Robert Tibshirani

Robert Tibshirani

16 packages on CRAN

1 packages on Bioconductor

acepack

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Two nonparametric methods for multiple regression transform selection are provided. The first, Alternative Conditional Expectations (ACE), is an algorithm to find the fixed point of maximal correlation, i.e. it finds a set of transformed response variables that maximizes R^2 using smoothing functions [see Breiman, L., and J.H. Friedman. 1985. "Estimating Optimal Transformations for Multiple Regression and Correlation". Journal of the American Statistical Association. 80:580-598. <doi:10.1080/01621459.1985.10478157>]. Also included is the Additivity Variance Stabilization (AVAS) method which works better than ACE when correlation is low [see Tibshirani, R.. 1986. "Estimating Transformations for Regression via Additivity and Variance Stabilization". Journal of the American Statistical Association. 83:394-405. <doi:10.1080/01621459.1988.10478610>]. A good introduction to these two methods is in chapter 16 of Frank Harrel's "Regression Modeling Strategies" in the Springer Series in Statistics.

clogitL1

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Tools for the fitting and cross validation of exact conditional logistic regression models with lasso and elastic net penalties. Uses cyclic coordinate descent and warm starts to compute the entire path efficiently.

compHclust

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Performs the complementary hierarchical clustering procedure and returns X' (the expected residual matrix) and a vector of the relative gene importances.

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Customized training is a simple technique for transductive learning, when the test covariates are known at the time of training. The method identifies a subset of the training set to serve as the training set for each of a few identified subsets in the training set. This package implements customized training for the glmnet() and cv.glmnet() functions.

FLLat

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Fits the Fused Lasso Latent Feature model, which is used for modeling multi-sample aCGH data to identify regions of copy number variation (CNV). Produces a set of features that describe the patterns of CNV and a set of weights that describe the composition of each sample. Also provides functions for choosing the optimal tuning parameters and the appropriate number of features, and for estimating the false discovery rate.

Interact

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This package searches for marginal interactions in a binary response model. Interact uses permutation methods to estimate false discovery rates for these marginal interactions and has some, limited visualization capabilities

lpc

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Implements the LPC method of Witten&Tibshirani(Annals of Applied Statistics 2008) for identification of significant genes in a microarray experiment.

neariso

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Implements a path algorithm for Near-Isotonic Regression. For more details see the help files.

npmr

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Fit multinomial logistic regression with a penalty on the nuclear norm of the estimated regression coefficient matrix, using proximal gradient descent. Reference: Powers S, Hastie T and Tibshirani R (2018) <doi:10.1177/1471082X18777669>.

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Ordered lasso and time-lag sparse regression. Ordered Lasso fits a linear model and imposes an order constraint on the coefficients. It writes the coefficients as positive and negative parts, and requires positive parts and negative parts are non-increasing and positive. Time-Lag Lasso generalizes the ordered Lasso to a general data matrix with multiple predictors. For more details, see Suo, X.,Tibshirani, R., (2014) 'An Ordered Lasso and Sparse Time-lagged Regression'.

pcLasso

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A method for fitting the entire regularization path of the principal components lasso for linear and logistic regression models. The algorithm uses cyclic coordinate descent in a path-wise fashion. See URL below for more information on the algorithm. See Tay, K., Friedman, J. ,Tibshirani, R., (2014) 'Principal component-guided sparse regression' <arXiv:1810.04651>.

pliable

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Fits a pliable lasso model. For details see Tibshirani and Friedman (2018) <arXiv:1712.00484>.

protoclass

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Greedy algorithm described in Bien and Tibshirani (2011) Prototype Selection for Interpretable Classification. Annals of Applied Statistics. 5(4). 2403-2424

relgam

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A method for fitting the entire regularization path of the reluctant generalized additive model (RGAM) for linear regression, logistic, Poisson and Cox regression models. See Tay, J. K., and Tibshirani, R., (2019) <arXiv:1912.01808> for details.

impute

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Imputation for microarray data (currently KNN only)

scout

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Implements the Scout method for regression, described in "Covariance-regularized regression and classification for high-dimensional problems", by Witten and Tibshirani (2008), Journal of the Royal Statistical Society, Series B 71(3): 615-636.

sparcl

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Implements the sparse clustering methods of Witten and Tibshirani (2010): "A framework for feature selection in clustering"; published in Journal of the American Statistical Association 105(490): 713-726.