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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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2025-03-25 |
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r-islasso
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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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2025-03-25 |
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r-isnullptr
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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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2025-03-25 |
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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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2025-03-25 |
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r-isingsampler
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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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2025-03-25 |
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r-isinglenzmc
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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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2025-03-25 |
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r-isa2
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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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2025-03-25 |
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r-isbf
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Selection of features for sparse regression estimation (like the LASSO). Selection of blocks of features when the regression parameter is sparse and constant by blocks (like the Fused-LASSO). Application to cgh arrays.
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2025-03-25 |
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r-irregular1
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Simulation and density evaluation of irregularly sampled stationary AR(1) processes with Gaussian errors using the algorithms described in Allévius (2018) <arXiv:1801.03791>.
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2025-03-25 |
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r-ipfp
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A fast (C) implementation of the iterative proportional fitting procedure.
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2025-03-25 |
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r-irishdirectorates
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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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2025-03-25 |
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r-irafnet
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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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2025-03-25 |
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r-intsurv
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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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2025-03-25 |
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r-intreggof
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Performs Goodness of Fit for regression models using Integrated Regression method. Works for several different fitting techniques.
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2025-03-25 |
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r-iotools
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Basic I/O tools for streaming and data parsing.
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2025-03-25 |
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r-intervalsurgeon
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Manipulate integer-bounded intervals including finding overlaps, piling and merging.
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2025-03-25 |
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r-interact
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This package searches for marginal interactions in a binary response model. Interact uses permutation methods to estimate false discovery rates for these marginal interactions and has some, limited visualization capabilities
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2025-03-25 |
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r-interep
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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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2025-03-25 |
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r-intervals
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Tools for working with and comparing sets of points and intervals.
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2025-03-25 |
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r-interp
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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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2025-03-25 |
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r-inca
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Specific functions are provided for rounding real weights to integers and performing an integer programming algorithm for calibration problems. They are useful for census-weights adjustments, or for performing linear regression with integer parameters. This research was supported in part by the U.S. Department of Agriculture, National Agriculture Statistics Service. The findings and conclusions in this publication are those of the authors and should not be construed to represent any official USDA, or US Government determination or policy.
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2025-03-25 |
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r-inplace
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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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2025-03-25 |
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r-independencetests
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Functions for testing mutual independence between many numerical random vectors or serial independence of a multivariate stationary sequence. The proposed test works when some or all of the marginal distributions are singular with respect to Lebesgue measure.
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2025-03-25 |
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r-infotheo
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This package implements various measures of information theory based on several entropy estimators.
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2025-03-25 |
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r-inarmix
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Fits mixtures models for longitudinal data. Appropriate when the data are counts and when the correlation structure is assumed to be AR(1).
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2025-03-25 |
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r-imptree
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Creation of imprecise classification trees. They rely on probability estimation within each node by means of either the imprecise Dirichlet model or the nonparametric predictive inference approach. The splitting variable is selected by the strategy presented in Fink and Crossman (2013) <http://www.sipta.org/isipta13/index.php?id=paper&paper=014.html>, but also the original imprecise information gain of Abellan and Moral (2003) <doi:10.1002/int.10143> is covered.
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2025-03-25 |
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r-immigrate
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Based on large margin principle, this package performs feature selection methods: "IM4E"(Iterative Margin-Maximization under Max-Min Entropy Algorithm); "Immigrate"(Iterative Max-Min Entropy Margin-Maximization with Interaction Terms Algorithm); "BIM"(Boosted version of IMMIGRATE algorithm); "Simba"(Iterative Search Margin Based Algorithm); "LFE"(Local Feature Extraction Algorithm). This package also performs prediction for the above feature selection methods.
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2025-03-25 |
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r-imputemdr
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This package provides various approaches to handling missing values for the MDR analysis to identify gene-gene interactions using biallelic marker data in genetic association studies
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2025-03-25 |
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r-imagine
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Provides fast application of image filters to data matrices, using R and C++ algorithms.
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2025-03-25 |
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r-im
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Compute moments of images and perform reconstruction from moments.
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2025-03-25 |
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r-image
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Performs mQTL (methylation quantitative-trait locus) mapping in bisulfite sequencing studies by fitting a binomial mixed model and then incorporating the allelic-specific methylation pattern. Based on Fan, Yue; Vilgalys, Tauras P.; Sun, Shiquan; Peng, Qinke; Tung, Jenny; Zhou, Xiang (2019) <doi:10.1101/615039>.
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2025-03-25 |
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r-iilasso
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Efficient algorithms for fitting linear / logistic regression model with Independently Interpretable Lasso. Takada, M., Suzuki, T., & Fujisawa, H. (2018). Independently Interpretable Lasso: A New Regularizer for Sparse Regression with Uncorrelated Variables. AISTATS. <http://proceedings.mlr.press/v84/takada18a/takada18a.pdf>.
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2025-03-25 |
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r-ifs
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Iterated Function Systems Estimator as in Iacus and La Torre (2005) <doi:10.1155/JAMDS.2005.33>.
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2025-03-25 |
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r-ieeeround
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A pair of functions for getting and setting the IEEE rounding mode for floating point computations.
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2025-03-25 |
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r-ifctools
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Provides utility functions to deal with Italian fiscal code ('codice fiscale').
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2025-03-25 |
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r-ifa
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The package performes Independent Factor Analysis
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2025-03-25 |
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r-idmtpreg
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Modeling of regression effects for transition probabilities in a progressive illness-death model. Azarang, Scheike, and de Una-Alvarez (2017) <doi:10.1002/sim.7245>.
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2025-03-25 |
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r-identity
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Calculate identity coefficients, based on Mark Abney's C code.
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2025-03-25 |
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r-idpmisc
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Different high-level graphics functions for displaying large datasets, displaying circular data in a very flexible way, finding local maxima, brewing color ramps, drawing nice arrows, zooming 2D-plots, creating figures with differently colored margin and plot region. In addition, the package contains auxiliary functions for data manipulation like omitting observations with irregular values or selecting data by logical vectors, which include NAs. Other functions are especially useful in spectroscopy and analyses of environmental data: robust baseline fitting, finding peaks in spectra, converting humidity measures.
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2025-03-25 |
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r-icemelt
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Estimates the parameters of the semiparametric linear transformation model using imputation method, naive method and regression calibration method when time-to-event is interval-censored and a covariate is measured with error. A right censoring indicator must be available. The methods implemented in this package can be found in Mandal, S., Wang, S. and Sinha, S. (2019+). Analysis of Linear Transformation Models with Covariate Measurement Error and Interval Censoring. (accepted, Statistics In Medicine).
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2025-03-25 |
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r-icr
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Provides functions to compute and plot Krippendorff's inter-coder reliability coefficient alpha and bootstrapped uncertainty estimates (Krippendorff 2004, ISBN:0761915443). The bootstrap routines are set up to make use of parallel threads where supported.
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2025-03-25 |
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r-icensmis
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We consider studies in which information from error-prone diagnostic tests or self-reports are gathered sequentially to determine the occurrence of a silent event. Using a likelihood-based approach incorporating the proportional hazards assumption, we provide functions to estimate the survival distribution and covariate effects. We also provide functions for power and sample size calculations for this setting. Please refer to Xiangdong Gu, Yunsheng Ma, and Raji Balasubramanian (2015) <doi: 10.1214/15-AOAS810>, Xiangdong Gu and Raji Balasubramanian (2016) <doi: 10.1002/sim.6962>, Xiangdong Gu, Mahlet G Tadesse, Andrea S Foulkes, Yunsheng Ma, and Raji Balasubramanian (2020) <doi: 10.1186/s12911-020-01223-w>.
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2025-03-25 |
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r-icranks
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Algorithms to construct simultaneous confidence intervals for the ranks of means mu_1,...,mu_n based on an independent Gaussian sample using multiple testing techniques.
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2025-03-25 |
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r-excel.link
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Allows access to data in running instance of Microsoft Excel (e. g. 'xl[a1] = xl[b2]*3' and so on). Graphics can be transferred with 'xl[a1] = current.graphics()'. Additionally there are function for reading/writing 'Excel' files - 'xl.read.file'/'xl.save.file'. They are not fast but able to read/write '*.xlsb'-files and password-protected files. There is an Excel workbook with examples of calling R from Excel in the 'doc' folder. It tries to keep things as simple as possible - there are no needs in any additional installations besides R, only 'VBA' code in the Excel workbook. Microsoft Excel is required for this package.
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2025-03-25 |
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openssl
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OpenSSL is an open-source implementation of the SSL and TLS protocols
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2025-03-25 |
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r-pkgdown
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Generate an attractive and useful website from a source package. 'pkgdown' converts your documentation, vignettes, 'README', and more to 'HTML' making it easy to share information about your package online.
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2025-03-25 |
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r-rematch2
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Wrappers on 'regexpr' and 'gregexpr' to return the match results in tidy data frames.
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2025-03-25 |
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r-rdsm
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Provides a threads-type programming environment for R. The package gives the R programmer the clearer, more concise shared memory world view, and in some cases gives superior performance as well. In addition, it enables parallel processing on very large, out-of-core matrices.
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2025-03-25 |
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r-highlight
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Syntax highlighter for R code based on the results of the R parser. Rendering in HTML and latex markup. Custom Sweave driver performing syntax highlighting of R code chunks.
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2025-03-25 |
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r-exporkit
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An R-interface to the Fortran package Expokit.
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2025-03-25 |
