Found 2024 packages in 0.02 seconds
Bayesian Graphical Models using MCMC
Interface to the JAGS MCMC library.
Bayesian Inference for Multinomial Models with Inequality Constraints
Implements Gibbs sampling and Bayes factors for multinomial models with
linear inequality constraints on the vector of probability parameters. As
special cases, the model class includes models that predict a linear order
of binomial probabilities (e.g., p[1] < p[2] < p[3] < .50) and mixture models
assuming that the parameter vector p must be inside the convex hull of a
finite number of predicted patterns (i.e., vertices). A formal definition of
inequality-constrained multinomial models and the implemented computational
methods is provided in: Heck, D.W., & Davis-Stober, C.P. (2019).
Multinomial models with linear inequality constraints: Overview and improvements
of computational methods for Bayesian inference. Journal of Mathematical
Psychology, 91, 70-87.
Bayesian Super Imposition by Translation and Rotation Growth Curve Analysis
The Super Imposition by Translation and Rotation (SITAR) model
is a shape-invariant nonlinear mixed effect model that fits a natural cubic
spline mean curve to the growth data and aligns individual-specific growth
curves to the underlying mean curve via a set of random effects (see Cole,
2010
Extract and Visualize the Results of Multivariate Data Analyses
Provides some easy-to-use functions to extract and visualize the output of multivariate data analyses, including 'PCA' (Principal Component Analysis), 'CA' (Correspondence Analysis), 'MCA' (Multiple Correspondence Analysis), 'FAMD' (Factor Analysis of Mixed Data), 'MFA' (Multiple Factor Analysis) and 'HMFA' (Hierarchical Multiple Factor Analysis) functions from different R packages. It contains also functions for simplifying some clustering analysis steps and provides 'ggplot2' - based elegant data visualization.
Algorithms and Framework for Nonnegative Matrix Factorization (NMF)
Provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.
Bayesian Network Structure Learning, Parameter Learning and Inference
Bayesian network structure learning, parameter learning and inference. This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC, Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu Search) and hybrid (MMHC, RSMAX2, H2PC) structure learning algorithms for discrete, Gaussian and conditional Gaussian networks, along with many score functions and conditional independence tests. The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented. Some utility functions (model comparison and manipulation, random data generation, arc orientation testing, simple and advanced plots) are included, as well as support for parameter estimation (maximum likelihood and Bayesian) and inference, conditional probability queries, cross-validation, bootstrap and model averaging. Development snapshots with the latest bugfixes are available from < https://www.bnlearn.com/>.
Vector Representing a Random Variable
Random vectors, called rvecs. An rvec holds multiple draws, but tries to behave like a standard R vector, including working well in data frames. Rvecs are useful for working with output from a simulation or a Bayesian analysis.
Fast Creation of Dummy (Binary) Columns and Rows from Categorical Variables
Creates dummy columns from columns that have categorical variables (character or factor types). You can also specify which columns to make dummies out of, or which columns to ignore. Also creates dummy rows from character, factor, and Date columns. This package provides a significant speed increase from creating dummy variables through model.matrix().
Bayesian Additive Regression Trees
Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary, categorical and time-to-event outcomes. For more information see Sparapani, Spanbauer and McCulloch
Tidy Data and 'Geoms' for Bayesian Models
Compose data for and extract, manipulate, and visualize posterior draws from Bayesian models ('JAGS', 'Stan', 'rstanarm', 'brms', 'MCMCglmm', 'coda', ...) in a tidy data format. Functions are provided to help extract tidy data frames of draws from Bayesian models and that generate point summaries and intervals in a tidy format. In addition, 'ggplot2' 'geoms' and 'stats' are provided for common visualization primitives like points with multiple uncertainty intervals, eye plots (intervals plus densities), and fit curves with multiple, arbitrary uncertainty bands.