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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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2025-04-22 |
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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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2025-04-22 |
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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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2025-04-22 |
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r-validatejsonr
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The current implementation uses the C++ library 'RapidJSON' to supply the schema functionality, it supports JSON Schema Draft v4. As of 2016-09-09, 'RapidJSON' passed 262 out of 263 tests in JSON Schema Test Suite (JSON Schema draft 4).
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2025-04-22 |
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r-unsystation
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Performs a test for second-order stationarity of time series based on unsystematic sub-samples.
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2025-04-22 |
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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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2025-04-22 |
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r-unix
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Bindings to system utilities found in most Unix systems such as POSIX functions which are not part of the Standard C Library.
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2025-04-22 |
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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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2025-04-22 |
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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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2025-04-22 |
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r-unifed
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Probability functions and family for glm() of the unifed distribution (Quijano Xacur, 2018; <arXiv:1812.00251>).
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2025-04-22 |
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r-unidoe
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Efficient procedures for constructing uniform design of experiments under various space-filling criteria. It is based on a stochastic and adaptive threshold accepting algorithm with flexible initialization, adaptive threshold, and stochastic evolution. The package may also construct the augmented uniform designs in a sequential manner.
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2025-04-22 |
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r-unfoldr
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Stereological unfolding of the joint size-shape-orientation distribution of spheroidal shaped particles.
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2025-04-22 |
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r-ump
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Does uniformly most powerful (UMP) and uniformly most powerful unbiased (UMPU) tests. At present only distribution implemented is binomial distribution. Also does fuzzy tests and confidence intervals (following Geyer and Meeden, 2005, <doi:10.1214/088342305000000340>) for the binomial distribution (one-tailed procedures based on UMP test and two-tailed procedures based on UMPU test).
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2025-04-22 |
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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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2025-04-22 |
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r-udpipe
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This natural language processing toolkit provides language-agnostic 'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency parsing' of raw text. Next to text parsing, the package also allows you to train annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided at <http://universaldependencies.org/format.html>. The techniques are explained in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0 with UDPipe', available at <doi:10.18653/v1/K17-3009>.
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2025-04-22 |
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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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2025-04-22 |
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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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2025-04-22 |
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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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2025-04-22 |
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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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2025-04-22 |
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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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2025-04-22 |
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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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2025-04-22 |
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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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2025-04-22 |
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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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2025-04-22 |
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r-tunepareto
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Generic methods for parameter tuning of classification algorithms using multiple scoring functions.
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2025-04-22 |
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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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2025-04-22 |
