|
r-rclone
|
public |
R version of 'GenClone' (a computer program to analyse genotypic data, test for clonality and describe spatial clonal organization, Arnaud-Haond & Belkhir 2007, <http://wwz.ifremer.fr/clonix/content/download/68205/903914/file/GenClone2.0.setup.zip>), this package allows clone handling as 'GenClone' does, plus the possibility to work with several populations, MultiLocus Lineages (MLL) custom definition and use, and p-value calculation for psex statistic (probability of originating from distinct sexual events) and psex_Fis statistic (taking account of Hardy-Weinberg equilibrium departure) as 'MLGsim'/'MLGsim2' (a program for detecting clones using a simulation approach, Stenberg et al. 2003).
|
2025-03-25 |
|
r-rclipboard
|
public |
Leverages the functionality of 'clipboard.js', a JavaScript library for HMTL5-based copy to clipboard from web pages (see <https://clipboardjs.com> for more information), and provides a reactive copy-to-clipboard UI button component, called 'rclipButton', for 'shiny' R applications.
|
2025-03-25 |
|
r-rclinicalcodes
|
public |
R tools for integrating with the www.clinicalcodes.org web repository
|
2025-03-25 |
|
r-rclean
|
public |
To create clearer, more concise code provides this toolbox helps coders to isolate the essential parts of a script that produces a chosen result, such as an object, tables and figures written to disk and even warnings and errors. This work was funded by US National Science Foundation grant SSI-1450277 for applications of End-to-End Data Provenance.
|
2025-03-25 |
|
r-rcites
|
public |
A programmatic interface to the Species+ <https://speciesplus.net/> database via the Species+/CITES Checklist API <https://api.speciesplus.net/>.
|
2025-03-25 |
|
r-rcircos
|
public |
A simple and flexible way to generate Circos 2D track plot images for genomic data visualization is implemented in this package. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation.
|
2025-03-25 |
|
r-rchoicedialogs
|
public |
Collection of portable choice dialog widgets
|
2025-03-25 |
|
r-rcheology
|
public |
Provides a dataset of functions in all base packages of R versions 1.0.1 onwards.
|
2025-03-25 |
|
r-rchallenge
|
public |
A simple data science challenge system using R Markdown and Dropbox <https://www.dropbox.com/>. It requires no network configuration, does not depend on external platforms like e.g. Kaggle <https://www.kaggle.com/> and can be easily installed on a personal computer.
|
2025-03-25 |
|
r-rcgmin
|
public |
Conjugate gradient minimization of nonlinear functions with box constraints incorporating the Dai/Yuan update. This implementation should be used in place of the "CG" algorithm of the optim() function.
|
2025-03-25 |
|
r-rcereal
|
public |
To facilitate using 'cereal' with Rcpp. 'cereal' is a header-only C++11 serialization library. 'cereal' takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. 'cereal' was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone. Please see <http://uscilab.github.io/cereal> for more information.
|
2025-03-25 |
|
r-rcelldata
|
public |
Example dataset for 'Rcell' package. Contains images and cell data object.
|
2025-03-25 |
|
r-rceim
|
public |
An implementation of a stochastic heuristic method for performing multidimensional function optimization. The method is inspired in the Cross-Entropy Method. It does not relies on derivatives, neither imposes particularly strong requirements into the function to be optimized. Additionally, it takes profit from multi-core processing to enable optimization of time-consuming functions.
|
2025-03-25 |
|
r-rcdklibs
|
public |
An R interface to the Chemistry Development Kit, a Java library for chemoinformatics. Given the size of the library itself, this package is not expected to change very frequently. To make use of the CDK within R, it is suggested that you use the 'rcdk' package. Note that it is possible to directly interact with the CDK using 'rJava'. However 'rcdk' exposes functionality in a more idiomatic way. The CDK library itself is released as LGPL and the sources can be obtained from <https://github.com/cdk/cdk>.
|
2025-03-25 |
|
r-rcc
|
public |
Functions to implement the parametric and non-parametric bootstrap confidence interval methods described in Morrison and Simon (2017) <arXiv:1702.06986>.
|
2025-03-25 |
|
r-rcbsubset
|
public |
Tools for optimal subset matching of treated units and control units in observational studies, with support for refined covariate balance constraints, (including fine and near-fine balance as special cases). A close relative is the 'rcbalance' package.
|
2025-03-25 |
|
r-rcbalance
|
public |
Tools for large, sparse optimal matching of treated units and control units in observational studies. Provisions are made for refined covariate balance constraints, which include fine and near-fine balance as special cases. Matches are optimal in the sense that they are computed as solutions to network optimization problems rather than greedy algorithms.
|
2025-03-25 |
|
r-rcarto
|
public |
This package makes some maps using shapefiles and dataframes. Five kinds of maps are available : proportionnal circles, proportionnal circles colored by a discretized quantitative variable, proportionnal circles colored by the modalities of a qualitative variable, choropleth and typology.
|
2025-03-25 |
|
r-rcarbon
|
public |
Enables the calibration and analysis of radiocarbon dates, often but not exclusively for the purposes of archaeological research. It includes functions not only for basic calibration, uncalibration, and plotting of one or more dates, but also a statistical framework for building demographic and related longitudinal inferences from aggregate radiocarbon date lists, including: Monte-Carlo simulation test (Timpson et al 2014 <doi:10.1016/j.jas.2014.08.011>), random mark permutation test (Crema et al 2016 <doi:10.1371/journal.pone.0154809>) and spatial permutation tests (Crema, Bevan, and Shennan 2017 <doi:10.1016/j.jas.2017.09.007>).
|
2025-03-25 |
|
r-rcapture
|
public |
Estimation of abundance and other of demographic parameters for closed populations, open populations and the robust design in capture-recapture experiments using loglinear models.
|
2025-03-25 |
|
r-rcane
|
public |
There are different numeric optimizations which are used in order to estimate coefficients in models such as linear regression and neural networks. This package covers parameter estimation in linear regression using different methods such as batch gradient descent, stochastic gradient descent, minibatch gradient descent and coordinate descent. Kiwiel, Krzysztof C (2001) <doi:10.1007/PL00011414> Yu Nesterov (2004) <ISBN:1-4020-7553-7> Ferguson, Thomas S (1982) <doi:10.1080/01621459.1982.10477894> Zeiler, Matthew D (2012) <arXiv:1212.5701> Wright, Stephen J (2015) <arXiv:1502.04759>.
|
2025-03-25 |
|
r-r.cache
|
public |
Memoization can be used to speed up repetitive and computational expensive function calls. The first time a function that implements memoization is called the results are stored in a cache memory. The next time the function is called with the same set of parameters, the results are momentarily retrieved from the cache avoiding repeating the calculations. With this package, any R object can be cached in a key-value storage where the key can be an arbitrary set of R objects. The cache memory is persistent (on the file system).
|
2025-03-25 |
|
r-rca
|
public |
Relational Class Analysis (RCA) is a method for detecting heterogeneity in attitudinal data (as described in Goldberg A., 2011, Am. J. Soc, 116(5)).
|
2025-03-25 |
|
r-rbtt
|
public |
Tu & Zhou (1999) <doi:10.1002/(SICI)1097-0258(19991030)18:20%3C2749::AID-SIM195%3E3.0.CO;2-C> showed that comparing the means of populations whose data-generating distributions are non-negative with excess zero observations is a problem of great importance in the analysis of medical cost data. In the same study, Tu & Zhou discuss that it can be difficult to control type-I error rates of general-purpose statistical tests for comparing the means of these particular data sets. This package allows users to perform a modified bootstrap-based t-test that aims to better control type-I error rates in these situations.
|
2025-03-25 |
|
r-rbtc
|
public |
Implementation of the RPC-JSON API for Bitcoin and utility functions for address creation and content analysis of the blockchain.
|
2025-03-25 |
|
r-rbmn
|
public |
Creation, manipulation, simulation of linear Gaussian Bayesian networks from text files and more...
|
2025-03-25 |
|
r-r.blip
|
public |
Allows the user to learn Bayesian networks from datasets containing thousands of variables. It focuses on score-based learning, mainly the 'BIC' and the 'BDeu' score functions. It provides state-of-the-art algorithms for the following tasks: (1) parent set identification - Mauro Scanagatta (2015) <http://papers.nips.cc/paper/5803-learning-bayesian-networks-with-thousands-of-variables>; (2) general structure optimization - Mauro Scanagatta (2018) <doi:10.1007/s10994-018-5701-9>, Mauro Scanagatta (2018) <http://proceedings.mlr.press/v73/scanagatta17a.html>; (3) bounded treewidth structure optimization - Mauro Scanagatta (2016) <http://papers.nips.cc/paper/6232-learning-treewidth-bounded-bayesian-networks-with-thousands-of-variables>; (4) structure learning on incomplete data sets - Mauro Scanagatta (2018) <doi:10.1016/j.ijar.2018.02.004>. Distributed under the LGPL-3 by IDSIA.
|
2025-03-25 |
|
r-rbldatalicense
|
public |
R interface to access prices and market data with the 'Bloomberg Data License' service from <https://www.bloomberg.com/professional/product/data-license/>. As a prerequisite, a valid Data License from 'Bloomberg' is needed together with the corresponding SFTP credentials and whitelisting of the IP from which accessing the service. This software and its author are in no way affiliated, endorsed, or approved by 'Bloomberg' or any of its affiliates. 'Bloomberg' is a registered trademark.
|
2025-03-25 |
|
r-rbitcoinchartsapi
|
public |
An R package for the BitCoinCharts.com API.
|
2025-03-25 |
|
r-rbitcoin
|
public |
Utilities related to Bitcoin. Unified markets API interface (bitstamp, kraken, btce, bitmarket). Both public and private API calls. Integration of data structures for all markets. Support SSL. Read Rbitcoin documentation (command: ?btc) for more information.
|
2025-03-25 |
|
r-rbit
|
public |
A simple implementation of Binary Indexed Tree by R. The BinaryIndexedTree class supports construction of Binary Indexed Tree from a vector, update of a value in the vector and query for the sum of a interval of the vector.
|
2025-03-25 |
|
r-rbiouml
|
public |
Functions for connecting to BioUML server, querying BioUML repository and launching BioUML analyses.
|
2025-03-25 |
|
r-rbenchmark
|
public |
rbenchmark is inspired by the Perl module Benchmark, and is intended to facilitate benchmarking of arbitrary R code. The library consists of just one function, benchmark, which is a simple wrapper around system.time. Given a specification of the benchmarking process (counts of replications, evaluation environment) and an arbitrary number of expressions, benchmark evaluates each of the expressions in the specified environment, replicating the evaluation as many times as specified, and returning the results conveniently wrapped into a data frame.
|
2025-03-25 |
|
r-raw
|
public |
In order to facilitate R instruction for actuaries, we have organized several sets of publicly available data of interest to non-life actuaries. In addition, we suggest a set of packages, which most practicing actuaries will use routinely. Finally, there is an R markdown skeleton for basic reserve analysis.
|
2025-03-25 |
|
r-rattle.data
|
public |
Contains the datasets used as default examples by the rattle package. The datasets themselves can be used independently of the rattle package to illustrate analytics, data mining, and data science tasks.
|
2025-03-25 |
|
r-ratios
|
public |
Calculation of ratios between two data sets containing environmental data like element concentrations by different methods. Additionally plant element concentrations can be corrected for adhering particles (soil, airborne dust).
|
2025-03-25 |
|
r-ratesci
|
public |
Computes confidence intervals for the rate (or risk) difference ('RD') or rate ratio (or relative risk, 'RR') for binomial proportions or Poisson rates, or for odds ratio ('OR', binomial only). Also confidence intervals for a single binomial or Poisson rate, and intervals for matched pairs. Includes skewness-corrected asymptotic score ('SCAS') methods, which have been developed in Laud (2017) <doi:10.1002/pst.1813> from Miettinen & Nurminen (1985) <doi:10.1002/sim.4780040211> and Gart & Nam (1988) <doi:10.2307/2531848>. Also includes MOVER methods (Method Of Variance Estimates Recovery) for all contrasts, derived from the Newcombe method but using equal-tailed Jeffreys intervals, and generalised for Bayesian applications incorporating prior information. So-called 'exact' methods for strictly conservative coverage are approximated using continuity corrections. Also includes methods for stratified calculations (e.g. meta-analysis), either assuming fixed effects or incorporating stratum heterogeneity.
|
2025-03-25 |
|
r-raters
|
public |
The kappa statistic implemented by Fleiss is a very popular index for assessing the reliability of agreement among multiple observers. It is used both in the psychological and in the psychiatric field. Other fields of application are typically medicine, biology and engineering. Unfortunately,the kappa statistic may behave inconsistently in case of strong agreement between raters, since this index assumes lower values than it would have been expected. We propose a modification kappa implemented by Fleiss in case of nominal and ordinal variables. Monte Carlo simulations are used both to testing statistical hypotheses and to calculating percentile bootstrap confidence intervals based on proposed statistic in case of nominal and ordinal data.
|
2025-03-25 |
|
r-rateratio.test
|
public |
A function which performs exact rate ratio tests and returns an object of class htest.
|
2025-03-25 |
|
r-ratelimitr
|
public |
Allows to limit the rate at which one or more functions can be called.
|
2025-03-25 |
|
r-ratedistortion
|
public |
An implementation of routines for solving rate-distortion problems. Rate-distortion theory is a field within information theory that examines optimal lossy compression. That is, given that some information must be lost, how can a communication channel be designed that minimizes the cost of communication error? Rate-distortion theory is concerned with the optimal (minimal cost) solution to such tradeoffs. An important tool for solving rate-distortion problems is the Blahut algorithm, developed by Richard Blahut and described in: . Blahut, R. E. (1972). Computation of channel capacity and rate-distortion functions. IEEE Transactions on Information Theory, IT-18(4), 460-473. . This package implements the basic Blahut algorithm, and additionally contains a number of `helper' functions, including a routine for searching for an information channel that minimizes cost subject to a constraint on information rate.
|
2025-03-25 |
|
r-rastervis
|
public |
Methods for enhanced visualization and interaction with raster data. It implements visualization methods for quantitative data and categorical data, both for univariate and multivariate rasters. It also provides methods to display spatiotemporal rasters, and vector fields. See the website for examples.
|
2025-03-25 |
|
r-rasterlist
|
public |
A S4 class has been created such that complex operations can be executed on each cells of a raster map. The raster of objects contains the traditional raster map with the addition of a list of generic objects: one object for each raster cells. It allows to write few lines of R code for complex map algebra. Two environmental applications about frequency analysis of raster map of precipitation and creation of a raster map of soil water retention curves have been presented.
|
2025-03-25 |
|
r-rasterize
|
public |
Provides R functions to selectively rasterize components of 'grid' output.
|
2025-03-25 |
|
r-rasciidoc
|
public |
Inspired by Karl Broman`s reader on using 'knitr' with 'asciidoc' (<http://kbroman.org/knitr_knutshell/pages/asciidoc.html>), this is merely a wrapper to 'knitr' and 'asciidoc'.
|
2025-03-25 |
|
r-rarity
|
public |
Allows calculation of rarity weights for species and indices of rarity for assemblages of species according to different methods (Leroy et al. 2012, Insect. Conserv. Divers. 5:159-168 <doi:10.1111/j.1752-4598.2011.00148.x>; Leroy et al. 2013, Divers. Distrib. 19:794-803 <doi:10.1111/ddi.12040>).
|
2025-03-25 |
|
r-raptor
|
public |
Performs wood cell anatomical data analyses on spatially explicit xylem (tracheids) datasets derived from thin sections of woody tissue. The package includes functions for visualisation, detection and alignment of continuous tracheid radial file (defined as rows) and individual tracheid position within an annual ring of coniferous species. This package is designed to be used with elaborate cell output, e.g. as provided with ROXAS (von Arx & Carrer, 2014 <doi:10.1016/j.dendro.2013.12.001>). The package has been validated for Picea abies, Larix Siberica, Pinus cembra and Pinus sylvestris.
|
2025-03-25 |
|
r-rapidxmlr
|
public |
Provides XML parsing capability through the 'Rapidxml' 'C++' header-only library.
|
2025-03-25 |
|
r-rapidjsonr
|
public |
Provides JSON parsing capability through the 'Rapidjson' 'C++' header-only library.
|
2025-03-25 |
|
r-rapiclient
|
public |
Access services specified in OpenAPI (formerly Swagger) format. It is not a code generator. Client is generated dynamically as a list of R functions.
|
2025-03-25 |
