Types

Type Members

trait CsvRow[T] extends AnyRef

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

Syntax for CsvRow
trait DataSet[D] extends AnyRef

Data set type class, for ABC methods
type DoubleState = DenseVector[Double]

Alias for a Breeze DenseVector[Double]
type HazardVec = DenseVector[Double]

Type for a SPN hazard vector
type IntState = DenseVector[Int]

Alias for a Breeze DenseVector[Int]
type LogLik = Double

Type representing log-likelihoods - just an alias for 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.
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] with Product with Serializable

Case class for SPNs that include an initial marking
trait Observation[O] extends CsvRow[O]

Observation type class, with implementations for Ints and Doubles
sealed trait Spn[S] extends AnyRef

Main trait for stochastic Petri nets (SPNs)
trait State[S] extends CsvRow[S]

State type class, with implementations for Breeze DenseVector Ints and Doubles
trait Thinnable[F[_]] extends AnyRef

A type class for things which can be "thinned", with an implementation for Stream.
A type class for things which can be "thinned", with an implementation for Stream. Useful for MCMC algorithms.
implicit class ThinnableSyntax[T, F[T]] extends AnyRef

Provision of the .thin syntax for Thinnable things
type Time = 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
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] with Product with Serializable

Case class for SPNs without an initial marking

Value Members

final def !=(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def ##(): Int

Definition Classes
AnyRef → Any
final def ==(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def asInstanceOf[T0]: T0

Definition Classes
Any
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
implicit val dvdObs: Observation[DoubleState]

Evidence that DoubleState belongs to the Observation type class
implicit val dvdState: State[DoubleState]

Evidence that DoubleState belongs to the State type class
implicit val dviObs: Observation[IntState]

Evidence that IntState belongs to the Observation type class
implicit val dviState: State[IntState]

Evidence that IntState belongs to the State type class
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def equals(arg0: Any): Boolean

Definition Classes
AnyRef → Any
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
final def getClass(): Class[_]

Definition Classes
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def hashCode(): Int

Definition Classes
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final def isInstanceOf[T0]: Boolean

Definition Classes
Any
final def ne(arg0: AnyRef): Boolean

Definition Classes
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final def notify(): Unit

Definition Classes
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final def notifyAll(): Unit

Definition Classes
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implicit val streamThinnable: Thinnable[Stream]

A Thinnable instance for Stream
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
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def toString(): String

Definition Classes
AnyRef → Any
implicit val tsdsDs: DataSet[Ts[DoubleState]]

Evidence that Ts[DoubleState] is a DataSet
implicit val tsisDs: DataSet[Ts[IntState]]

Evidence that Ts[IntState] is a DataSet
final def wait(): Unit

Definition Classes
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Annotations
@throws( ... )
final def wait(arg0: Long, arg1: Int): Unit

Definition Classes
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Annotations
@throws( ... )
final def wait(arg0: Long): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )

Related Doc: package smfsb

object Types

Type Members

trait CsvRow[T] extends AnyRef

implicit class CsvRowSyntax[T] extends AnyRef

trait DataSet[D] extends AnyRef

type DoubleState = DenseVector[Double]

type HazardVec = DenseVector[Double]

type IntState = DenseVector[Int]

type LogLik = Double

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] with Product with Serializable

trait Observation[O] extends CsvRow[O]

sealed trait Spn[S] extends AnyRef

trait State[S] extends CsvRow[S]

trait Thinnable[F[_]] extends AnyRef

implicit class ThinnableSyntax[T, F[T]] extends AnyRef

type Time = Double

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

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] with Product with Serializable

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

final def asInstanceOf[T0]: T0

def clone(): AnyRef

implicit val dvdObs: Observation[DoubleState]

implicit val dvdState: State[DoubleState]

implicit val dviObs: Observation[IntState]

implicit val dviState: State[IntState]

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

final def getClass(): Class[_]

def hashCode(): Int

final def isInstanceOf[T0]: Boolean

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

implicit val streamThinnable: Thinnable[Stream]

final def synchronized[T0](arg0: ⇒ T0): T0

def toString(): String

implicit val tsdsDs: DataSet[Ts[DoubleState]]

implicit val tsisDs: DataSet[Ts[IntState]]

final def wait(): Unit

final def wait(arg0: Long, arg1: Int): Unit

final def wait(arg0: Long): Unit

Inherited from AnyRef

Inherited from Any

Ungrouped