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Matrix - Sparse and Dense Matrix Classes and Methods

A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.

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openblas

16.87 score 1 stars 9.7k dependents 49k scripts 155k downloads

zoo - S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)

An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.

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16.56 score 3.1k dependents 40k scripts 835k downloads

colorspace - A Toolbox for Manipulating and Assessing Colors and Palettes

Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided along with corresponding ggplot2 color scales. Color palette choice is aided by an interactive app (with either a Tcl/Tk or a shiny graphical user interface) and shiny apps with an HCL color picker and a color vision deficiency emulator. Plotting functions for displaying and assessing palettes include color swatches, visualizations of the HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation functions include: desaturation, lightening/darkening, mixing, and simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly). Details can be found on the project web page at <https://colorspace.R-Forge.R-project.org/> and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical Software, <doi:10.18637/jss.v096.i01>).

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15.26 score 2.7k dependents 13k scripts 484k downloads

xtable - Export Tables to LaTeX or HTML

Coerce data to LaTeX and HTML tables.

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14.94 score 2.5k dependents 23k scripts 618k downloads

sandwich - Robust Covariance Matrix Estimators

Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC) covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC) covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators); clustered covariances (one-way and multi-way); panel and panel-corrected covariances; outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted to other classes through S3 methods. Details can be found in Zeileis et al. (2020) <doi:10.18637/jss.v095.i01>, Zeileis (2004) <doi:10.18637/jss.v011.i10> and Zeileis (2006) <doi:10.18637/jss.v016.i09>.

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14.56 score 1.0k dependents 10k scripts 255k downloads

numDeriv - Accurate Numerical Derivatives

Methods for calculating (usually) accurate numerical first and second order derivatives. Accurate calculations are done using 'Richardson''s' extrapolation or, when applicable, a complex step derivative is available. A simple difference method is also provided. Simple difference is (usually) less accurate but is much quicker than 'Richardson''s' extrapolation and provides a useful cross-check. Methods are provided for real scalar and vector valued functions.

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14.31 score 1 stars 3.6k dependents 2.7k scripts 882k downloads

multcomp - Simultaneous Inference in General Parametric Models

Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models. The package includes demos reproducing analyzes presented in the book "Multiple Comparisons Using R" (Bretz, Hothorn, Westfall, 2010, CRC Press).

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13.89 score 391 dependents 14k scripts 168k downloads

robustbase - Basic Robust Statistics

"Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.

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openblas

13.61 score 497 dependents 3.1k scripts 92k downloads

survey - Analysis of Complex Survey Samples

Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase and multiphase subsampling designs. Graphics. PPS sampling without replacement. Small-area estimation. Dual-frame designs.

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cpp

13.59 score 1 stars 242 dependents 15k scripts 89k downloads

coin - Conditional Inference Procedures in a Permutation Test Framework

Conditional inference procedures for the general independence problem including two-sample, K-sample (non-parametric ANOVA), correlation, censored, ordered and multivariate problems described in <doi:10.18637/jss.v028.i08>.

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13.19 score 82 dependents 2.2k scripts 44k downloads

tm - Text Mining Package

A framework for text mining applications within R.

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cpp

12.74 score 91 dependents 19k scripts 33k downloads

GPArotation - GPA Factor Rotation

Gradient Projection Algorithm Rotation for Factor Analysis. See '?GPArotation.Intro' for more details.

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12.44 score 1 stars 395 dependents 1.7k scripts 169k downloads

partykit - A Toolkit for Recursive Partytioning

A toolkit with infrastructure for representing, summarizing, and visualizing tree-structured regression and classification models. This unified infrastructure can be used for reading/coercing tree models from different sources ('rpart', 'RWeka', 'PMML') yielding objects that share functionality for print()/plot()/predict() methods. Furthermore, new and improved reimplementations of conditional inference trees (ctree()) and model-based recursive partitioning (mob()) from the 'party' package are provided based on the new infrastructure. A description of this package was published by Hothorn and Zeileis (2015) <https://jmlr.org/papers/v16/hothorn15a.html>.

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12.38 score 95 dependents 2.5k scripts 21k downloads

carData - Companion to Applied Regression Data Sets

Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage (2019).

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11.85 score 1.1k dependents 1.3k scripts 338k downloads

copula - Multivariate Dependence with Copulas

Classes (S4) of commonly used elliptical, Archimedean, extreme-value and other copula families, as well as their rotations, mixtures and asymmetrizations. Nested Archimedean copulas, related tools and special functions. Methods for density, distribution, random number generation, bivariate dependence measures, Rosenblatt transform, Kendall distribution function, perspective and contour plots. Fitting of copula models with potentially partly fixed parameters, including standard errors. Serial independence tests, copula specification tests (independence, exchangeability, radial symmetry, extreme-value dependence, goodness-of-fit) and model selection based on cross-validation. Empirical copula, smoothed versions, and non-parametric estimators of the Pickands dependence function.

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11.71 score 97 dependents 1.7k scripts 12k downloads

MatrixModels - Modelling with Sparse and Dense Matrices

Generalized Linear Modelling with sparse and dense 'Matrix' matrices, using modular prediction and response module classes.

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11.69 score 1 stars 1.7k dependents 182 scripts 406k downloads

expm - Matrix Exponential, Log, 'etc'

Computation of the matrix exponential, logarithm, sqrt, and related quantities, using traditional and modern methods.

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openblas

11.66 score 455 dependents 2.2k scripts 76k downloads

randtoolbox - Toolbox for Pseudo and Quasi Random Number Generation and Random Generator Tests

Provides (1) pseudo random generators - general linear congruential generators, multiple recursive generators and generalized feedback shift register (SF-Mersenne Twister algorithm (<doi:10.1007/978-3-540-74496-2_36>) and WELL (<doi:10.1145/1132973.1132974>) generators); (2) quasi random generators - the Torus algorithm, the Sobol sequence, the Halton sequence (including the Van der Corput sequence) and (3) some generator tests - the gap test, the serial test, the poker test, see, e.g., Gentle (2003) <doi:10.1007/b97336>. Take a look at the Distribution task view of types and tests of random number generators. The package can be provided without the 'rngWELL' dependency on demand. Package in Memoriam of Diethelm and Barbara Wuertz.

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11.54 score 1 stars 87 dependents 697 scripts 15k downloads

minqa - Derivative-Free Optimization Algorithms by Quadratic Approximation

Derivative-free optimization by quadratic approximation based on an interface to Fortran implementations by M. J. D. Powell.

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cpp

11.49 score 1 stars 1.9k dependents 378 scripts 436k downloads

party - A Laboratory for Recursive Partytioning

A computational toolbox for recursive partitioning. The core of the package is ctree(), an implementation of conditional inference trees which embed tree-structured regression models into a well defined theory of conditional inference procedures. This non-parametric class of regression trees is applicable to all kinds of regression problems, including nominal, ordinal, numeric, censored as well as multivariate response variables and arbitrary measurement scales of the covariates. Based on conditional inference trees, cforest() provides an implementation of Breiman's random forests. The function mob() implements an algorithm for recursive partitioning based on parametric models (e.g. linear models, GLMs or survival regression) employing parameter instability tests for split selection. Extensible functionality for visualizing tree-structured regression models is available. The methods are described in Hothorn et al. (2006) <doi:10.1198/106186006X133933>, Zeileis et al. (2008) <doi:10.1198/106186008X319331> and Strobl et al. (2007) <doi:10.1186/1471-2105-8-25>.

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openblas

11.33 score 32 dependents 3.5k scripts 27k downloads

Rmpfr - Interface R to MPFR - Multiple Precision Floating-Point Reliable

Arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental ("special") functions. To this end, the package interfaces to the 'LGPL' licensed 'MPFR' (Multiple Precision Floating-Point Reliable) Library which itself is based on the 'GMP' (GNU Multiple Precision) Library.

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mpfr4gmp

10.94 score 88 dependents 640 scripts 29k downloads

betareg - Beta Regression

Beta regression for modeling beta-distributed dependent variables on the open unit interval (0, 1), e.g., rates and proportions, see Cribari-Neto and Zeileis (2010) <doi:10.18637/jss.v034.i02>. Moreover, extended-support beta regression models can accommodate dependent variables with boundary observations at 0 and/or 1, see Kosmidis and Zeileis (2025) <doi:10.1093/jrsssc/qlaf039>. For the classical beta regression model, alternative specifications are provided: Bias-corrected and bias-reduced estimation, finite mixture models, and recursive partitioning for beta regression, see Grün, Kosmidis, and Zeileis (2012) <doi:10.18637/jss.v048.i11>.

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quarto

10.57 score 23 dependents 1.6k scripts 21k downloads

surveillance - Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

Statistical methods for the modeling and monitoring of time series of counts, proportions and categorical data, as well as for the modeling of continuous-time point processes of epidemic phenomena. The monitoring methods focus on aberration detection in count data time series from public health surveillance of communicable diseases, but applications could just as well originate from environmetrics, reliability engineering, econometrics, or social sciences. The package implements many typical outbreak detection procedures such as the (improved) Farrington algorithm, or the negative binomial GLR-CUSUM method of Hoehle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>. A novel CUSUM approach combining logistic and multinomial logistic modeling is also included. The package contains several real-world data sets, the ability to simulate outbreak data, and to visualize the results of the monitoring in a temporal, spatial or spatio-temporal fashion. A recent overview of the available monitoring procedures is given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>. For the retrospective analysis of epidemic spread, the package provides three endemic-epidemic modeling frameworks with tools for visualization, likelihood inference, and simulation. hhh4() estimates models for (multivariate) count time series following Paul and Held (2011) <doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>. twinSIR() models the susceptible-infectious-recovered (SIR) event history of a fixed population, e.g, epidemics across farms or networks, as a multivariate point process as proposed by Hoehle (2009) <doi:10.1002/bimj.200900050>. twinstim() estimates self-exciting point process models for a spatio-temporal point pattern of infective events, e.g., time-stamped geo-referenced surveillance data, as proposed by Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>. A recent overview of the implemented space-time modeling frameworks for epidemic phenomena is given by Meyer et al. (2017) <doi:10.18637/jss.v077.i11>.

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cpp

10.30 score 2 stars 4 dependents 395 scripts 1.2k downloads

Polychrome - Qualitative Palettes with Many Colors

Tools for creating, viewing, and assessing qualitative palettes with many (20-30 or more) colors. See Coombes and colleagues (2019) <doi:10.18637/jss.v090.c01>.

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9.76 score 22 dependents 1.9k scripts 3.1k downloads

pcalg - Methods for Graphical Models and Causal Inference

Functions for causal structure learning and causal inference using graphical models. The main algorithms for causal structure learning are PC (for observational data without hidden variables), FCI and RFCI (for observational data with hidden variables), and GIES (for a mix of data from observational studies (i.e. observational data) and data from experiments involving interventions (i.e. interventional data) without hidden variables). For causal inference the IDA algorithm, the Generalized Backdoor Criterion (GBC), the Generalized Adjustment Criterion (GAC) and some related functions are implemented. Functions for incorporating background knowledge are provided.

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openblascpp

8.94 score 17 dependents 1.3k scripts 6.7k downloads

WRS2 - A Collection of Robust Statistical Methods

A collection of robust statistical methods based on Wilcox' WRS functions. It implements robust t-tests (independent and dependent samples), robust ANOVA (including between-within subject designs), quantile ANOVA, robust correlation, robust mediation, and nonparametric ANCOVA models based on robust location measures.

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8.57 score 10 dependents 608 scripts 10k downloads

tuneR - Analysis of Music and Speech

Analyze music and speech, extract features like MFCCs, handle wave files and their representation in various ways, read mp3, read midi, perform steps of a transcription, ... Also contains functions ported from the 'rastamat' 'Matlab' package.

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7.87 score 45 dependents 1.2k scripts 4.4k downloads

POT - Generalized Pareto Distribution and Peaks Over Threshold

Some functions useful to perform a Peak Over Threshold analysis in univariate and bivariate cases, see Beirlant et al. (2004) <doi:10.1002/0470012382>. A user guide is available in the vignette.

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7.31 score 4 dependents 170 scripts 908 downloads

grImport - Importing Vector Graphics

Functions for converting, importing, and drawing PostScript pictures in R plots.

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6.89 score 8 dependents 97 scripts 4.2k downloads

mada - Meta-Analysis of Diagnostic Accuracy

Provides functions for diagnostic meta-analysis. Next to basic analysis and visualization the bivariate Model of Reitsma et al. (2005) that is equivalent to the HSROC of Rutter & Gatsonis (2001) can be fitted. A new approach based to diagnostic meta-analysis of Holling et al. (2012) is also available. Standard methods like summary, plot and so on are provided.

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6.67 score 3 dependents 95 scripts 5.5k downloads

RHRV - Heart Rate Variability Analysis of ECG Data

Allows users to import data files containing heartbeat positions in the most broadly used formats, to remove outliers or points with unacceptable physiological values present in the time series, to plot HRV data, and to perform time domain, frequency domain and nonlinear HRV analysis. See Garcia et al. (2017) <DOI:10.1007/978-3-319-65355-6>.

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6.57 score 2 dependents 78 scripts 966 downloads

isotone - Active Set and Generalized PAVA for Isotone Optimization

Contains two main functions: one for solving general isotone regression problems using the pool-adjacent-violators algorithm (PAVA); another one provides a framework for active set methods for isotone optimization problems with arbitrary order restrictions. Various types of loss functions are prespecified.

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6.50 score 14 dependents 99 scripts 1.9k downloads

RandVar - Implementation of Random Variables

Implements random variables by means of S4 classes and methods.

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6.07 score 6 dependents 76 scripts 2.1k downloads

Gifi - Multivariate Analysis with Optimal Scaling

Implements various Gifi methods in a user-friendly way: categorical principal component analysis (princals), multiple correspondence analysis (homals), monotone regression analysis (morals).

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5.96 score 1 dependents 64 scripts 623 downloads

SpatialExtremes - Modelling Spatial Extremes

Tools for the statistical modelling of spatial extremes using max-stable processes, copula or Bayesian hierarchical models. More precisely, this package allows (conditional) simulations from various parametric max-stable models, analysis of the extremal spatial dependence, the fitting of such processes using composite likelihoods or least square (simple max-stable processes only), model checking and selection and prediction. Other approaches (although not completely in agreement with the extreme value theory) are available such as the use of (spatial) copula and Bayesian hierarchical models assuming the so-called conditional assumptions. The latter approaches is handled through an (efficient) Gibbs sampler. Some key references: Davison et al. (2012) <doi:10.1214/11-STS376>, Padoan et al. (2010) <doi:10.1198/jasa.2009.tm08577>, Dombry et al. (2013) <doi:10.1093/biomet/ass067>.

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openblas

5.86 score 5 dependents 220 scripts 1.1k downloads

grImport2 - Importing 'SVG' Graphics

Functions for importing external vector images and drawing them as part of 'R' plots. This package is different from the 'grImport' package because, where that package imports 'PostScript' format images, this package imports 'SVG' format images. Furthermore, this package imports a specific subset of 'SVG', so external images must be preprocessed using a package like 'rsvg' to produce 'SVG' that this package can import. 'SVG' features that are not supported by 'R' graphics, e.g., gradient fills, can be imported and then exported via the 'gridSVG' package.

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5.81 score 15 dependents 128 scripts 5.7k downloads

wordspace - Distributional Semantic Models in R

An interactive laboratory for research on distributional semantic models ('DSM', see <https://en.wikipedia.org/wiki/Distributional_semantics> for more information).

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cppopenmp

5.43 score 4 dependents 217 scripts 1.0k downloads

GNE - Computation of Generalized Nash Equilibria

Compute standard and generalized Nash Equilibria of non-cooperative games. Optimization methods available are nonsmooth reformulation, fixed-point formulation, minimization problem and constrained-equation reformulation. See e.g. Kanzow and Facchinei (2010), <doi:10.1007/s10479-009-0653-x>.

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5.18 score 1 stars 19 scripts 258 downloads

EasyABC - Efficient Approximate Bayesian Computation Sampling Schemes

Enables launching a series of simulations of a computer code from the R session, and to retrieve the simulation outputs in an appropriate format for post-processing treatments. Five sequential sampling schemes and three coupled-to-MCMC schemes are implemented.

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5.15 score 3 dependents 264 scripts 463 downloads

RobAStBase - Robust Asymptotic Statistics

Base S4-classes and functions for robust asymptotic statistics.

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4.93 score 3 dependents 69 scripts 3.5k downloads

PCDimension - Finding the Number of Significant Principal Components

Implements methods to automate the Auer-Gervini graphical Bayesian approach for determining the number of significant principal components. Automation uses clustering, change points, or simple statistical models to distinguish "long" from "short" steps in a graph showing the posterior number of components as a function of a prior parameter. See <doi:10.1101/237883>.

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clustering

4.68 score 6 dependents 42 scripts 1.6k downloads

metRology - Support for Metrological Applications

Provides classes and calculation and plotting functions for metrology applications, including measurement uncertainty estimation and inter-laboratory metrology comparison studies.

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4.47 score 5 stars 5 dependents 197 scripts 767 downloads

ROptEst - Optimally Robust Estimation

R infrastructure for optimally robust estimation in general smoothly parameterized models using S4 classes and methods as described Kohl, M., Ruckdeschel, P., and Rieder, H. (2010), <doi:10.1007/s10260-010-0133-0>, and in Rieder, H., Kohl, M., and Ruckdeschel, P. (2008), <doi:10.1007/s10260-007-0047-7>.

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4.43 score 1 dependents 71 scripts 3.2k downloads

Mercator - Clustering and Visualizing Distance Matrices

Defines the classes used to explore, cluster and visualize distance matrices, especially those arising from binary data. See Abrams and colleagues, 2021, <doi:10.1093/bioinformatics/btab037>.

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clustering

4.43 score 1 dependents 30 scripts 681 downloads

Thresher - Threshing and Reaping for Principal Components

Defines the classes used to identify outliers (threshing) and compute the number of significant principal components and number of clusters (reaping) in a joint application of PCA and hierarchical clustering. See Wang et al., 2018, <doi:10.1186/s12859-017-1998-9>.

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clustering

4.41 score 5 dependents 43 scripts 334 downloads

frontier - Stochastic Frontier Analysis

Maximum Likelihood Estimation of Stochastic Frontier Production and Cost Functions. Two specifications are available: the error components specification with time-varying efficiencies (Battese and Coelli, 1992, <doi:10.1007/BF00158774>) and a model specification in which the firm effects are directly influenced by a number of variables (Battese and Coelli, 1995, <doi:10.1007/BF01205442>).

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fortran

4.34 score 2 dependents 248 scripts 1.5k downloads

Sleuth2 - Data Sets from Ramsey and Schafer's "Statistical Sleuth (2nd Ed)"

Data sets from Ramsey, F.L. and Schafer, D.W. (2002), "The Statistical Sleuth: A Course in Methods of Data Analysis (2nd ed)", Duxbury.

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4.20 score 281 scripts 2.8k downloads

tframe - Time Frame Coding Kernel

A kernel of functions for programming time series methods in a way that is relatively independently of the representation of time. Also provides plotting, time windowing, and some other utility functions which are specifically intended for time series. See the Guide distributed as a vignette, or '?tframe.Intro' for more details. (User utilities are in package 'tfplot'.)

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4.05 score 1 dependents 37 scripts 433 downloads

RobLox - Optimally Robust Influence Curves and Estimators for Location and Scale

Functions for the determination of optimally robust influence curves and estimators in case of normal location and/or scale (see Chapter 8 in Kohl (2005) <https://epub.uni-bayreuth.de/839/2/DissMKohl.pdf>).

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3.91 score 100 scripts 2.0k downloads

Umpire - Simulating Realistic Gene Expression and Clinical Data

The Ultimate Microrray Prediction, Reality and Inference Engine (UMPIRE) is a package to facilitate the simulation of realistic microarray data sets with links to associated outcomes. See Zhang and Coombes (2012) <doi:10.1186/1471-2105-13-S13-S1>. Version 2.0 adds the ability to simulate realistic mixed-typed clinical data.

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3.69 score 81 scripts 318 downloads

Modeler - Classes and Methods for Training and Using Binary Prediction Models

Defines classes and methods to learn models and use them to predict binary outcomes. These are generic tools, but we also include specific examples for many common classifiers.

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microarrayclustering

3.59 score 1 dependents 13 scripts 584 downloads

loa - Lattice Options and Add-Ins

Various plots and functions that make use of the lattice/trellis plotting framework. The plots, which include loaPlot(), loaMapPlot() and trianglePlot(), and use panelPal(), a function that extends 'lattice' and 'hexbin' package methods to automate plot subscript and panel-to-panel and panel-to-key synchronization/management.

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openjdk

3.33 score 2 dependents 18 scripts 936 downloads

RobExtremes - Optimally Robust Estimation for Extreme Value Distributions

Optimally robust estimation for extreme value distributions using S4 classes and methods (based on packages 'distr', 'distrEx', 'distrMod', 'RobAStBase', and 'ROptEst'); the underlying theoretic results can be found in Ruckdeschel and Horbenko, (2013 and 2012), \doi{10.1080/02331888.2011.628022} and \doi{10.1007/s00184-011-0366-4}.

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3.18 score 38 scripts 461 downloads

aspect - A General Framework for Multivariate Analysis with Optimal Scaling

Contains various functions for optimal scaling. One function performs optimal scaling by maximizing an aspect (i.e. a target function such as the sum of eigenvalues, sum of squared correlations, squared multiple correlations, etc.) of the corresponding correlation matrix. Another function performs implements the LINEALS approach for optimal scaling by minimization of an aspect based on pairwise correlations and correlation ratios. The resulting correlation matrix and category scores can be used for further multivariate methods such as structural equation models.

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3.08 score 2 dependents 10 scripts 768 downloads

gridGraphviz - Drawing Graphs with 'grid'

Functions for drawing node-and-edge graphs that have been laid out by 'graphviz'. This provides an alternative rendering to that provided by the 'Rgraphviz' package, with two main advantages: the rendering provided by 'gridGraphviz' should be more similar to what 'graphviz' itself would draw; and rendering with 'grid' allows for post-hoc customisations using the named viewports and grobs that 'gridGraphviz' produces.

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2.78 score 1 dependents 2 scripts 238 downloads

corpora - Statistics and Data Sets for Corpus Frequency Data

Utility functions for the statistical analysis of corpus frequency data. This package is a companion to the open-source course "Statistical Inference: A Gentle Introduction for Computational Linguists and Similar Creatures" ('SIGIL').

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2.72 score 53 scripts 389 downloads

anacor - Simple and Canonical Correspondence Analysis

Performs simple and canonical CA (covariates on rows/columns) on a two-way frequency table (with missings) by means of SVD. Different scaling methods (standard, centroid, Benzecri, Goodman) as well as various plots including confidence ellipsoids are provided.

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2.72 score 26 scripts 794 downloads

signal - Signal Processing

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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9.44 score 159 dependents 1.5k scripts 39k downloads

stabledist - Stable Distribution Functions

Density, Probability and Quantile functions, and random number generation for (skew) stable distributions, using the parametrizations of Nolan.

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9.39 score 1 stars 230 dependents 103 scripts 27k downloads

CHNOSZ - Thermodynamic Calculations and Diagrams for Geochemistry

An integrated set of tools for thermodynamic calculations in aqueous geochemistry and geobiochemistry. Functions are provided for writing balanced reactions to form species from user-selected basis species and for calculating the standard molal properties of species and reactions, including the standard Gibbs energy and equilibrium constant. Calculations of the non-equilibrium chemical affinity and equilibrium chemical activity of species can be portrayed on diagrams as a function of temperature, pressure, or activity of basis species; in two dimensions, this gives a maximum affinity or predominance diagram. The diagrams have formatted chemical formulas and axis labels, and water stability limits can be added to Eh-pH, oxygen fugacity- temperature, and other diagrams with a redox variable. The package has been developed to handle common calculations in aqueous geochemistry, such as solubility due to complexation of metal ions, mineral buffers of redox or pH, and changing the basis species across a diagram ("mosaic diagrams"). CHNOSZ also implements a group additivity algorithm for the standard thermodynamic properties of proteins.

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9.37 score 5 dependents 281 scripts 1.2k downloads

exams - Automatic Generation of Exams in R

Automatic generation of exams based on exercises in Markdown or LaTeX format, possibly including R code for dynamic generation of exercise elements. Exercise types include single-choice and multiple-choice questions, arithmetic problems, string questions, and combinations thereof (cloze). Output formats include standalone files (PDF, HTML, Docx, ODT, ...), Moodle XML, QTI 1.2, QTI 2.1, Blackboard, Canvas, OpenOlat, ILIAS, TestVision, Particify, ARSnova, Kahoot!, Grasple, and TCExam. In addition to fully customizable PDF exams, a standardized PDF format (NOPS) is provided that can be printed, scanned, and automatically evaluated.

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8.98 score 1 stars 7 dependents 2.3k scripts 3.5k downloads

FME - A Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability and Monte Carlo Analysis

Provides functions to help in fitting models to data, to perform Monte Carlo, sensitivity and identifiability analysis. It is intended to work with models be written as a set of differential equations that are solved either by an integration routine from package 'deSolve', or a steady-state solver from package 'rootSolve'. However, the methods can also be used with other types of functions.

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8.95 score 7 dependents 451 scripts 6.2k downloads

systemfit - Estimating Systems of Simultaneous Equations

Econometric estimation of simultaneous systems of linear and nonlinear equations using Ordinary Least Squares (OLS), Weighted Least Squares (WLS), Seemingly Unrelated Regressions (SUR), Two-Stage Least Squares (2SLS), Weighted Two-Stage Least Squares (W2SLS), and Three-Stage Least Squares (3SLS) as suggested, e.g., by Zellner (1962) <doi:10.2307/2281644>, Zellner and Theil (1962) <doi:10.2307/1911287>, and Schmidt (1990) <doi:10.1016/0304-4076(90)90127-F>.

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8.94 score 21 dependents 509 scripts 15k downloads

ClassDiscovery - Classes and Methods for "Class Discovery" with Microarrays or Proteomics

Defines the classes used for "class discovery" problems in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class discovery primarily consists of unsupervised clustering methods with attempts to assess their statistical significance.

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microarrayclustering

8.86 score 11 dependents 189 scripts 1.9k downloads

GeneralizedHyperbolic - The Generalized Hyperbolic Distribution

Functions for the hyperbolic and related distributions. Density, distribution and quantile functions and random number generation are provided for the hyperbolic distribution, the generalized hyperbolic distribution, the generalized inverse Gaussian distribution and the skew-Laplace distribution. Additional functionality is provided for the hyperbolic distribution, normal inverse Gaussian distribution and generalized inverse Gaussian distribution, including fitting of these distributions to data. Linear models with hyperbolic errors may be fitted using hyperblmFit.

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8.54 score 1 stars 34 dependents 167 scripts 16k downloads

sampleSelection - Sample Selection Models

Two-step and maximum likelihood estimation of Heckman-type sample selection models: standard sample selection models (Tobit-2), endogenous switching regression models (Tobit-5), sample selection models with binary dependent outcome variable, interval regression with sample selection (only ML estimation), and endogenous treatment effects models. These methods are described in the three vignettes that are included in this package and in econometric textbooks such as Greene (2011, Econometric Analysis, 7th edition, Pearson).

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8.51 score 5 dependents 457 scripts 8.0k downloads

distr - Object Oriented Implementation of Distributions

S4-classes and methods for distributions.

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8.44 score 36 dependents 447 scripts 4.8k downloads

linprog - Linear Programming / Optimization

Can be used to solve Linear Programming / Linear Optimization problems by using the simplex algorithm.

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8.40 score 175 dependents 106 scripts 23k downloads

crch - Censored Regression with Conditional Heteroscedasticity

Different approaches to censored or truncated regression with conditional heteroscedasticity are provided. First, continuous distributions can be used for the (right and/or left censored or truncated) response with separate linear predictors for the mean and variance. Second, cumulative link models for ordinal data (obtained by interval-censoring continuous data) can be employed for heteroscedastic extended logistic regression (HXLR). In the latter type of models, the intercepts depend on the thresholds that define the intervals. Infrastructure for working with censored or truncated normal, logistic, and Student-t distributions, i.e., d/p/q/r functions and distributions3 objects.

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quarto

8.08 score 3 dependents 143 scripts 5.4k downloads

ROI - R Optimization Infrastructure

The R Optimization Infrastructure ('ROI') <doi:10.18637/jss.v094.i15> is a sophisticated framework for handling optimization problems in R. Additional information can be found on the 'ROI' homepage <http://roi.r-forge.r-project.org/>.

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7.92 score 50 dependents 712 scripts 7.9k downloads

cobs - Constrained B-Splines (Sparse Matrix Based)

Qualitatively Constrained (Regression) Smoothing Splines via Linear Programming and Sparse Matrices.

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7.80 score 21 dependents 198 scripts 10k downloads

Bessel - Computations and Approximations for Bessel Functions

Computations for Bessel function for complex, real and partly 'mpfr' (arbitrary precision) numbers; notably interfacing TOMS 644; approximations for large arguments, experiments, etc.

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7.69 score 17 dependents 215 scripts 7.5k downloads

mlt - Most Likely Transformations

Likelihood-based estimation of conditional transformation models via the most likely transformation approach described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291> and Hothorn (2020) <DOI:10.18637/jss.v092.i01>. Shift-scale (Siegfried et al, 2023, <DOI:10.1080/00031305.2023.2203177>) and multivariate (Klein et al, 2022, <DOI:10.1111/sjos.12501>) transformation models are part of this package. A package vignette is available from <DOI:10.32614/CRAN.package.mlt.docreg> and more convenient user interfaces to many models from <DOI:10.32614/CRAN.package.tram>.

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7.66 score 8 dependents 92 scripts 5.6k downloads

Rglpk - R/GNU Linear Programming Kit Interface

R interface to the GNU Linear Programming Kit. 'GLPK' is open source software for solving large-scale linear programming (LP), mixed integer linear programming ('MILP') and other related problems.

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glpk

7.54 score 52 dependents 300 scripts 12k downloads

nor1mix - Normal aka Gaussian 1-d Mixture Models

Onedimensional Normal (i.e. Gaussian) Mixture Models (S3) Classes, for, e.g., density estimation or clustering algorithms research and teaching; providing the widely used Marron-Wand densities. Efficient random number generation and graphics. Fitting to data by efficient ML (Maximum Likelihood) or traditional EM estimation.

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7.51 score 55 dependents 116 scripts 8.5k downloads

censReg - Censored Regression (Tobit) Models

Maximum Likelihood estimation of censored regression (Tobit) models with cross-sectional and panel data.

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7.50 score 1 dependents 180 scripts 5.9k downloads

oompaBase - Class Unions, Matrix Operations, and Color Schemes for OOMPA

Provides the class unions that must be preloaded in order for the basic tools in the OOMPA (Object-Oriented Microarray and Proteomics Analysis) project to be defined and loaded. It also includes vectorized operations for row-by-row means, variances, and t-tests. Finally, it provides new color schemes. Details on the packages in the OOMPA project can be found at <http://oompa.r-forge.r-project.org/>.

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infrastructure

7.35 score 20 dependents 48 scripts 2.6k downloads

SkewHyperbolic - The Skew Hyperbolic Student t-Distribution

Functions are provided for the density function, distribution function, quantiles and random number generation for the skew hyperbolic t-distribution. There are also functions that fit the distribution to data. There are functions for the mean, variance, skewness, kurtosis and mode of a given distribution and to calculate moments of any order about any centre. To assess goodness of fit, there are functions to generate a Q-Q plot, a P-P plot and a tail plot.

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7.34 score 1 stars 25 dependents 15 scripts 15k downloads

fExtremes - Rmetrics - Modelling Extreme Events in Finance

Provides functions for analysing and modelling extreme events in financial time Series. The topics include: (i) data pre-processing, (ii) explorative data analysis, (iii) peak over threshold modelling, (iv) block maxima modelling, (v) estimation of VaR and CVaR, and (vi) the computation of the extreme index.

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7.15 score 1 stars 4 dependents 186 scripts 799 downloads

tram - Transformation Models

Formula-based user-interfaces to specific transformation models implemented in package 'mlt' (<DOI:10.32614/CRAN.package.mlt>, <DOI:10.32614/CRAN.package.mlt.docreg>). Available models include Cox models, some parametric survival models (Weibull, etc.), models for ordered categorical variables, normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression (Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to transformation models for clustered data is provided (Barbanti and Hothorn, 2022, <DOI:10.1093/biostatistics/kxac048>) and a tutorial explains applications in survival analysis (Siegfried et al., 2025, <DOI:10.48550/arXiv.2402.06428>). Multivariate conditional transformation models (Klein et al, 2022, <DOI:10.1111/sjos.12501>) and shift-scale transformation models (Siegfried et al, 2023, <DOI:10.1080/00031305.2023.2203177>) can be fitted as well. The package contains an implementation of a doubly robust score test, described in Kook et al. (2024, <DOI:10.1080/01621459.2024.2395588>).

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7.12 score 6 dependents 212 scripts 3.6k downloads

zipfR - Statistical Models for Word Frequency Distributions

Statistical models and utilities for the analysis of word frequency distributions. The utilities include functions for loading, manipulating and visualizing word frequency data and vocabulary growth curves. The package also implements several statistical models for the distribution of word frequencies in a population. (The name of this package derives from the most famous word frequency distribution, Zipf's law.)

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6.95 score 12 dependents 207 scripts 4.0k downloads

glmertree - Generalized Linear Mixed Model Trees

Recursive partitioning based on (generalized) linear mixed models (GLMMs) combining lmer()/glmer() from 'lme4' and lmtree()/glmtree() from 'partykit'. The fitting algorithm is described in more detail in Fokkema, Smits, Zeileis, Hothorn & Kelderman (2018; <DOI:10.3758/s13428-017-0971-x>). For detecting and modeling subgroups in growth curves with GLMM trees see Fokkema & Zeileis (2024; <DOI:10.3758/s13428-024-02389-1>).

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6.44 score 3 dependents 51 scripts 5.0k downloads

basefun - Infrastructure for Computing with Basis Functions

Some very simple infrastructure for basis functions.

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6.42 score 9 dependents 21 scripts 5.1k downloads

Sleuth3 - Data Sets from Ramsey and Schafer's "Statistical Sleuth (3rd Ed)"

Data sets from Ramsey, F.L. and Schafer, D.W. (2013), "The Statistical Sleuth: A Course in Methods of Data Analysis (3rd ed)", Cengage Learning.

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6.42 score 894 scripts 1.1k downloads

ClassComparison - Classes and Methods for "Class Comparison" Problems on Microarrays

Defines the classes used for "class comparison" problems in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class comparison includes tests for differential expression; see Simon's book for details on typical problem types.

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microarraydifferentialexpressionmultiplecomparisons

6.40 score 3 dependents 47 scripts 389 downloads

fPortfolio - Rmetrics - Portfolio Selection and Optimization

A collection of functions to optimize portfolios and to analyze them from different points of view. If the suggested package 'bcp' is not availble from CRAN, it can be installed from the archive, e.g. <https://cran.r-project.org/src/contrib/Archive/bcp/bcp_4.0.3.tar.gz>.

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6.39 score 1 stars 2 dependents 316 scripts 1.0k downloads

variables - Variable Descriptions

Abstract descriptions of (yet) unobserved variables.

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6.36 score 10 dependents 16 scripts 5.0k downloads

distrMod - Object Oriented Implementation of Probability Models

Implements S4 classes for probability models based on packages 'distr' and 'distrEx'.

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6.35 score 5 dependents 149 scripts 2.5k downloads

TailRank - The Tail-Rank Statistic

Implements the tail-rank statistic for selecting biomarkers from a microarray data set, an efficient nonparametric test focused on the distributional tails. See <https://gitlab.com/krcoombes/coombeslab/-/blob/master/doc/papers/tolstoy-new.pdf>.

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6.33 score 2 dependents 60 scripts 603 downloads

distrEx - Extensions of Package 'distr'

Extends package 'distr' by functionals, distances, and conditional distributions.

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6.25 score 16 dependents 127 scripts 3.6k downloads

DPQ - Density, Probability, Quantile ('DPQ') Computations

Computations for approximations and alternatives for the 'DPQ' (Density (pdf), Probability (cdf) and Quantile) functions for probability distributions in R. Primary focus is on (central and non-central) beta, gamma and related distributions such as the chi-squared, F, and t. -- For several distribution functions, provide functions implementing formulas from Johnson, Kotz, and Kemp (1992) <doi:10.1002/bimj.4710360207> and Johnson, Kotz, and Balakrishnan (1995) for discrete or continuous distributions respectively. This is for the use of researchers in these numerical approximation implementations, notably for my own use in order to improve standard R pbeta(), qgamma(), ..., etc: {'"dpq"'-functions}.

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6.18 score 1 dependents 61 scripts 3.5k downloads

lokern - Kernel Regression Smoothing with Local or Global Plug-in Bandwidth

Kernel regression smoothing with adaptive local or global plug-in bandwidth selection.

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5.97 score 5 dependents 81 scripts 3.9k downloads

setRNG - Set (Normal) Random Number Generator and Seed

Provides utilities to help set and record the setting of the seed and the uniform and normal generators used when a random experiment is run. The utilities can be used in other functions that do random experiments to simplify recording and/or setting all the necessary information for reproducibility. See the vignette and reference manual for examples.

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5.93 score 6 dependents 26 scripts 4.5k downloads

tscount - Analysis of Count Time Series

Likelihood-based methods for model fitting and assessment, prediction and intervention analysis of count time series following generalized linear models are provided, see Liboschik et al. (2017) <doi:10.18637/jss.v082.i05>. Models with the identity and with the logarithmic link function are allowed. The conditional distribution can be Poisson or Negative Binomial.

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5.81 score 1 dependents 155 scripts 2.0k downloads

truncreg - Truncated Gaussian Regression Models

Estimation of models for truncated Gaussian variables by maximum likelihood.

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5.75 score 6 dependents 65 scripts 7.9k downloads

RNetLogo - Provides an Interface to the Agent-Based Modelling Platform 'NetLogo'

Interface to use and access Wilensky's 'NetLogo' (Wilensky 1999) from R using either headless (no GUI) or interactive GUI mode. Provides functions to load models, execute commands, and get values from reporters. Mostly analogous to the 'NetLogo' 'Mathematica' Link <https://github.com/NetLogo/Mathematica-Link>.

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openjdk

5.72 score 1 dependents 176 scripts 357 downloads

mlt.docreg - Most Likely Transformations: Documentation and Regression Tests

Additional documentation, a package vignette and regression tests for package mlt.

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5.63 score 1.2k downloads

fAssets - Rmetrics - Analysing and Modelling Financial Assets

A collection of functions to manage, to investigate and to analyze data sets of financial assets from different points of view.

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5.53 score 1 stars 3 dependents 30 scripts 828 downloads

R2MLwiN - Running 'MLwiN' from Within R

An R command interface to the 'MLwiN' multilevel modelling software package.

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5.52 score 236 scripts 398 downloads

oompaData - Data to Illustrate OOMPA Algorithms

This is a data-only package to provide example data for other packages that are part of the "Object-Oriented Microrray and Proteomics Analysis" suite of packages. These are described in more detail at the package URL.

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5.49 score 13 dependents 16 scripts 1.6k downloads

arrayhelpers - Convenience Functions for Arrays

Some convenient functions to work with arrays.

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5.48 score 30 dependents 61 scripts 5.5k downloads

genoPlotR - Plot Publication-Grade Gene and Genome Maps

Draws gene or genome maps and comparisons between these, in a publication-grade manner. Starting from simple, common files, it will draw postscript or PDF files that can be sent as such to journals.

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5.48 score 151 scripts 511 downloads

ROI.plugin.glpk - 'ROI' Plug-in 'GLPK'

Enhances the 'R' Optimization Infrastructure ('ROI') package by registering the free 'GLPK' solver. It allows for solving mixed integer linear programming ('MILP') problems as well as all variants/combinations of 'LP', 'IP'.

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5.47 score 6 dependents 423 scripts 3.9k downloads

qualV - Qualitative Validation Methods

Qualitative methods for the validation of dynamic models. It contains (i) an orthogonal set of deviance measures for absolute, relative and ordinal scale and (ii) approaches accounting for time shifts. The first approach transforms time to take time delays and speed differences into account. The second divides the time series into interval units according to their main features and finds the longest common subsequence (LCS) using a dynamic programming algorithm.

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5.37 score 1 stars 38 dependents 56 scripts 1.8k downloads

JM - Joint Modeling of Longitudinal and Survival Data

Shared parameter models for the joint modeling of longitudinal and time-to-event data.

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5.32 score 2 stars 1 dependents 199 scripts 3.5k downloads

lpridge - Local Polynomial (Ridge) Regression

Local Polynomial Regression with Ridging.

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5.23 score 2 dependents 19 scripts 328 downloads

Rsymphony - SYMPHONY in R

An R interface to the SYMPHONY solver for mixed-integer linear programs.

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coinor-symphony

5.20 score 6 dependents 151 scripts 5.8k downloads

PreProcess - Basic Functions for Pre-Processing Microarrays

Provides classes to pre-process microarray gene expression data as part of the OOMPA collection of packages described at <http://oompa.r-forge.r-project.org/>.

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microarraypreprocessing

5.18 score 50 scripts 357 downloads

fRegression - Rmetrics - Regression Based Decision and Prediction

A collection of functions for linear and non-linear regression modelling. It implements a wrapper for several regression models available in the base and contributed packages of R.

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5.16 score 1 stars 23 scripts 385 downloads

plasma - Partial LeAst Squares for Multiomic Analysis

Contains tools for supervised analyses of incomplete, overlapping multiomics datasets. Applies partial least squares in multiple steps to find models that predict survival outcomes. See Yamaguchi et al. (2023) <doi:10.1101/2023.03.10.532096>.

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5.16 score 24 scripts 654 downloads

VarSelLCM - Variable Selection for Model-Based Clustering of Mixed-Type Data Set with Missing Values

Full model selection (detection of the relevant features and estimation of the number of clusters) for model-based clustering (see reference here <doi:10.1007/s11222-016-9670-1>). Data to analyze can be continuous, categorical, integer or mixed. Moreover, missing values can occur and do not necessitate any pre-processing. Shiny application permits an easy interpretation of the results.

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openblascpp

4.98 score 2 dependents 53 scripts 465 downloads

cotram - Count Transformation Models

Count transformation models featuring parameters interpretable as discrete hazard ratios, odds ratios, reverse-time discrete hazard ratios, or transformed expectations. An appropriate data transformation for a count outcome and regression coefficients are simultaneously estimated by maximising the exact discrete log-likelihood using the computational framework provided in package 'mlt', technical details are given in Siegfried & Hothorn (2020) <DOI:10.1111/2041-210X.13383>. The package also contains an experimental implementation of multivariate count transformation models with an application to multi-species distribution models <DOI:10.48550/arXiv.2201.13095>.

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4.76 score 2 dependents 8 scripts 973 downloads

robustX - 'eXtra' / 'eXperimental' Functionality for Robust Statistics

Robustness -- 'eXperimental', 'eXtraneous', or 'eXtraordinary' Functionality for Robust Statistics. Hence methods which are not well established, often related to methods in package 'robustbase'. Amazingly, 'BACON()', originally by Billor, Hadi, and Velleman (2000) <doi:10.1016/S0167-9473(99)00101-2> has become established in places. The "barrow wheel" `rbwheel()` is from Stahel and Mächler (2009) <doi:10.1111/j.1467-9868.2009.00706.x>.

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4.75 score 2 dependents 29 scripts 631 downloads

trtf - Transformation Trees and Forests

Recursive partytioning of transformation models with corresponding random forest for conditional transformation models as described in 'Transformation Forests' (Hothorn and Zeileis, 2021, <doi:10.1080/10618600.2021.1872581>) and 'Top-Down Transformation Choice' (Hothorn, 2018, <DOI:10.1177/1471082X17748081>).

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4.73 score 12 scripts 4.6k downloads

fCopulae - Rmetrics - Bivariate Dependence Structures with Copulae

Provides a collection of functions to manage, to investigate and to analyze bivariate financial returns by Copulae. Included are the families of Archemedean, Elliptical, Extreme Value, and Empirical Copulae.

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4.60 score 1 stars 3 dependents 35 scripts 873 downloads

agrmt - Calculate Concentration and Dispersion in Ordered Rating Scales

Calculates concentration and dispersion in ordered rating scales. It implements various measures of concentration and dispersion to describe what researchers variably call agreement, concentration, consensus, dispersion, or polarization among respondents in ordered data. It also implements other related measures to classify distributions. In addition to a generic city-block based concentration measure and a generic dispersion measure, the package implements various measures, including van der Eijk's (2001) <DOI: 10.1023/A:1010374114305> measure of agreement A, measures of concentration by Leik, Tatsle and Wierman, Blair and Lacy, Kvalseth, Berry and Mielke, Reardon, and Garcia-Montalvo and Reynal-Querol. Furthermore, the package provides an implementation of Galtungs AJUS-system to classify distributions, as well as a function to identify the position of multiple modes.

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4.57 score 62 scripts 805 downloads

cordillera - Calculation of the OPTICS Cordillera

Functions for calculating the OPTICS Cordillera. The OPTICS Cordillera measures the amount of 'clusteredness' in a numeric data matrix within a distance-density based framework for a given minimum number of points comprising a cluster, as described in Rusch, Hornik, Mair (2018) <doi:10.1080/10618600.2017.1349664>. We provide an R native version with methods for printing, summarizing, and plotting the result.

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4.56 score 1 stars 2 dependents 5 scripts 306 downloads

plgraphics - User Oriented Plotting Functions

Plots with high flexibility and easy handling, including informative regression diagnostics for many models.

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4.36 score 19 scripts 217 downloads

fNonlinear - Rmetrics - Nonlinear and Chaotic Time Series Modelling

Provides a collection of functions for testing various aspects of univariate time series including independence and neglected nonlinearities. Further provides functions to investigate the chaotic behavior of time series processes and to simulate different types of chaotic time series maps.

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4.26 score 1 stars 3 dependents 16 scripts 527 downloads

stops - Structure Optimized Proximity Scaling

Methods that use flexible variants of multidimensional scaling (MDS) which incorporate parametric nonlinear distance transformations and trade-off the goodness-of-fit fit with structure considerations to find optimal hyperparameters, also known as structure optimized proximity scaling (STOPS) (Rusch, Mair & Hornik, 2023,<doi:10.1007/s11222-022-10197-w>). The package contains various functions, wrappers, methods and classes for fitting, plotting and displaying different 1-way MDS models with ratio, interval, ordinal optimal scaling in a STOPS framework. These cover essentially the functionality of the package smacofx, including Torgerson (classical) scaling with power transformations of dissimilarities, SMACOF MDS with powers of dissimilarities, Sammon mapping with powers of dissimilarities, elastic scaling with powers of dissimilarities, spherical SMACOF with powers of dissimilarities, (ALSCAL) s-stress MDS with powers of dissimilarities, r-stress MDS, MDS with powers of dissimilarities and configuration distances, elastic scaling powers of dissimilarities and configuration distances, Sammon mapping powers of dissimilarities and configuration distances, power stress MDS (POST-MDS), approximate power stress, Box-Cox MDS, local MDS, Isomap, curvilinear component analysis (CLCA), curvilinear distance analysis (CLDA) and sparsified (power) multidimensional scaling and (power) multidimensional distance analysis (experimental models from smacofx influenced by CLCA). All of these models can also be fit by optimizing over hyperparameters based on goodness-of-fit fit only (i.e., no structure considerations). The package further contains functions for optimization, specifically the adaptive Luus-Jaakola algorithm and a wrapper for Bayesian optimization with treed Gaussian process with jumps to linear models, and functions for various c-structuredness indices. Hyperparameter optimization can be done with a number of techniques but we recommend either Bayesian optimization or particle swarm. For using "Kriging", users need to install a version of the archived 'DiceOptim' R package.

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openjdk

4.21 score 1 stars 27 scripts 316 downloads

FFD - Freedom from Disease

Functions, S4 classes/methods and a graphical user interface (GUI) to design surveys to substantiate freedom from disease using a modified hypergeometric function (see Cameron and Baldock, 1997, <doi:10.1016/s0167-5877(97)00081-0>). Herd sensitivities are computed according to sampling strategies "individual sampling" or "limited sampling" (see M. Ziller, T. Selhorst, J. Teuffert, M. Kramer and H. Schlueter, 2002, <doi:10.1016/S0167-5877(01)00245-8>). Methods to compute the a-posteriori alpha-error are implemented. Risk-based targeted sampling is supported.

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4.20 score 20 scripts 290 downloads

cops - Cluster Optimized Proximity Scaling

Multidimensional scaling (MDS) methods that aim at pronouncing the clustered appearance of the configuration (Rusch, Mair & Hornik, 2021, <doi:10.1080/10618600.2020.1869027>). They achieve this by transforming proximities/distances with explicit power functions and penalizing the fitting criterion with a clusteredness index, the OPTICS Cordillera (Rusch, Hornik & Mair, 2018, <doi:10.1080/10618600.2017.1349664>). There are two variants: One for finding the configuration directly (COPS-C) for any Minkowski distance with given explicit power transformations and implicit ratio, interval and nonmetric optimal scaling transformations (Borg & Groenen, 2005, ISBN:978-0-387-28981-6), and one for using the augmented fitting criterion to find optimal hyperparameters for the explicit transformations (P-COPS). The package contains various functions, wrappers, methods and classes for fitting, plotting and displaying a large number of different MDS models (most of the functionality in smacofx) in the COPS framework. The package further contains a function for pattern search optimization, the ``Adaptive Luus-Jaakola Algorithm'' (Rusch, Mair & Hornik, 2021,<doi:10.1080/10618600.2020.1869027>) and a functions to calculate the phi-distances for count data or histograms.

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4.16 score 1 stars 24 scripts 305 downloads

TopKLists - Inference, Aggregation and Visualization for Top-K Ranked Lists

For multiple ranked input lists (full or partial) representing the same set of N objects, the package TopKLists offers (1) statistical inference on the lengths of informative top-k lists, (2) stochastic aggregation of full or partial lists, and (3) graphical tools for the statistical exploration of input lists, and for the visualization of aggregation results.

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4.11 score 1 dependents 43 scripts 330 downloads

NormalLaplace - The Normal Laplace Distribution

Functions for the normal Laplace distribution. Currently, it provides limited functionality. Density, distribution and quantile functions, random number generation, and moments are provided.

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4.10 score 1 stars 9 scripts 303 downloads

CommonJavaJars - Useful libraries for building a Java based GUI under R

Useful libraries for building a Java based GUI under R

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4.08 score 4 dependents 3 scripts 511 downloads

tramME - Transformation Models with Mixed Effects

Likelihood-based estimation of mixed-effects transformation models using the Template Model Builder ('TMB', Kristensen et al., 2016) <doi:10.18637/jss.v070.i05>. The technical details of transformation models are given in Hothorn et al. (2018) <doi:10.1111/sjos.12291>. Likelihood contributions of exact, randomly censored (left, right, interval) and truncated observations are supported. The random effects are assumed to be normally distributed on the scale of the transformation function, the marginal likelihood is evaluated using the Laplace approximation, and the gradients are calculated with automatic differentiation (Tamasi & Hothorn, 2021) <doi:10.32614/RJ-2021-075>. Penalized smooth shift terms can be defined using 'mgcv'.

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cppopenmp

4.06 score 3 scripts 1.2k downloads

tramnet - Penalized Transformation Models

Partially penalized versions of specific transformation models implemented in package 'mlt'. Available models include a fully parametric version of the Cox model, other parametric survival models (Weibull, etc.), models for binary and ordered categorical variables, normal and transformed-normal (Box-Cox type) linear models, and continuous outcome logistic regression. Hyperparameter tuning is facilitated through model-based optimization functionalities from package 'mlr3MBO'. The methodology is described in Kook et al. (2021) <doi:10.32614/RJ-2021-054>. Transformation models and model-based optimization are described in Hothorn et al. (2019) <doi:10.1111/sjos.12291> and Bischl et al. (2016) <doi:10.48550/arXiv.1703.03373>, respectively.

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4.00 score 2 scripts 1.0k downloads

tramvs - Optimal Subset Selection for Transformation Models

Greedy optimal subset selection for transformation models (Hothorn et al., 2018, <doi:10.1111/sjos.12291> ) based on the abess algorithm (Zhu et al., 2020, <doi:10.1073/pnas.2014241117> ). Applicable to models from packages 'tram' and 'cotram'. Application to shift-scale transformation models are described in Siegfried et al. (2024, <doi:10.1080/00031305.2023.2203177>).

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4.00 score 9 scripts 1.0k downloads

ROI.plugin.symphony - 'SYMPHONY' Plug-in for the 'R' Optimization Interface

Enhances the R Optimization Infrastructure ('ROI') package by registering the 'SYMPHONY' open-source solver from the COIN-OR suite. It allows for solving mixed integer linear programming (MILP) problems as well as all variants/combinations of LP, IP.

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3.79 score 4 dependents 38 scripts 1.4k downloads

ROI.plugin.quadprog - 'quadprog' Plug-in for the 'R' Optimization Infrastructure

Enhances the R Optimization Infrastructure ('ROI') package by registering the 'quadprog' solver. It allows for solving quadratic programming (QP) sproblems.

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3.70 score 1 dependents 145 scripts 1.1k downloads

distrSim - Simulation Classes Based on Package 'distr'

S4-classes for setting up a coherent framework for simulation within the distr family of packages.

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3.68 score 4 dependents 7 scripts 363 downloads

mpmi - Mixed-pair mutual information estimators

Uses a kernel smoothing approach to calculate Mutual Information for comparisons between all types of variables including continuous vs continuous, continuous vs discrete and discrete vs discrete. Uses a nonparametric bias correction giving Bias Corrected Mutual Information (BCMI). Implemented efficiently in Fortran 95 with OpenMP and suited to large genomic datasets.

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fortran

3.65 score 45 scripts 313 downloads

ROI.plugin.ecos - 'ECOS' Plugin for the 'R' Optimization Infrastructure

Enhances the 'R' Optimization Infrastructure ('ROI') package with the Embedded Conic Solver ('ECOS') for solving conic optimization problems.

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3.62 score 2 dependents 29 scripts 2.4k downloads

distrDoc - Documentation for 'distr' Family of R Packages

Provides documentation in form of a common vignette to packages 'distr', 'distrEx', 'distrMod', 'distrSim', 'distrTEst', 'distrTeach', and 'distrEllipse'.

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3.60 score 5 scripts 478 downloads

smacofx - Flexible Multidimensional Scaling and 'smacof' Extensions

Flexible multidimensional scaling (MDS) methods and extensions to the package 'smacof'. This package contains various functions, wrappers, methods and classes for fitting, plotting and displaying a large number of different flexible MDS models. These are: Torgerson scaling (Torgerson, 1958, ISBN:978-0471879459) with powers, Sammon mapping (Sammon, 1969, <doi:10.1109/T-C.1969.222678>) with ratio and interval optimal scaling, Multiscale MDS (Ramsay, 1977, <doi:10.1007/BF02294052>) with ratio and interval optimal scaling, s-stress MDS (ALSCAL; Takane, Young & De Leeuw, 1977, <doi:10.1007/BF02293745>) with ratio and interval optimal scaling, elastic scaling (McGee, 1966, <doi:10.1111/j.2044-8317.1966.tb00367.x>) with ratio and interval optimal scaling, r-stress MDS (De Leeuw, Groenen & Mair, 2016, <https://rpubs.com/deleeuw/142619>) with ratio, interval, splines and nonmetric optimal scaling, power-stress MDS (POST-MDS; Buja & Swayne, 2002 <doi:10.1007/s00357-001-0031-0>) with ratio and interval optimal scaling, restricted power-stress (Rusch, Mair & Hornik, 2021, <doi:10.1080/10618600.2020.1869027>) with ratio and interval optimal scaling, approximate power-stress with ratio optimal scaling (Rusch, Mair & Hornik, 2021, <doi:10.1080/10618600.2020.1869027>), Box-Cox MDS (Chen & Buja, 2013, <https://jmlr.org/papers/v14/chen13a.html>), local MDS (Chen & Buja, 2009, <doi:10.1198/jasa.2009.0111>), curvilinear component analysis (Demartines & Herault, 1997, <doi:10.1109/72.554199>), curvilinear distance analysis (Lee, Lendasse & Verleysen, 2004, <doi:10.1016/j.neucom.2004.01.007>), nonlinear MDS with optimal dissimilarity powers functions (De Leeuw, 2024, <https://github.com/deleeuw/smacofManual/blob/main/smacofPO(power)/smacofPO.pdf>), sparsified (power) MDS and sparsified multidimensional (power) distance analysis aka extended curvilinear (power) component analysis and extended curvilinear (power) distance analysis (Rusch, 2024, <doi:10.57938/355bf835-ddb7-42f4-8b85-129799fc240e>). Some functions are suitably flexible to allow any other sensible combination of explicit power transformations for weights, distances and input proximities with implicit ratio, interval, splines or nonmetric optimal scaling of the input proximities. Most functions use a Majorization-Minimization algorithm. Currently the methods are only available for one-mode two-way data (symmetric dissimilarity matrices).

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3.56 score 1 stars 2 dependents 1 scripts 272 downloads

cardidates - Identification of Cardinal Dates in Ecological Time Series

Identification of cardinal dates (begin, time of maximum, end of mass developments) in ecological time series using fitted Weibull functions.

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3.34 score 22 scripts 282 downloads

ROI.plugin.neos - 'NEOS' Plug-in for the 'R' Optimization Interface

Enhances the 'R' Optimization Infrastructure ('ROI') package with a connection to the 'neos' server. 'ROI' optimization problems can be directly be sent to the 'neos' server and solution obtained in the typical 'ROI' style.

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3.33 score 7 scripts 2.2k downloads

QSARdata - Quantitative Structure Activity Relationship (QSAR) Data Sets

Molecular descriptors and outcomes for several public domain data sets

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3.22 score 81 scripts 2.1k downloads

ROI.plugin.alabama - 'alabama' Plug-in for the 'R' Optimization Infrastructure

Enhances the R Optimization Infrastructure ('ROI') package with the 'alabama' solver for solving nonlinear optimization problems.

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2.80 score 18 scripts 3.5k downloads

multiColl - Collinearity Detection in a Multiple Linear Regression Model

The detection of worrying approximate collinearity in a multiple linear regression model is a problem addressed in all existing statistical packages. However, we have detected deficits regarding to the incorrect treatment of qualitative independent variables and the role of the intercept of the model. The objective of this package is to correct these deficits. In this package will be available detection and treatment techniques traditionally used as the recently developed. D.A. Belsley (1982) <doi:10.1016/0304-4076(82)90020-3>. D. A. Belsley (1991, ISBN: 978-0471528890). C. Garcia, R. Salmeron and C.B. Garcia (2019) <doi:10.1080/00949655.2018.1543423>. R. Salmeron, C.B. Garcia and J. Garcia (2018) <doi:10.1080/00949655.2018.1463376>. G.W. Stewart (1987) <doi:10.1214/ss/1177013444>.

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2.78 score 1 dependents 20 scripts 268 downloads

ROI.models.miplib - 'ROI' Access to 'MIPLIB' 2010 Benchmark Instances

The mixed integer programming library 'MIPLIB' (see <http://miplib.zib.de/>) is commonly used to compare the performance of mixed integer optimization solvers. This package provides functions to access 'MIPLIB' from the 'R' Optimization Infrastructure ('ROI'). More information about 'MIPLIB' can be found in the paper by Koch et al. available at <http://mpc.zib.de/index.php/MPC/article/viewFile/56/28>. The 'README.md' file illustrates how to use this package.

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2.70 score 5 scripts 282 downloads

ROI.plugin.optimx - 'optimx' Plug-in for the 'R' Optimization Infrastructure

Enhances the R Optimization Infrastructure ('ROI') package with the 'optimx' package.

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2.48 score 1 dependents 5 scripts 261 downloads

ROI.plugin.ipop - 'ipop' Plug-in for the 'R' Optimization Interface

Enhances the 'R' Optimization Infrastructure ('ROI') package by registering the 'ipop' solver from package 'kernlab'.

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2.00 score 2 scripts 258 downloads

Eagle - Multiple Locus Association Mapping on a Genome-Wide Scale

An implementation of multiple-locus association mapping on a genome-wide scale. 'Eagle' can handle inbred or outbred study populations, populations of arbitrary unknown complexity, and data larger than the memory capacity of the computer. Since 'Eagle' is based on linear mixed models, it is best suited to the analysis of data on continuous traits. However, it can tolerate non-normal data. 'Eagle' reports, as its findings, the best set of snp in strongest association with a trait. To perform an analysis, run 'OpenGUI()'. This opens a web browser to the menu-driven user interface for the input of data, and for performing genome-wide analysis.

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cppopenmp

3.51 score 32 scripts 311 downloads

distrEllipse - S4 Classes for Elliptically Contoured Distributions

Distribution (S4-)classes for elliptically contoured distributions (based on package 'distr').

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3.33 score 1 dependents 18 scripts 360 downloads

DPQmpfr - DPQ (Density, Probability, Quantile) Distribution Computations using MPFR

An extension to the 'DPQ' package with computations for 'DPQ' (Density (pdf), Probability (cdf) and Quantile) functions, where the functions here partly use the 'Rmpfr' package and hence the underlying 'MPFR' and 'GMP' C libraries.

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3.33 score 2 scripts 3.6k downloads

sirad - Functions for Calculating Daily Solar Radiation and Evapotranspiration

Calculating daily global solar radiation at horizontal surface using several well-known models (i.e. Angstrom-Prescott, Supit-Van Kappel, Hargreaves, Bristow and Campbell, and Mahmood-Hubbard), and model calibration based on ground-truth data, and (3) model auto-calibration. The FAO Penmann-Monteith equation to calculate evapotranspiration is also included.

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3.24 score 86 scripts 306 downloads

copulaData - Data Sets for Copula Modeling

Data sets used for copula modeling in addition to those in the R package 'copula'. These include a random subsample from the US National Education Longitudinal Study (NELS) of 1988 and nursing home data from Wisconsin.

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3.18 score 7 scripts 791 downloads

simest - Constrained Single Index Model Estimation

Estimation of function and index vector in single index model ('sim') with (and w/o) shape constraints including different smoothness conditions. See, e.g., Kuchibhotla and Patra (2020) <doi:10.3150/19-BEJ1183>.

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3.18 score 15 scripts 467 downloads

RCytoGPS - Using Cytogenetics Data in R

Defines classes and methods to process text-based cytogenetics using the CytoGPS web site, then import the results into R for further analysis and graphing.

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3.12 score 33 scripts 305 downloads

mpm - Multivariate Projection Methods

Exploratory graphical analysis of multivariate data, specifically gene expression data with different projection methods: principal component analysis, correspondence analysis, spectral map analysis.

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3.10 score 3 dependents 14 scripts 426 downloads

distrTEst - Estimation and Testing Classes Based on Package 'distr'

Evaluation (S4-)classes based on package distr for evaluating procedures (estimators/tests) at data/simulation in a unified way.

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3.08 score 1 dependents 3 scripts 389 downloads

distrTeach - Extensions of Package 'distr' for Teaching Stochastics/Statistics in Secondary School

Provides flexible examples of LLN and CLT for teaching purposes in secondary school.

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3.08 score 1 dependents 9 scripts 341 downloads

RobAStRDA - Interpolation Grids for Packages of the 'RobASt' - Family of Packages

Includes 'sysdata.rda' file for packages of the 'RobASt' - family of packages; is currently used by package 'RobExtremes' only.

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3.08 score 1 dependents 376 downloads

WayFindR - Computing Graph Structures on WikiPathways

Converts pathways from 'WikiPathways' GPML format or 'KEGG' KGML format into 'igraph' objects. Includes tools to find all cycles in the resulting graphs and determine which ones involve negative feedback (inhibition).

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3.07 score 13 scripts 674 downloads

RPointCloud - Visualizing Topological Loops and Voids

Visualizations to explain the results of a topological data analysis. The goal of topological data analysis is to identify persistent topological structures, such as loops (topological circles) and voids (topological spheres), in data sets. The output of an analysis using the 'TDA' package is a Rips diagram (named after the mathematician Eliyahu Rips). The goal of 'RPointCloud' is to fill in these holes in the data by providing tools to visualize the features that help explain the structures found in the Rips diagram. See McGee and colleagues (2024) <doi:10.1101/2024.05.16.593927>.

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2.92 score 28 scripts 183 downloads

plugdensity - Plug-in Kernel Density Estimation

Kernel density estimation with global bandwidth selection via "plug-in".

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2.90 score 3 scripts 343 downloads

NameNeedle - Using Needleman-Wunsch to Match Sample Names

The Needleman-Wunsch global alignment algorithm can be used to find approximate matches between sample names in different data sets. See Wang et al. (2010) <doi:10.4137/CIN.S5613>.

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2.73 score 1 stars 1 dependents 18 scripts 528 downloads

BimodalIndex - The Bimodality Index

Defines the functions used to compute the bimodal index as defined by Wang et al. (2009) <https://pmc.ncbi.nlm.nih.gov/articles/PMC2730180/>, <doi:10.4137/CIN.S2846>.

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microarray

2.65 score 1 dependents 15 scripts 392 downloads

distrRmetrics - Distribution Classes for Distributions from Rmetrics

S4-distribution classes based on package distr for distributions from packages 'fBasics' and 'fGarch'.

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2.60 score 7 scripts 265 downloads

lagsarlmtree - Spatial Lag Model Trees

Model-based linear model trees adjusting for spatial correlation using a simultaneous autoregressive spatial lag, Wagner and Zeileis (2019) <doi:10.1111/geer.12146>.

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2.60 score 3 scripts 217 downloads

integIRTy - Integrating Multiple Modalities of High Throughput Assays Using Item Response Theory

Provides a systematic framework for integrating multiple modalities of assays profiled on the same set of samples. The goal is to identify genes that are altered in cancer either marginally or consistently across different assays. The heterogeneity among different platforms and different samples are automatically adjusted so that the overall alteration magnitude can be accurately inferred. See Tong and Coombes (2012) <doi:10.1093/bioinformatics/bts561>.

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2.41 score 26 scripts 332 downloads

NewmanOmics - Extending the Newman Studentized Range Statistic to Transcriptomics

Extends the classical Newman studentized range statistic in various ways that can be applied to genome-scale transcriptomic or other expression data.

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2.30 score 20 scripts 305 downloads

SIBERG - Systematic Identification of Bimodally Expressed Genes Using RNAseq Data

Provides models to identify bimodally expressed genes from RNAseq data based on the Bimodality Index. SIBERG models the RNAseq data in the finite mixture modeling framework and incorporates mechanisms for dealing with RNAseq normalization. Three types of mixture models are implemented, namely, the mixture of log normal, negative binomial, or generalized Poisson distribution. See Tong et al. (2013) <doi:10.1093/bioinformatics/bts713>.

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2.30 score 20 scripts 255 downloads

pems.utils - Portable Emissions (and Other Mobile) Measurement System Utilities

Utility functions for the handling, analysis and visualisation of data from portable emissions measurement systems ('PEMS') and other similar mobile activity monitoring devices. The package includes a dedicated 'pems' data class that manages many of the quality control, unit handling and data archiving issues that can hinder efforts to standardise 'PEMS' research.

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openjdk

2.28 score 19 scripts 321 downloads

GenAlgo - Classes and Methods to Use Genetic Algorithms for Feature Selection

Defines classes and methods that can be used to implement genetic algorithms for feature selection. The idea is that we want to select a fixed number of features to combine into a linear classifier that can predict a binary outcome, and can use a genetic algorithm heuristically to select an optimal set of features.

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microarrayclustering

2.28 score 19 scripts 357 downloads

CrossValidate - Classes and Methods for Cross Validation of "Class Prediction" Algorithms

Defines classes and methods to cross-validate various binary classification algorithms used for "class prediction" problems.

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microarrayclustering

2.20 score 16 scripts 308 downloads

ROI.plugin.scs - 'SCS' Plug-in for the 'R' Optimization Infrastructure

Enhances the 'R' Optimization Infrastructure ('ROI') package with the 'SCS' solver for solving convex cone problems.

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2.15 score 14 scripts 310 downloads

ROI.plugin.deoptim - 'DEoptim' and 'DEoptimR' Plugin for the 'R' Optimization Interface

Enhances the R Optimization Infrastructure ('ROI') package with the 'DEoptim' and 'DEoptimR' package. 'DEoptim' is used for unconstrained optimization and 'DEoptimR' for constrained optimization.

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2.15 score 14 scripts 303 downloads

ROI.plugin.nloptr - 'nloptr' Plug-in for the 'R' Optimization Infrastructure

Enhances the R Optimization Infrastructure ('ROI') package with the 'NLopt' solver for solving nonlinear optimization problems.

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2.11 score 13 scripts 335 downloads

CloneSeeker - Seeking and Finding Clones in Copy Number and Sequencing Data

Defines the classes and functions used to simulate and to analyze data sets describing copy number variants and, optionally, sequencing mutations in order to detect clonal subsets. See Zucker et al. (2019) <doi:10.1093/bioinformatics/btz057>.

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2.00 score 8 scripts 194 downloads

SVAlignR - Recovering Structure of Long Molecules from Structural Variation Data

Implements a method to combine multiple levels of multiple sequence alignment to uncover the structure of complex DNA rearrangements.

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2.00 score 10 scripts 236 downloads

SillyPutty - Silly Putty Clustering

Implements a simple, novel clustering algorithm based on optimizing the silhouette width. See <doi:10.1101/2023.11.07.566055> for details.

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clustering

2.00 score 6 scripts 205 downloads

ROI.plugin.msbinlp - 'Multi-Solution' Binary Linear Problem Plug-in for the 'R' Optimization Interface

Enhances the 'R' Optimization Infrastructure ('ROI') package with the possibility to obtain multiple solutions for linear problems with binary variables. The main function is copied (with small modifications) from the relations package.

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2.00 score 6 scripts 284 downloads

ROI.plugin.osqp - 'osqp' Plugin for the 'R' Optimization Infrastructure

Enhances the 'R' Optimization Infrastructure ('ROI') package with the quadratic solver 'OSQP'. More information about 'OSQP' can be found at <https://osqp.org>.

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2.00 score 2 scripts 260 downloads

softclassval - Soft Classification Performance Measures

An extension of sensitivity, specificity, positive and negative predictive value to continuous predicted and reference memberships in [0, 1].

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2.00 score 8 scripts 194 downloads