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gR

catnet

A package that handles discrete Bayesian network models and provides inference using the frequentist approach

parcor

The package estimates the matrix of partial correlations based on different regularized regression methods: lasso, adaptive lasso, PLS, and Ridge Regression. In addition, the package provides model selection for lasso, adaptive lasso and Ridge regression based on cross-validation.

gRc

Estimation, model selection and other aspects of statistical inference in Graphical Gaussian models with edge and vertex symmetries (Graphical Gaussian models with colours)

gRain

A package for probability propagation in graphical independence networks, also known as probabilistic expert systems or Bayesian networks.

ergm

An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGM). "ergm" is a part of the "statnet" suite of packages for network analysis.

diagram

Visualises simple graphs (networks) based on a transition matrix, utilities to plot flow diagrams, visualising webs, electrical networks, ... Support for the books "A practical guide to ecological modelling - using R as a simulation platform" by Karline Soetaert and Peter M.J. Herman (2009). Springer. and the book "Solving Differential Equations in R" by Karline Soetaert, Jeff Cash and Francesca Mazzia. Springer. Includes demo(flowchart), demo(plotmat), demo(plotweb)

pcalg

Standard and robust estimation of the equivalence class of a Directed Acyclic Graph (DAG) via the PC-Algorithm. The equivalence class is represented by its (unique) Completete Partially Directed Acyclic Graph (CPDAG). Furthermore, a PAG instead of a CPDAG can be estimated if latent variables and/or selection variables are assumed to be present. FCI and RFCI are available for estimating PAGs. Functions for causal inference using the IDA algorithm (based on do-calculus of Judea Pearl) are provided for CPDAGs.

mimR

An R interface to MIM for graphical modelling in R

BRugs

Fully-interactive R interface to the OpenBUGS software for Bayesian analysis using MCMC sampling. Runs natively and stably in 32-bit R under Windows. Versions running on Linux and on 64-bit R under Windows are in "beta" status and less efficient.

rbugs

Functions to prepare files needed for running BUGS in batch-mode, and running BUGS from R. Support for Linux and Windows systems with OpenBugs is emphasized.