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r-discretefdr
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Multiple testing procedures described in the paper Döhler, Durand and Roquain (2018) "New FDR bounds for discrete and heterogeneous tests" <doi:10.1214/18-EJS1441>. The main procedures of the paper (HSU and HSD), their adaptive counterparts (AHSU and AHSD), and the HBR variant are available and are coded to take as input a set of observed p-values and their discrete support under the null. A function to compute such p-values and supports for Fisher's exact tests is also provided, along with a wrapper allowing to apply discrete procedures directly from contingency tables.
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2025-04-22 |
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r-detestset
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Solvers and test set for stiff and non-stiff differential equations, and differential algebraic equations. 'Mazzia, F., Cash, J.R. and K. Soetaert, 2012. DOI: 10.1016/j.cam.2012.03.014'.
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2025-04-22 |
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r-delt
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We implement methods for estimating multivariate densities. We include a discretized kernel estimator, an adaptive histogram (a greedy histogram and a CART-histogram), stagewise minimization, and bootstrap aggregation.
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2025-04-22 |
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r-datautils
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Contains facilities such as getting the current timestamp in decimal seconds, computing interval w.r.t. a reference timestamp, and custom plotting with error bars.
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2025-04-22 |
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r-bitrina
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Provides methods for the binarization and trinarization of one-dimensional data and some visualization functions.
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2025-04-22 |
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r-binarize
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Provides methods for the binarization of one-dimensional data and some visualization functions.
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2025-04-22 |
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r-bigreadr
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Read large text files by splitting them in smaller files. Package bigreadr also provides some convenient wrappers of fread/fwrite.
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2025-04-22 |
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r-diphiseq
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Implements the algorithm described in Jun Li and Alicia T. Lamere, "DiPhiSeq: Robust comparison of expression levels on RNA-Seq data with large sample sizes" (Unpublished). Detects not only genes that show different average expressions ("differential expression", DE), but also genes that show different diversities of expressions in different groups ("differentially dispersed", DD). DD genes can be important clinical markers. 'DiPhiSeq' uses a redescending penalty on the quasi-likelihood function, and thus has superior robustness against outliers and other noise. Updates from version 0.1.0: (1) Added the option of using adaptive initial value for phi. (2) Added a function for estimating the proportion of outliers in the data. (3) Modified the input parameter names for clarity, and modified the output format for the main function.
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2025-04-22 |
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r-dint
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S3 classes and methods to create and work with year-quarter, year-month and year-isoweek vectors. Basic arithmetic operations (such as adding and subtracting) are supported, as well as formatting and converting to and from standard R date types.
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2025-04-22 |
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r-dinamic
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This function implements the DiNAMIC procedure for assessing the statistical significance of recurrent DNA copy number aberrations (Bioinformatics (2011) 27(5) 678 - 685).
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2025-04-22 |
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r-digitalpcr
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The assay sensitivity is the minimum number of copies that the digital PCR assay can detect. Users provide serial dilution results in the format of counts of positive and total reaction wells. The output is the estimated assay sensitivity and the copy number per well in the initial dilute.
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2025-04-22 |
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r-diffr
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An R interface to the 'codediff' JavaScript library (a copy of which is included in the package, see <https://github.com/danvk/codediff.js> for information). Allows for visualization of the difference between 2 files, usually text files or R scripts, in a browser.
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2025-04-22 |
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r-diffpriv
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An implementation of major general-purpose mechanisms for privatizing statistics, models, and machine learners, within the framework of differential privacy of Dwork et al. (2006) <doi:10.1007/11681878_14>. Example mechanisms include the Laplace mechanism for releasing numeric aggregates, and the exponential mechanism for releasing set elements. A sensitivity sampler (Rubinstein & Alda, 2017) <arXiv:1706.02562> permits sampling target non-private function sensitivity; combined with the generic mechanisms, it permits turn-key privatization of arbitrary programs.
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2025-04-22 |
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r-diffmeshgp
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This R function implements the nonstationary Kriging model proposed by Tuo, Wu and Yu (2014) <DOI:10.1080/00401706.2013.842935> for analyzing multi-fidelity computer outputs. This function computes the maximum likelihood estimates for the model parameters as well as the predictive means and variances of the exact solution (i.e., the conceptually highest fidelity).
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2025-04-22 |
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r-diffee
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This is an R implementation of Fast and Scalable Learning of Sparse Changes in High-Dimensional Gaussian Graphical Model Structure (DIFFEE). The DIFFEE algorithm can be used to fast estimate the differential network between two related datasets. For instance, it can identify differential gene network from datasets of case and control. By performing data-driven network inference from two high-dimensional data sets, this tool can help users effectively translate two aggregated data blocks into knowledge of the changes among entities between two Gaussian Graphical Model. Please run demo(diffeeDemo) to learn the basic functions provided by this package. For further details, please read the original paper: Beilun Wang, Arshdeep Sekhon, Yanjun Qi (2018) <arXiv:1710.11223>.
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2025-04-22 |
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r-difconet
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Estimation of DIFferential COexpressed NETworks using diverse and user metrics. This package is basically used for three functions related to the estimation of differential coexpression. First, to estimate differential coexpression where the coexpression is estimated, by default, by Spearman correlation. For this, a metric to compare two correlation distributions is needed. The package includes 6 metrics. Some of them needs a threshold. A new metric can also be specified as a user function with specific parameters (see difconet.run). The significance is be estimated by permutations. Second, to generate datasets with controlled differential correlation data. This is done by either adding noise, or adding specific correlation structure. Third, to show the results of differential correlation analyses. Please see <http://bioinformatica.mty.itesm.mx/difconet> for further information.
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2025-04-22 |
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r-diezeit
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A wrapper for the ZEIT ONLINE Content API, available at <http://developer.zeit.de>. 'diezeit' gives access to articles and corresponding metadata from the ZEIT archive and from ZEIT ONLINE. A personal API key is required for usage.
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2025-04-22 |
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r-dielectric
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Physical constants. Gold, silver and glass permittivities, together with spline interpolation functions.
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2025-04-22 |
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r-didacticboost
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A basic, clear implementation of tree-based gradient boosting designed to illustrate the core operation of boosting models. Tuning parameters (such as stochastic subsampling, modified learning rate, or regularization) are not implemented. The only adjustable parameter is the number of training rounds. If you are looking for a high performance boosting implementation with tuning parameters, consider the 'xgboost' package.
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2025-04-22 |
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r-dicionariosibge
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This package contains the dictionaries for reading microdata from IBGE (Brazilian Institute of Geography and Statistics) surveys PNAD, PME and POF.
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2025-04-22 |
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r-dice
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This package provides utilities to calculate the probabilities of various dice-rolling events, such as the probability of rolling a four-sided die six times and getting a 4, a 3, and either a 1 or 2 among the six rolls (in any order); the probability of rolling two six-sided dice three times and getting a 10 on the first roll, followed by a 4 on the second roll, followed by anything but a 7 on the third roll; or the probabilities of each possible sum of rolling five six-sided dice, dropping the lowest two rolls, and summing the remaining dice.
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2025-04-22 |
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r-diaplt
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Visualize one-factor data frame. Beads plot consists of diamonds of each factor of each data series. A diamond indicates average and range. Look over a data frame with many numeric columns and a factor column.
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2025-04-22 |
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r-dialrjars
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Collects 'libphonenumber' jars required for the 'dialr' package.
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2025-04-22 |
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r-diagonals
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Several tools for handling block-matrix diagonals and similar constructs are implemented. Block-diagonal matrices can be extracted or removed using two small functions implemented here. In addition, non-square matrices are supported. Block diagonal matrices occur when two dimensions of a data set are combined along one edge of a matrix. For example, trade-flow data in the 'decompr' and 'gvc' packages have each country-industry combination occur along both edges of the matrix.
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2025-04-22 |
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r-di
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A set of utilities for calculating the Deficit (frailty) Index (DI) in gerontological studies. The deficit index was first proposed by Arnold Mitnitski and Kenneth Rockwood and represents a proxy measure of aging and also can be served as a sensitive predictor of survival. For more information, see (i)"Accumulation of Deficits as a Proxy Measure of Aging" by Arnold B. Mitnitski et al. (2001), The Scientific World Journal 1, <DOI:10.1100/tsw.2001.58>; (ii) "Frailty, fitness and late-life mortality in relation to chronological and biological age" by Arnold B Mitnitski et al. (2001), BMC Geriatrics2002 2(1), <DOI:10.1186/1471-2318-2-1>.
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2025-04-22 |
