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r-tsss
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Functions for statistical analysis, modeling and simulation of time series with state space model, based on the methodology in Kitagawa (1993, ISBN: 4-00-007703-1 and 2005, ISBN: 4-00-005455-4).
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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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r-tserieschaos
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Routines for the analysis of nonlinear time series. This work is largely inspired by the TISEAN project, by Rainer Hegger, Holger Kantz and Thomas Schreiber: <http://www.mpipks-dresden.mpg.de/~tisean/>.
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2025-03-25 |
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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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2025-03-25 |
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r-tsdfgs
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Determining training set for genomic selection using a genetic algorithm (Holland J.H. (1975) <DOI:10.1145/1216504.1216510>) or simple exchange algorithm (change an individual every iteration). Three different criteria are used in both algorithms, which are r-score (Ou J.H., Liao C.T. (2018) <DOI:10.6342/NTU201802290>), PEV-score (Akdemir D. et al. (2015) <DOI:10.1186/s12711-015-0116-6>) and CD-score (Laloe D. (1993) <DOI:10.1186/1297-9686-25-6-557>). Phenotypic data for candidate set is not necessary for all these methods. By using it, one may readily determine a training set that can be expected to provide a better training set comparing to random sampling.
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2025-03-25 |
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r-tsc
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Performs the two-sample comparisons using the following exact test procedures: the exact likelihood-ratio test (LRT) for equality of two normal populations proposed in Zhang et al. (2012); the combined test based on the LRT and Shapiro-Wilk test for normality via the Bonferroni correction technique; the newly proposed density-based empirical likelihood (DBEL) ratio test. To calculate p-values of the DBEL procedures, three procedures are used: (a) the traditional Monte Carlo (MC) method implemented in C++, (b) a new interpolation method based on regression techniques to operate with tabulated critical values of the test statistic; (c) a Bayesian type method that uses the tabulated critical values as the prior information and MC generated DBEL-test-statistic's values as data.
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2025-03-25 |
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r-trustoptim
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Trust region algorithm for nonlinear optimization. Efficient when the Hessian of the objective function is sparse (i.e., relatively few nonzero cross-partial derivatives). See Braun, M. (2014) <doi:10.18637/jss.v060.i04>.
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2025-03-25 |
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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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2025-03-25 |
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r-truncgof
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Goodness-of-fit tests and some adjusted exploratory tools allowing for left truncated data
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2025-03-25 |
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r-tripack
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A constrained two-dimensional Delaunay triangulation package providing both triangulation and generation of voronoi mosaics of irregular spaced data.
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2025-03-25 |
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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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2025-03-25 |
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r-triebeard
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'Radix trees', or 'tries', are key-value data structures optimised for efficient lookups, similar in purpose to hash tables. 'triebeard' provides an implementation of 'radix trees' for use in R programming and in developing packages with 'Rcpp'.
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2025-03-25 |
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r-trialsize
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functions and examples in Sample Size Calculation in Clinical Research.
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2025-03-25 |
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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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2025-03-25 |
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r-treeman
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S4 class and methods for intuitive and efficient phylogenetic tree manipulation.
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2025-03-25 |
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r-tree
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Classification and regression trees.
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2025-03-25 |
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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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2025-03-25 |
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r-transurv
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A structural transformation model for a latent, quasi-independent truncation time as a function of the observed dependent truncation time and the event time, and an unknown dependence parameter. The dependence parameter is chosen to minimize the conditional Kendall's tau (Martin and Betensky, 2005) <doi:10.1198/016214504000001538>. The marginal distribution for the truncation time and the event time are completely left unspecified.
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2025-03-25 |
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r-transport
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Solve optimal transport problems. Compute Wasserstein distances (a.k.a. Kantorovitch, Fortet--Mourier, Mallows, Earth Mover's, or minimal L_p distances), return the corresponding transference plans, and display them graphically. Objects that can be compared include grey-scale images, (weighted) point patterns, and mass vectors.
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2025-03-25 |
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r-tracerer
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'BEAST2' (<http://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'Tracer' (<http://tree.bio.ed.ac.uk/software/tracer/>) is a GUI tool to parse and analyze the files generated by 'BEAST2'. This package provides a way to parse and analyze 'BEAST2' input files without active user input, but using R function calls instead.
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2025-03-25 |
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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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2025-03-25 |
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r-tp.idm
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Estimation of transition probabilities for the illness-death model. Both the Aalen-Johansen estimator for a Markov model and a novel non-Markovian estimator by de Una-Alvarez and Meira-Machado (2015) <doi:10.1111/biom.12288>, see also Balboa and de Una-Alvarez (2018) <doi:10.18637/jss.v083.i10>, are included.
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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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r-tmg
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Random number generation of truncated multivariate Gaussian distributions using Hamiltonian Monte Carlo. The truncation is defined using linear and/or quadratic polynomials.
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2025-03-25 |
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r-tmcn
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A Text mining toolkit for Chinese, which includes facilities for Chinese string processing, Chinese NLP supporting, encoding detecting and converting. Moreover, it provides some functions to support 'tm' package in Chinese.
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2025-03-25 |
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r-tmb
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With this tool, a user should be able to quickly implement complex random effect models through simple C++ templates. The package combines 'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain an efficient implementation of the applied Laplace approximation with exact derivatives. Key features are: Automatic sparseness detection, parallelism through 'BLAS' and parallel user templates.
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2025-03-25 |
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r-tis
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Functions and S3 classes for time indexes and time indexed series, which are compatible with FAME frequencies.
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2025-03-25 |
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r-tinflex
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A universal non-uniform random number generator for quite arbitrary distributions with piecewise twice differentiable densities.
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2025-03-25 |
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r-timsac
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Functions for statistical analysis, prediction and control of time series based mainly on Akaike and Nakagawa (1988) <ISBN 978-90-277-2786-2>.
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2025-03-25 |
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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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2025-03-25 |
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r-timereg
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Programs for Martinussen and Scheike (2006), `Dynamic Regression Models for Survival Data', Springer Verlag. Plus more recent developments. Additive survival model, semiparametric proportional odds model, fast cumulative residuals, excess risk models and more. Flexible competing risks regression including GOF-tests. Two-stage frailty modelling. PLS for the additive risk model. Lasso in the 'ahaz' package.
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2025-03-25 |
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r-timechange
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Efficient routines for manipulation of date-time objects while accounting for time-zones and daylight saving times. The package includes utilities for updating of date-time components (year, month, day etc.), modification of time-zones, rounding of date-times, period addition and subtraction etc. Parts of the 'CCTZ' source code, released under the Apache 2.0 License, are included in this package. See <https://github.com/google/cctz> for more details.
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2025-03-25 |
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r-tiff
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This package provides an easy and simple way to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors.
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2025-03-25 |
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r-threearmedtrials
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Design and analyze three-arm non-inferiority or superiority trials which follow a gold-standard design, i.e. trials with an experimental treatment, an active, and a placebo control. Method for the following distributions are implemented: Poisson (Mielke and Munk (2009) <arXiv:0912.4169>), negative binomial (Muetze et al. (2016) <doi:10.1002/sim.6738>), normal (Pigeot et al. (2003) <doi:10.1002/sim.1450>; Hasler et al. (2009) <doi:10.1002/sim.3052>), binary (Friede and Kieser (2007) <doi:10.1002/sim.2543>), nonparametric (Muetze et al. (2017) <doi:10.1002/sim.7176>), exponential (Mielke and Munk (2009) <arXiv:0912.4169>).
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2025-03-25 |
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r-thgenetics
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A step-up test for genetic rare variants in a gene or in a pathway. The method determines an optimal grouping of rare variants analytically. The method has been described in Hoffmann TJ, Marini NJ, and Witte JS (2010) <doi:10.1371/journal.pone.0013584>.
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2025-03-25 |
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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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2025-03-25 |
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r-tfmpvalue
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In putative Transcription Factor Binding Sites (TFBSs) identification from sequence/alignments, we are interested in the significance of certain match score. TFMPvalue provides the accurate calculation of P-value with score threshold for Position Weight Matrices, or the score with given P-value. It is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet and Varre (2007) <DOI:10.1186/1748-7188-2-15>.
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2025-03-25 |
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r-tfcox
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In Cox's proportional hazard model, covariates are modeled as linear function and may not be flexible. This package implements additive trend filtering Cox proportional hazards model as proposed in Jiacheng Wu & Daniela Witten (2019) "Flexible and Interpretable Models for Survival Data", Journal of Computational and Graphical Statistics, <DOI:10.1080/10618600.2019.1592758>. The fitted functions are piecewise polynomial with adaptively chosen knots.
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2025-03-25 |
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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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2025-03-25 |
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r-textreg
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Function for sparse regression on raw text, regressing a labeling vector onto a feature space consisting of all possible phrases.
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2025-03-25 |
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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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2025-03-25 |
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r-rgdal
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Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ.4' library. The 'GDAL' and 'PROJ.4' libraries are external to the package, and, when installing the package from source, must be correctly installed first. From 'rgdal' 1.4.1, provision is made for 'PROJ6' accommodation, with 'PROJ6' functionality to follow; from 1.4.1 'rgdal' will build and function when 'PROJ' >= 6. Both 'GDAL' raster and 'OGR' vector map data can be imported into R, and 'GDAL' raster data and 'OGR' vector data exported. Use is made of classes defined in the 'sp' package. Windows and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and 'Expat') are provided on 'CRAN'.
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2025-03-25 |
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r-rootwishart
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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.
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2025-03-25 |
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r-rootsolve
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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.
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2025-03-25 |
