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r-sparsehessianfd
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Estimates Hessian of a scalar-valued function, and returns it in a sparse Matrix format. The sparsity pattern must be known in advance. The algorithm is especially efficient for hierarchical models with a large number of heterogeneous units. See Braun, M. (2017) <doi:10.18637/jss.v082.i10>.
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2025-03-25 |
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r-sparcl
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public |
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.
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2025-03-25 |
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r-spam64
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Provides the Fortran code of the R package 'spam' with 64-bit integers. Loading this package together with the R package spam enables the sparse matrix class spam to handle huge sparse matrices with more than 2^31-1 non-zero elements.
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2025-03-25 |
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r-spam
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Set of functions for sparse matrix algebra. Differences with other sparse matrix packages are: (1) we only support (essentially) one sparse matrix format, (2) based on transparent and simple structure(s), (3) tailored for MCMC calculations within G(M)RF. (4) and it is fast and scalable (with the extension package spam64).
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2025-03-25 |
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r-spacejam
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This package provides an extension of conditional independence (CIG) and directed acyclic graph (DAG) estimation to the case where conditional relationships are (non-linear) additive models.
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2025-03-25 |
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r-space
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Partial correlation estimation with joint sparse regression model
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2025-03-25 |
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r-soundexbr
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The SoundexBR package provides an algorithm for decoding names into phonetic codes, as pronounced in Portuguese. The goal is for homophones to be encoded to the same representation so that they can be matched despite minor differences in spelling. The algorithm mainly encodes consonants; a vowel will not be encoded unless it is the first letter. The soundex code resultant consists of a four digits long string composed by one letter followed by three numerical digits: the letter is the first letter of the name, and the digits encode the remaining consonants.
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2025-03-25 |
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r-soobench
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Collection of different single objective test functions useful for benchmarks and algorithm development.
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2025-03-25 |
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r-sommer
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Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects and unknown variance-covariance structures (i.e. heterogeneous and unstructured variance models) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>). ML/REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms. Designed for genomic prediction and genome wide association studies (GWAS), particularly focused in the p > n problem (more coefficients than observations) and dense known covariance structures for levels of random effects. Spatial models can also be fitted using i.e. the two-dimensional spline functionality available in sommer.
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2025-03-25 |
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r-som
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Self-Organizing Map (with application in gene clustering).
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2025-03-25 |
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r-softrandomforest
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Performs random forests for soft decision trees for a classification problem. Current limitations are for a maximum depth of 5 resulting in 16 terminal nodes. Some data cleaning is required before input. Final graphic output requires currently requires exporting to 'Microsoft Excel' for visualization. Method based on Irsoy, Yildiz and Alpaydin (2012, ISBN: 978-4-9906441-1-6).
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2025-03-25 |
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r-softimpute
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Iterative methods for matrix completion that use nuclear-norm regularization. There are two main approaches.The one approach uses iterative soft-thresholded svds to impute the missing values. The second approach uses alternating least squares. Both have an "EM" flavor, in that at each iteration the matrix is completed with the current estimate. For large matrices there is a special sparse-matrix class named "Incomplete" that efficiently handles all computations. The package includes procedures for centering and scaling rows, columns or both, and for computing low-rank SVDs on large sparse centered matrices (i.e. principal components)
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2025-03-25 |
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r-soda
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public |
Functions, examples and other software related to the book "Software for Data Analysis: Programming with R". See package?SoDA for an overview.
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2025-03-25 |
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r-socialnetworks
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Generates social networks using either of two approaches: using either pairwise distances or territorial area intersections.
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2025-03-25 |
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r-social
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A set of functions to quantify and visualise social autocorrelation.
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2025-03-25 |
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r-soccer
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Functions for evaluating tournament predictions, simulating results from individual soccer matches and tournaments. See <http://sandsynligvis.dk/2018/08/03/world-cup-prediction-winners/> for more information.
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2025-03-25 |
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r-sobolsequence
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R implementation of S. Joe and F. Y. Kuo(2008) <DOI:10.1137/070709359>. The implementation is based on the data file new-joe-kuo-6.21201 <http://web.maths.unsw.edu.au/~fkuo/sobol/>.
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2025-03-25 |
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r-snnr
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Solve the problem of over-parameterization in neural networks for genomic selection. Daniel Gianola, Hayrettin OkutEmail, Kent A Weigel and Guilherme JM Rosa (2011) <doi:10.1186/1471-2156-12-87>.
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2025-03-25 |
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r-snipem
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public |
Snipping methods optimally removing scattered cells for robust estimation and cluster analysis.
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2025-03-25 |
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r-snappier
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public |
Compression and decompression with 'Snappy'.
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2025-03-25 |
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r-snakecharmr
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public |
Run 'Python' code, make function calls, assign and retrieve variables, etc. from R. A fork from 'rPython' which uses 'jsonlite', 'Rcpp' and has several fixes and improvements.
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2025-03-25 |
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r-smoothsurv
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Contains, as a main contribution, a function to fit a regression model with possibly right, left or interval censored observations and with the error distribution expressed as a mixture of G-splines. Core part of the computation is done in compiled C++ written using the Scythe Statistical Library Version 0.3.
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2025-03-25 |
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r-smoothhazard
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Estimation of two-state (survival) models and irreversible illness- death models with possibly interval-censored,left-truncated and right-censored data. Proportional intensities regression models can be specified to allow for covariates effects separately for each transition. We use either a parametric approach with Weibull baseline intensities or a semi-parametric approach with M-splines approximation of baseline intensities in order to obtain smooth estimates of the hazard functions. Parameter estimates are obtained by maximum likelihood in the parametric approach and by penalized maximum likelihood in the semi-parametric approach.
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2025-03-25 |
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r-smma
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Efficient design matrix free procedure for solving a soft maximin problem for large scale array-tensor structured models. Currently Lasso and SCAD penalized estimation is implemented.
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2025-03-25 |
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r-smitidvisu
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public |
Visualisation tools for 'SMITIDstruct' package. Allow to visualize host timeline, transmission tree, index diversities and variant graph using HTMLwidgets. It mainly using D3JS javascript framework.
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2025-03-25 |
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r-smisc
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A collection of functions for statistical computing and data manipulation in R. Includes routines for data ingestion, operating on dataframes and matrices, conversion to and from lists, converting factors, filename manipulation, programming utilities, parallelization, plotting, statistical and mathematical operations, and time series.
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2025-03-25 |
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r-smfsb
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Code and data for modelling and simulation of stochastic kinetic biochemical network models. It contains the code and data associated with the second and third editions of the book Stochastic Modelling for Systems Biology, published by Chapman & Hall/CRC Press.
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2025-03-25 |
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r-sme
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public |
Fit smoothing-splines mixed-effects models to replicated functional data sets and visualise the results.
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2025-03-25 |
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r-smds
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Symbolic multidimensional scaling for interval-valued dissimilarities. The hypersphere model and the hyperbox model are available.
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2025-03-25 |
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r-smc
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public |
particle filtering, auxiliary particle filtering and sequential Monte Carlo algorithms
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2025-03-25 |
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r-smac
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This package provides a solution path for L1-penalized angle-based classification. Three loss functions are implemented in smac, including the deviance loss in logistic regression, the exponential loss in boosting, and the proximal support vector machine loss.
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2025-03-25 |
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r-smaa
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Implementation of the Stochastic Multi-Criteria Acceptability Analysis (SMAA) family of Multiple Criteria Decision Analysis (MCDA) methods.
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2025-03-25 |
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r-sm
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This is software linked to the book 'Applied Smoothing Techniques for Data Analysis - The Kernel Approach with S-Plus Illustrations' Oxford University Press.
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2025-03-25 |
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r-slp
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Interface for creation of 'slp' class smoother objects for use in Generalized Additive Models (as implemented by packages 'gam' and 'mgcv').
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2025-03-25 |
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r-slope
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Efficient procedures for Sorted L1 Penalized Estimation (SLOPE). The sorted L1 norm is useful for statistical estimation and testing, particularly for variable selection in the linear model.
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2025-03-25 |
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r-slhd
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Generate the optimal Latin Hypercube Designs (LHDs) for computer experiments with quantitative factors and the optimal Sliced Latin Hypercube Designs (SLHDs) for computer experiments with both quantitative and qualitative factors. Details of the algorithm can be found in Ba, S., Brenneman, W. A. and Myers, W. R. (2015), "Optimal Sliced Latin Hypercube Designs," Technometrics. Important function in this package is "maximinSLHD".
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2025-03-25 |
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r-slfm
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Set of tools to find coherent patterns in microarray data using a Bayesian Sparse Latent Factor Model - SLFM; see Duarte and Mayrink (2015) <DOI:10.1007/978-3-319-12454-4_15>. Considerable effort has been put into making slfm fast and memory efficient, turning it an interesting alternative to simpler methods in terms of execution time. It implements versions of the SLFM based on two type of mixtures priors for the loadings: one relying on a degenerate component at zero and the other using a small variance normal distribution for the spike part of the mixture. It also implements additional functions to allow pre-processing procedures for the data and to fit the model for a large number of probesets or genes.
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2025-03-25 |
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r-skda
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public |
Sparse (Multicategory) Kernel Discriminant Analysis does variable selection for nonparametric classification
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2025-03-25 |
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r-skat
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public |
Functions for kernel-regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently compute SNP-set level p-values.
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2025-03-25 |
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r-sitmo
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public |
Provided within are two high quality and fast PPRNGs that may be used in an 'OpenMP' parallel environment. In addition, there is a generator for one dimensional low-discrepancy sequence. The objective of this library to consolidate the distribution of the 'sitmo' (C++98 & C++11), 'threefry' and 'vandercorput' (C++11-only) engines on CRAN by enabling others to link to the header files inside of 'sitmo' instead of including a copy of each engine within their individual package. Lastly, the package contains example implementations using the 'sitmo' package and three accompanying vignette that provide additional information.
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2025-03-25 |
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r-simputation
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public |
Easy to use interfaces to a number of imputation methods that fit in the not-a-pipe operator of the 'magrittr' package.
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2025-03-25 |
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r-simone
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Implements the inference of co-expression networks based on partial correlation coefficients from either steady-state or time-course transcriptomic data. Note that with both type of data this package can deal with samples collected in different experimental conditions and therefore not identically distributed. In this particular case, multiple but related networks are inferred on one simone run.
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2025-03-25 |
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r-simmer
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public |
A process-oriented and trajectory-based Discrete-Event Simulation (DES) package for R. It is designed as a generic yet powerful framework. The architecture encloses a robust and fast simulation core written in 'C++' with automatic monitoring capabilities. It provides a rich and flexible R API that revolves around the concept of trajectory, a common path in the simulation model for entities of the same type. Documentation about 'simmer' is provided by several vignettes included in this package, via the paper by Ucar, Smeets & Azcorra (2019, <doi:10.18637/jss.v090.i02>), and the paper by Ucar, Hernández, Serrano & Azcorra (2018, <doi:10.1109/MCOM.2018.1700960>); see 'citation("simmer")' for details.
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2025-03-25 |
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r-siminf
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Provides an efficient and very flexible framework to conduct data-driven epidemiological modeling in realistic large scale disease spread simulations. The framework integrates infection dynamics in subpopulations as continuous-time Markov chains using the Gillespie stochastic simulation algorithm and incorporates available data such as births, deaths and movements as scheduled events at predefined time-points. Using C code for the numerical solvers and 'OpenMP' (if available) to divide work over multiple processors ensures high performance when simulating a sample outcome. One of our design goals was to make the package extendable and enable usage of the numerical solvers from other R extension packages in order to facilitate complex epidemiological research. The package contains template models and can be extended with user-defined models.
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2025-03-25 |
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r-similar
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An implementation of a novel method to quantify the similarity the code-base of R functions by means of program dependence graphs. Possible use cases include detection of code clones for improving software quality and of plagiarism among students' homework assignments.
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2025-03-25 |
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r-simframe
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A general framework for statistical simulation.
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2025-03-25 |
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r-simecol
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An object oriented framework to simulate ecological (and other) dynamic systems. It can be used for differential equations, individual-based (or agent-based) and other models as well. It supports structuring of simulation scenarios (to avoid copy and paste) and aims to improve readability and re-usability of code.
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2025-03-25 |
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r-sim.diffproc
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It provides users with a wide range of tools to simulate, estimate, analyze, and visualize the dynamics of stochastic differential systems in both forms Ito and Stratonovich. Statistical analysis with parallel Monte Carlo and moment equations methods of SDE's. Enabled many searchers in different domains to use these equations to modeling practical problems in financial and actuarial modeling and other areas of application, e.g., modeling and simulate of first passage time problem in shallow water using the attractive center (Boukhetala K, 1996) ISBN:1-56252-342-2.
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2025-03-25 |
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r-simctest
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Algorithms for the implementation and evaluation of Monte Carlo tests, as well as for their use in multiple testing procedures.
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2025-03-25 |
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r-simcdm
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Provides efficient R and 'C++' routines to simulate cognitive diagnostic model data for Deterministic Input, Noisy "And" Gate ('DINA') and reduced Reparameterized Unified Model ('rRUM') from Culpepper and Hudson (2017) <doi: 10.1177/0146621617707511>, Culpepper (2015) <doi:10.3102/1076998615595403>, and de la Torre (2009) <doi:10.3102/1076998607309474>.
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2025-03-25 |
