Package

com.github.jonnylaw

model

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package model

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Type Members

  1. case class Branch[A](left: Tree[A], right: Tree[A]) extends Tree[A] with Product with Serializable

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  2. case class BranchParameter(left: Parameters, right: Parameters) extends Parameters with Product with Serializable

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  3. case class BrownianParameter(m0: DenseVector[Double], c0: DenseVector[Double], mu: DenseVector[Double], sigma: DenseVector[Double]) extends SdeParameter with Product with Serializable

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  4. trait Collection[F[_]] extends Foldable[F] with MonoidK[F] with Monad[F]

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    A typeclass representing a Collection with a few additional features required for implementing the particle filter

  5. case class CredibleInterval(lower: Double, upper: Double) extends Product with Serializable

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    Credible intervals from a set of samples in a distribution

    Credible intervals from a set of samples in a distribution

    lower

    the lower interval

    upper

    the upper interval

  6. sealed trait Data extends AnyRef

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    A single observation of a time series

  7. trait DataService extends AnyRef

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  8. type Eta = Double

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  9. case class Filter[F[_]](mod: Model, resample: Resample[F, State])(implicit evidence$1: Collection[F]) extends ParticleFilter[F] with Product with Serializable

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  10. case class FilterLgcp(mod: Model, resample: Resample[List, State], precision: Int) extends ParticleFilter[List] with Product with Serializable

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  11. case class FilterParallel(mod: Model, resample: Resample[ParVector, State], parallelism: Int) extends ParticleFilter[ParVector] with Product with Serializable

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    Particle filter which uses ParVector to represent the collection of particles, parallelism specifies the level of parallelism using a scala.concurrent.forkjoin.ForkJoinPool

    Particle filter which uses ParVector to represent the collection of particles, parallelism specifies the level of parallelism using a scala.concurrent.forkjoin.ForkJoinPool

    mod

    the model to use for filtering

    resample

    the resampling scheme

    parallelism

    the level of parallism

  12. case class FilterSequential(mod: Model, resample: Resample[List, State]) extends ParticleFilter[List] with Product with Serializable

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  13. case class ForecastOut(t: Time, obs: Observation, obsIntervals: CredibleInterval, eta: Double, etaIntervals: CredibleInterval, state: State, stateIntervals: IndexedSeq[CredibleInterval]) extends Product with Serializable

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    Forecast data

    Forecast data

    t

    the time of the observation

    obs

    an observation of the process

    obsIntervals

    the upper and lower credible intervals of the observation

    state

    the untransformed latent state

    stateIntervals

    the intervals of the latent state

  14. type Gamma = Double

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  15. case class Leaf[A](value: A) extends Tree[A] with Product with Serializable

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  16. case class LeafParameter(scale: Option[Double], sdeParam: SdeParameter) extends Parameters with Product with Serializable

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  17. type LogLikelihood = Double

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  18. case class MetropState(ll: LogLikelihood, params: Parameters, accepted: Int) extends Product with Serializable

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    The state of the metropolis-hastings algorithms

    The state of the metropolis-hastings algorithms

    ll

    the log-likelihood of the observations given the latent state and the current parameters

    params

    the current set of parameters

    accepted

    the total number of accepted moves in the metropolis hastings algorithm

  19. trait MetropolisHastings extends AnyRef

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  20. trait Model extends AnyRef

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  21. type Observation = Double

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  22. case class ObservationWithState(t: Time, observation: Observation, eta: Eta, gamma: Gamma, sdeState: State) extends Data with Product with Serializable

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    A single observation of a time series, containing a realisation of the filtering state

    A single observation of a time series, containing a realisation of the filtering state

    observation

    pi(eta), the observation

    eta

    g(gamma), the latent state transformed by the linking-function

    gamma

    f(x_t), the latent state transformed by the linear transformation

    sdeState

    x_t

  23. case class OrnsteinParameter(m0: DenseVector[Double], c0: DenseVector[Double], theta: DenseVector[Double], alpha: DenseVector[Double], sigma: DenseVector[Double]) extends SdeParameter with Product with Serializable

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  24. sealed trait Parameters extends AnyRef

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  25. trait ParticleFilter[F[_]] extends AnyRef

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  26. case class ParticleMetropolis(logLikelihood: (Parameters) ⇒ LogLikelihood, initialParams: Parameters, proposal: (Parameters) ⇒ Rand[Parameters], prior: (Parameters) ⇒ LogLikelihood) extends MetropolisHastings with Product with Serializable

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    Implementation of the particle metropolis algorithm

    Implementation of the particle metropolis algorithm

    logLikelihood

    a function from parameters to LogLikelihood

    initialParams

    the starting parameters for the metropolis algorithm

    proposal

    a SYMMETRIC proposal distribution for the metropolis algorithm (eg. Gaussian)

  27. case class ParticleMetropolisHastings(logLikelihood: (Parameters) ⇒ LogLikelihood, transitionProb: (Parameters, Parameters) ⇒ LogLikelihood, proposal: (Parameters) ⇒ Rand[Parameters], initialParams: Parameters, prior: (Parameters) ⇒ LogLikelihood) extends MetropolisHastings with Product with Serializable

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    Implementation of the particle metropolis hastings algorithm specified prior distribution

    Implementation of the particle metropolis hastings algorithm specified prior distribution

    logLikelihood

    a function from parameters to LogLikelihood

    proposal

    a generic proposal distribution for the metropolis algorithm (eg. Gaussian)

    initialParams

    the starting parameters for the metropolis algorithm

  28. case class PfOut(time: Time, observation: Option[Observation], eta: Double, etaIntervals: CredibleInterval, state: State, stateIntervals: IndexedSeq[CredibleInterval]) extends Product with Serializable

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    A class representing a return type for the particle filter, containing the state and associated credible intervals

    A class representing a return type for the particle filter, containing the state and associated credible intervals

    time

    the time of the process

    observation

    an optional observation, note discretely observed processes cannot be seen at all time points continuously

    state

    the mean of the empirical filtering distribution at time 'time'

  29. case class PfState[F[_]](t: Time, observation: Option[Observation], particles: F[State], ll: LogLikelihood, ess: Int) extends Product with Serializable

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    Representation of the state of the particle filter, where the particles are in a Collection typeclass defined in package.scala

    Representation of the state of the particle filter, where the particles are in a Collection typeclass defined in package.scala

    t

    the time of the current observation

    observation

    the current observation at time t

    particles

    a collection containing an approximate sample from the filtering distribution p(x(t) | y(t0:t))

    ll

    the estimated log-likelihood of the path given the observations so far

    ess

    the effective sample size

  30. type Resample[F[_], A] = (F[A], F[LogLikelihood]) ⇒ F[A]

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  31. trait Sde extends AnyRef

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  32. sealed trait SdeParameter extends AnyRef

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  33. case class SimulatedData(model: Model) extends DataService with Product with Serializable

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  34. type State = Tree[DenseVector[Double]]

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  35. case class StateSpace(time: Time, state: State) extends Product with Serializable

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    Representing a realisation from a stochastic differential equation

  36. type StepFunction = (SdeParameter) ⇒ (State, TimeIncrement) ⇒ Rand[State]

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  37. type Time = Double

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  38. type TimeIncrement = Double

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  39. case class TimedObservation(t: Time, observation: Observation) extends Data with Product with Serializable

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    A single observation of a time series

    A single observation of a time series

    observation

    pi(eta), the observation

  40. sealed trait Tree[A] extends AnyRef

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    A binary tree implementation, to be used when combining models Hopefully this simplifies "zooming" into values and changing them

  41. type UnparamModel = Kleisli[Id, Parameters, Model]

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  42. type UnparamSde = Kleisli[Id, SdeParameter, Sde]

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Value Members

  1. object EmptyParameter extends Parameters with Product with Serializable

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  2. object Model

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  3. object Parameters

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  4. object ParticleFilter

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  5. object Sde

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  6. object SdeParameter

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  7. object SimulateData

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  8. object Tree

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  9. implicit def credibleIntervalsShow: Show[CredibleInterval]

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  10. implicit def dataShow(implicit S: Show[State]): Show[Data]

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  11. implicit def filterOutShow(implicit S: Show[State], C: Show[CredibleInterval]): Show[PfOut]

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  12. implicit def filterShow[F[_]](implicit arg0: Collection[F], S: Show[State]): Show[PfState[F]]

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  13. implicit def forecastOutShow(implicit S: Show[State]): Show[ForecastOut]

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  14. implicit def fromProcess[F[_], A](iter: Process[A]): Stream[F, A]

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  15. implicit def itersShow(implicit S: Show[Parameters]): Show[MetropState]

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  16. implicit def listCollection: Collection[List]

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  17. implicit def numericDenseVector: Numeric[DenseVector[Double]]

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  18. implicit def parVectorCollection: Collection[ParVector]

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  19. implicit def parameterShow(implicit S: Show[SdeParameter]): Show[Parameters]

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  20. implicit def randMonad: Monad[Rand]

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  21. implicit def sdeParamShow: Show[SdeParameter]

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  22. implicit val stateShow: Show[State]

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