Balasubramanian Narasimhan

Balasubramanian Narasimhan

16 packages on CRAN

1 packages on Bioconductor

ASSISTant

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Clinical trial design for subgroup selection in three-stage group sequential trial. Includes facilities for design, exploration and analysis of such trials. An implementation of the initial DEFUSE-3 trial is also provided as a vignette.

bcaboot

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Computation of bootstrap confidence intervals in an almost automatic fashion.

cubature

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R wrappers around the cubature C library of Steven G. Johnson for adaptive multivariate integration over hypercubes and the Cuba C library of Thomas Hahn for deterministic and Monte Carlo integration. Scalar and vector interfaces for cubature and Cuba routines are provided; the vector interfaces are highly recommended as demonstrated in the package vignette.

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Empirical Bayes methods for learning prior distributions from data. An unknown prior distribution (g) has yielded (unobservable) parameters, each of which produces a data point from a parametric exponential family (f). The goal is to estimate the unknown prior ("g-modeling") by deconvolution and Empirical Bayes methods.

distcomp

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Implementing algorithms and fitting models when sites (possibly remote) share computation summaries rather than actual data over HTTP with a master R process (using 'opencpu', for example). A stratified Cox model and a singular value decomposition are provided. The former makes direct use of code from the R 'survival' package. (That is, the underlying Cox model code is derived from that in the R 'survival' package.) Sites may provide data via several means: CSV files, Redcap API, etc. An extensible design allows for new methods to be added in the future and includes facilities for local prototyping and testing. Web applications are provided (via 'shiny') for the implemented methods to help in designing and deploying the computations.

ECOSolveR

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R interface to the Embedded COnic Solver (ECOS), an efficient and robust C library for convex problems. Conic and equality constraints can be specified in addition to integer and boolean variable constraints for mixed-integer problems. This R interface is inspired by the python interface and has similar calling conventions.

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Homomorphic computations in R for privacy-preserving applications. Currently only the Paillier Scheme is implemented.

impute

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Imputation for microarray data (currently KNN only)

locfdr

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Computation of local false discovery rates.

sglr

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Functions for computing power and boundaries for pre-licensure vaccine trials using the Generalized Likelihood Ratio tests proposed by Shih, Lai, Heyse and Chen

sp23design

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Provides methods for generating, exploring and executing seamless Phase II-III designs of Lai, Lavori and Shih using generalized likelihood ratio statistics. Includes pdf and source files that describe the entire R implementation with the relevant mathematical details.

CVXR

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An object-oriented modeling language for disciplined convex programming (DCP). It allows the user to formulate convex optimization problems in a natural way following mathematical convention and DCP rules. The system analyzes the problem, verifies its convexity, converts it into a canonical form, and hands it off to an appropriate solver to obtain the solution.

glmnet

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Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial regression. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the papers listed in the URL below.

owl

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Efficient implementations for Sorted L-One Penalized Estimation (SLOPE): generalized linear models regularized with the sorted L1-norm (Bogdan et al. (2015) <doi:10/gfgwzt>) or, equivalently, ordered weighted L1-norm (OWL). Supported models include ordinary least-squares regression, binomial regression, multinomial regression, and Poisson regression. Both dense and sparse predictor matrices are supported. In addition, the package features predictor screening rules that enable fast and efficient solutions to high-dimensional problems.

pamr

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Some functions for sample classification in microarrays.

samr

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Significance Analysis of Microarrays for differential expression analysis, RNAseq data and related problems.

scs

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Solves convex cone programs via operator splitting. Can solve: linear programs ('LPs'), second-order cone programs ('SOCPs'), semidefinite programs ('SDPs'), exponential cone programs ('ECPs'), and power cone programs ('PCPs'), or problems with any combination of those cones. 'SCS' uses 'AMD' (a set of routines for permuting sparse matrices prior to factorization) and 'LDL' (a sparse 'LDL' factorization and solve package) from 'SuiteSparse' (<http://www.suitesparse.com>).