a random seed generated by the system rather than a seedepi-sim2The number of lineages at the end of a simulation.epi-simGenerate exponentially distributed random variates with inhomogeneous rate starting from a particular point in time. Assuming the stepFunc" is the intensity of arrivals and t0! is the start time this returns t1 the time of the next arrival.epi-simGenerate exponentially distributed random variates with inhomogeneous rate.TODO The algorithm used here generates more variates than are needed. It would be nice to use a more efficient implementation.epi-simHelper function for converting between the Maybe monad and the Either monad.epi-simThe events from the simulationepi-sim Step functionepi-sim Start timeepi-sim Generatorepi-simTimerepi-sim Step functionepi-sim Generator. None#$%epi-simThe parameters of the logistic-BDSD process. This process allows for infections, removals, sampling and disasters.epi-simCreate an simulation configuration or return an error message if this is not possible.epi-sim=Defines how a single random event is simulated in this model.epi-sim.condition upon at least two sequenced samples.   None#$(fepi-sim&Return a BDS-process parameters objectNote that this requires that the rates are all positive, if they are not it will return Nothing.epi-simConfiguration 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.epi-sim birth rateepi-sim death rateepi-sim sample rateepi-sim4Duration of the simulation after starting at time 0.epi-sim.condition upon at least two sequenced samples.epi-simBirth, Death and Sampling rates None#$*epi-simbirth rate, death rate, sampling rate, catastrophe specification, occurrence rate and disaster specificationepi-simConfiguration of a birth-death-sampling-occurrence-disaster simulationepi-sim;The way in which random events are generated in this model.epi-simDuration of the simulationepi-sim.condition upon at least two sequenced samples.epi-simBirth, Death, Sampling, Catastrophe probability, Occurrence rates and Disaster probabilities  Safe-Inferred* !"#$%&'()*+,--..//0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnnoopqqrstuvwxyz{|}~~                                                                            $epi-sim-0.4.2-4l1mCHWa7vKLa54bgYWgDREpidemic.Types.PopulationEpidemic.Types.TimeEpidemic.Types.ParameterEpidemic.Types.EventsEpidemic.Types.SimulationEpidemic.Types.ObservationsEpidemic.Types.NewickEpidemicEpidemic.UtilityEpidemic.Model.LogisticBDSDEpidemic.Model.InhomogeneousBDSEpidemic.Model.BDSCOD Paths_epi_simPeoplePerson Identifier PopulationsusceptiblePeopleinfectiousPeople removedPeople isInfectedasPeopleincludesPersonhaveCommonPeople nullPeople numPeople addPerson removePersonpersonByteString$fToJSONIdentifier$fFromJSONIdentifier$fToJSONPerson$fFromJSONPerson$fToJSONPeople$fFromJSONPeople $fShowPeople $fEqPeople$fGenericPeople $fShowPerson$fGenericPerson $fEqPerson$fShowIdentifier$fGenericIdentifier$fEqIdentifierTimed TimeDelta AbsoluteTime timeDeltatimeAfterDeltaasTimed isAscending cadlagValuediracDeltaValuehasTimenextTimeallTimes$fToJSONAbsoluteTime$fFromJSONAbsoluteTime$fToJSONTimeDelta$fFromJSONTimeDelta$fSemigroupTimed $fToJSONTimed$fFromJSONTimed$fGenericTimed $fEqTimed $fShowTimed$fGenericTimeDelta $fEqTimeDelta$fShowTimeDelta$fOrdTimeDelta$fGenericAbsoluteTime$fEqAbsoluteTime$fShowAbsoluteTime$fOrdAbsoluteTime ProbabilityRateModelParametersrNaught eventRate birthProb EpidemicTreeBranchLeafShoot EpidemicEvent InfectionRemovalIndividualSamplePopulationSample Extinction StoppingTime indSampTime indSampPerson indSampSeq popSampTime popSampPeople popSampSeqisExtinctionOrStopping eventTime derivedFrommaybeEpidemicTree$fOrdEpidemicEvent$fToJSONEpidemicEvent$fFromJSONEpidemicEvent$fShowEpidemicTree$fEqEpidemicTree$fShowEpidemicEvent$fGenericEpidemicEvent$fEqEpidemicEventSimulationRandEventSimulationStateTerminatedSimulationSimulationConfigurationscRates scPopulationscNewIdentifier scStartTime scSimDurationscValidPopulationscRequireCherry$fEqSimulationState$fShowSimulationStateReconstructedTreeRBranchRLeafPointProcessEvents ObservationpointProcessEventsmaybeReconstructedTreeobservedEventsreconstructedTreeEvents$fToJSONObservation$fFromJSONObservation$fShowReconstructedTree$fEqReconstructedTree$fShowObservation$fOrdObservation$fEqObservation$fGenericObservationNewickasNewickStringampersandBuilder colonBuilderleftBraceBuilderrightBraceBuilder commaBuildercatastrophePeopleBuilder$fNewickReconstructedTree eventPopDeltafirstSchedulednoScheduledEventpersonsInEventpeopleInEventsinfected infectedBy allEventsNTreeNSubtreeNLeaf NInternal NBranchSetNBranchNLengthNNameinitialIdentifier newPerson selectElem randomPersonsortcount'simulationWithGenIO simulationisReconTreeLeaf simulation'simulationWithSystemRandom finalSizeinhomExponential randInhomExp maybeToRight$fShowNSubtree$fShowNBranchSet $fShowNBranch $fShowNTree $fEqNTree $fEqNSubtree$fEqNBranchSet $fEqNBranchLogisticBDSDPopulationLogisticBDSDParametersparamsBirthRateparamsCapacityparamsDeathRateparamsSamplingRateparamsDisasters configuration randomEvent"$fPopulationLogisticBDSDPopulation=$fModelParametersLogisticBDSDParametersLogisticBDSDPopulation$fShowLogisticBDSDPopulation$fShowLogisticBDSDParameters InhomBDSPop InhomBDSRates inhomBDSRates$fPopulationInhomBDSPop)$fModelParametersInhomBDSRatesInhomBDSPop$fShowInhomBDSPopBDSCODPopulationBDSCODParameters$fPopulationBDSCODPopulation1$fModelParametersBDSCODParametersBDSCODPopulation$fShowBDSCODPopulationversion getBinDir getLibDir getDynLibDir getDataDir getLibexecDir getSysconfDirgetDataFileName