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r-wavethresh
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Performs 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.
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2023-06-16 |
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r-vifcp
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Contains a function to support the following paper: Xiaoping Shi, Xiang-Sheng Wang, Dongwei Wei, Yuehua Wu (2016), <DOI:10.1007/s00180-015-0587-5>, A sequential multiple change-point detection procedure via VIF regression, Computational Statistics, 31(2): 671-691.
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2023-06-16 |
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r-vbsr
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Efficient algorithm for solving ultra-sparse regularized regression models using a variational Bayes algorithm with a spike (l0) prior. Algorithm is solved on a path, with coordinate updates, and is capable of generating very sparse models. There are very general model diagnostics for controling type-1 error included in this package.
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2023-06-16 |
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r-valorate
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The algorithm implemented in this package was designed to quickly estimates the distribution of the log-rank especially for heavy unbalanced groups. VALORATE estimates the null distribution and the p-value of the log-rank test based on a recent formulation. For a given number of alterations that define the size of survival groups, the estimation involves a weighted sum of distributions that are conditional on a co-occurrence term where mutations and events are both present. The estimation of conditional distributions is quite fast allowing the analysis of large datasets in few minutes <http://bioinformatica.mty.itesm.mx/valorate>.
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2023-06-16 |
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r-trapezoid
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The trapezoid package provides dtrapezoid, ptrapezoid, qtrapezoid, and rtrapezoid functions for the trapezoidal distribution.
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2023-06-16 |
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r-touch
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R implementation of the software tools developed in the H-CUP (Healthcare Cost and Utilization Project) <https://www.hcup-us.ahrq.gov> and AHRQ (Agency for Healthcare Research and Quality) <https://www.ahrq.gov>. It currently contains functions for mapping ICD-9 codes to the AHRQ comorbidity measures and translating ICD-9 (resp. ICD-10) codes to ICD-10 (resp. ICD-9) codes based on GEM (General Equivalence Mappings) from CMS (Centers for Medicare and Medicaid Services).
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2023-06-16 |
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r-uniisoregression
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Perform L1 or L2 isotonic and unimodal regression on 1D weighted or unweighted input vector and isotonic regression on 2D weighted or unweighted input vector. It also performs L infinity isotonic and unimodal regression on 1D unweighted input vector. Reference: Quentin F. Stout (2008) <doi:10.1016/j.csda.2008.08.005>. Spouge, J., Wan, H. & Wilbur, W.(2003) <doi:10.1023/A:1023901806339>. Q.F. Stout (2013) <doi:10.1007/s00453-012-9628-4>.
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2023-06-16 |
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r-ulid
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Universally unique identifiers ('UUIDs') can be suboptimal for many uses-cases because they aren't the most character efficient way of encoding 128 bits of randomness; v1/v2 versions are impractical in many environments, as they require access to a unique, stable MAC address; v3/v5 versions require a unique seed and produce randomly distributed IDs, which can cause fragmentation in many data structures; v4 provides no other information than randomness which can cause fragmentation in many data structures. 'ULIDs' (<https://github.com/ulid/spec>) have 128-bit compatibility with 'UUID', 1.21e+24 unique 'ULIDs' per millisecond, are lexicographically sortable, canonically encoded as a 26 character string, as opposed to the 36 character 'UUID', use Crockford's 'base32' for better efficiency and readability (5 bits per character), are case insensitive, have no special characters (i.e. are 'URL' safe) and have a onotonic sort order (correctly detects and handles the same millisecond).
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2023-06-16 |
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r-twophaseind
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Estimation of gene-treatment interactions in randomized clinical trials exploiting gene-treatment independence.
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2023-06-16 |
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r-tvd
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Total Variation Denoising is a regularized denoising method which effectively removes noise from piecewise constant signals whilst preserving edges. This package contains a C++ implementation of Condat's very fast 1D squared error loss TVD algorithm. Additional methods and loss functions may be added in future versions.
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2023-06-16 |
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r-tree
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Classification and regression trees.
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2023-06-16 |
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r-waffect
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waffect (pronounced 'double-u affect' for 'weighted affectation') is a package to simulate phenotypic (case or control) datasets under a disease model H1 such that the total number of cases is constant across all the simulations (the constrain in the title). The package also makes it possible to generate phenotypes in the case of more than two classes, so that the number of phenotypes belonging to each class is constant across all the simulations. waffect is used to assess empirically the statistical power of Genome Wide Association studies.
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2023-06-16 |
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r-vlmc
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Functions, Classes & Methods for estimation, prediction, and simulation (bootstrap) of Variable Length Markov Chain ('VLMC') Models.
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2023-06-16 |
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r-vigor
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Conducts linear regression using variational Bayesian inference, particularly optimized for genome-wide association mapping and whole-genome prediction which use a number of DNA markers as the explanatory variables. Provides seven regression models which select the important variables (i.e., the variables related to response variables) among the given explanatory variables in different ways (i.e., model structures).
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2023-06-16 |
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r-tvsmiss
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Use a regularization likelihood method to achieve variable selection purpose. Likelihood can be worked with penalty lasso, smoothly clipped absolute deviations (SCAD), and minimax concave penalty (MCP). Tuning parameter selection techniques include cross validation (CV), Bayesian information criterion (BIC) (low and high), stability of variable selection (sVS), stability of BIC (sBIC), and stability of estimation (sEST). More details see Jiwei Zhao, Yang Yang, and Yang Ning (2018) <arXiv:1703.06379> "Penalized pairwise pseudo likelihood for variable selection with nonignorable missing data." Statistica Sinica.
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2023-06-16 |
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r-topmodel
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Set of hydrological functions including an R implementation of the hydrological model TOPMODEL, which is based on the 1995 FORTRAN version by Keith Beven. From version 0.7.0, the package is put into maintenance mode.
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2023-06-16 |
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r-tgcd
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Deconvolving thermoluminescence glow curves according to various kinetic models (first-order, second-order, general-order, and mixed-order) using a modified Levenberg-Marquardt algorithm. It provides the possibility of setting constraints or fixing any of parameters. It offers an interactive way to initialize parameters by clicking with a mouse on a plot at positions where peak maxima should be located. The optimal estimate is obtained by "trial-and-error". It also provides routines for simulating first-order, second-order, and general-order glow peaks.
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2023-06-16 |
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r-unmarked
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Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates.
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2023-06-16 |
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r-twocop
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This package implements the nonparametric test of equality between two copulas proposed by Remillard and Scaillet in their 2009 JMVA paper.
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2023-06-16 |
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r-truncnorm
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Density, probability, quantile and random number generation functions for the truncated normal distribution.
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2023-06-16 |
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r-vca
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ANOVA and REML estimation of linear mixed models is implemented, once following Searle et al. (1991, ANOVA for unbalanced data), once making use of the 'lme4' package. The primary objective of this package is to perform a variance component analysis (VCA) according to CLSI EP05-A3 guideline "Evaluation of Precision of Quantitative Measurement Procedures" (2014). There are plotting methods for visualization of an experimental design, plotting random effects and residuals. For ANOVA type estimation two methods for computing ANOVA mean squares are implemented (SWEEP and quadratic forms). The covariance matrix of variance components can be derived, which is used in estimating confidence intervals. Linear hypotheses of fixed effects and LS means can be computed. LS means can be computed at specific values of covariables and with custom weighting schemes for factor variables. See ?VCA for a more comprehensive description of the features.
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2023-06-16 |
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r-tsp
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Basic infrastructure and some algorithms for the traveling salesperson problem (also traveling salesman problem; TSP). The package provides some simple algorithms and an interface to the Concorde TSP solver and its implementation of the Chained-Lin-Kernighan heuristic. The code for Concorde itself is not included in the package and has to be obtained separately.
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2023-06-16 |
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r-tokenizers.bpe
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Unsupervised text tokenizer focused on computational efficiency. Wraps the 'YouTokenToMe' library <https://github.com/VKCOM/YouTokenToMe> which is an implementation of fast Byte Pair Encoding (BPE) <https://www.aclweb.org/anthology/P16-1162>.
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2023-06-16 |
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r-tokenbrowser
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Create browsers for reading full texts from a token list format. Information obtained from text analyses (e.g., topic modeling, word scaling) can be used to annotate the texts.
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2023-06-16 |
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r-tmvnsim
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Importance sampling from the truncated multivariate normal using the GHK (Geweke-Hajivassiliou-Keane) simulator. Unlike Gibbs sampling which can get stuck in one truncation sub-region depending on initial values, this package allows truncation based on disjoint regions that are created by truncation of absolute values. The GHK algorithm uses simple Cholesky transformation followed by recursive simulation of univariate truncated normals hence there are also no convergence issues. Importance sample is returned along with sampling weights, based on which, one can calculate integrals over truncated regions for multivariate normals.
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2023-06-16 |
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r-wcorr
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Calculates Pearson, Spearman, polychoric, and polyserial correlation coefficients, in weighted or unweighted form. The package implements tetrachoric correlation as a special case of the polychoric and biserial correlation as a specific case of the polyserial.
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2023-06-16 |
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r-waveslim
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Basic wavelet routines for time series (1D), image (2D) and array (3D) analysis. The code provided here is based on wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002). All figures in chapters 4-7 of GSW (2001) are reproducible using this package and R code available at the book website(s) below.
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2023-06-16 |
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r-tth
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C source code and R wrappers for the tth/ttm TeX to HTML/MathML translators.
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2023-06-16 |
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r-tshrc
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Two-stage procedure compares hazard rate functions, which may or may not cross each other.
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2023-06-16 |
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r-tpmsm
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Estimation of transition probabilities for the illness-death model and or the three-state progressive model.
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2023-06-16 |
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r-vbdm
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Efficient algorithm for solving discrete mixture regression model for rare variant association analysis. Uses variational Bayes algorithm to efficiently search over model space. Outputs an approximate likelihood ratio test as well as variant level posterior probabilities of association.
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2023-06-16 |
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r-unine
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Implementation of "light" stemmers for French, German, Italian, Spanish, Portuguese, Finnish, Swedish. They are based on the same work as the "light" stemmers found in 'SolR' <https://lucene.apache.org/solr/> or 'ElasticSearch' <https://www.elastic.co/fr/products/elasticsearch>. A "light" stemmer consists in removing inflections only for noun and adjectives. Indexing verbs for these languages is not of primary importance compared to nouns and adjectives. The stemming procedure for French is described in (Savoy, 1999) <doi:10.1002/(SICI)1097-4571(1999)50:10%3C944::AID-ASI9%3E3.3.CO;2-H>.
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2023-06-16 |
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r-twosamples
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Fast randomization based two sample tests. Testing the hypothesis that two samples come from the same distribution using randomization to create p-values. Included tests are: Kolmogorov-Smirnov, Kuiper, Cramer-von Mises, and Anderson-Darling. There is also a very efficient test based on the Wasserstein Distance. The default test 'two_sample' builds on the Wasserstein distance by using a weighting scheme like that of Anderson-Darling. We also include the permutation scheme to make test building simple for others.
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2023-06-16 |
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r-tweedie
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Maximum likelihood computations for Tweedie families, including the series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>), and related methods.
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2023-06-16 |
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r-trialsize
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functions and examples in Sample Size Calculation in Clinical Research.
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2023-06-16 |
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r-topicmodels
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Provides an interface to the C code for Latent Dirichlet Allocation (LDA) models and Correlated Topics Models (CTM) by David M. Blei and co-authors and the C++ code for fitting LDA models using Gibbs sampling by Xuan-Hieu Phan and co-authors.
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2023-06-16 |
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r-timetools
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Objects to manipulate sequential and seasonal time series. Sequential time series based on time instants and time durations are handled. Both can be regularly or unevenly spaced (overlapping durations are allowed). Only POSIX* format are used for dates and times. The following classes are provided : 'POSIXcti', 'POSIXctp', 'TimeIntervalDataFrame', 'TimeInstantDataFrame', 'SubtimeDataFrame' ; methods to switch from a class to another and to modify the time support of series (hourly time series to daily time series for instance) are also defined. Tools provided can be used for instance to handle environmental monitoring data (not always produced on a regular time base).
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2023-06-16 |
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r-texttinyr
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It offers functions for splitting, parsing, tokenizing and creating a vocabulary for big text data files. Moreover, it includes functions for building a document-term matrix and extracting information from those (term-associations, most frequent terms). It also embodies functions for calculating token statistics (collocations, look-up tables, string dissimilarities) and functions to work with sparse matrices. Lastly, it includes functions for Word Vector Representations (i.e. 'GloVe', 'fasttext') and incorporates functions for the calculation of (pairwise) text document dissimilarities. The source code is based on 'C++11' and exported in R through the 'Rcpp', 'RcppArmadillo' and 'BH' packages.
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2023-06-16 |
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r-websocket
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Provides a 'WebSocket' client interface for R. 'WebSocket' is a protocol for low-overhead real-time communication: <https://en.wikipedia.org/wiki/WebSocket>.
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2023-06-16 |
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r-vlad
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Contains functions to set up risk-adjusted quality control charts in health care. For the variable life adjusted display (VLAD) proposed by Lovegrove et al. (1997) <doi:10.1016/S0140-6736(97)06507-0> signaling rules derived in Wittenberg et al. (2018) <doi: 10.1002/sim.7647> are implemented. Additionally, for the risk-adjusted cumulative sum chart based on log-likelihood ratio statistic introduced by Steiner et al. (2000) <doi:10.1093/biostatistics/1.4.441> average run length and control limits can be computed.
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2023-06-16 |
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r-varband
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Implementation of the variable banding procedure for modeling local dependence and estimating precision matrices that is introduced in Yu & Bien (2016) and is available at <https://arxiv.org/abs/1604.07451>.
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2023-06-16 |
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r-ucminf
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An algorithm for general-purpose unconstrained non-linear optimization. The algorithm is of quasi-Newton type with BFGS updating of the inverse Hessian and soft line search with a trust region type monitoring of the input to the line search algorithm. The interface of 'ucminf' is designed for easy interchange with 'optim'.
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2023-06-16 |
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r-tuwmodel
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The model, developed at the Vienna University of Technology, is a lumped conceptual rainfall-runoff model, following the structure of the HBV model. The model can also be run in a semi-distributed fashion. The model runs on a daily or shorter time step and consists of a snow routine, a soil moisture routine and a flow routing routine. See Parajka, J., R. Merz, G. Bloeschl (2007) <DOI:10.1002/hyp.6253> Uncertainty and multiple objective calibration in regional water balance modelling: case study in 320 Austrian catchments, Hydrological Processes, 21, 435-446.
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2023-06-16 |
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r-tsentropies
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Computes various entropies of given time series. This is the initial version that includes ApEn() and SampEn() functions for calculating approximate entropy and sample entropy. Approximate entropy was proposed by S.M. Pincus in "Approximate entropy as a measure of system complexity", Proceedings of the National Academy of Sciences of the United States of America, 88, 2297-2301 (March 1991). Sample entropy was proposed by J. S. Richman and J. R. Moorman in "Physiological time-series analysis using approximate entropy and sample entropy", American Journal of Physiology, Heart and Circulatory Physiology, 278, 2039-2049 (June 2000). This package also contains FastApEn() and FastSampEn() functions for calculating fast approximate entropy and fast sample entropy. These are newly designed very fast algorithms, resulting from the modification of the original algorithms. The calculated values of these entropies are not the same as the original ones, but the entropy trend of the analyzed time series determines equally reliably. Their main advantage is their speed, which is up to a thousand times higher. A scientific article describing their properties has been submitted to The Journal of Supercomputing and in present time it is waiting for the acceptance.
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2023-06-16 |
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r-triosgl
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Fit a trio model via penalized maximum likelihood. The model is fit for a path of values of the penalty parameter. This package is based on Noah Simon, et al. (2011) <doi:10.1080/10618600.2012.681250>.
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2023-06-16 |
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r-treeperm
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An implementation of permutation tests in R, supporting both exact and asymptotic K sample test of data locations. The p value of exact tests is found using tree algorithms. Tree algorithms treat permutations of input data as tree nodes and perform constraint depth-first searches for permutations that fall into the critical region of a test systematically. Pruning of tree search and optimisations at C level enable exact tests for certain large data sets.
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2023-06-16 |
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r-rmecabko
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An 'Rcpp' interface for Eunjeon project <http://eunjeon.blogspot.com/>. The 'mecab-ko' and 'mecab-ko-dic' is based on a C++ library, and part-of-speech tagging with them is useful when the spacing of source Korean text is not correct. This package provides part-of-speech tagging and tokenization function for Korean text.
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2023-06-16 |
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r-robustreg
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Linear regression functions using Huber and bisquare psi functions. Optimal weights are calculated using IRLS algorithm.
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2023-06-16 |
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r-rlt
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Random forest with a variety of additional features for regression, classification and survival analysis. The features include: parallel computing with OpenMP, embedded model for selecting the splitting variable (based on Zhu, Zeng & Kosorok, 2015), subject weight, variable weight, tracking subjects used in each tree, etc.
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2023-06-16 |
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r-restrictedmvn
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A fast Gibbs sampler for multivariate normal with affine constraints.
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2023-06-16 |
