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r-snipem
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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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Compression and decompression with 'Snappy'.
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2025-03-25 |
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r-snakecharmr
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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, see Lund, Mogensen and Hansen (2019) <arXiv:1805.02407>. 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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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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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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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. Tervonen, T. and Figueira, J. R. (2008) <doi:10.1002/mcda.407>.
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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 implementations for Sorted L-One Penalized Estimation (SLOPE): generalized linear models regularized with the sorted L1-norm (Bogdan et al. (2015) <doi:10/gfgwzt>). 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.
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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 gene expression (microarray) data using a Bayesian Sparse Latent Factor Model (SLFM) <DOI:10.1007/978-3-319-12454-4_15>. Considerable effort has been put to build a fast and memory efficient package, which makes this proposal an interesting and computationally convenient alternative to study patterns of gene expressions exhibited in matrices. The package contains the implementation of two versions of the model based on different mixture priors for the loadings: one relies on a degenerate component at zero and the other uses a small variance normal distribution for the spike part of the mixture.
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2025-03-25 |
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r-skda
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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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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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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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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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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. For more details see the paper by Widgren, Bauer, Eriksson and Engblom (2019) <doi:10.18637/jss.v091.i12>. The package also provides functionality to fit models to time series data using the Approximate Bayesian Computation Sequential Monte Carlo ('ABC-SMC') algorithm of Toni and others (2009) <doi:10.1098/rsif.2008.0172>.
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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 of 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 amongst students' assignments.
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2025-03-25 |
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r-simframe
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A general framework for statistical simulation, which allows researchers to make use of a wide range of simulation designs with minimal programming effort. The package provides functionality for drawing samples from a distribution or a finite population, for adding outliers and missing values, as well as for visualization of the simulation results. It follows a clear object-oriented design and supports parallel computing to increase computational performance.
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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 SDEs <doi:10.18637/jss.v096.i02>. 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 |
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r-signal
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A set of signal processing functions originally written for 'Matlab' and 'Octave'. Includes filter generation utilities, filtering functions, resampling routines, and visualization of filter models. It also includes interpolation functions.
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2025-03-25 |
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r-shrinkcovmat
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Provides nonparametric Steinian shrinkage estimators of the covariance matrix that are suitable in high dimensional settings, that is when the number of variables is larger than the sample size.
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2025-03-25 |
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r-shp2graph
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Functions for converting network data from a SpatialLinesDataFrame object to an 'igraph'-Class object.
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2025-03-25 |
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r-shiftr
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Fast enrichment analysis for locally correlated statistics via circular permutations. The analysis can be performed at multiple significance thresholds for both primary and auxiliary data sets with efficient correction for multiple testing.
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2025-03-25 |
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r-sharpdata
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Functions and data sets inspired by data sharpening - data perturbation to achieve improved performance in nonparametric estimation, as described in Choi, E., Hall, P. and Rousson, V. (2000). Capabilities for enhanced local linear regression function and derivative estimation are included, as well as an asymptotically correct iterated data sharpening estimator for any degree of local polynomial regression estimation. A cross-validation-based bandwidth selector is included which, in concert with the iterated sharpener, will often provide superior performance, according to a median integrated squared error criterion. Sample data sets are provided to illustrate function usage.
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2025-03-25 |
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r-sgloptim
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Fast generic solver for sparse group lasso optimization problems. The loss (objective) function must be defined in a C++ module. The optimization problem is solved using a coordinate gradient descent algorithm. Convergence of the algorithm is established (see reference) and the algorithm is applicable to a broad class of loss functions. Use of parallel computing for cross validation and subsampling is supported through the 'foreach' and 'doParallel' packages. Development version is on GitHub, please report package issues on GitHub.
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2025-03-25 |
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r-sglasso
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RCON(V, E) models are a kind of restriction of the Gaussian Graphical Models defined by a set of equality constraints on the entries of the concentration matrix. 'sglasso' package implements the structured graphical lasso (sglasso) estimator proposed in Abbruzzo et al. (2014) for the weighted l1-penalized RCON(V, E) model. Two cyclic coordinate algorithms are implemented to compute the sglasso estimator, i.e. a cyclic coordinate minimization (CCM) and a cyclic coordinate descent (CCD) algorithm.
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2025-03-25 |
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r-sgl
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Fit a regularized generalized linear model via penalized maximum likelihood. The model is fit for a path of values of the penalty parameter. Fits linear, logistic and Cox models.
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2025-03-25 |
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r-sgeostat
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An Object-oriented Framework for Geostatistical Modeling in S+ containing functions for variogram estimation, variogram fitting and kriging as well as some plot functions. Written entirely in S, therefore works only for small data sets in acceptable computing time.
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2025-03-25 |
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r-sfs
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An implementation of the Similarity-First Search algorithm (SFS), a combinatorial algorithm which can be used to solve the seriation problem and to recognize some structured weighted graphs. The SFS algorithm represents a generalization to weighted graphs of the graph search algorithm Lexicographic Breadth-First Search (Lex-BFS), a variant of Breadth-First Search. The SFS algorithm reduces to Lex-BFS when applied to binary matrices (or, equivalently, unweighted graphs). Hence this library can be also considered for Lex-BFS applications such as recognition of graph classes like chordal or unit interval graphs. In fact, the SFS seriation algorithm implemented in this package is a multisweep algorithm, which consists in repeating a finite number of SFS iterations (at most n sweeps for a matrix of size n). If the data matrix has a Robinsonian structure, then the ranking returned by the multistep SFS algorithm is a Robinson ordering of the input matrix. Otherwise the algorithm can be used as a heuristic to return a ranking partially satisfying the Robinson property.
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2025-03-25 |
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r-sets
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Data structures and basic operations for ordinary sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets, customizable sets, and intervals.
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2025-03-25 |
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r-sequoia
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Multi-generational pedigree inference from incomplete data on hundreds of SNPs, including parentage assignment and sibship clustering. See Huisman (2017) (<DOI:10.1111/1755-0998.12665>) for more information.
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2025-03-25 |
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r-sequences
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Educational package used in R courses to illustrate object-oriented programming and package development. Using biological sequences (DNA and RNA) as a working example.
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2025-03-25 |
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r-seqminer
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Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.
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2025-03-25 |
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r-seqmeta
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Computes necessary information to meta analyze region-based tests for rare genetic variants (e.g. SKAT, T1) in individual studies, and performs meta analysis.
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2025-03-25 |
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r-seqcbs
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This is a method for DNA Copy Number Profiling using Next-Generation Sequencing. It has new model and test statistics based on non-homogeneous Poisson Processes with change point models. It uses an adaptation of Circular Binary Segmentation. Also included are methods for point-wise Bayesian Confidence Interval and model selection method for the change-point model. A case and a control sample reads (normal and tumor) are required.
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2025-03-25 |
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r-sensitivitypstrat
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This package provides functions to perform principal stratification sensitivity analyses on datasets.
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2025-03-25 |
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r-semver
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Tools and functions for parsing, rendering and operating on semantic version strings. Semantic versioning is a simple set of rules and requirements that dictate how version numbers are assigned and incremented as outlined at <http://semver.org>.
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2025-03-25 |
