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r-cleancall
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Wrapper of .Call() that runs exit handlers to clean up C resources. Helps managing C (non-R) resources while using the R API.
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2023-06-16 |
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r-chunkr
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Read tables chunk by chunk using a C++ backend and a simple R interface.
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2023-06-16 |
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r-cetcolor
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Collection of perceptually uniform colour maps made by Peter Kovesi (2015) "Good Colour Maps: How to Design Them" <arXiv:1509.03700> at the Centre for Exploration Targeting (CET).
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2023-06-16 |
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r-cernaseek
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Provides several functions to identify and analyse miRNA sponge, including popular methods for identifying miRNA sponge interactions, two types of global ceRNA regulation prediction methods and four types of context-specific prediction methods( Li Y et al.(2017) <doi:10.1093/bib/bbx137>), which are based on miRNA-messenger RNA regulation alone, or by integrating heterogeneous data, respectively. In addition, For predictive ceRNA relationship pairs, this package provides several downstream analysis algorithms, including regulatory network analysis and functional annotation analysis, as well as survival prognosis analysis based on expression of ceRNA ternary pair.
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2023-06-16 |
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r-cengam
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Implementation of Tobit type I and type II families for censored regression using the 'mgcv' package, based on methods detailed in Woods (2016) <doi:10.1080/01621459.2016.1180986>.
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2023-06-16 |
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r-cbsodatar
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The data and meta data from Statistics Netherlands (<https://www.cbs.nl>) can be browsed and downloaded. The client uses the open data API of Statistics Netherlands.
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2023-06-16 |
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r-catt
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This function conducts the Cochran-Armitage trend test to a 2 by k contingency table. It will report the test statistic (Z) and p-value.A linear trend in the frequencies will be calculated, because the weights (0,1,2) will be used by default.
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2023-06-16 |
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r-calibrate
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Package for drawing calibrated scales with tick marks on (non-orthogonal) variable vectors in scatterplots and biplots.
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2023-06-16 |
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r-cbinom
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Implementation of the d/p/q/r family of functions for a continuous analog to the standard discrete binomial with continuous size parameter and continuous support with x in [0, size + 1], following Ilienko (2013) <arXiv:1303.5990>.
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2023-06-16 |
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r-chillmodels
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Calculates the chilling and heat accumulation for studies of the temperate fruit trees. The models in this package are: Utah (Richardson et al., 1974, ISSN:0018-5345), Positive Chill Units - PCU (Linsley-Noaks et al., 1995, ISSN:1017-0316), GDH-A - Growing Degree Hours by Anderson et al.(1986, ISSN:0567-7572), GDH-R - Growing Degree Hours by Richardson et al.(1975, ISSN:0018-5345), North Carolina (Shaltout e Unrath, 1983, ISSN:0003-1062), Landsberg Model (Landsberg, 1974, ISSN:0305-7364), Q10 Model (Bidabe, 1967, ISSN:0031-9368), Jones Model (Jones et al., 2013 <DOI:10.1111/j.1438-8677.2012.00590.x>), Low-Chill Model (Gilreath and Buchanan, 1981, ISSN:0003-1062), Model for Cherry "Sweetheart" (Guak and Nielsen, 2013 <DOI:10.1007/s13580-013-0140-9>), Model for apple "Gala" (Guak and Nielsen, 2013 <DOI:10.1007/s13580-013-0140-9>), Taiwan Model (Lu et al., 2012 <DOI:10.17660/ActaHortic.2012.962.35>), Dynamic Model (Fishman et al., 1987, ISSN:0022-5193) adapted from the function Dynamic_Model() of the 'chillR' package (Luedeling, 2018), Unified Model (Chuine et al., 2016 <DOI:10.1111/gcb.13383>) and Heat Restriction model.
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2023-06-16 |
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r-cherry
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Provides an alternative approach to multiple testing by calculating a simultaneous upper confidence bounds for the number of true null hypotheses among any subset of the hypotheses of interest, using the methods of Goeman and Solari (2011) <doi:10.1214/11-STS356>.
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2023-06-16 |
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r-cld2
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Bindings to Google's C++ library Compact Language Detector 2 (see <https://github.com/cld2owners/cld2#readme> for more information). Probabilistically detects over 80 languages in plain text or HTML. For mixed-language input it returns the top three detected languages and their approximate proportion of the total classified text bytes (e.g. 80% English and 20% French out of 1000 bytes). There is also a 'cld3' package on CRAN which uses a neural network model instead.
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2023-06-16 |
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r-cheb
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Discrete Linear Chebyshev Approximation
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2023-06-16 |
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r-cc
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Tools for creating and visualizing statistical process control charts. Control charts are used for monitoring measurement processes, such as those occurring in manufacturing. The objective is to monitor the history of such processes and flag outlying measurements: out-of-control signals. Montgomery, D. (2009, ISBN:978-0-470-16992-6) contains an extensive discussion of the methodology.
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2023-06-16 |
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r-cec2013
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This package provides R wrappers for the C implementation of 28 benchmark functions defined for the Special Session and Competition on Real-Parameter Single Objective Optimization at CEC-2013. The focus of this package is to provide an open-source and multi-platform implementation of the CEC2013 benchmark functions, in order to make easier for researchers to test the performance of new optimization algorithms in a reproducible way. The original C code (Windows only) was provided by Jane Jing Liang, while GNU/Linux comments were made by Janez Brest. This package was gently authorised for publication on CRAN by Ponnuthurai Nagaratnam Suganthan. The official documentation is available at http://www.ntu.edu.sg/home/EPNSugan/index_files/CEC2013/CEC2013.htm. Bugs reports/comments/questions are very welcomed (in English, Spanish or Italian).
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2023-06-16 |
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r-changepointshd
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This implements the methods developed in, L. Bybee and Y. Atchade. (2018). Contains a series of methods for estimating change-points given user specified black-box models. The methods include binary segmentation for multiple change-point estimation. For estimating each individual change-point the package includes simulated annealing, brute force, and, for Gaussian graphical models, an applications specific rank-one update implementation. Additionally, code for estimating Gaussian graphical models is included. The goal of this package is to allow for the efficient estimation of change-points in complicated models with high dimensional data.
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2023-06-16 |
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r-censusapi
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A wrapper for the U.S. Census Bureau APIs that returns data frames of Census data and metadata. Available datasets include the Decennial Census, American Community Survey, Small Area Health Insurance Estimates, Small Area Income and Poverty Estimates, Population Estimates and Projections, and more.
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2023-06-16 |
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r-cdnmoney
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Components of Canadian Credit Aggregates and Monetary Aggregates with continuity adjustments.
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2023-06-16 |
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r-ccremover
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Implements a method for identifying and removing the cell-cycle effect from scRNA-Seq data. The description of the method is in Barron M. and Li J. (2016) <doi:10.1038/srep33892>. Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data. Submitted. Different from previous methods, ccRemover implements a mechanism that formally tests whether a component is cell-cycle related or not, and thus while it often thoroughly removes the cell-cycle effect, it preserves other features/signals of interest in the data.
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2023-06-16 |
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r-chi
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Light weight implementation of the standard distribution functions for the chi distribution, wrapping those for the chi-squared distribution in the stats package.
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2023-06-16 |
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r-chemospecutils
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Functions supporting the common needs of packages 'ChemoSpec' and 'ChemoSpec2D'.
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2023-06-16 |
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r-changepointtesting
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A multiple testing procedure for clustered alternative hypotheses. It is assumed that the p-values under the null hypotheses follow U(0,1) and that the distributions of p-values from the alternative hypotheses are stochastically smaller than U(0,1). By aggregating information, this method is more sensitive to detecting signals of low magnitude than standard methods. Additionally, sporadic small p-values appearing within a null hypotheses sequence are avoided by averaging on the neighboring p-values.
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2023-06-16 |
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r-chandwich
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Performs adjustments of a user-supplied independence loglikelihood function using a robust sandwich estimator of the parameter covariance matrix, based on the methodology in Chandler and Bate (2007) <doi:10.1093/biomet/asm015>. This can be used for cluster correlated data when interest lies in the parameters of the marginal distributions or for performing inferences that are robust to certain types of model misspecification. Functions for profiling the adjusted loglikelihoods are also provided, as are functions for calculating and plotting confidence intervals, for single model parameters, and confidence regions, for pairs of model parameters. Nested models can be compared using an adjusted likelihood ratio test.
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2023-06-16 |
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r-clues
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We developed the clues R package to provide functions for automatically estimating the number of clusters and getting the final cluster partition without any input parameter except the stopping rule for convergence. The package also provides functions to evaluate and compare the performances of partitions of a data set both numerically and graphically.
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2023-06-16 |
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r-clrdag
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Provides MLEdag() for constrained maximum likelihood estimation and likelihood ratio test of a large directed acyclic graph. The algorithms are described in the paper by Li, Shen, and Pan (2019) <doi:10.1080/01621459.2019.1623042>.
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2023-06-16 |
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r-cifsmry
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Estimate of cumulative incidence function in two samples. Provide weighted summary statistics based on various methods and weights.
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2023-06-16 |
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r-chi2x3way
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Provides two index partitions for three-way contingency tables: partition of the association measure chi-squared and of the predictability index tau under several representative hypotheses about the expected frequencies (hypothesized probabilities).
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2023-06-16 |
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r-censregmod
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Fits univariate censored linear regression model under Normal or Student-t distribution
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2023-06-16 |
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r-cdft
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This package proposes a statistical downscaling method for cumulative distribution functions (CDF), as well as the computation of the Cram\`er-von Mises statistics U, and the Kolmogorov-Smirnov statistics KS.
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2023-06-16 |
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r-cgh
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Functions to analyze microarray comparative genome hybridization data using the Smith-Waterman algorithm
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2023-06-16 |
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r-cbsem
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The composites are linear combinations of their indicators in composite based structural equation models. Structural models are considered consisting of two blocks. The indicators of the exogenous composites are named by X, the indicators of the endogenous by Y. Reflective relations are given by arrows pointing from the composite to their indicators. Their values are called loadings. In a reflective-reflective scenario all indicators have loadings. Arrows are pointing to their indicators only from the endogenous composites in the formative-reflective scenario. There are no loadings at all in the formative-formative scenario. The covariance matrices are computed for these three scenarios. They can be used to simulate these models. These models can also be estimated and a segmentation procedure is included as well.
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2023-06-16 |
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r-cchs
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Contains a function, also called 'cchs', that calculates Estimator III of Borgan et al (2000), <DOI:10.1023/A:1009661900674>. This estimator is for fitting a Cox proportional hazards model to data from a case-cohort study where the subcohort was selected by stratified simple random sampling.
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2023-06-16 |
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r-caroline
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The caroline R library contains dozens of functions useful for: database migration (dbWriteTable2), database style joins & aggregation (nerge, groupBy & bestBy), data structure conversion (nv, tab2df), legend table making (sstable & leghead), plot annotation (labsegs & mvlabs), data visualization (violins, pies & raPlot), character string manipulation (m & pad), file I/O (write.delim), batch scripting and more. The package's greatest contributions lie in the database style merge, aggregation and interface functions as well as in it's extensive use and propagation of row, column and vector names in most functions.
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2023-06-16 |
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r-capwire
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Fits models from Miller et al. 2005 to estimate population sizes from natural populations. Several models are implemented. Package also includes functions to perform a likelihood ratio test to choose between models, perform parametric bootstrapping to obtain confidence intervals and multiple functions to simulate data.
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2023-06-16 |
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r-canvasxpress
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Enables creation of visualizations using the CanvasXpress framework in R. CanvasXpress is a standalone JavaScript library for reproducible research with complete tracking of data and end-user modifications stored in a single PNG image that can be played back. See <http://canvasxpress.org> for more information.
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2023-06-16 |
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r-calacs
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Implements several string comparison algorithms, including calACS (count all common subsequences), lenACS (calculate the lengths of all common subsequences), and lenLCS (calculate the length of the longest common subsequence). Some algorithms differentiate between the more strict definition of subsequence, where a common subsequence cannot be separated by any other items, from its looser counterpart, where a common subsequence can be interrupted by other items. This difference is shown in the suffix of the algorithm (-Strict vs -Loose). For example, q-w is a common subsequence of q-w-e-r and q-e-w-r on the looser definition, but not on the more strict definition. calACSLoose Algorithm from Wang, H. All common subsequences (2007) IJCAI International Joint Conference on Artificial Intelligence, pp. 635-640.
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2023-06-16 |
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r-cclust
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Convex Clustering methods, including K-means algorithm, On-line Update algorithm (Hard Competitive Learning) and Neural Gas algorithm (Soft Competitive Learning), and calculation of several indexes for finding the number of clusters in a data set.
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2023-06-16 |
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r-bigalgebra
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This package provides arithmetic functions for R matrix and big.matrix objects.
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2023-06-16 |
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r-chcn
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A compilation of historical through contemporary climate measurements scraped from the Environment Canada Website Including tools for scraping data, creating metadata and formating temperature files.
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2023-06-16 |
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r-clusrank
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Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test) for clustered data.
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2023-06-16 |
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r-cklrt
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Composite Kernel Machine Regression based on Likelihood Ratio Test (CKLRT): in this package, we develop a kernel machine regression framework to model the overall genetic effect of a SNP-set, considering the possible GE interaction. Specifically, we use a composite kernel to specify the overall genetic effect via a nonparametric function and we model additional covariates parametrically within the regression framework. The composite kernel is constructed as a weighted average of two kernels, one corresponding to the genetic main effect and one corresponding to the GE interaction effect. We propose a likelihood ratio test (LRT) and a restricted likelihood ratio test (RLRT) for statistical significance. We derive a Monte Carlo approach for the finite sample distributions of LRT and RLRT statistics. (N. Zhao, H. Zhang, J. Clark, A. Maity, M. Wu. Composite Kernel Machine Regression based on Likelihood Ratio Test with Application for Combined Genetic and Gene-environment Interaction Effect (Submitted).)
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2023-06-16 |
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r-circularddm
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Circular drift-diffusion model for continuous reports.
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2023-06-16 |
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r-bigtabulate
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Extend the bigmemory package with 'table', 'tapply', and 'split' support for 'big.matrix' objects. The functions may also be used with native R matrices for improving speed and memory-efficiency.
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2023-06-16 |
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r-ceriolioutlierdetection
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Implements the iterated RMCD method of Cerioli (2010) for multivariate outlier detection via robust Mahalanobis distances. Also provides the finite-sample RMCD method discussed in the paper, as well as the methods provided in Hardin and Rocke (2005) <doi:10.1198/106186005X77685> and Green and Martin (2017).
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2023-06-16 |
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r-catencoders
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Contains some commonly used categorical variable encoders, such as 'LabelEncoder' and 'OneHotEncoder'. Inspired by the encoders implemented in Python 'sklearn.preprocessing' package (see <http://scikit-learn.org/stable/modules/preprocessing.html>).
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2023-06-16 |
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r-carlit
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Functions to calculate and plot ecological quality ratios (EQR) as specified by Ballesteros et al. 2007.
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2023-06-16 |
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r-care1
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The R package CARE1, the first part of the program CARE (Capture-Recapture) in http://chao.stat.nthu.edu.tw/softwareCE.html, can be used to analyze epidemiological data via sample coverage approach (Chao et al. 2001a). Based on the input of records from several incomplete lists (or samples) of individuals, the R package CARE1 provides output of population size estimate and related statistics.
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2023-06-16 |
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r-cfa
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Analysis of configuration frequencies for simple and repeated measures, multiple-samples CFA, hierarchical CFA, bootstrap CFA, functional CFA, Kieser-Victor CFA, and Lindner's test using a conventional and an accelerated algorithm.
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2023-06-16 |
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r-cdlasso
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Coordinate Descent Algorithms for Lasso Penalized L1, L2, and Logistic Regression
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2023-06-16 |
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r-bigmap
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Unsupervised clustering protocol for large scale structured data, based on a low dimensional representation of the data. Dimensionality reduction is performed using a parallelized implementation of the t-Stochastic Neighboring Embedding algorithm (Garriga J. and Bartumeus F. (2018), <arXiv:1812.09869>).
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2023-06-16 |
