|
r-bmrv
|
public |
Provides two Bayesian models for detecting the association between rare genetic variants and a trait that can be continuous, ordinal or binary. Bayesian latent variable collapsing model (BLVCM) detects interaction effect and is dedicated to twin design while it can also be applied to independent samples. Hierarchical Bayesian multiple regression model (HBMR) incorporates genotype uncertainty information and can be applied to either independent or family samples. Furthermore, it deals with continuous, binary and ordinal traits.
|
2025-04-22 |
|
r-bmixture
|
public |
Provides statistical tools for Bayesian estimation for finite mixture of distributions, mainly mixture of Gamma, Normal and t-distributions. The package is implemented the recent improvements in Bayesian literature for the finite mixture of distributions, including Mohammadi and et al. (2013) <doi:10.1007/s00180-012-0323-3> and Mohammadi and Salehi-Rad (2012) <doi:10.1080/03610918.2011.588358>.
|
2025-04-22 |
|
r-bmix
|
public |
This is a bare-bones implementation of sampling algorithms for a variety of Bayesian stick-breaking (marginally DP) mixture models, including particle learning and Gibbs sampling for static DP mixtures, particle learning for dynamic BAR stick-breaking, and DP mixture regression. The software is designed to be easy to customize to suit different situations and for experimentation with stick-breaking models. Since particles are repeatedly copied, it is not an especially efficient implementation.
|
2025-04-22 |
|
r-bmamevt
|
public |
Toolkit for Bayesian estimation of the dependence structure in multivariate extreme value parametric models.
|
2025-04-22 |
|
r-blsm
|
public |
Provides a Bayesian latent space model for complex networks, either weighted or unweighted. Given an observed input graph, the estimates for the latent coordinates of the nodes are obtained through a Bayesian MCMC algorithm. The overall likelihood of the graph depends on a fundamental probability equation, which is defined so that ties are more likely to exist between nodes whose latent space coordinates are close. The package is mainly based on the model by Hoff, Raftery and Handcock (2002) <doi:10.1198/016214502388618906> and contains some extra features (e.g., removal of the Procrustean step, weights implemented as coefficients of the latent distances, 3D plots). The original code related to the above model was retrieved from <https://www.stat.washington.edu/people/pdhoff/Code/hoff_raftery_handcock_2002_jasa/>. Users can inspect the MCMC simulation, create and customize insightful graphical representations or apply clustering techniques.
|
2025-04-22 |
|
r-blr
|
public |
Bayesian Linear Regression.
|
2025-04-22 |
|
r-blockmodels
|
public |
Latent and Stochastic Block Model estimation by a Variational EM algorithm. Various probability distribution are provided (Bernoulli, Poisson...), with or without covariates.
|
2025-04-22 |
|
r-blockforest
|
public |
A random forest variant 'block forest' ('BlockForest') tailored to the prediction of binary, survival and continuous outcomes using block-structured covariate data, for example, clinical covariates plus measurements of a certain omics data type or multi-omics data, that is, data for which measurements of different types of omics data and/or clinical data for each patient exist. Examples of different omics data types include gene expression measurements, mutation data and copy number variation measurements. Block forest are presented in Hornung & Wright (2019). The package includes four other random forest variants for multi-omics data: 'RandomBlock', 'BlockVarSel', 'VarProb', and 'SplitWeights'. These were also considered in Hornung & Wright (2019), but performed worse than block forest in their comparison study based on 20 real multi-omics data sets. Therefore, we recommend to use block forest ('BlockForest') in applications. The other random forest variants can, however, be consulted for academic purposes, for example, in the context of further methodological developments. Reference: Hornung, R. & Wright, M. N. (2019) Block Forests: random forests for blocks of clinical and omics covariate data. BMC Bioinformatics 20:358. <doi:10.1186/s12859-019-2942-y>.
|
2025-04-22 |
|
r-blockfest
|
public |
An R implementation of an extension of the 'BayeScan' software (Foll, 2008) <DOI:10.1534/genetics.108.092221> for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this new approach is the identification of genomic regions, genes, or gene sets containing one or more SNPs that evolved under directional selection.
|
2025-04-22 |
|
r-blatr
|
public |
A wrapper around the 'Blat' command line SMTP mailer for Windows. 'Blat' is public domain software, but be sure to read the license before use. It can be found at the Blat website http://www.blat.net.
|
2025-04-22 |
|
r-bkpc
|
public |
Bayesian kernel projection classifier is a nonlinear multicategory classifier which performs the classification of the projections of the data to the principal axes of the feature space. A Gibbs sampler is implemented to find the posterior distributions of the parameters.
|
2025-04-22 |
|
r-bivrec
|
public |
Alternating recurrent event data arise frequently in biomedical and social sciences where 2 types of events such as hospital admissions and discharge occur alternatively over time. As such we implement a collection of non-parametric and semiparametric methods to analyze such data. The main functions are biv.rec.fit() and biv.rec.np(). Use biv.rec.fit() for estimation of covariate effects on the two alternating event gap times (xij and yij) using semiparametric methods. The method options are "Lee.et.al" and "Chang". Use biv.rec.np() for estimation of the joint cumulative distribution function (cdf) for the two alternating events gap times (xij and yij) as well as the marginal survival function for type I gap times (xij) and the conditional cdf of the type II gap times (yij) given an interval of type I gap times (xij) in a non-parametric fashion. The package also provides options to simulate and visualize the data and results of analysis.
|
2025-04-22 |
|
r-bitsqueezr
|
public |
Provides a implementation of floating-point quantization algorithms for use in precision-preserving compression, similar to the approach taken in the 'netCDF operators' (NCO) software package and described in Zender (2016) <doi:10.5194/gmd-2016-63>.
|
2025-04-22 |
|
r-bitrugs
|
public |
MCMC methods to estimate transmission dynamics and infection routes in hospitals using genomic sampling data.
|
2025-04-22 |
|
r-biopn
|
public |
bioPN is a package suited to perform simulation of deterministic and stochastic systems of biochemical reaction networks. Models are defined using a subset of Petri Nets, in a way that is close at how chemical reactions are defined. For deterministic solutions, bioPN creates the associated system of differential equations "on the fly", and solves it with a Runge Kutta Dormand Prince 45 explicit algorithm. For stochastic solutions, bioPN offers variants of Gillespie algorithm, or SSA. For hybrid deterministic/stochastic, it employs the Haseltine and Rawlings algorithm, that partitions the system in fast and slow reactions. bioPN algorithms are developed in C to achieve adequate performance.
|
2025-04-22 |
|
r-bio3d
|
public |
Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
|
2025-04-22 |
|
r-binostics
|
public |
Calculates graph theoretic scagnostics. Scagnostics describe various measures of interest for pairs of variables, based on their appearance on a scatterplot. They are useful tool for discovering interesting or unusual scatterplots from a scatterplot matrix, without having to look at every individual plot.
|
2025-04-22 |
|
r-binom
|
public |
Constructs confidence intervals on the probability of success in a binomial experiment via several parameterizations
|
2025-04-22 |
|
r-bild
|
public |
Performs logistic regression for binary longitudinal data, allowing for serial dependence among observations from a given individual and a random intercept term. Estimation is via maximization of the exact likelihood of a suitably defined model. Missing values and unbalanced data are allowed, with some restrictions.
|
2025-04-22 |
|
r-bigvar
|
public |
Estimates VAR and VARX models with structured Lasso Penalties.
|
2025-04-22 |
|
r-bigtcr
|
public |
For studying recurrent disease and death with competing risks, comparisons based on the well-known cumulative incidence function can be confounded by different prevalence rates of the competing events. Alternatively, comparisons of the conditional distribution of the survival time given the failure event type are more relevant for investigating the prognosis of different patterns of recurrence disease. This package implements a nonparametric estimator for the conditional cumulative incidence function and a nonparametric conditional bivariate cumulative incidence function for the bivariate gap times proposed in Huang et al. (2016) <doi:10.1111/biom.12494>.
|
2025-04-22 |
|
r-bigsplines
|
public |
Fits smoothing spline regression models using scalable algorithms designed for large samples. Seven marginal spline types are supported: linear, cubic, different cubic, cubic periodic, cubic thin-plate, ordinal, and nominal. Random effects and parametric effects are also supported. Response can be Gaussian or non-Gaussian: Binomial, Poisson, Gamma, Inverse Gaussian, or Negative Binomial.
|
2025-04-22 |
|
r-biglmm
|
public |
Regression for data too large to fit in memory. This package functions exactly like the 'biglm' package, but works with later versions of R.
|
2025-04-22 |
|
r-biglm
|
public |
Regression for data too large to fit in memory
|
2025-04-22 |
|
r-bigintegeralgos
|
public |
Features the multiple polynomial quadratic sieve algorithm for factoring large integers and a vectorized factoring function that returns the complete factorization of an integer. Utilizes the C library GMP (GNU Multiple Precision Arithmetic) and classes created by Antoine Lucas et al. found in the 'gmp' package.
|
2025-04-22 |
