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r-ecctmc
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Draw sample paths for endpoint-conditioned continuous time Markov chains via modified rejection sampling or uniformization.
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2023-06-16 |
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r-drmdel
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Dual empirical likelihood (DEL) inference under semiparametric density ratio models (DRM) in the presence of multiple samples, including population cumulative distribution function estimation, quantile estimation and comparison, density estimation, composite hypothesis testing for DRM parameters which encompasses testing for changes in population distribution functions as a special case, etc.
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2023-06-16 |
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r-document
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Have you ever been tempted to create 'roxygen2'-style documentation comments for one of your functions that was not part of one of your packages (yet)? This is exactly what this package is about: running 'roxygen2' on (chunks of) a single code file.
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2023-06-16 |
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r-divmelt
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This package has tools for analyzing DNA melting data to generate HRM scores, the DNA diversity measure output of the HRM Diversity Assay. For additional documentation visit http://code.google.com/p/divmelt/.
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2023-06-16 |
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r-distance.sample.size
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Calculates the study size (either number of detections, or proportion of region that should be covered) to achieve a target precision for the estimated abundance. The calculation allows for the penalty due to unknown detection function, and for overdispersion. The user must specify a guess at the true detection function.
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2023-06-16 |
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r-dovalidation
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Local linear hazard estimator and its multiplicatively bias correction, including three bandwidth selection methods: best one-sided cross-validation, double one-sided cross-validation, and standard cross-validation.
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2023-06-16 |
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r-displayhts
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A package containing R functions for displaying data and results from high-throughput screening experiments.
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2023-06-16 |
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r-distributiontest
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Provides new types of omnibus tests which are generally much more powerful than traditional tests (including the Kolmogorov-Smirnov, Cramer-von Mises and Anderson-Darling tests),see Zhang (2002) <doi:10.1111/1467-9868.00337>.
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2023-06-16 |
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r-discretization
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This package is a collection of supervised discretization algorithms. It can also be grouped in terms of top-down or bottom-up, implementing the discretization algorithms.
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2023-06-16 |
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r-discriminer
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Functions for Discriminant Analysis and Classification purposes covering various methods such as descriptive, geometric, linear, quadratic, PLS, as well as qualitative discriminant analyses
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2023-06-16 |
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r-discsurv
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Provides data transformations, estimation utilities, predictive evaluation measures and simulation functions for discrete time survival analysis.
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2023-06-16 |
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r-disparityfilter
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The disparity filter algorithm is a network reduction technique to identify the 'backbone' structure of a weighted network without destroying its multi-scale nature. The algorithm is documented in M. Angeles Serrano, Marian Boguna and Alessandro Vespignani in "Extracting the multiscale backbone of complex weighted networks", Proceedings of the National Academy of Sciences 106 (16), 2009. This implementation of the algorithm supports both directed and undirected networks.
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2023-06-16 |
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r-doubleexpseq
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Differential exon usage test for RNA-Seq data via an empirical Bayes shrinkage method for the dispersion parameter the utilizes inclusion-exclusion data to analyze the propensity to skip an exon across groups. The input data consists of two matrices where each row represents an exon and the columns represent the biological samples. The first matrix is the count of the number of reads expressing the exon for each sample. The second matrix is the count of the number of reads that either express the exon or explicitly skip the exon across the samples, a.k.a. the total count matrix. Dividing the two matrices yields proportions representing the propensity to express the exon versus skipping the exon for each sample.
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2023-06-16 |
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r-dpglasso
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fits the primal graphical lasso, via one-at-a-time block-coordinate descent.
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2023-06-16 |
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r-dlm
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Provides routines for Maximum likelihood, Kalman filtering and smoothing, and Bayesian analysis of Normal linear State Space models, also known as Dynamic Linear Models.
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2023-06-16 |
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r-distributionutils
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Utilities are provided which are of use in the packages I have developed for dealing with distributions. Currently these packages are GeneralizedHyperbolic, VarianceGamma, and SkewHyperbolic and NormalLaplace. Each of these packages requires DistributionUtils. Functionality includes sample skewness and kurtosis, log-histogram, tail plots, moments by integration, changing the point about which a moment is calculated, functions for testing distributions using inversion tests and the Massart inequality. Also includes an implementation of the incomplete Bessel K function.
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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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r-devrate
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A set of functions to quantify the relationship between development rate and temperature and to build phenological models. The package comprises a set of models and estimated parameters borrowed from a literature review in ectotherms. The methods and literature review are described in Rebaudo et al. (2018) <doi:10.1111/2041-210X.12935> and Rebaudo and Rabhi (2018) <doi:10.1111/eea.12693>. An example can be found in Rebaudo et al. (2017) <doi:10.1007/s13355-017-0480-5>.
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2023-06-16 |
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r-dfmta
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Phase I/II adaptive dose-finding design for single-agent Molecularly Targeted Agent (MTA), according to the paper "Phase I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau Determination using Adaptive Randomization", Riviere Marie-Karelle et al. (2016) <doi:10.1177/0962280216631763>.
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2023-06-16 |
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r-documair
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Production of R packages from tagged comments introduced within the code and a minimum of additional documentation files.
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2023-06-16 |
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r-dismo
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Functions for species distribution modeling, that is, predicting entire geographic distributions form occurrences at a number of sites and the environment at these sites.
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2023-06-16 |
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r-dialrjars
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Collects 'libphonenumber' jars required for the 'dialr' package.
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2023-06-16 |
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r-devfunc
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A concise check of the format of one or multiple input arguments (data type, length or value) is provided. Since multiple input arguments can be tested simultaneously, a lengthly list of checks at the beginning of your function can be avoided, hereby enhancing the readability and maintainability of your code.
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2023-06-16 |
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r-deriv
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R-based solution for symbolic differentiation. It admits user-defined function as well as function substitution in arguments of functions to be differentiated. Some symbolic simplification is part of the work.
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2023-06-16 |
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r-deming
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Generalized Deming regression, Theil-Sen regression and Passing-Bablock regression functions.
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2023-06-16 |
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r-demetics
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This package allows to calculate the fixation index Gst (Nei, 1973) and the differentiation index D (Jost, 2008) pairwise between or averaged over several populations. P-values, stating the significance of differentiation, and 95 percent confidence intervals can be estimated using bootstrap resamplings. In the case that more than two populations are compared pairwise, the p-values are adjusted by bonferroni correction and in several other ways due to the multiple comparison from one data set.
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2023-06-16 |
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r-deltd
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It plots densities by using asymmetrical kernels which belong to life time distributions and calculate its related MSE. For details see Chen (2000), Jin and Kawczak (2003) and Salha et al. (2014) <doi:10.12988/pms.2014.4616>.
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2023-06-16 |
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r-dfphase1
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Statistical methods for retrospectively detecting changes in location and/or dispersion of univariate and multivariate variables. Data values are assumed to be independent, can be individual (one observation at each instant of time) or subgrouped (more than one observation at each instant of time). Control limits are computed, often using a permutation approach, so that a prescribed false alarm probability is guaranteed without making any parametric assumptions on the stable (in-control) distribution.
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2023-06-16 |
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r-appestimation
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Calculating predictive model performance measures adjusted for predictor distributions using density ratio method (Sugiyama et al., (2012, ISBN:9781139035613)). L1 and L2 error for continuous outcome and C-statistics for binomial outcome are computed.
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2023-06-16 |
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r-dpcid
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Differential partial correlation identification with the ridge and the fusion penalties.
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2023-06-16 |
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r-dixontest
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For outlier detection in small and normally distributed samples the ratio test of Dixon (Q-test) can be used. Density, distribution function, quantile function and random generation for Dixon's ratio statistics are provided as wrapper functions. The core applies McBane's Fortran functions <doi:10.18637/jss.v016.i03> that use Gaussian quadrature for a numerical solution.
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2023-06-16 |
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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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2023-06-16 |
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r-dgmb
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A set of functions have been implemented to generate random data to perform Monte Carlo simulations on structural models with formative constructs and interaction and nonlinear effects (Two-Step PLS Mode B structural models). The setup of the true model considers a simple structure with three formative exogenous constructs related to one formative endogenous construct. The routines take into account the interaction and nonlinear effects of the exogenous constructs on the endogenous construct.
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2023-06-16 |
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r-dfcompare
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Compares two dataframes with a common key and returns the delta records. The package will return three dataframes that contain the added, changed, and deleted records.
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2023-06-16 |
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r-dbemplikenorm
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Test for joint assessment of normality
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2023-06-16 |
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r-cytobankbridger
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A collection of tools that leverage the CytobankAPI R package <https://cran.r-project.org/web/packages/CytobankAPI/vignettes/cytobank-quickstart.html> to complete more complex workflows, and add/extend various Cytobank features.
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2023-06-16 |
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r-delaporte
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Provides probability mass, distribution, quantile, random-variate generation, and method-of-moments parameter-estimation functions for the Delaporte distribution. The Delaporte is a discrete probability distribution which can be considered the convolution of a negative binomial distribution with a Poisson distribution. Alternatively, it can be considered a counting distribution with both Poisson and negative binomial components. It has been studied in actuarial science as a frequency distribution which has more variability than the Poisson, but less than the negative binomial.
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2023-06-16 |
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r-discretelaplace
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Probability mass function, distribution function, quantile function, random generation and estimation for the skew discrete Laplace distributions.
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2023-06-16 |
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r-dlib
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Interface for 'Rcpp' users to 'dlib' <http://dlib.net> which is a 'C++' toolkit containing machine learning algorithms and computer vision tools. It is used in a wide range of domains including robotics, embedded devices, mobile phones, and large high performance computing environments. This package allows R users to use 'dlib' through 'Rcpp'.
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2023-06-16 |
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r-divo
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A set of tools for empirical analysis of diversity (a number and frequency of different types in population) and similarity (a number and frequency of shared types in two populations) in biological or ecological systems.
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2023-06-16 |
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r-distory
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Geodesic distance between phylogenetic trees and associated functions.
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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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r-denseflmm
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Estimation of functional linear mixed models for densely sampled data based on functional principal component analysis.
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2023-06-16 |
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r-delta
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Measure of agreement delta was originally by MartÃn & Femia (2004) <DOI:10.1348/000711004849268>. Since then has been considered as agreement measure for different fields, since their behavior is usually better than the usual kappa index by Cohen (1960) <DOI:10.1177/001316446002000104>. The main issue with delta is that can not be computed by hand contrary to kappa. The current algorithm is based on the Version 5 of the delta windows program that can be found on <https://www.ugr.es/~bioest/software/delta/cmd.php?seccion=downloads>.
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2023-06-16 |
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r-denpro
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We provide tools to (1) visualize multivariate density functions and density estimates with level set trees, (2) visualize level sets with shape trees, (3) visualize multivariate data with tail trees, (4) visualize scales of multivariate density estimates with mode graphs and branching maps, and (5) visualize anisotropic spread with 2D volume functions and 2D probability content functions. Level set trees visualize mode structure, shape trees visualize shapes of level sets of unimodal densities, and tail trees visualize connected data sets. The kernel estimator is implemented but the package may also be applied for visualizing other density estimates.
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2023-06-16 |
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r-deisotoper
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Provides a low-level interface for a deisotoper container implemented in the 'Java' programming language and means of S3 helper functions for plotting and debugging isotopes of mass spectrometric data. The deisotoper algorithm detects and aggregates peaks which belong to the same isotopic cluster of a given mass spectrum.
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2023-06-16 |
