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r-coretdt
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Use to analysis case-parent trio sequencing studies. Test the compound heterozygous and recessive disease models
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2023-06-16 |
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r-copula.surv
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Perform association analysis of bivariate survival data based on copula models. Two different ways to estimate the association parameter in copula models are implemented. A goodness-of-fit test for a given copula model is implemented. See Emura, Lin and Wang (2010) <doi.org/10.1016/j.csda.2010.03.013> for details.
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2023-06-16 |
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r-constellation
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Examine any number of time series data frames to identify instances in which various criteria are met within specified time frames. In clinical medicine, these types of events are often called "constellations of signs and symptoms", because a single condition depends on a series of events occurring within a certain amount of time of each other. This package was written to work with any number of time series data frames and is optimized for speed to work well with data frames with millions of rows.
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2023-06-16 |
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r-covr
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Track and report code coverage for your package and (optionally) upload the results to a coverage service like 'Codecov' <http://codecov.io> or 'Coveralls' <http://coveralls.io>. Code coverage is a measure of the amount of code being exercised by a set of tests. It is an indirect measure of test quality and completeness. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code.
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2023-06-16 |
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r-contfrac
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Various utilities for evaluating continued fractions.
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2023-06-16 |
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r-ddrtree
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Provides an implementation of the framework of reversed graph embedding (RGE) which projects data into a reduced dimensional space while constructs a principal tree which passes through the middle of the data simultaneously. DDRTree shows superiority to alternatives (Wishbone, DPT) for inferring the ordering as well as the intrinsic structure of the single cell genomics data. In general, it could be used to reconstruct the temporal progression as well as bifurcation structure of any datatype.
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2023-06-16 |
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r-dbscan
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A fast reimplementation of several density-based algorithms of the DBSCAN family for spatial data. Includes the DBSCAN (density-based spatial clustering of applications with noise) and OPTICS (ordering points to identify the clustering structure) clustering algorithms HDBSCAN (hierarchical DBSCAN) and the LOF (local outlier factor) algorithm. The implementations use the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided.
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2023-06-16 |
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r-datagraph
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Functions to save either '.dtable' or '.dtbin' files that can be read by DataGraph, a graphing and analysis application for macOS. Can save a data frame, collection of data frames and sequences of data frames and individual vectors. For more information see <https://www.visualdatatools.com/DataGraph/Help/DataFiles/R/index.html>.
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2023-06-16 |
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r-cusum
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Provides functions for constructing and evaluating CUSUM charts and RA-CUSUM charts with focus on false signal probability.
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2023-06-16 |
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r-crossdes
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Contains functions for the construction of carryover balanced crossover designs. In addition contains functions to check given designs for balance.
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2023-06-16 |
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r-crone
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Functions to carry out the most important crystallographic calculations for crystal structures made of 1d Gaussian-shaped atoms, especially useful for methods development. Main reference: E. Smith, G. Evans, J. Foadi (2017) <doi:10.1088/1361-6404/aa8188>.
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2023-06-16 |
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r-cp
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Functions for calculating the conditional power for different models in survival time analysis within randomized clinical trials with two different treatments to be compared and survival as an endpoint.
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2023-06-16 |
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r-conspline
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Given response y, continuous predictor x, and covariate matrix, the relationship between E(y) and x is estimated with a shape constrained regression spline. Function outputs fits and various types of inference.
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2023-06-16 |
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r-cmpcontrol
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The main purpose of this package is to juxtapose the different control limits obtained by modelling a data set through the COM-Poisson distribution vs. the classical Poisson distribution. Accordingly, this package offers the ability to compute the COM-Poisson parameter estimates and plot associated Shewhart control charts for a given data set.
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2023-06-16 |
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r-cubist
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Regression modeling using rules with added instance-based corrections.
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2023-06-16 |
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r-crimcv
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A finite mixture of Zero-Inflated Poisson (ZIP) models for analyzing criminal trajectories.
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2023-06-16 |
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r-corlink
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A matrix of agreement patterns and counts for record pairs is the input for the procedure. An EM algorithm is used to impute plausible values for missing record pairs. A second EM algorithm, incorporating possible correlations between per-field agreement, is used to estimate posterior probabilities that each pair is a true match - i.e. constitutes the same individual.
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2023-06-16 |
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r-conclust
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There are 4 main functions in this package: ckmeans(), lcvqe(), mpckm() and ccls(). They take an unlabeled dataset and two lists of must-link and cannot-link constraints as input and produce a clustering as output.
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2023-06-16 |
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r-cointmonitor
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We propose a consistent monitoring procedure to detect a structural change from a cointegrating relationship to a spurious relationship. The procedure is based on residuals from modified least squares estimation, using either Fully Modified, Dynamic or Integrated Modified OLS. It is inspired by Chu et al. (1996) <DOI:10.2307/2171955> in that it is based on parameter estimation on a pre-break "calibration" period only, rather than being based on sequential estimation over the full sample. See the discussion paper <DOI:10.2139/ssrn.2624657> for further information. This package provides the monitoring procedures for both the cointegration and the stationarity case (while the latter is just a special case of the former one) as well as printing and plotting methods for a clear presentation of the results.
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2023-06-16 |
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r-aptools
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We provide tools to estimate two prediction accuracy metrics, the average positive predictive values (AP) as well as the well-known AUC (the area under the receiver operator characteristic curve) for risk scores. The outcome of interest is either binary or censored event time. Note that for censored event time, our functions' estimates, the AP and the AUC, are time-dependent for pre-specified time interval(s). A function that compares the APs of two risk scores/markers is also included. Optional outputs include positive predictive values and true positive fractions at the specified marker cut-off values, and a plot of the time-dependent AP versus time (available for event time data).
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2023-06-16 |
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r-corelearn
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A suite of machine learning algorithms written in C++ with the R interface contains several learning techniques for classification and regression. Predictive models include e.g., classification and regression trees with optional constructive induction and models in the leaves, random forests, kNN, naive Bayes, and locally weighted regression. All predictions obtained with these models can be explained and visualized with the 'ExplainPrediction' package. This package is especially strong in feature evaluation where it contains several variants of Relief algorithm and many impurity based attribute evaluation functions, e.g., Gini, information gain, MDL, and DKM. These methods can be used for feature selection or discretization of numeric attributes. The OrdEval algorithm and its visualization is used for evaluation of data sets with ordinal features and class, enabling analysis according to the Kano model of customer satisfaction. Several algorithms support parallel multithreaded execution via OpenMP. The top-level documentation is reachable through ?CORElearn.
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2023-06-16 |
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r-concreg
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Implements concordance regression which can be used to estimate generalized odds of concordance. Can be used for non- and semi-parametric survival analysis with non-proportional hazards, for binary and for continuous outcome data.
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2023-06-16 |
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r-datamap
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datamap utilizes variable bindings and objects of class "UserDefinedDatabase" to provide a simple mapping system to foreign objects. Maps can be used as environments or attached to the search path, and changes to either are persistent. Mapped foreign objects are fetched in real-time and are never cached by the mapping system.
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2023-06-16 |
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r-ctt
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A collection of common test and item analyses from a classical test theory (CTT) framework. Analyses can be applied to both dichotomous and polytomous data. Functions provide reliability analyses (alpha), item statistics, disctractor analyses, disattenuated correlations, scoring routines, and empirical ICCs.
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2023-06-16 |
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r-credentials
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Setup and retrieve HTTPS and SSH credentials for use with 'git' and other services. For HTTPS remotes the package interfaces the 'git-credential' utility which 'git' uses to store HTTP usernames and passwords. For SSH remotes we provide convenient functions to find or generate appropriate SSH keys. The package both helps the user to setup a local git installation, and also provides a back-end for git/ssh client libraries to authenticate with existing user credentials.
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2023-06-16 |
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r-confsam
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For multiple testing. Computes estimates and confidence bounds for the False Discovery Proportion (FDP), the fraction of false positives among all rejected hypotheses. The methods in the package use permutations of the data. Doing so, they take into account the dependence structure in the data.
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2023-06-16 |
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r-condmvnorm
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Computes conditional multivariate normal probabilities, random deviates and densities.
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2023-06-16 |
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r-compr
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Different tools for describing and analysing paired comparison data are presented. Main methods are estimation of products scores according Bradley Terry Luce model. A segmentation of the individual could be conducted on the basis of a mixture distribution approach. The number of classes can be tested by the use of Monte Carlo simulations. This package deals also with multi-criteria paired comparison data.
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2023-06-16 |
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r-coop
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Fast implementations of the co-operations: covariance, correlation, and cosine similarity. The implementations are fast and memory-efficient and their use is resolved automatically based on the input data, handled by R's S3 methods. Full descriptions of the algorithms and benchmarks are available in the package vignettes.
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2023-06-16 |
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r-conconpiwifun
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Continuous convex piecewise linear (ccpl) resp. quadratic (ccpq) functions can be implemented with sorted breakpoints and slopes. This includes functions that are ccpl (resp. ccpq) on a convex set (i.e. an interval or a point) and infinite out of the domain. These functions can be very useful for a large class of optimisation problems. Efficient manipulation (such as log(N) insertion) of such data structure is obtained with map standard template library of C++ (that hides balanced trees). This package is a wrapper on such a class based on Rcpp modules.
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2023-06-16 |
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r-compboost
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C++ implementation of component-wise boosting implementation of component-wise boosting written in C++ to obtain high runtime performance and full memory control. The main idea is to provide a modular class system which can be extended without editing the source code. Therefore, it is possible to use R functions as well as C++ functions for custom base-learners, losses, logging mechanisms or stopping criteria.
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2023-06-16 |
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r-dap
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An implementation of Discriminant Analysis via Projections (DAP) method for high-dimensional binary classification in the case of unequal covariance matrices. See Irina Gaynanova and Tianying Wang (2018) <arXiv:1711.04817v2>.
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2023-06-16 |
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r-daly
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The DALY Calculator is a free, open-source Graphical User Interface (GUI) for stochastic disability-adjusted life year (DALY) calculation.
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2023-06-16 |
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r-cyclertools
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A suite of functions for analysing cycling data.
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2023-06-16 |
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r-curstatci
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Computes the maximum likelihood estimator, the smoothed maximum likelihood estimator and pointwise bootstrap confidence intervals for the distribution function under current status data. Groeneboom and Hendrickx (2017) <doi:10.1214/17-EJS1345>.
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2023-06-16 |
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r-cptcity
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Incorporates colour gradients from the 'cpt-city' web archive available at <http://soliton.vm.bytemark.co.uk/pub/cpt-city/>.
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2023-06-16 |
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r-care
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Implements the regression approach of Zuber and Strimmer (2011) "High-dimensional regression and variable selection using CAR scores" SAGMB 10: 34, <DOI:10.2202/1544-6115.1730>. CAR scores measure the correlation between the response and the Mahalanobis-decorrelated predictors. The squared CAR score is a natural measure of variable importance and provides a canonical ordering of variables. This package provides functions for estimating CAR scores, for variable selection using CAR scores, and for estimating corresponding regression coefficients. Both shrinkage as well as empirical estimators are available.
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2023-06-16 |
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r-corrdna
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Can be useful for finding associations among different positions in a position-wise aligned sequence dataset. The approach adopted for finding associations among positions is based on the latent multivariate normal distribution.
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2023-06-16 |
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r-condreg
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Based on \url{http://statistics.stanford.edu/~ckirby/techreports/GEN/2012/2012-10.pdf}
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2023-06-16 |
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r-concordance
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A set of utilities for matching products in different classification codes used in international trade research. It supports concordance between HS (Combined), ISIC Rev. 2,3, and SITC1,2,3,4 product classification codes, as well as BEC, NAICS, and SIC classifications. It also provides code nomenclature / descriptions look-up, Rauch classification look-up (via concordance to SITC2) and trade elasticity look-up (via concordance to SITC2/3 or HS3.ss).
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2023-06-16 |
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r-concor
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The four functions svdcp (cp for column partitioned), svdbip or svdbip2 (bip for bi-partitioned), and svdbips (s for a simultaneous optimization of one set of r solutions), correspond to a "SVD by blocks" notion, by supposing each block depending on relative subspaces, rather than on two whole spaces as usual SVD does. The other functions, based on this notion, are relative to two column partitioned data matrices x and y defining two sets of subsets xi and yj of variables and amount to estimate a link between xi and yj for the pair (xi, yj) relatively to the links associated to all the other pairs.
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2023-06-16 |
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r-complognormal
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Computes the probability density function, cumulative distribution function, quantile function, random numbers of any composite model based on the lognormal distribution.
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2023-06-16 |
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r-cloneseeker
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Defines the classes and functions used to simulate and to analyze data sets describing copy number variants and, optionally, sequencing mutations in order to detect clonal subsets. See Zucker et al. (2019) <doi:10.1093/bioinformatics/btz057>.
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2023-06-16 |
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r-csp
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Provides the Correlates of State Policy data set for easy use in R.
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2023-06-16 |
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r-cshapes
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Package for CShapes, a GIS dataset of country boundaries (1946-today). Includes functions for data extraction and the computation of distance matrices and -lists.
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2023-06-16 |
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r-crtsize
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Sample size estimation in cluster (group) randomized trials. Contains traditional power-based methods, empirical smoothing (Rotondi and Donner, 2009), and updated meta-analysis techniques (Rotondi and Donner, 2012).
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2023-06-16 |
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r-crossval
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Contains generic functions for performing cross validation and for computing diagnostic errors.
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2023-06-16 |
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r-crochet
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Functions to help implement the extraction / subsetting / indexing function '[' and replacement function '[<-' of custom matrix-like types (based on S3, S4, etc.), modeled as closely to the base matrix class as possible (with tests to prove it).
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2023-06-16 |
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r-cr
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This package contains R-functions to perform power calculation in a group sequential clinical trial with censored survival data and possibly unequal patient allocation between treatment and control groups. The fuctions can also be used to determine the study duration in a clinical trial with censored survival data as the sum of the accrual duration, which determines the sample size in a traditional sense, and the follow-up duration, which more or less controls the number of events to be observed. This package also contains R functions and methods to display the computed results.
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2023-06-16 |
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r-cpgassoc
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Is designed to test for association between methylation at CpG sites across the genome and a phenotype of interest, adjusting for any relevant covariates. The package can perform standard analyses of large datasets very quickly with no need to impute the data. It can also handle mixed effects models with chip or batch entering the model as a random intercept. Also includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites.
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2023-06-16 |
