% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/phasic-package.R
\docType{package}
\name{phasic-package}
\alias{phasic-package}
\title{phasic: Phase-Type Distribution Algorithms}
\description{
High-performance library for computing with phase-type distributions using graph-based algorithms. Provides R interface to Python implementation via 'reticulate'. Phase-type distributions model time until absorption in continuous or discrete-time Markov chains. Includes methods for graph construction via create_graph(), reward transformation, moment computation, trace-based elimination with record_elimination_trace(), and Bayesian inference via Stein Variational Gradient Descent (SVGD). Implements algorithms from Røikjer, Hobolth & Munch (2022) \doi{10.1007/s11222-022-10155-6}.

High-performance library for computing with phase-type distributions using
graph-based algorithms. This R package provides an interface to the Python
implementation via reticulate.
}
\details{
Phase-type distributions model the time until absorption in continuous or
discrete-time Markov chains. This package uses graph-based algorithms that
are 10-100x faster than traditional matrix methods for sparse systems.

Key features:
\itemize{
\item Graph construction with callbacks or manual building
\item PDF/PMF computation via forward algorithm
\item Reward transformation for multivariate distributions
\item Trace-based elimination for efficient parameter evaluation
\item Bayesian inference via SVGD (Stein Variational Gradient Descent)
\item JAX integration for automatic differentiation
}
}
\section{Main functions}{

\itemize{
\item \code{\link{create_graph}}: Create phase-type distribution graph
\item \code{\link{record_elimination_trace}}: Record trace for efficient evaluation
\item \code{\link{run_svgd}}: Bayesian inference via SVGD
\item \code{\link{Graph}}: R6 class for graph objects
}
}

\references{
Røikjer, T., Hobolth, A., & Munch, K. (2022).
Phase-type distributions in population genetics.
\emph{Statistics and Computing}, 32(5), 1-21.
\doi{10.1007/s11222-022-10155-6}
}
\seealso{
Useful links:
\itemize{
  \item \url{https://github.com/munch-group/phasic}
  \item Report bugs at \url{https://github.com/munch-group/phasic/issues}
}


Useful links:
\itemize{
  \item \url{https://github.com/munch-group/phasic}
  \item Report bugs at \url{https://github.com/munch-group/phasic/issues}
}

}
\author{
\strong{Maintainer}: Kasper Munch \email{kaspermunch@birc.au.dk}

Authors:
\itemize{
  \item Tobias Røikjer
  \item Asger Hobolth
}

}
\keyword{internal}
