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r-discretelaplace
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public |
Probability mass function, distribution function, quantile function, random generation and estimation for the skew discrete Laplace distributions.
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2024-01-16 |
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r-disclap
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public |
The discrete Laplace exponential family for use in fitting generalized linear models.
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2024-01-16 |
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r-dineq
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public |
Decomposition of (income) inequality by population sub groups. For a decomposition on a single variable the mean log deviation can be used (see Mookherjee Shorrocks (1982) <DOI:10.2307/2232673>). For a decomposition on multiple variables a regression based technique can be used (see Fields (2003) <DOI:10.1016/s0147-9121(03)22001-x>). Recentered influence function regression for marginal effects of the (income or wealth) distribution (see Firpo et al. (2009) <DOI:10.3982/ECTA6822>). Some extensions to inequality functions to handle weights and/or missings.
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2024-01-16 |
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r-discfrail
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public |
Functions for fitting Cox proportional hazards models for grouped time-to-event data, where the shared group-specific frailties have a discrete nonparametric distribution. The methods proposed in the package is described by Gasperoni, F., Ieva, F., Paganoni, A. M., Jackson, C. H., Sharples, L. (2018) <doi:10.1093/biostatistics/kxy071>. There are also functions for simulating from these models, with a nonparametric or a parametric baseline hazard function.
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2024-01-16 |
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r-dirmult
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public |
Estimate parameters in Dirichlet-Multinomial and compute log-likelihoods.
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2024-01-16 |
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r-directstandardisation
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public |
Calculate adjusted means and proportions of a variable by groups defined by another variable by direct standardisation, standardised to the structure of the dataset.
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2024-01-16 |
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r-directlabels
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public |
An extensible framework for automatically placing direct labels onto multicolor 'lattice' or 'ggplot2' plots. Label positions are described using Positioning Methods which can be re-used across several different plots. There are heuristics for examining "trellis" and "ggplot" objects and inferring an appropriate Positioning Method.
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2024-01-16 |
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r-directedclustering
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public |
Allows the computation of clustering coefficients for directed and weighted networks by using different approaches. It allows to compute clustering coefficients that are not present in 'igraph' package. A description of clustering coefficients can be found in "Directed clustering in weighted networks: a new perspective", Clemente, G.P., Grassi, R. (2017), <doi:10.1016/j.chaos.2017.12.007>.
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2024-01-16 |
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r-directeffects
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public |
A set of functions to estimate the controlled direct effect of treatment fixing a potential mediator to a specific value. Implements the sequential g-estimation estimator described in Vansteelandt (2009) <doi:10.1097/EDE.0b013e3181b6f4c9> and Acharya, Blackwell, and Sen (2016) <doi:10.1017/S0003055416000216>.
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2024-01-16 |
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r-diphiseq
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public |
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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2024-01-16 |
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r-dint
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public |
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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2024-01-16 |
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r-dimora
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public |
The implemented methods are: Standard Bass model, Generalized Bass model (with rectangular shock, exponential shock, and mixed shock. You can choose to add from 1 to 3 shocks), Guseo-Guidolin model and Variable Potential Market model, and UCRCD model. The Bass model consists of a simple differential equation that describes the process of how new products get adopted in a population, the Generalized Bass model is a generalization of the Bass model in which there is a "carrier" function x(t) that allows to change the speed of time sliding. In some real processes the reachable potential of the resource available in a temporal instant may appear to be not constant over time, because of this we use Variable Potential Market model, in which the Guseo-Guidolin has a particular specification for the market function. The UCRCD model (Unbalanced Competition and Regime Change Diachronic) is a diffusion model used to capture the dynamics of the competitive or collaborative transition.
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2024-01-16 |
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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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2024-01-16 |
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r-digitize
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public |
Import data from a digital image; it requires user input for calibration and to locate the data points. The end result is similar to 'DataThief' and other other programs that 'digitize' published plots or graphs.
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2024-01-16 |
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r-diffusionmap
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public |
Implements diffusion map method of data parametrization, including creation and visualization of diffusion map, clustering with diffusion K-means and regression using adaptive regression model. Richards (2009) <doi:10.1088/0004-637X/691/1/32>.
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2024-01-16 |
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r-dimensionsr
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public |
A set of tools to extract bibliographic content from 'Digital Science Dimensions' using 'DSL' API <https://www.dimensions.ai/dimensions-apis/>.
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2024-01-16 |
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r-difr
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public |
Provides a collection of standard methods to detect differential item functioning among dichotomously scored items. Methods for uniform and non-uniform DIF, based on test-score or IRT methods, for comparing two or more than two groups of respondents, are available (Magis, Beland, Tuerlinckx and De Boeck,A General Framework and an R Package for the Detection of Dichotomous Differential Item Functioning, Behavior Research Methods, 42, 2010, 847-862 <doi:10.3758/BRM.42.3.847>).
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2024-01-16 |
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r-diffviewer
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public |
A HTML widget that shows differences between files (text, images, and data frames).
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2024-01-16 |
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r-digitalpcr
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public |
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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2024-01-16 |
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r-diffcor
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public |
Computations of Fisher's z-tests concerning different kinds of correlation differences. Additionally, approaches to estimating statistical power via Monte Carlo simulations are implemented.
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2024-01-16 |
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r-diffdf
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public |
Functions for comparing two data.frames against each other. The core functionality is to provide a detailed breakdown of any differences between two data.frames as well as providing utility functions to help narrow down the source of problems and differences.
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2024-01-16 |
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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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2024-01-16 |
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r-diffpriv
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public |
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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2024-01-16 |
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r-did2s
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public |
Estimates Two-way Fixed Effects difference-in-differences/event-study models using the approach proposed by Gardner (2021) <doi:10.48550/arXiv.2207.05943>. To avoid the problems caused by OLS estimation of the Two-way Fixed Effects model, this function first estimates the fixed effects and covariates using untreated observations and then in a second stage, estimates the treatment effects.
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2024-01-16 |
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r-diffee
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public |
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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2024-01-16 |
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r-dictionar6
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public |
Efficient object-oriented R6 dictionary capable of holding objects of any class, including R6. Typed and untyped dictionaries are provided as well as the 'usual' dictionary methods that are available in other OOP languages, for example listing keys, items, values, and methods to get/set these.
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2024-01-16 |
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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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2024-01-16 |
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r-did
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The standard Difference-in-Differences (DID) setup involves two periods and two groups -- a treated group and untreated group. Many applications of DID methods involve more than two periods and have individuals that are treated at different points in time. This package contains tools for computing average treatment effect parameters in Difference in Differences setups with more than two periods and with variation in treatment timing using the methods developed in Callaway and Sant'Anna (2021) <doi:10.1016/j.jeconom.2020.12.001>. The main parameters are group-time average treatment effects which are the average treatment effect for a particular group at a a particular time. These can be aggregated into a fewer number of treatment effect parameters, and the package deals with the cases where there is selective treatment timing, dynamic treatment effects, calendar time effects, or combinations of these. There are also functions for testing the Difference in Differences assumption, and plotting group-time average treatment effects.
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2024-01-16 |
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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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2024-01-16 |
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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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2024-01-16 |
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r-dict
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public |
A key-value dictionary data structure based on R6 class which is designed to be similar usages with other languages dictionary (e.g. 'Python') with reference semantics and extendabilities by R6.
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2024-01-16 |
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r-dials
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public |
Many models contain tuning parameters (i.e. parameters that cannot be directly estimated from the data). These tools can be used to define objects for creating, simulating, or validating values for such parameters.
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2024-01-16 |
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r-diagram
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public |
Visualises simple graphs (networks) based on a transition matrix, utilities to plot flow diagrams, visualising webs, electrical networks, etc. Support for the book "A practical guide to ecological modelling - using R as a simulation platform" by Karline Soetaert and Peter M.J. Herman (2009), Springer. and the book "Solving Differential Equations in R" by Karline Soetaert, Jeff Cash and Francesca Mazzia (2012), Springer. Includes demo(flowchart), demo(plotmat), demo(plotweb).
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2024-01-16 |
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r-dichromat
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None |
Collapse red-green or green-blue distinctions to simulate the effects of different types of color-blindness.
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2024-01-16 |
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r-diceeval
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public |
Estimation, validation and prediction of models of different types : linear models, additive models, MARS,PolyMARS and Kriging.
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2024-01-16 |
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r-dharma
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The 'DHARMa' package uses a simulation-based approach to create readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed models. Currently supported are linear and generalized linear (mixed) models from 'lme4' (classes 'lmerMod', 'glmerMod'), 'glmmTMB' 'GLMMadaptive' and 'spaMM', generalized additive models ('gam' from 'mgcv'), 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model classes. Moreover, externally created simulations, e.g. posterior predictive simulations from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well. The resulting residuals are standardized to values between 0 and 1 and can be interpreted as intuitively as residuals from a linear regression. The package also provides a number of plot and test functions for typical model misspecification problems, such as over/underdispersion, zero-inflation, and residual spatial and temporal autocorrelation.
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2024-01-16 |
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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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2024-01-16 |
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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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2024-01-16 |
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r-dialrjars
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Collects 'libphonenumber' jars required for the 'dialr' package.
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2024-01-16 |
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r-dialr
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public |
Parse, format, and validate international phone numbers using Google's 'libphonenumber' java library, <https://github.com/google/libphonenumber>.
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2024-01-16 |
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r-diagrammersvg
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public |
Allows for export of DiagrammeR Graphviz objects to SVG.
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2024-01-16 |
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r-diagrammer
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None |
Build graph/network structures using functions for stepwise addition and deletion of nodes and edges. Work with data available in tables for bulk addition of nodes, edges, and associated metadata. Use graph selections and traversals to apply changes to specific nodes or edges. A wide selection of graph algorithms allow for the analysis of graphs. Visualize the graphs and take advantage of any aesthetic properties assigned to nodes and edges.
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2024-01-16 |
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r-di
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public |
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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2024-01-16 |
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r-dfa.cancor
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public |
Produces SPSS- and SAS-like output for linear discriminant function analysis and canonical correlation analysis. The methods are described in Manly & Alberto (2017, ISBN:9781498728966), Rencher (2002, ISBN:0-471-41889-7), and Tabachnik & Fidell (2019, ISBN:9780134790541).
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2024-01-16 |
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r-diagonals
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public |
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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2024-01-16 |
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r-dhh
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public |
The density, cumulative distribution, quantiles, and i.i.d random variables of a heavy-headed distribution. For more information, please see the vignette.
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2024-01-16 |
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r-detectseparation
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public |
Provides pre-fit and post-fit methods for detecting separation and infinite maximum likelihood estimates in generalized linear models with categorical responses. The pre-fit methods apply on binomial-response generalized liner models such as logit, probit and cloglog regression, and can be directly supplied as fitting methods to the glm() function. They solve the linear programming problems for the detection of separation developed in Konis (2007, <https://ora.ox.ac.uk/objects/uuid:8f9ee0d0-d78e-4101-9ab4-f9cbceed2a2a>) using 'ROI' <https://cran.r-project.org/package=ROI> or 'lpSolveAPI' <https://cran.r-project.org/package=lpSolveAPI>. The post-fit methods apply to models with categorical responses, including binomial-response generalized linear models and multinomial-response models, such as baseline category logits and adjacent category logits models; for example, the models implemented in the 'brglm2' <https://cran.r-project.org/package=brglm2> package. The post-fit methods successively refit the model with increasing number of iteratively reweighted least squares iterations, and monitor the ratio of the estimated standard error for each parameter to what it has been in the first iteration. According to the results in Lesaffre & Albert (1989, <https://www.jstor.org/stable/2345845>), divergence of those ratios indicates data separation.
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2024-01-16 |
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r-dfoptim
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public |
Derivative-Free optimization algorithms. These algorithms do not require gradient information. More importantly, they can be used to solve non-smooth optimization problems.
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2024-01-16 |
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r-dfidx
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public |
Provides extended data frames, with a special data frame column which contains two indexes, with potentially a nesting structure.
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2024-01-16 |
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r-details
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public |
Create a details HTML tag around R objects to place in a Markdown, 'Rmarkdown' and 'roxygen2' documentation.
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2024-01-16 |
