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r-reports
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Assists in writing reports and presentations by providing a frame work that brings together existing R, LaTeX/.docx and Pandoc tools. The package is designed to be used with RStudio, MiKTex/Tex Live/LibreOffice, knitr, knitcitations, Pandoc and pander. The user will want to download these free programs/packages to maximize the effectiveness of the reports package. Functions with two letter names are general text formatting functions for copying text from articles for inclusion as a citation.
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2025-03-25 |
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r-reportroc
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Provides an easy way to report the results of ROC analysis, including: 1. an ROC curve. 2. the value of Cutoff, AUC (Area Under Curve), ACC (accuracy), SEN (sensitivity), SPE (specificity), PLR (positive likelihood ratio), NLR (negative likelihood ratio), PPV (positive predictive value), NPV (negative predictive value).
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2025-03-25 |
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r-reportreg
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Provides an easy way to report the results of regression analysis, including: 1. Proportional hazards regression from function 'coxph' of package 'survival'; 2. Conditional logistic regression from function 'clogit' of package 'survival'; 3. Ordered logistic regression from function 'polr' of package 'MASS'; 4. Binary logistic regression from function 'glm' of package 'stats'; 5. Linear regression from function 'lm' of package 'stats'; 6. Risk regression model for survival analysis with competing risks from function 'FGR' of package 'riskRegression'; 7. Multilevel model from function 'lme' of package 'nlme'.
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2025-03-25 |
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r-repogenerator
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Generates a project and repo for easy initialization of a GitHub repo for R workshops. The repo includes a README with instructions to ensure that all users have the needed packages, an 'RStudio' project with the right directories and the proper data. The repo can then be used for hosting code taught during the workshop.
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2025-03-25 |
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r-repo
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A data manager meant to avoid manual storage/retrieval of data to/from the file system. It builds one (or more) centralized repository where R objects are stored with rich annotations, including corresponding code chunks, and easily searched and retrieved.
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2025-03-25 |
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r-repec
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Utilities for accessing RePEc (Research Papers in Economics) through a RESTful API. You can request a code and get detailed information at the following page: <https://ideas.repec.org/api.html>.
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2025-03-25 |
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r-repeatedhighdim
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Global tests for expression data of high-dimensional sets of molecular features.
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2025-03-25 |
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r-rentrez
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Provides an R interface to the NCBI's 'EUtils' API, allowing users to search databases like 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> and 'PubMed' <https://www.ncbi.nlm.nih.gov/pubmed/>, process the results of those searches and pull data into their R sessions.
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2025-03-25 |
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r-renpow
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Supports calculations and visualization for renewable power systems and the environment. Analysis and graphical tools for DC and AC circuits and their use in electric power systems. Analysis and graphical tools for thermodynamic cycles and heat engines, supporting efficiency calculations in coal-fired power plants, gas-fired power plants. Calculations of carbon emissions and atmospheric CO2 dynamics. Analysis of power flow and demand for the grid, as well as power models for microgrids and off-grid systems. Provides resource and power generation for hydro power, wind power, and solar power.
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2025-03-25 |
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r-remindr
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Insert/extract text "reminders" into/from function source code comments or as the "comment" attribute of any object. The former can be handy in development as reminders of e.g. argument requirements, expected objects in the calling environment, required options settings, etc. The latter can be used to provide information of the object and as simple manual "tooltips" for users, among other things.
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2025-03-25 |
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r-relvalanalysis
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Classes and functions for analyzing the performance of portfolios relative to a benchmark.
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2025-03-25 |
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r-relimp
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Functions to facilitate inference on the relative importance of predictors in a linear or generalized linear model, and a couple of useful Tcl/Tk widgets.
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2025-03-25 |
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r-reliar
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A collection of utilities for some reliability models/probability distributions.
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2025-03-25 |
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r-reliability
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Functions for estimating parameters in software reliability models. Only infinite failure models are implemented so far.
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2025-03-25 |
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r-relen
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This function computes the relative entropy (H) as an index for qualitative variation of a factor.
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2025-03-25 |
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r-relaxo
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Relaxed Lasso is a generalisation of the Lasso shrinkage technique for linear regression. Both variable selection and parameter estimation is achieved by regular Lasso, yet both steps do not necessarily use the same penalty parameter. The results include all standard Lasso solutions but allow often for sparser models while having similar or even slightly better predictive performance if many predictor variables are present. The package depends on the LARS package.
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2025-03-25 |
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r-relaxnet
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Extends the glmnet package with "relaxation", done by running glmnet once on the entire predictor matrix, then again on each different subset of variables from along the regularization path. Relaxation may lead to improved prediction accuracy for truly sparse data generating models, as well as fewer false positives (i.e. fewer noncontributing predictors in the final model). Penalty may be lasso (alpha = 1) or elastic net (0 < alpha < 1). For this version, family may be "gaussian" or "binomial" only. Takes advantage of fast FORTRAN code from the glmnet package.
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2025-03-25 |
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r-relatable
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Functions to safely map from a vector of keys to a vector of values, determine properties of a given relation, or ensure a relation conforms to a given type, such as many-to-many, one-to-many, injective, surjective, or bijective. Permits default return values for use similar to a vectorised switch statement, as well as safely handling large vectors, NAs, and duplicate mappings.
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2025-03-25 |
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r-relabeloadings
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In confirmatory factor analysis (CFA), structural constraints typically ensure that the model is identified up to all possible reflections, i.e., column sign changes of the matrix of loadings. Such reflection invariance is problematic for Bayesian CFA when the reflection modes are not well separated in the posterior distribution. Imposing rotational constraints -- fixing some loadings to be zero or positive in order to pick a factor solution that corresponds to one reflection mode -- may not provide a satisfactory solution for Bayesian CFA. The function 'relabel' uses the relabeling algorithm of Erosheva and Curtis to correct for sign invariance in MCMC draws from CFA models. The MCMC draws should come from Bayesian CFA models that are fit without rotational constraints.
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2025-03-25 |
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r-rela
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Item analysis with alpha standard error and principal axis factoring for continuous variable scales (with plots).
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2025-03-25 |
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r-rel
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Derives point estimates with confidence intervals for Bennett et als S, Cohen's kappa, Conger's kappa, Fleiss' kappa, Gwet's AC, intraclass correlation coefficients, Krippendorff's alpha, Scott's pi, the standard error of measurement, and weighted kappa.
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2025-03-25 |
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r-reinstallr
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Search R files for not installed packages and run install.packages.
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2025-03-25 |
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r-reinforcelearn
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Implements reinforcement learning environments and algorithms as described in Sutton & Barto (1998, ISBN:0262193981). The Q-Learning algorithm can be used with function approximation, eligibility traces (Singh & Sutton (1996) <doi:10.1007/BF00114726>) and experience replay (Mnih et al. (2013) <arXiv:1312.5602>).
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2025-03-25 |
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r-rehh.data
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Contains example data for the 'rehh' package.
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2025-03-25 |
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r-regtest
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Functions for unary and binary regression tests
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2025-03-25 |
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r-regsubseq
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For a sequence of event occurence times, we are interested in finding subsequences in it that are too "regular". We define regular as being significantly different from a homogeneous Poisson process. The departure from the Poisson process is measured using a L1 distance. See Di and Perlman 2007 for more details.
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2025-03-25 |
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r-regspec
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Computes linear Bayesian spectral estimates from multirate data for second-order stationary time series. Provides credible intervals and methods for plotting various spectral estimates.
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2025-03-25 |
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r-regsel
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Functions for fitting linear and generalized linear models with variable selection. The functions can automatically do Stepwise Regression, Lasso or Elastic Net as variable selection methods. Lasso and Elastic net are improved and handle factors better (they can either include or exclude all factor levels).
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2025-03-25 |
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r-regressionfactory
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The expander functions rely on the mathematics developed for the Hessian-definiteness invariance theorem for linear projection transformations of variables, described in authors' paper, to generate the full, high-dimensional gradient and Hessian from the lower-dimensional derivative objects. This greatly relieves the computational burden of generating the regression-function derivatives, which in turn can be fed into any optimization routine that utilizes such derivatives. The theorem guarantees that Hessian definiteness is preserved, meaning that reasoning about this property can be performed in the low-dimensional space of the base distribution. This is often a much easier task than its equivalent in the full, high-dimensional space. Definiteness of Hessian can be useful in selecting optimization/sampling algorithms such as Newton-Raphson optimization or its sampling equivalent, the Stochastic Newton Sampler. Finally, in addition to being a computational tool, the regression expansion framework is of conceptual value by offering new opportunities to generate novel regression problems.
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2025-03-25 |
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r-regress
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Functions to fit Gaussian linear model by maximising the residual log likelihood where the covariance structure can be written as a linear combination of known matrices. Can be used for multivariate models and random effects models. Easy straight forward manner to specify random effects models, including random interactions. Code now optimised to use Sherman Morrison Woodbury identities for matrix inversion in random effects models. We've added the ability to fit models using any kernel as well as a function to return the mean and covariance of random effects conditional on the data (BLUPs).
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2025-03-25 |
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r-regpro
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Tools are provided for (1) nonparametric regression (kernel, local linear), (2) semiparametric regression (single index, additive models), and (3) quantile regression (linear, kernel).
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2025-03-25 |
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r-regexselect
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'shiny' extension that adds regular expression filtering capabilities to the choice vector of the select list.
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2025-03-25 |
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r-regexpipes
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Provides wrappers around base::grep() where the first argument is standardized to take the data object. This makes it less of a pain to use regular expressions with 'magrittr' or other pipe operators.
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2025-03-25 |
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r-regent
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Produces population distribution of disease risk and statistical risk categories, and predicts risks for individuals with genotype information.
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2025-03-25 |
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r-regclust
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This package clusters regression coefficients using the methods of clustering through linear regression models (CLM) (Qin and Self 2006). Maximum likelihood approach is used to infer the parameters for each cluster. Bayesian information criterion (BIC) combined with Bootstrapped maximum volume (BMV) criterion are used to determine the number of clusters.
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2025-03-25 |
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r-refset
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Provides subsets with reference semantics, i.e. subsets which automatically reflect changes in the original object, and which optionally update the original object when they are changed.
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2025-03-25 |
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r-refnr
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A tool for refining data frame with formulas.
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2025-03-25 |
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r-refmanager
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Provides tools for importing and working with bibliographic references. It greatly enhances the 'bibentry' class by providing a class 'BibEntry' which stores 'BibTeX' and 'BibLaTeX' references, supports 'UTF-8' encoding, and can be easily searched by any field, by date ranges, and by various formats for name lists (author by last names, translator by full names, etc.). Entries can be updated, combined, sorted, printed in a number of styles, and exported. 'BibTeX' and 'BibLaTeX' '.bib' files can be read into 'R' and converted to 'BibEntry' objects. Interfaces to 'NCBI Entrez', 'CrossRef', and 'Zotero' are provided for importing references and references can be created from locally stored 'PDF' files using 'Poppler'. Includes functions for citing and generating a bibliography with hyperlinks for documents prepared with 'RMarkdown' or 'RHTML'.
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2025-03-25 |
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r-reffreeewas
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Reference-free method for conducting EWAS while deconvoluting DNA methylation arising as mixtures of cell types. The older method (Houseman et al., 2014,<doi:10.1093/bioinformatics/btu029>) is similar to surrogate variable analysis (SVA and ISVA), except that it makes additional use of a biological mixture assumption. The newer method (Houseman et al., 2016, <doi:10.1186/s12859-016-1140-4>) is similar to non-negative matrix factorization, with additional constraints and additional utilities.
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2025-03-25 |
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r-reemtree
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This package estimates regression trees with random effects as a way to use data mining techniques to describe longitudinal or panel data.
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2025-03-25 |
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r-redmonder
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Provide color schemes for maps (and other graphics) based on the color palettes of several Microsoft(r) products. Forked from 'RColorBrewer' v1.1-2.
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2025-03-25 |
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r-redas
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Provides functions used in the 'R: Einführung durch angewandte Statistik' (second edition).
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2025-03-25 |
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r-records
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Functions for generating k-record values and k-record times
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2025-03-25 |
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r-recorder
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A lightweight toolkit to validate new observations when computing their predictions with a predictive model. The validation process consists of two steps: (1) record relevant statistics and meta data of the variables in the original training data for the predictive model and (2) use these data to run a set of basic validation tests on the new set of observations.
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2025-03-25 |
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r-recombinator
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Turns nested lists into data.frames in an orderly manner.
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2025-03-25 |
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r-recoder
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Simple, easy to use, and flexible functionality for recoding variables. It allows for simple piecewise definition of transformations.
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2025-03-25 |
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r-recipa
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Pathways in a database could have many redundancies among them. This package allows the user to set a maximum value for the proportion of these redundancies.
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2025-03-25 |
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r-rechonest
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The 'Echo nest' <http://the.echonest.com> is the industry's leading music intelligence company, providing developer with deepest understanding of music content and music fans. This package can be used to access artist's data including songs, blogs, news, reviews etc. Song's data including audio summary, style, danceability, tempo etc can also be accessed.
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2025-03-25 |
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r-reca
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Relevant Component Analysis (RCA) tries to find a linear transformation of the feature space such that the effect of irrelevant variability is reduced in the transformed space.
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2025-03-25 |
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r-rebus.base
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Build regular expressions piece by piece using human readable code. This package contains core functionality, and is primarily intended to be used by package developers.
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2025-03-25 |
