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.
Last updated 11 hours ago
1 stars 20.47 score 1 dependencies 11010 dependentsnumDeriv - 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.
Last updated 1 years ago
15.56 score 0 dependencies 2828 dependentsmvtnorm - Multivariate Normal and t Distributions
Computes multivariate normal and t probabilities, quantiles, random deviates, and densities. Log-likelihoods for multivariate Gaussian models and Gaussian copulae parameterised by Cholesky factors of covariance or precision matrices are implemented for interval-censored and exact data, or a mix thereof. Score functions for these log-likelihoods are available. A class representing multiple lower triangular matrices and corresponding methods are part of this package.
Last updated 16 days ago
15.14 score 0 dependencies 2430 dependentsMatrixModels - Modelling with Sparse and Dense Matrices
Modelling with sparse and dense 'Matrix' matrices, using modular prediction and response module classes.
Last updated 3 months ago
1 stars 15.03 score 2 dependencies 2489 dependentsexpm - Matrix Exponential, Log, 'etc'
Computation of the matrix exponential, logarithm, sqrt, and related quantities, using traditional and modern methods.
Last updated 7 months ago
9.75 score 2 dependencies 411 dependentsGPArotation - GPA Factor Rotation
Gradient Projection Algorithm Rotation for Factor Analysis. See '?GPArotation.Intro' for more details.
Last updated 1 years ago
8.63 score 0 dependencies 216 dependentssignal - 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.
Last updated 8 months ago
7.36 score 1 dependencies 141 dependentsROI - 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/>.
Last updated 1 years ago
6.05 score 4 dependencies 45 dependentsFME - 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.
Last updated 1 years ago
4.94 score 8 dependencies 9 dependentsRglpk - 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.
Last updated 7 months ago
4.86 score 1 dependencies 48 dependentsRcmdr - R Commander
A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Last updated 6 months ago
4 stars 4.31 score 124 dependencies 37 dependentsqualV - 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.
Last updated 1 years ago
3.80 score 1 dependencies 25 dependentsRandVar - Implementation of Random Variables
Implements random variables by means of S4 classes and methods.
Last updated 6 months ago
2.37 score 5 dependencies 7 dependentsROI.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'.
Last updated 1 years ago
2.33 score 6 dependencies 8 dependentstscount - 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.
Last updated 1 years ago
2.25 score 1 dependencies 1 dependentsdistrSim - Simulation Classes Based on Package 'distr'
S4-classes for setting up a coherent framework for simulation within the distr family of packages.
Last updated 5 months ago
2.02 score 5 dependencies 3 dependentsRobAStBase - Robust Asymptotic Statistics
Base S4-classes and functions for robust asymptotic statistics.
Last updated 6 months ago
1.98 score 13 dependencies 4 dependentsRobLoxBioC - Infinitesimally Robust Estimators for Preprocessing -Omics Data
Functions for the determination of optimally robust influence curves and estimators for preprocessing omics data, in particular gene expression data (Kohl and Deigner (2010), <doi:10.1186/1471-2105-11-583>).
Last updated 6 months ago
1.82 score 89 dependenciesdistrTEst - 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.
Last updated 5 months ago
1.71 score 6 dependencies 1 dependentsGNE - 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>.
Last updated 1 years ago
1.71 score 6 dependenciesdistrRmetrics - Distribution Classes for Distributions from Rmetrics
S4-distribution classes based on package distr for distributions from packages 'fBasics' and 'fGarch'.
Last updated 5 months ago
1.53 score 18 dependenciesROptEst - 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>.
Last updated 6 months ago
1.48 score 14 dependencies 1 dependentsRobLox - 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>).
Last updated 6 months ago
1.47 score 17 dependencies 1 dependentsRobAStRDA - 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.
Last updated 6 months ago
1.47 score 0 dependencies 1 dependentsROI.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.
Last updated 1 years ago
1.43 score 8 dependencies 3 dependentsskellam - Densities and Sampling for the Skellam Distribution
Functions for the Skellam distribution, including: density (pmf), cdf, quantiles and regression.
Last updated 6 months ago
1.38 score 0 dependencies 1 dependentsROI.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.
Last updated 1 years ago
1.27 score 6 dependencies 2 dependentsROI.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.
Last updated 1 years ago
1.27 score 6 dependencies 2 dependentsRobExtremes - 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}.
Last updated 6 months ago
1.25 score 19 dependencieswordspace - 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).
Last updated 7 months ago
1.21 score 7 dependencies 2 dependentsROI.plugin.optimx - 'optimx' Plug-in for the 'R' Optimization Infrastructure
Enhances the R Optimization Infrastructure ('ROI') package with the 'optimx' package.
Last updated 1 years ago
0.94 score 9 dependencies 1 dependentsROI.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.
Last updated 1 years ago
0.69 score 11 dependenciesROI.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.
Last updated 1 years ago
0.64 score 6 dependenciesROI.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.
Last updated 1 years ago
0.63 score 5 dependenciesROI.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.
Last updated 1 years ago
0.63 score 7 dependenciesROI.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'.
Last updated 1 years ago
0.62 score 6 dependenciesSillyPutty - 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.
Last updated 6 months ago
0.09 score 27 dependenciesNameNeedle - 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>.
Last updated 11 months ago
1 stars 0.09 score 0 dependenciesRCytoGPS - 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.
Last updated 8 months ago
0.00 score 1 dependenciesxtable - Export Tables to LaTeX or HTML
Coerce data to LaTeX and HTML tables.
Last updated 4 years ago
14.84 score 0 dependencies 2224 dependentszoo - 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.
Last updated 1 months ago
14.70 score 1 dependencies 2060 dependentscar - Companion to Applied Regression
Functions to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage, 2019.
Last updated 2 months ago
12.31 score 59 dependencies 843 dependentscarData - Companion to Applied Regression Data Sets
Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage (2019).
Last updated 2 months ago
11.92 score 0 dependencies 859 dependentsrobustbase - 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.
Last updated 18 days ago
10.25 score 1 dependencies 458 dependentsmultcomp - 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).
Last updated 9 days ago
9.91 score 9 dependencies 334 dependentssurvey - 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.
Last updated 22 days ago
9.07 score 9 dependencies 218 dependentslatticeExtra - Extra Graphical Utilities Based on Lattice
Building on the infrastructure provided by the lattice package, this package provides several new high-level functions and methods, as well as additional utilities such as panel and axis annotation functions.
Last updated 2 years ago
8.75 score 9 dependencies 228 dependentsstabledist - Stable Distribution Functions
Density, Probability and Quantile functions, and random number generation for (skew) stable distributions, using the parametrizations of Nolan.
Last updated 16 days ago
1 stars 8.07 score 0 dependencies 209 dependentstm - Text Mining Package
A framework for text mining applications within R.
Last updated 3 months ago
7.75 score 7 dependencies 93 dependentscoin - 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>.
Last updated 30 days ago
7.54 score 13 dependencies 69 dependentslinprog - Linear Programming / Optimization
Can be used to solve Linear Programming / Linear Optimization problems by using the simplex algorithm.
Last updated 2 years ago
7.25 score 1 dependencies 142 dependentsRmpfr - R 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.
Last updated 13 days ago
7.06 score 1 dependencies 130 dependentspolycor - Polychoric and Polyserial Correlations
Computes polychoric and polyserial correlations by quick "two-step" methods or ML, optionally with standard errors; tetrachoric and biserial correlations are special cases.
Last updated 3 years ago
6.56 score 4 dependencies 71 dependentsgenoPlotR - 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.
Last updated 4 years ago
6.11 score 7 dependenciesWRS2 - 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.
Last updated 3 months ago
5.85 score 4 dependencies 8 dependentstuneR - 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.
Last updated 3 months ago
5.44 score 2 dependencies 42 dependentsnor1mix - 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.
Last updated 3 months ago
5.12 score 0 dependencies 52 dependentsmlogit - Multinomial Logit Models
Maximum Likelihood estimation of random utility discrete choice models, as described in Kenneth Train (2009) Discrete Choice Methods with Simulations <doi:10.1017/CBO9780511805271>.
Last updated 4 years ago
5.06 score 8 dependencies 14 dependentsdtw - Dynamic Time Warping Algorithms
A comprehensive implementation of dynamic time warping (DTW) algorithms in R. DTW computes the optimal (least cumulative distance) alignment between points of two time series. Common DTW variants covered include local (slope) and global (window) constraints, subsequence matches, arbitrary distance definitions, normalizations, minimum variance matching, and so on. Provides cumulative distances, alignments, specialized plot styles, etc., as described in Giorgino (2009) <doi:10.18637/jss.v031.i07>.
Last updated 2 years ago
5 stars 4.70 score 1 dependencies 47 dependentsGeneralizedHyperbolic - 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.
Last updated 16 days ago
1 stars 4.42 score 2 dependencies 25 dependentsSkewHyperbolic - 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.
Last updated 16 days ago
1 stars 4.18 score 3 dependencies 19 dependentsdistr - Object Oriented Implementation of Distributions
S4-classes and methods for distributions.
Last updated 5 months ago
4.11 score 3 dependencies 26 dependentssystemfit - 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>.
Last updated 1 years ago
4.10 score 63 dependencies 21 dependentsPolychrome - 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>.
Last updated 3 months ago
3.87 score 2 dependencies 22 dependentsClassDiscovery - 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.
Last updated 3 months ago
3.83 score 6 dependencies 9 dependentsBessel - 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.
Last updated 7 days ago
3.74 score 2 dependencies 15 dependentsmlt - 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>.
Last updated 8 days ago
3.72 score 17 dependencies 10 dependentsmodEvA - Model Evaluation and Analysis
Analyses species distribution models and evaluates their performance. It includes functions for variation partitioning, extracting variable importance, computing several metrics of model discrimination and calibration performance, optimizing prediction thresholds based on a number of criteria, performing multivariate environmental similarity surface (MESS) analysis, and displaying various analytical plots. Initially described in Barbosa et al. (2013) <doi:10.1111/ddi.12100>.
Last updated 2 months ago
3.66 score 2 dependencies 2 dependentsarrayhelpers - Convenience Functions for Arrays
Some convenient functions to work with arrays.
Last updated 4 years ago
3.60 score 1 dependencies 23 dependentsvariables - Variable Descriptions
Abstract descriptions of (yet) unobserved variables.
Last updated 8 days ago
3.59 score 0 dependencies 12 dependentsoompaBase - 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/>.
Last updated 3 months ago
3.58 score 1 dependencies 18 dependentsPOT - 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.
Last updated 2 years ago
3.56 score 0 dependencies 3 dependentsRHRV - 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>.
Last updated 2 months ago
3.56 score 101 dependencies 1 dependentscobs - Constrained B-Splines (Sparse Matrix Based)
Qualitatively Constrained (Regression) Smoothing Splines via Linear Programming and Sparse Matrices.
Last updated 3 months ago
3.56 score 7 dependencies 19 dependentsbasefun - Infrastructure for Computing with Basis Functions
Some very simple infrastructure for basis functions.
Last updated 8 days ago
3.53 score 5 dependencies 11 dependentsR2MLwiN - Running 'MLwiN' from Within R
An R command interface to the 'MLwiN' multilevel modelling software package.
Last updated 1 months ago
3.22 score 44 dependenciesoompaData - 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.
Last updated 3 months ago
3.17 score 0 dependencies 12 dependentsisotone - 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.
Last updated 3 months ago
3.13 score 1 dependencies 12 dependentsfExtremes - 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.
Last updated 16 days ago
1 stars 3.11 score 15 dependencies 4 dependentsdistrEx - Extensions of Package 'distr'
Extends package 'distr' by functionals, distances, and conditional distributions.
Last updated 5 months ago
3.09 score 4 dependencies 11 dependentsmlt.docreg - Most Likely Transformations: Documentation and Regression Tests
Additional documentation, a package vignette and regression tests for package mlt.
Last updated 8 days ago
3.00 score 73 dependenciescensReg - Censored Regression (Tobit) Models
Maximum Likelihood estimation of censored regression (Tobit) models with cross-sectional and panel data.
Last updated 3 months ago
2.99 score 18 dependencies 2 dependentsfAssets - 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.
Last updated 16 days ago
1 stars 2.95 score 36 dependencies 3 dependentsfUnitRoots - Rmetrics - Modelling Trends and Unit Roots
Provides four addons for analyzing trends and unit roots in financial time series: (i) functions for the density and probability of the augmented Dickey-Fuller Test, (ii) functions for the density and probability of MacKinnon's unit root test statistics, (iii) reimplementations for the ADF and MacKinnon Test, and (iv) an 'urca' Unit Root Test Interface for Pfaff's unit root test suite.
Last updated 16 days ago
1 stars 2.93 score 10 dependenciesfPortfolio - Rmetrics - Portfolio Selection and Optimization
A collection of functions to optimize portfolios and to analyze them from different points of view.
Last updated 16 days ago
1 stars 2.88 score 48 dependencies 2 dependentsRNetLogo - 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>.
Last updated 7 years ago
2.77 score 12 dependencies 1 dependentsfImport - Rmetrics - Importing Economic and Financial Data
Provides a collection of utility functions to download and manage data sets from the Internet or from other sources.
Last updated 16 days ago
1 stars 2.67 score 2 dependenciesgrImport - Importing Vector Graphics
Functions for converting, importing, and drawing PostScript pictures in R plots.
Last updated 2 days ago
2.66 score 1 dependencies 7 dependentsfRegression - 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.
Last updated 16 days ago
1 stars 2.65 score 15 dependenciestrtf - 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>).
Last updated 8 days ago
2.63 score 29 dependenciestbm - Transformation Boosting Machines
Boosting the likelihood of conditional and shift transformation models as introduced in \doi{10.1007/s11222-019-09870-4}.
Last updated 8 days ago
2.61 score 27 dependenciestramvs - 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'.
Last updated 8 days ago
2.61 score 33 dependenciestruncreg - Truncated Gaussian Regression Models
Estimation of models for truncated Gaussian variables by maximum likelihood.
Last updated 6 years ago
2.60 score 7 dependencies 7 dependentslokern - Kernel Regression Smoothing with Local or Global Plug-in Bandwidth
Kernel regression smoothing with adaptive local or global plug-in bandwidth selection.
Last updated 3 months ago
2.50 score 1 dependencies 5 dependentsGifi - Multivariate Analysis with Optimal Scaling
Implements categorical principal component analysis ('PRINCALS'), multiple correspondence analysis ('HOMALS'), monotone regression analysis ('MORALS'). It replaces the 'homals' package.
Last updated 3 months ago
2.49 score 1 dependencies 1 dependentszipfR - 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.)
Last updated 4 years ago
2.47 score 0 dependencies 10 dependentsdistrMod - Object Oriented Implementation of Probability Models
Implements S4 classes for probability models based on packages 'distr' and 'distrEx'.
Last updated 5 months ago
2.41 score 6 dependencies 6 dependentsClassComparison - 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.
Last updated 3 months ago
2.36 score 4 dependencies 2 dependentssetRNG - 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.
Last updated 5 months ago
2.35 score 0 dependencies 5 dependentssse - Sample Size Estimation
Provides functions to evaluate user-defined power functions for a parameter range, and draws a sensitivity plot. It also provides a resampling procedure for semi-parametric sample size estimation and methods for adding information to a Sweave report.
Last updated 3 years ago
2.27 score 1 dependenciesTailRank - 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>.
Last updated 3 months ago
2.24 score 5 dependencies 3 dependentslpridge - Local Polynomial (Ridge) Regression
Local Polynomial Regression with Ridging.
Last updated 3 months ago
2.24 score 0 dependencies 2 dependentscordillera - 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.
Last updated 30 days ago
1 stars 2.19 score 3 dependencies 2 dependentsDPQmpfr - 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.
Last updated 7 days ago
2.06 score 4 dependenciesplasma - 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>.
Last updated 3 months ago
1.83 score 158 dependenciesRsymphony - SYMPHONY in R
An R interface to the SYMPHONY solver for mixed-integer linear programs.
Last updated 3 years ago
1.74 score 0 dependencies 4 dependentsloa - Lattice Options and Add-Ins
Various plots and functions that make use of the lattice/trellis plotting framework. The plots, which include loaPlot(), RgoogleMapsPlot() and trianglePlot(), 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.
Last updated 1 months ago
1.72 score 37 dependencies 2 dependentsCommonJavaJars - Useful libraries for building a Java based GUI under R
Useful libraries for building a Java based GUI under R
Last updated 10 years ago
1.72 score 0 dependencies 4 dependentsdistrTeach - Extensions of Package 'distr' for Teaching Stochastics/Statistics in Secondary School
Provides flexible examples of LLN and CLT for teaching purposes in secondary school.
Last updated 5 months ago
1.71 score 5 dependencies 1 dependentsanacor - 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.
Last updated 3 months ago
1.66 score 79 dependenciesmpm - 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.
Last updated 13 years ago
1.66 score 2 dependencies 3 dependentsVarSelLCM - 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.
Last updated 5 years ago
1.65 score 52 dependencies 1 dependentslpsymphony - Symphony integer linear programming solver in R
This package was derived from Rsymphony_0.1-17 from CRAN. These packages provide an R interface to SYMPHONY, an open-source linear programming solver written in C++. The main difference between this package and Rsymphony is that it includes the solver source code (SYMPHONY version 5.6), while Rsymphony expects to find header and library files on the users' system. Thus the intention of lpsymphony is to provide an easy to install interface to SYMPHONY. For Windows, precompiled DLLs are included in this package.
Last updated 3 months ago
bioconductor-package
1.58 score 0 dependencies 3 dependentsEasyABC - 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.
Last updated 2 years ago
1.54 score 16 dependencies 3 dependentsdistrEllipse - S4 Classes for Elliptically Contoured Distributions
Distribution (S4-)classes for elliptically contoured distributions (based on package 'distr').
Last updated 5 months ago
1.53 score 8 dependenciestframe - 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'.)
Last updated 5 months ago
1.49 score 0 dependencies 3 dependentsplugdensity - Plug-in Kernel Density Estimation
Kernel density estimation with global bandwidth selection via "plug-in".
Last updated 3 months ago
1.48 score 0 dependenciescorpora - 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').
Last updated 2 months ago
1.48 score 0 dependenciesmetRology - Support for Metrological Applications
Provides classes and calculation and plotting functions for metrology applications, including measurement uncertainty estimation and inter-laboratory metrology comparison studies.
Last updated 6 years ago
4 stars 1.45 score 4 dependencies 4 dependentscopulaData - 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.
Last updated 2 months ago
1.42 score 0 dependenciesTopKLists - 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.
Last updated 9 years ago
1.26 score 70 dependencies 1 dependentsPCDimension - 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>.
Last updated 2 years ago
1.16 score 12 dependencies 4 dependentsQSARdata - Quantitative Structure Activity Relationship (QSAR) Data Sets
Molecular descriptors and outcomes for several public domain data sets
Last updated 13 years ago
1.05 score 0 dependenciestm.plugin.europresse - Import Articles from 'Europresse' Using the 'tm' Text Mining Framework
Provides a 'tm' Source to create corpora from articles exported from the 'Europresse' content provider as HTML files. It is able to read both text content and meta-data information (including source, date, title, author and pages).
Last updated 8 years ago
1.02 score 9 dependencies 1 dependentssirad - 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.
Last updated 8 years ago
0.92 score 6 dependenciesrvif - Collinearity Detection using RVIF and Graphical Methods
The detection of troubling approximate collinearity in a multiple linear regression model is a classical problem in Econometrics. The objective of this package is to detect it using the variance inflation factor redefined and the scatterplot between the variance inflation factor and the coefficient of variation.
Last updated 2 years ago
0.73 score 1 dependenciespems.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.
Last updated 1 years ago
0.62 score 51 dependenciesJM - Joint Modeling of Longitudinal and Survival Data
Shared parameter models for the joint modeling of longitudinal and time-to-event data.
Last updated 2 years ago
2 stars 0.23 score 5 dependenciesgridGraphviz - 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.
Last updated 2 years ago
1.10 score 3 dependencies 1 dependentstfplot - Time Frame User Utilities
Utilities for simple manipulation and quick plotting of time series data. These utilities use the 'tframe' package which provides a programming kernel for time series. Extensions to 'tframe' provided in 'tframePlus' can also be used. See the Guide vignette for examples.
Last updated 5 months ago
1.05 score 1 dependenciesThresher - 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>.
Last updated 3 months ago
1.00 score 24 dependencies 3 dependentsfrontier - 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>).
Last updated 12 days ago
0.91 score 19 dependenciestframePlus - Time Frame Coding Kernel Extensions
Extensions and additional 'tframe' utilities.
Last updated 5 months ago
0.75 score 3 dependenciesmpmi - 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.
Last updated 11 years ago
0.64 score 1 dependenciessoftclassval - Soft Classification Performance Measures
An extension of sensitivity, specificity, positive and negative predictive value to continuous predicted and reference memberships in [0, 1].
Last updated 8 years ago
0.62 score 2 dependenciesMercator - 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>.
Last updated 3 months ago
0.36 score 76 dependencies 1 dependentsModeler - 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.
Last updated 5 years ago
0.23 score 18 dependencies 1 dependentsBimodalIndex - The Bimodality Index
Defines the functions used to compute the bimodal index as defined by Wang et al. (2009) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2730180/>, <doi:10.4137/CIN.S2846>.
Last updated 5 years ago
0.23 score 3 dependencies 1 dependentsWayFindR - Computing Graph Structures on WikiPathways
Converts pathways from 'WikiPathways' GPML format into 'igraph' objects. Includes tools to find all cycles in the resulting graphs and determine which ones involve negative feedback (inhibition).
Last updated 4 months ago
0.00 score 12 dependenciesCloneSeeker - 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>.
Last updated 2 years ago
0.00 score 76 dependenciesUmpire - 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.
Last updated 4 years ago
0.00 score 73 dependenciesGenAlgo - 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.
Last updated 4 years ago
0.00 score 8 dependencies