|
r-rootwishart
|
public |
Functions for hypothesis testing in single and double Wishart settings, based on Roy's largest root. This test statistic is especially useful in multivariate analysis. The computations are based on results by Chiani (2014) <DOI:10.1016/j.jmva.2014.04.002> and Chiani (2016) <DOI:10.1016/j.jmva.2015.10.007>. They use the fact that the CDF is related to the Pfaffian of a matrix that can be computed in a finite number of iterations. This package takes advantage of the Boost and Eigen C++ libraries to perform multi-precision linear algebra.
|
2023-06-16 |
|
r-rodeo
|
public |
Provides an R6 class and several utility methods to facilitate the implementation of models based on ordinary differential equations. The heart of the package is a code generator that creates compiled 'Fortran' (or 'R') code which can be passed to a numerical solver. There is direct support for solvers contained in packages 'deSolve' and 'rootSolve'.
|
2023-06-16 |
|
r-robustblme
|
public |
Bayesian robust fitting of linear mixed effects models through weighted likelihood equations and approximate Bayesian computation as proposed by Ruli et al. (2017) <arXiv:1706.01752>.
|
2023-06-16 |
|
r-rmixtcompio
|
public |
Mixture Composer <https://github.com/modal-inria/MixtComp> is a project to build mixture models with heterogeneous data sets and partially missing data management. It includes models for real, categorical, counting, functional and ranking data. This package contains the minimal R interface of the C++ 'MixtComp' library.
|
2023-06-16 |
|
r-rgeos
|
public |
Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. The 'GEOS' library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'. ('rgeos' >= 0.5-1): Up to and including 'GEOS' 3.7.1, topological operations succeeded with some invalid geometries for which the same operations fail from and including 'GEOS' 3.7.2. The 'checkValidity=' argument defaults and structure have been changed, from default FALSE to integer default '0L' for 'GEOS' < 3.7.2 (no check), '1L' 'GEOS' >= 3.7.2 (check and warn). A value of '2L' is also provided that may be used, assigned globally using 'set_RGEOS_CheckValidity(2L)', or locally using the 'checkValidity=2L' argument, to attempt zero-width buffer repair if invalid geometries are found. The previous default (FALSE, now '0L') is fastest and used for 'GEOS' < 3.7.2, but will not warn users of possible problems before the failure of topological operations that previously succeeded.
|
2023-06-16 |
|
r-rexpokit
|
public |
Wraps some of the matrix exponentiation utilities from EXPOKIT (<http://www.maths.uq.edu.au/expokit/>), a FORTRAN library that is widely recommended for matrix exponentiation (Sidje RB, 1998. "Expokit: A Software Package for Computing Matrix Exponentials." ACM Trans. Math. Softw. 24(1): 130-156). EXPOKIT includes functions for exponentiating both small, dense matrices, and large, sparse matrices (in sparse matrices, most of the cells have value 0). Rapid matrix exponentiation is useful in phylogenetics when we have a large number of states (as we do when we are inferring the history of transitions between the possible geographic ranges of a species), but is probably useful in other ways as well.
|
2023-06-16 |
|
r-redm
|
public |
A new implementation of EDM algorithms based on research software previously developed for internal use in the Sugihara Lab (UCSD/SIO). Contains C++ compiled objects that use time delay embedding to perform state-space reconstruction and nonlinear forecasting and an R interface to those objects using 'Rcpp'. It supports both the simplex projection method from Sugihara & May (1990) <DOI:10.1038/344734a0> and the S-map algorithm in Sugihara (1994) <DOI:10.1098/rsta.1994.0106>. In addition, this package implements convergent cross mapping as described in Sugihara et al. (2012) <DOI:10.1126/science.1227079> and multiview embedding as described in Ye & Sugihara (2016) <DOI:10.1126/science.aag0863>.
|
2023-06-16 |
|
r-robustgasp
|
public |
Robust parameter estimation and prediction of Gaussian stochastic process emulators. It allows for robust parameter estimation and prediction using Gaussian stochastic process emulator. It also implements the parallel partial Gaussian stochastic process emulator for computer model with massive outputs See the reference: Mengyang Gu and Jim Berger, 2016, Annals of Applied Statistics; Mengyang Gu, Xiaojing Wang and Jim Berger, 2018, Annals of Statistics.
|
2023-06-16 |
|
r-rnifti
|
public |
Provides very fast read and write access to images stored in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between compiled C and interpreted R code. Also provides a C/C++ API that can be used by other packages. Not to be confused with 'RNiftyReg', which performs image registration.
|
2023-06-16 |
|
r-rlda
|
public |
Estimates the Bayesian LDA model for mixed-membership clustering based on different types of data (i.e., Multinomial, Bernoulli, and Binomial entries). Albuquerque, Valle and Li (2019) <doi:10.1016/j.knosys.2018.10.024>.
|
2023-06-16 |
|
r-rgb
|
public |
Classes and methods to efficiently handle (slice, annotate, draw ...) genomic features (such as genes or transcripts), and an interactive interface to browse them.
|
2023-06-16 |
|
r-rexperigen
|
public |
Provides convenience functions to communicate with an Experigen server: Experigen (<http://github.com/aquincum/experigen>) is an online framework for creating linguistic experiments, and it stores the results on a dedicated server. This package can be used to retrieve the results from the server, and it is especially helpful with registered experiments, as authentication with the server has to happen.
|
2023-06-16 |
|
r-reordercluster
|
public |
Tools for performing the leaf reordering for the dendrogram that preserves the hierarchical clustering result and at the same time tries to group instances from the same class together.
|
2023-06-16 |
|
r-refinr
|
public |
These functions take a character vector as input, identify and cluster similar values, and then merge clusters together so their values become identical. The functions are an implementation of the key collision and ngram fingerprint algorithms from the open source tool Open Refine <http://openrefine.org/>. More info on key collision and ngram fingerprint can be found here <https://github.com/OpenRefine/OpenRefine/wiki/Clustering-In-Depth>.
|
2023-06-16 |
|
r-robfitcongraph
|
public |
Contains a single function named robFitConGraph() which includes two algorithms for robust estimation of scatter matrices subject to zero-constraints in its inverse. The methodology is described in Vogel & Tyler (2014) <doi:10.1093/biomet/asu041>. See robFitConGraph() function documentation for further details.
|
2023-06-16 |
|
r-rnetcarto
|
public |
It provides functions to compute the modularity and modularity-related roles in networks. It is a wrapper around the rgraph library (Guimera & Amaral, 2005, doi:10.1038/nature03288).
|
2023-06-16 |
|
r-ring
|
public |
Circular / ring buffers in R and C. There are a couple of different buffers here with different implementations that represent different trade-offs.
|
2023-06-16 |
|
r-ri2by2
|
public |
Computes attributable effects based confidence interval, permutation test confidence interval, or asymptotic confidence interval for the the average treatment effect on a binary outcome.
|
2023-06-16 |
|
r-remmap
|
public |
remMap is developed for fitting multivariate response regression models under the high-dimension-low-sample-size setting
|
2023-06-16 |
|
r-reglogit
|
public |
Regularized (polychotomous) logistic regression by Gibbs sampling. The package implements subtly different MCMC schemes with varying efficiency depending on the data type (binary v. binomial, say) and the desired estimator (regularized maximum likelihood, or Bayesian maximum a posteriori/posterior mean, etc.) through a unified interface.
|
2023-06-16 |
|
r-recosystem
|
public |
R wrapper of the 'libmf' library <http://www.csie.ntu.edu.tw/~cjlin/libmf/> for recommender system using matrix factorization. It is typically used to approximate an incomplete matrix using the product of two matrices in a latent space. Other common names for this task include "collaborative filtering", "matrix completion", "matrix recovery", etc. High performance multi-core parallel computing is supported in this package.
|
2023-06-16 |
|
r-rodbcext
|
public |
An extension for RODBC package adding support for parameterized queries.
|
2023-06-16 |
|
r-rmargint
|
public |
Three robust marginal integration procedures for additive models based on local polynomial kernel smoothers. As a preliminary estimator of the multivariate function for the marginal integration procedure, a first approach uses local constant M-estimators, a second one uses local polynomials of order 1 over all the components of covariates, and the third one uses M-estimators based on local polynomials but only in the direction of interest. For this last approach, estimators of the derivatives of the additive functions can be obtained. All three procedures can compute predictions for points outside the training set if desired. See Boente and Martinez (2017) <doi:10.1007/s11749-016-0508-0> for details.
|
2023-06-16 |
|
r-rmalschains
|
public |
An implementation of an algorithm family for continuous optimization called memetic algorithms with local search chains (MA-LS-Chains). Memetic algorithms are hybridizations of genetic algorithms with local search methods. They are especially suited for continuous optimization.
|
2023-06-16 |
|
r-rltp
|
public |
R interface to the 'LTP'-Cloud service for Natural Language Processing in Chinese (http://www.ltp-cloud.com/).
|
2023-06-16 |
|
r-rlm
|
public |
Robust fitting of linear model which can take response in matrix form.
|
2023-06-16 |
|
r-rlibeemd
|
public |
An R interface for libeemd (Luukko, Helske, Räsänen, 2016) <doi:10.1007/s00180-015-0603-9>, a C library of highly efficient parallelizable functions for performing the ensemble empirical mode decomposition (EEMD), its complete variant (CEEMDAN), the regular empirical mode decomposition (EMD), and bivariate EMD (BEMD). Due to the possible portability issues CRAN version no longer supports OpenMP, you can install OpenMP-supported version from GitHub: <https://github.com/helske/Rlibeemd/>.
|
2023-06-16 |
|
r-ridge
|
public |
Linear and logistic ridge regression functions. Additionally includes special functions for genome-wide single-nucleotide polymorphism (SNP) data.
|
2023-06-16 |
|
r-rfit
|
public |
R estimation and inference for linear models. Estimation is for general scores and a library of commonly used score functions is included.
|
2023-06-16 |
|
r-robustgam
|
public |
This package provides robust estimation for generalized additive models. It implements a fast and stable algorithm in Wong, Yao and Lee (2013). The implementation also contains three automatic selection methods for smoothing parameter. They are designed to be robust to outliers. For more details, see Wong, Yao and Lee (2013).
|
2023-06-16 |
|
r-robfilter
|
public |
A set of functions to filter time series based on concepts from robust statistics.
|
2023-06-16 |
|
r-robcp
|
public |
Provides robust methods to detect change-points in uni- or multivariate time series. They can cope with corrupted data and heavy tails. One can detect changes in location, scale and dependence structure of a possibly multivariate time series. Procedures are based on Huberized versions of CUSUM tests proposed in Duerre and Fried (2019) <arXiv:1905.06201>.
|
2023-06-16 |
|
r-rngwell19937
|
public |
Long period linear random number generator WELL19937a by F. Panneton, P. L'Ecuyer and M. Matsumoto. The initialization algorithm allows to seed the generator with a numeric vector of an arbitrary length and uses MRG32k5a by P. L'Ecuyer to achieve good quality of the initialization. The output function may be set to provide numbers from the interval (0,1) with 53 (the default) or 32 random bits. WELL19937a is of similar type as Mersenne Twister and has the same period. WELL19937a is slightly slower than Mersenne Twister, but has better equidistribution and "bit-mixing" properties and faster recovery from states with prevailing zeros than Mersenne Twister. All WELL generators with orders 512, 1024, 19937 and 44497 can be found in randtoolbox package.
|
2023-06-16 |
|
r-rngwell
|
public |
It is a dedicated package to WELL pseudo random generators, which were introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software. But this package is not intended to be used directly, you are strongly __encouraged__ to use the 'randtoolbox' package, which depends on this package.
|
2023-06-16 |
|
r-rngsetseed
|
public |
A function setVectorSeed() is provided. Its argument is a numeric vector of an arbitrary nonzero length, whose components have integer values from [0, 2^32-1]. The input vector is transformed using AES (Advanced Encryption Standard) algorithm into an initial state of Mersenne-Twister random number generator. The function provides a better alternative to the R base function set.seed(), if the input vector is a single integer. Initializing a stream of random numbers with a vector is a convenient way to obtain several streams, each of which is identified by several integer indices.
|
2023-06-16 |
|
r-rmkdiscrete
|
public |
Sundry discrete probability distributions and helper functions.
|
2023-06-16 |
|
r-rjacgh
|
public |
Bayesian analysis of CGH microarrays fitting Hidden Markov Chain models. The selection of the number of states is made via their posterior probability computed by Reversible Jump Markov Chain Monte Carlo Methods. Also returns probabilistic common regions for gains/losses.
|
2023-06-16 |
|
r-riskparityportfolio
|
public |
Fast design of risk parity portfolios for financial investment. The goal of the risk parity portfolio formulation is to equalize or distribute the risk contributions of the different assets, which is missing if we simply consider the overall volatility of the portfolio as in the mean-variance Markowitz portfolio. In addition to the vanilla formulation, where the risk contributions are perfectly equalized subject to no shortselling and budget constraints, many other formulations are considered that allow for box constraints and shortselling, as well as the inclusion of additional objectives like the expected return and overall variance. See vignette for a detailed documentation and comparison, with several illustrative examples. The package is based on the papers: Y. Feng, and D. P. Palomar (2015). SCRIP: Successive Convex Optimization Methods for Risk Parity Portfolio Design. IEEE Trans. on Signal Processing, vol. 63, no. 19, pp. 5285-5300. <doi:10.1109/TSP.2015.2452219>. F. Spinu (2013), An Algorithm for Computing Risk Parity Weights. <doi:10.2139/ssrn.2297383>. T. Griveau-Billion, J. Richard, and T. Roncalli (2013). A fast algorithm for computing High-dimensional risk parity portfolios. <arXiv:1311.4057>.
|
2023-06-16 |
|
r-retimes
|
public |
Reaction time analysis by maximum likelihood
|
2023-06-16 |
|
r-rootsolve
|
public |
Routines to find the root of nonlinear functions, and to perform steady-state and equilibrium analysis of ordinary differential equations (ODE). Includes routines that: (1) generate gradient and jacobian matrices (full and banded), (2) find roots of non-linear equations by the 'Newton-Raphson' method, (3) estimate steady-state conditions of a system of (differential) equations in full, banded or sparse form, using the 'Newton-Raphson' method, or by dynamically running, (4) solve the steady-state conditions for uni-and multicomponent 1-D, 2-D, and 3-D partial differential equations, that have been converted to ordinary differential equations by numerical differencing (using the method-of-lines approach). Includes fortran code.
|
2023-06-16 |
|
r-robeth
|
public |
Locations problems, M-estimates of coefficients and scale in linear regression, Weights for bounded influence regression, Covariance matrix of the coefficient estimates, Asymptotic relative efficiency of regression M-estimates, Robust testing in linear models, High breakdown point regression, M-estimates of covariance matrices, M-estimates for discrete generalized linear models.
|
2023-06-16 |
|
r-rkvo
|
public |
This package provides functionality to read files containing observations which consist of arbitrary key/value pairs.
|
2023-06-16 |
|
r-rgeode
|
public |
Provides the hybrid Bayesian method Geometric Density Estimation. On the one hand, it scales the dimension of our data, on the other it performs inference. The method is fully described in the paper "Scalable Geometric Density Estimation" by Y. Wang, A. Canale, D. Dunson (2016) <http://proceedings.mlr.press/v51/wang16e.pdf>.
|
2023-06-16 |
|
r-rnomni
|
public |
Genetic association tests that use the rank-based inverse normal transformation (INT). These tests are recommend for continuous traits with non-normally distributed residuals. INT-based tests robustly control the type I error in settings where standard linear regression does not. Moreover, INT-based tests dominate standard linear regression in terms of power. INT-based tests may be classified into two types: tests that directly transform the phenotype (D-INT) and tests that transform phenotypic residuals (I-INT). Our omnibus test (O-INT) adaptively combines D-INT and I-INT into a single robust and statistically powerful approach.
|
2023-06-16 |
|
r-rmi
|
public |
Provides mutual information estimators based on k-nearest neighbor estimators by A. Kraskov, et al. (2004) <doi:10.1103/PhysRevE.69.066138>, S. Gao, et al. (2015) <http://proceedings.mlr.press/v38/gao15.pdf> and local density estimators by W. Gao, et al. (2017) <doi:10.1109/ISIT.2017.8006749>.
|
2023-06-16 |
|
r-rlof
|
public |
R parallel implementation of Local Outlier Factor(LOF) which uses multiple CPUs to significantly speed up the LOF computation for large datasets. (Note: The overall performance depends on the computers especially the number of the cores).It also supports multiple k values to be calculated in parallel, as well as various distance measures in addition to the default Euclidean distance.
|
2023-06-16 |
|
r-rip46
|
public |
Utility functions and S3 classes for IPv4 and IPv6 addresses, including conversion to and from binary representation.
|
2023-06-16 |
|
r-relsurv
|
public |
Contains functions for analysing relative survival data, including nonparametric estimators of net (marginal relative) survival, relative survival ratio, crude mortality, methods for fitting and checking additive and multiplicative regression models, transformation approach, methods for dealing with population mortality tables.
|
2023-06-16 |
|
r-robustaft
|
public |
R functions for the computation of the truncated maximum likelihood and the robust accelerated failure time regression for gaussian and log-Weibull case.
|
2023-06-16 |
|
r-rnetcdf
|
public |
An interface to the NetCDF file format designed by Unidata for efficient storage of array-oriented scientific data and descriptions. The R interface is closely based on the C API of the NetCDF library, and it includes calendar conversions from the Unidata UDUNITS library. The current implementation supports all operations on NetCDF datasets in classic and 64-bit offset file formats, and NetCDF4-classic format is supported for reading and modification of existing files.
|
2023-06-16 |
