scala-smfsb/smfsb

smfsb

package smfsb

Type members

Classlikes

object Abc

Functions for parameter inference using ABC (and ABC-SMC) methods

Functions for parameter inference using ABC (and ABC-SMC) methods

trait CsvRow[T]

Type class for vectors that can be rendered to a CSV string (and a Breeze DenseVector[Double]), extended by State

Type class for vectors that can be rendered to a CSV string (and a Breeze DenseVector[Double]), extended by State

class CsvRowSyntax[T](value: T)

Syntax for CsvRow

Syntax for CsvRow

trait DataSet[D]

Data set type class, for ABC methods

Data set type class, for ABC methods

case class MarkedSpn[S](species: List[String], m: S, pre: DenseMatrix[Int], post: DenseMatrix[Int], h: (S, Time) => HazardVec)(implicit evidence$2: State[S]) extends Spn[S]

Case class for SPNs that include an initial marking

Case class for SPNs that include an initial marking

object Mcmc

Functions for constucting generic Metropolis-Hastings MCMC algorithms, and associated utilities. Can be used in conjunction with an unbiased estimate of marginal model likelihood for constructing pseudo-marginal MCMC algorithms, such as PMMH pMCMC.

Functions for constucting generic Metropolis-Hastings MCMC algorithms, and associated utilities. Can be used in conjunction with an unbiased estimate of marginal model likelihood for constructing pseudo-marginal MCMC algorithms, such as PMMH pMCMC.

object Mll

Functions associated with particle filtering of Markov process models against time series data and the computation of marginal model likelihoods.

Functions associated with particle filtering of Markov process models against time series data and the computation of marginal model likelihoods.

case class PMatrix[T](x: Int, y: Int, r: Int, c: Int, data: ParVector[T])

Comonadic pointed 2d image/matrix type (parallel implementation), used by the spatial simulation functions.

Comonadic pointed 2d image/matrix type (parallel implementation), used by the spatial simulation functions.

Companion
object
case object PMatrix
Companion
class
case class PVector[T](cur: Int, vec: ParVector[T])

Comonadic pointed vector type (parallel implementation), used by the spatial simulation functions.

Comonadic pointed vector type (parallel implementation), used by the spatial simulation functions.

object Sim

Functions for simulating data associated with a Markov process given an appropriate transition kernel.

Functions for simulating data associated with a Markov process given an appropriate transition kernel.

object Spatial

All functions and utilities relating to spatial simulation

All functions and utilities relating to spatial simulation

sealed trait Spn[S]

Main trait for stochastic Petri nets (SPNs)

Main trait for stochastic Petri nets (SPNs)

object SpnModels

Some example SPN models, each of which can be instantiated with either discrete or continous states.

Some example SPN models, each of which can be instantiated with either discrete or continous states.

trait State[S] extends CsvRow[S]

State type class, with implementations for Breeze DenseVector Ints and Doubles

State type class, with implementations for Breeze DenseVector Ints and Doubles

object Step

Functions which accept a Spn and return a function for simulating from the transition kernel of that model

Functions which accept a Spn and return a function for simulating from the transition kernel of that model

trait Thinnable[F[_]]

A type class for things which can be "thinned", with an implementation for Stream. Useful for MCMC algorithms.

A type class for things which can be "thinned", with an implementation for Stream. Useful for MCMC algorithms.

class ThinnableSyntax[T, F[T]](value: F[T])

Provision of the .thin syntax for Thinnable things

Provision of the .thin syntax for Thinnable things

case class UnmarkedSpn[S](species: List[String], pre: DenseMatrix[Int], post: DenseMatrix[Int], h: (S, Time) => HazardVec)(implicit evidence$1: State[S]) extends Spn[S]

Case class for SPNs without an initial marking

Case class for SPNs without an initial marking

Types

type DoubleState = DenseVector[Double]

Alias for a Breeze DenseVector[Double]

Alias for a Breeze DenseVector[Double]

type HazardVec = DenseVector[Double]

Type for a SPN hazard vector

Type for a SPN hazard vector

type IntState = DenseVector[Int]

Alias for a Breeze DenseVector[Int]

Alias for a Breeze DenseVector[Int]

type LogLik = Double

Type representing log-likelihoods - just an alias for Double. All likelihoods in this library are on a log scale. There should be no raw likelihoods passed into or out of any user-facing function.

Type representing log-likelihoods - just an alias for Double. All likelihoods in this library are on a log scale. There should be no raw likelihoods passed into or out of any user-facing function.

type Time = Double

Type representing time, but just an alias for Double

Type representing time, but just an alias for Double

type Ts[S] = List[(Time, S)]

The main time series class, for representing output from simulation functions, and for observed time course data

The main time series class, for representing output from simulation functions, and for observed time course data

Implicits

Implicits

implicit val dvdState: State[DoubleState]

Evidence that DoubleState belongs to the State type class

Evidence that DoubleState belongs to the State type class

implicit val dviState: State[IntState]

Evidence that IntState belongs to the State type class

Evidence that IntState belongs to the State type class

implicit val streamThinnable: Thinnable[LazyList]

A Thinnable instance for Stream

A Thinnable instance for Stream

implicit val tsdsDs: DataSet[Ts[DoubleState]]

Evidence that Ts[DoubleState] is a DataSet

Evidence that Ts[DoubleState] is a DataSet

implicit val tsisDs: DataSet[Ts[IntState]]

Evidence that Ts[IntState] is a DataSet

Evidence that Ts[IntState] is a DataSet