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r-kernelknn
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public |
Extends the simple k-nearest neighbors algorithm by incorporating numerous kernel functions and a variety of distance metrics. The package takes advantage of 'RcppArmadillo' to speed up the calculation of distances between observations.
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2024-01-16 |
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r-kerndwd
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public |
A novel implementation that solves the linear distance weighted discrimination and the kernel distance weighted discrimination. Reference: Wang and Zou (2018) <doi:10.1111/rssb.12244>.
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2024-01-16 |
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r-kere
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public |
An efficient algorithm inspired by majorization-minimization principle for solving the entire solution path of a flexible nonparametric expectile regression estimator constructed in a reproducing kernel Hilbert space.
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2024-01-16 |
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r-kendall
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public |
Computes the Kendall rank correlation and Mann-Kendall trend test. See documentation for use of block bootstrap when there is autocorrelation.
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2024-01-16 |
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r-kappalab
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public |
S4 tool box for capacity (or non-additive measure, fuzzy measure) and integral manipulation in a finite setting. It contains routines for handling various types of set functions such as games or capacities. It can be used to compute several non-additive integrals: the Choquet integral, the Sugeno integral, and the symmetric and asymmetric Choquet integrals. An analysis of capacities in terms of decision behavior can be performed through the computation of various indices such as the Shapley value, the interaction index, the orness degree, etc. The well-known M�bius transform, as well as other equivalent representations of set functions can also be computed. Kappalab further contains seven capacity identification routines: three least squares based approaches, a method based on linear programming, a maximum entropy like method based on variance minimization, a minimum distance approach and an unsupervised approach based on parametric entropies. The functions contained in Kappalab can for instance be used in the framework of multicriteria decision making or cooperative game theory.
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2024-01-16 |
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r-joinerml
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public |
Fits the joint model proposed by Henderson and colleagues (2000) <doi:10.1093/biostatistics/1.4.465>, but extended to the case of multiple continuous longitudinal measures. The time-to-event data is modelled using a Cox proportional hazards regression model with time-varying covariates. The multiple longitudinal outcomes are modelled using a multivariate version of the Laird and Ware linear mixed model. The association is captured by a multivariate latent Gaussian process. The model is estimated using a Monte Carlo Expectation Maximization algorithm. This project was funded by the Medical Research Council (Grant number MR/M013227/1).
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2024-01-16 |
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r-kamila
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public |
Implements methods for clustering mixed-type data, specifically combinations of continuous and nominal data. Special attention is paid to the often-overlooked problem of equitably balancing the contribution of the continuous and categorical variables. This package implements KAMILA clustering, a novel method for clustering mixed-type data in the spirit of k-means clustering. It does not require dummy coding of variables, and is efficient enough to scale to rather large data sets. Also implemented is Modha-Spangler clustering, which uses a brute-force strategy to maximize the cluster separation simultaneously in the continuous and categorical variables. For more information, see Foss, Markatou, Ray, & Heching (2016) <doi:10.1007/s10994-016-5575-7> and Foss & Markatou (2018) <doi:10.18637/jss.v083.i13>.
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2024-01-16 |
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r-junctions
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public |
Individual based simulations of hybridizing populations, where the accumulation of junctions is tracked. Furthermore, mathematical equations are provided to verify simulation outcomes. Both simulations and mathematical equations are based on Janzen (2018, <doi:10.1101/058107>) and Janzen (2020, <doi:10.1101/2020.09.10.292441>).
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2024-01-16 |
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r-jomo
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public |
Similarly to package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation (Carpenter and Kenward, 2013) <doi:10.1002/9781119942283>. Novel aspects of 'jomo' are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.
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2024-01-16 |
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r-juliacall
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public |
Provides an R interface to 'Julia', which is a high-level, high-performance dynamic programming language for numerical computing, see <https://julialang.org/> for more information. It provides a high-level interface as well as a low-level interface. Using the high level interface, you could call any 'Julia' function just like any R function with automatic type conversion. Using the low level interface, you could deal with C-level SEXP directly while enjoying the convenience of using a high-level programming language like 'Julia'.
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2024-01-16 |
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r-jsonify
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public |
Conversions between 'R' objects and Javascript Object Notation (JSON) using the 'rapidjsonr' library <https://CRAN.R-project.org/package=rapidjsonr>.
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2024-01-16 |
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r-jqr
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public |
Client for 'jq', a 'JSON' processor (<https://jqlang.github.io/jq/>), written in C. 'jq' allows the following with 'JSON' data: index into, parse, do calculations, cut up and filter, change key names and values, perform conditionals and comparisons, and more.
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2024-01-16 |
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r-jpeg
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None |
This package provides an easy and simple way to read, write and display bitmap images stored in the JPEG format. It can read and write both files and in-memory raw vectors.
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2024-01-16 |
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r-jousboost
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public |
Implements under/oversampling for probability estimation. To be used with machine learning methods such as AdaBoost, random forests, etc.
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2024-01-16 |
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r-jinjar
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public |
Template engine powered by the 'inja' C++ library. Users write a template document, using syntax inspired by the 'Jinja' Python package, and then render the final document by passing data from R. The template syntax supports features such as variables, loops, conditions and inheritance.
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2024-01-16 |
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r-jointdiag
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public |
Different algorithms to perform approximate joint diagonalization of a finite set of square matrices. Depending on the algorithm, orthogonal or non-orthogonal diagonalizer is found. These algorithms are particularly useful in the context of blind source separation. Original publications of the algorithms can be found in Ziehe et al. (2004), Pham and Cardoso (2001) <doi:10.1109/78.942614>, Souloumiac (2009) <doi:10.1109/TSP.2009.2016997>, Vollgraff and Obermayer <doi:10.1109/TSP.2006.877673>. An example of application in the context of Brain-Computer Interfaces EEG denoising can be found in Gouy-Pailler et al (2010) <doi:10.1109/TBME.2009.2032162>.
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2024-01-16 |
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r-jmotif
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public |
Implements time series z-normalization, SAX, HOT-SAX, VSM, SAX-VSM, RePair, and RRA algorithms facilitating time series motif (i.e., recurrent pattern), discord (i.e., anomaly), and characteristic pattern discovery along with interpretable time series classification.
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2024-01-16 |
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r-jiebar
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public |
Chinese text segmentation, keyword extraction and speech tagging For R.
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2024-01-16 |
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r-jmi
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public |
Computes the Jackknife Mutual Information (JMI) between two random vectors and provides the p-value for dependence tests. See Zeng, X., Xia, Y. and Tong, H. (2018) <doi:10.1073/pnas.1715593115>.
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2024-01-16 |
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r-isotone
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public |
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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2024-01-16 |
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r-jfa
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public |
Provides statistical methods for auditing as implemented in JASP for Audit (Derks et al., 2021 <doi:10.21105/joss.02733>). First, the package makes it easy for an auditor to plan a statistical sample, select the sample from the population, and evaluate the misstatement in the sample compliant with international auditing standards. Second, the package provides statistical methods for auditing data, including tests of digit distributions and repeated values. Finally, the package includes methods for auditing algorithms on the aspect of fairness and bias. Next to classical statistical methodology, the package implements Bayesian equivalents of these methods whose statistical underpinnings are described in Derks et al. (2021) <doi:10.1111/ijau.12240>, Derks et al. (2021) <doi:10.31234/osf.io/kzqp5>, and Derks et al. (2022) <doi:10.31234/osf.io/8nf3e>.
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2024-01-16 |
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r-javagd
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public |
Graphics device routing all graphics commands to a Java program. The actual functionality of the JavaGD depends on the Java-side implementation. Simple AWT and Swing implementations are included.
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2024-01-16 |
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r-irtoys
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public |
A collection of functions useful in learning and practicing IRT, which can be combined into larger programs. Provides basic CTT analysis, a simple common interface to the estimation of item parameters in IRT models for binary responses with three different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME, EAP, WLE, plausible values), item and person fit statistics, scaling methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich array of parametric and non-parametric (kernel) plots. Estimates and plots Haberman's interaction model when all items are dichotomously scored.
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2024-01-16 |
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r-jade
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public |
Cardoso's JADE algorithm as well as his functions for joint diagonalization are ported to R. Also several other blind source separation (BSS) methods, like AMUSE and SOBI, and some criteria for performance evaluation of BSS algorithms, are given. The package is described in Miettinen, Nordhausen and Taskinen (2017) <doi:10.18637/jss.v076.i02>.
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2024-01-16 |
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r-jacobieigen
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public |
Implements the classical Jacobi algorithm for the eigenvalues and eigenvectors of a real symmetric matrix, both in pure 'R' and in 'C++' using 'Rcpp'. Mainly as a programming example for teaching purposes.
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2024-01-16 |
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r-isospecr
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public |
IsoSpec is a fine structure calculator used for obtaining the most probable masses of a chemical compound given the frequencies of the composing isotopes and their masses. It finds the smallest set of isotopologues with a given probability. The probability is assumed to be that of the product of multinomial distributions, each corresponding to one particular element and parametrized by the frequencies of finding these elements in nature. These numbers are supplied by IUPAC - the International Union of Pure and Applied Chemistry. See: Lacki, Valkenborg, Startek (2020) <DOI:10.1021/acs.analchem.0c00959> and Lacki, Startek, Valkenborg, Gambin (2017) <DOI:10.1021/acs.analchem.6b01459> for the description of the algorithms used.
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2024-01-16 |
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r-isoband
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public |
A fast C++ implementation to generate contour lines (isolines) and contour polygons (isobands) from regularly spaced grids containing elevation data.
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2024-01-16 |
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r-iso
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public |
Linear order and unimodal order (univariate) isotonic regression; bivariate isotonic regression with linear order on both variables.
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2024-01-16 |
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r-isnullptr
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public |
Check if an 'externalptr' is a null pointer. R does currently not have a native function for that purpose. This package contains a C function that returns TRUE in case of a null pointer.
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2024-01-16 |
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r-islasso
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public |
An implementation of the induced smoothing (IS) idea to lasso regularization models to allow estimation and inference on the model coefficients (currently hypothesis testing only). Linear, logistic, Poisson and gamma regressions with several link functions are implemented. The algorithm is described in the original paper; see <doi:10.1177/0962280219842890> and discussed in a tutorial <doi:10.13140/RG.2.2.16360.11521>.
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2024-01-16 |
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r-island
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public |
Develops stochastic models based on the Theory of Island Biogeography (TIB) of MacArthur and Wilson (1967) <doi:10.1023/A:1016393430551> and extensions. It implements methods to estimate colonization and extinction rates (including environmental variables) given presence-absence data, simulates community assembly, and performs model selection.
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2024-01-16 |
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r-isingsampler
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public |
Sample states from the Ising model and compute the probability of states. Sampling can be done for any number of nodes, but due to the intractibility of the Ising model the distribution can only be computed up to ~10 nodes.
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2024-01-16 |
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r-isinglenzmc
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public |
Classical Ising Model is a land mark system in statistical physics.The model explains the physics of spin glasses and magnetic materials, and cooperative phenomenon in general, for example phase transitions and neural networks.This package provides utilities to simulate one dimensional Ising Model with Metropolis and Glauber Monte Carlo with single flip dynamics in periodic boundary conditions. Utility functions for exact solutions are provided.
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2024-01-16 |
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r-isa2
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public |
The ISA is a biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix.
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2024-01-16 |
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r-irlba
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None |
Fast and memory efficient methods for truncated singular value decomposition and principal components analysis of large sparse and dense matrices.
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2024-01-16 |
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r-irace
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public |
Iterated race is an extension of the Iterated F-race method for the automatic configuration of optimization algorithms, that is, (offline) tuning their parameters by finding the most appropriate settings given a set of instances of an optimization problem. M. López-Ibáñez, J. Dubois-Lacoste, L. Pérez Cáceres, T. Stützle, and M. Birattari (2016) <doi:10.1016/j.orp.2016.09.002>.
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2024-01-16 |
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r-irafnet
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public |
Provides a flexible integrative algorithm that allows information from prior data, such as protein protein interactions and gene knock-down, to be jointly considered for gene regulatory network inference.
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2024-01-16 |
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r-irishdirectorates
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public |
Provides the dataset and an implementation of the method illustrated in Friel, N., Rastelli, R., Wyse, J. and Raftery, A.E. (2016) <DOI:10.1073/pnas.1606295113>.
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2024-01-16 |
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r-ipred
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public |
Improved predictive models by indirect classification and bagging for classification, regression and survival problems as well as resampling based estimators of prediction error.
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2024-01-16 |
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r-ipfp
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public |
A fast (C) implementation of the iterative proportional fitting procedure.
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2024-01-16 |
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r-iotools
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public |
Basic I/O tools for streaming and data parsing.
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2024-01-16 |
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r-intsurv
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public |
Contains implementations of integrative survival analysis routines, including regular Cox cure rate model proposed by Kuk and Chen (1992) <doi:10.1093/biomet/79.3.531> via an EM algorithm proposed by Sy and Taylor (2000) <doi:10.1111/j.0006-341X.2000.00227.x>, regularized Cox cure rate model with elastic net penalty following Masud et al. (2018) <doi:10.1177/0962280216677748>, and Zou and Hastie (2005) <doi:10.1111/j.1467-9868.2005.00503.x>, and weighted concordance index for cure models proposed by Asano and Hirakawa (2017) <doi:10.1080/10543406.2017.1293082>.
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2024-01-16 |
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r-intreggof
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public |
Performs Goodness of Fit for regression models using Integrated Regression method. Works for several different fitting techniques.
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2024-01-16 |
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r-intervalsurgeon
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public |
Manipulate integer-bounded intervals including finding overlaps, piling and merging.
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2024-01-16 |
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r-intervals
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public |
Tools for working with and comparing sets of points and intervals.
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2024-01-16 |
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r-interp
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public |
Bivariate data interpolation on regular and irregular grids, either linear or using splines are the main part of this package. It is intended to provide FOSS replacement functions for the ACM licensed akima::interp and tripack::tri.mesh functions. Linear interpolation is implemented in interp::interp(..., method="linear"), this corresponds to the call akima::interp(..., linear=TRUE) which is the default setting and covers most of akima::interp use cases in depending packages. A re-implementation of Akimas irregular grid spline interpolation (akima::interp(..., linear=FALSE)) is now also available via interp::interp(..., method="akima"). Estimators for partial derivatives are now also available in interp::locpoly(), these are a prerequisite for the spline interpolation. The basic part is a GPLed triangulation algorithm (sweep hull algorithm by David Sinclair) providing the starting point for the irregular grid interpolator. As side effect this algorithm is also used to provide replacements for almost all functions of the tripack package which also suffers from the same ACM license restrictions. All functions are designed to be backward compatible with their akima / tripack counterparts.
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2024-01-16 |
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r-interep
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public |
Extensive penalized variable selection methods have been developed in the past two decades for analyzing high dimensional omics data, such as gene expressions, single nucleotide polymorphisms (SNPs), copy number variations (CNVs) and others. However, lipidomics data have been rarely investigated by using high dimensional variable selection methods. This package incorporates our recently developed penalization procedures to conduct interaction analysis for high dimensional lipidomics data with repeated measurements. The core module of this package is developed in C++. The development of this software package and the associated statistical methods have been partially supported by an Innovative Research Award from Johnson Cancer Research Center, Kansas State University.
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2024-01-16 |
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r-inplace
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public |
It provides in-place operators for R that are equivalent to '+=', '-=', '*=', '/=' in C++. Those can be applied on integer|double vectors|matrices. You have also access to sweep operations (in-place).
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2024-01-16 |
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r-immunarch
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public |
A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq) and single-cell sequencing (scRNAseq). Immunarch implements most of the widely used AIRR analysis methods, such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor databases and clonotype tracking in vaccination and cancer studies. A successor to our previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.
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2024-01-16 |
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r-infotheo
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public |
This package implements various measures of information theory based on several entropy estimators.
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2024-01-16 |
