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r-lmoments
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Contains functions to estimate L-moments and trimmed L-moments from the data. Also contains functions to estimate the parameters of the normal polynomial quantile mixture and the Cauchy polynomial quantile mixture from L-moments and trimmed L-moments.
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2025-04-22 |
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r-lmm
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It implements Expectation/Conditional Maximization Either (ECME) and rapidly converging algorithms as well as Bayesian inference for linear mixed models, which is described in Schafer, J.L. (1998) "Some improved procedures for linear mixed models". Dept. of Statistics, The Pennsylvania State University.
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2025-04-22 |
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r-lmenbbayes
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The functions in this package implement the safety monitoring procedures proposed in the paper titled "A flexible mixed effect negative binomial regression model for detecting unusual increases in MRI lesion counts in individual multiple sclerosis patients" by Kondo, Y., Zhao, Y. and Petkau, A.J. The procedure first models longitudinally collected count variables with a negative binomial mixed-effect regression model. To account for the correlation among repeated measures from the same patient, the model has subject-specific random intercept, which is modelled with the infinite mixture of Beta distributions, very flexible distribution that theoretically allows any form. The package also has the option of a single beta distribution for random effects. These mixed-effect models could be useful beyond the application of the safety monitoring. The inference is based on MCMC samples and this package contains a Gibbs sampler to sample from the posterior distribution of the negative binomial mixed-effect regression model. Based on the fitted model, the personalized activity index is computed for each patient. Lastly, this package is companion to R package lmeNB, which contains the functions to compute the Personalized Activity Index in the frequentist framework.
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2025-04-22 |
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r-lm.br
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Exact significance tests for a changepoint in linear or multiple linear regression. Confidence regions with exact coverage probabilities for the changepoint. Based on Knowles, Siegmund and Zhang (1991) <doi:10.1093/biomet/78.1.15>.
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2025-04-22 |
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r-ljr
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Fits and tests logistic joinpoint models.
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2025-04-22 |
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r-littler
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A scripting and command-line front-end is provided by 'r' (aka 'littler') as a lightweight binary wrapper around the GNU R language and environment for statistical computing and graphics. While R can be used in batch mode, the r binary adds full support for both 'shebang'-style scripting (i.e. using a hash-mark-exclamation-path expression as the first line in scripts) as well as command-line use in standard Unix pipelines. In other words, r provides the R language without the environment.
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2025-04-22 |
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r-lintools
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Variable elimination (Gaussian elimination, Fourier-Motzkin elimination), Moore-Penrose pseudoinverse, reduction to reduced row echelon form, value substitution, projecting a vector on the convex polytope described by a system of (in)equations, simplify systems by removing spurious columns and rows and collapse implied equalities, test if a matrix is totally unimodular, compute variable ranges implied by linear (in)equalities.
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2025-04-22 |
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r-linerr
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Fits a linear excess relative risk model by maximum likelihood, possibly including several variables and allowing for lagged exposures.
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2025-04-22 |
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r-linkcomm
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Link communities reveal the nested and overlapping structure in networks, and uncover the key nodes that form connections to multiple communities. linkcomm provides a set of tools for generating, visualizing, and analysing link communities in networks of arbitrary size and type. The linkcomm package also includes tools for generating, visualizing, and analysing Overlapping Cluster Generator (OCG) communities. Kalinka and Tomancak (2011) <doi:10.1093/bioinformatics/btr311>.
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2025-04-22 |
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r-limsolve
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Functions that (1) find the minimum/maximum of a linear or quadratic function: min or max (f(x)), where f(x) = ||Ax-b||^2 or f(x) = sum(a_i*x_i) subject to equality constraints Ex=f and/or inequality constraints Gx>=h, (2) sample an underdetermined- or overdetermined system Ex=f subject to Gx>=h, and if applicable Ax~=b, (3) solve a linear system Ax=B for the unknown x. It includes banded and tridiagonal linear systems.
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2025-04-22 |
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r-liger
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Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states. The original algorithm is detailed in Subramanian et al. with 'Java' implementations available through the Broad Institute (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>). The 'liger' package provides a lightweight R implementation of this enrichment test on a list of values (Fan et al., 2017 <doi:10.5281/zenodo.887386>). Given a list of values, such as p-values or log-fold changes derived from differential expression analysis or other analyses comparing biological states, this package enables you to test a priori defined set of genes for enrichment to enable interpretability of highly significant or high fold-change genes.
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2025-04-22 |
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r-libsoc
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Handle 'PharmML' (Pharmacometrics Markup Language) standard output (SO) XML files. SO files can be created, read, manipulated and written through a data binding from the XML structure to a tree structure of R objects.
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2025-04-22 |
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r-liblinear
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A wrapper around the LIBLINEAR C/C++ library for machine learning (available at <https://www.csie.ntu.edu.tw/~cjlin/liblinear/>). LIBLINEAR is a simple library for solving large-scale regularized linear classification and regression. It currently supports L2-regularized classification (such as logistic regression, L2-loss linear SVM and L1-loss linear SVM) as well as L1-regularized classification (such as L2-loss linear SVM and logistic regression) and L2-regularized support vector regression (with L1- or L2-loss). The main features of LiblineaR include multi-class classification (one-vs-the rest, and Crammer & Singer method), cross validation for model selection, probability estimates (logistic regression only) or weights for unbalanced data. The estimation of the models is particularly fast as compared to other libraries.
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2025-04-22 |
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r-liblinear.acf
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Solving the linear SVM problem with coordinate descent is very efficient and is implemented in one of the most often used packages, 'LIBLINEAR' (available at http://www.csie.ntu.edu.tw/~cjlin/liblinear). It has been shown that the uniform selection of coordinates can be accelerated by using an online adaptation of coordinate frequencies (ACF). This package implements ACF and is based on 'LIBLINEAR' as well as the 'LiblineaR' package (<https://cran.r-project.org/package=LiblineaR>). It currently supports L2-regularized L1-loss as well as L2-loss linear SVM. Similar to 'LIBLINEAR' multi-class classification (one-vs-the rest, and Crammer & Singer method) and cross validation for model selection is supported. The training of the models based on ACF is much faster than standard 'LIBLINEAR' on many problems.
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2025-04-22 |
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r-lhs
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Provides a number of methods for creating and augmenting Latin Hypercube Samples and Orthogonal Array Latin Hypercube Samples.
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2025-04-22 |
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r-lgarch
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Simulation and estimation of univariate and multivariate log-GARCH models. The main functions of the package are: lgarchSim(), mlgarchSim(), lgarch() and mlgarch(). The first two functions simulate from a univariate and a multivariate log-GARCH model, respectively, whereas the latter two estimate a univariate and multivariate log-GARCH model, respectively.
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2025-04-22 |
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r-lfe
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Transforms away factors with many levels prior to doing an OLS. Useful for estimating linear models with multiple group fixed effects, and for estimating linear models which uses factors with many levels as pure control variables. See Gaure (2013) <doi:10.1016/j.csda.2013.03.024> Includes support for instrumental variables, conditional F statistics for weak instruments, robust and multi-way clustered standard errors, as well as limited mobility bias correction (Gaure 2014 <doi:10.1002/sta4.68>). WARNING: This package is NOT under active development anymore, no further improvements are to be expected, and the package is at risk of being removed from CRAN.
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2025-04-22 |
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r-lemarns
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Set up, run and explore the outputs of the Length-based Multi-species model (LeMans; Hall et al. 2006 <doi:10.1139/f06-039>), focused on the marine environment.
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2025-04-22 |
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r-lexrankr
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An R implementation of the LexRank algorithm described by G. Erkan and D. R. Radev (2004) <DOI:10.1613/jair.1523>.
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2025-04-22 |
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r-leadercluster
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The leader clustering algorithm provides a means for clustering a set of data points. Unlike many other clustering algorithms it does not require the user to specify the number of clusters, but instead requires the approximate radius of a cluster as its primary tuning parameter. The package provides a fast implementation of this algorithm in n-dimensions using Lp-distances (with special cases for p=1,2, and infinity) as well as for spatial data using the Haversine formula, which takes latitude/longitude pairs as inputs and clusters based on great circle distances.
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2025-04-22 |
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r-lda
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Implements latent Dirichlet allocation (LDA) and related models. This includes (but is not limited to) sLDA, corrLDA, and the mixed-membership stochastic blockmodel. Inference for all of these models is implemented via a fast collapsed Gibbs sampler written in C. Utility functions for reading/writing data typically used in topic models, as well as tools for examining posterior distributions are also included.
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2025-04-22 |
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r-lcopula
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Collections of functions allowing random number generations and estimation of 'Liouville' copulas, as described in Belzile and Neslehova (2017) <doi:10.1016/j.jmva.2017.05.008>.
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2025-04-22 |
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r-lcmm
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Estimation of various extensions of the mixed models including latent class mixed models, joint latent class mixed models, mixed models for curvilinear outcomes, mixed models for multivariate longitudinal outcomes using a maximum likelihood estimation method (Proust-Lima, Philipps, Liquet (2017) <doi:10.18637/jss.v078.i02>).
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2025-04-22 |
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r-lcmcr
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Bayesian population size estimation using non parametric latent-class models.
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2025-04-22 |
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r-lbfgsb3c
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Interfacing to Nocedal et al. L-BFGS-B.3.0 (See <http://users.iems.northwestern.edu/~nocedal/lbfgsb.html>) limited memory BFGS minimizer with bounds on parameters. This is a fork of 'lbfgsb3'. This registers a 'R' compatible 'C' interface to L-BFGS-B.3.0 that uses the same function types and optimization as the optim() function (see writing 'R' extensions and source for details). This package also adds more stopping criteria as well as allowing the adjustment of more tolerances.
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2025-04-22 |
