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r-plsdepot
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public |
plsdepot contains different methods for PLS analysis of one or two data tables such as Tucker's Inter-Battery, NIPALS, SIMPLS, SIMPLS-CA, PLS Regression, and PLS Canonical Analysis. The main reference for this software is the awesome book (in French) 'La Regression PLS: Theorie et Pratique' by Michel Tenenhaus.
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2023-06-16 |
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r-rtorch
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'R' implementation and interface of the Machine Learning platform 'PyTorch' <https://pytorch.org/> developed in 'Python'. It requires a 'conda' environment with 'torch' and 'torchvision' to provide 'PyTorch' functions, methods and classes. The key object in 'PyTorch' is the tensor which is in essence a multidimensional array. These tensors are fairly flexible to perform calculations in CPUs as well as 'GPUs' to accelerate the process.
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2023-06-16 |
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r-rsubgroup
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A collection of efficient and effective tools and algorithms for subgroup discovery and analytics. The package integrates an R interface to the org.vikamine.kernel library of the VIKAMINE system (http://www.vikamine.org) implementing subgroup discovery, pattern mining and analytics in Java.
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2023-06-16 |
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r-rsm
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Provides functions to generate response-surface designs, fit first- and second-order response-surface models, make surface plots, obtain the path of steepest ascent, and do canonical analysis. A good reference on these methods is Chapter 10 of Wu, C-F J and Hamada, M (2009) "Experiments: Planning, Analysis, and Parameter Design Optimization" ISBN 978-0-471-69946-0.
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2023-06-16 |
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r-rslp
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Implements the "Stemming Algorithm for the Portuguese Language" <DOI:10.1109/SPIRE.2001.10024>.
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2023-06-16 |
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r-rsarules
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Implements the Gibbs sampling algorithm to randomly sample association rules with one pre-chosen item as the consequent from a transaction dataset. The Gibbs sampling algorithm was proposed in G. Qian, C.R. Rao, X. Sun and Y. Wu (2016) <DOI:10.1073/pnas.1604553113>.
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2023-06-16 |
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r-rolldown
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public |
R Markdown output formats based on JavaScript libraries such as 'Scrollama' (<https://github.com/russellgoldenberg/scrollama>) for storytelling.
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2023-06-16 |
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r-rode
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public |
Show physics, math and engineering students how an ODE solver is made and how effective R classes can be for the construction of the equations that describe natural phenomena. Inspiration for this work comes from the book on "Computer Simulations in Physics" by Harvey Gould, Jan Tobochnik, and Wolfgang Christian. Book link: <http://www.compadre.org/osp/items/detail.cfm?ID=7375>.
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2023-06-16 |
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r-rnetlogo
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Interface to use and access Wilensky's 'NetLogo' (Wilensky 1999) from R using either headless (no GUI) or interactive GUI mode. Provides functions to load models, execute commands, and get values from reporters. Mostly analogous to the 'NetLogo' 'Mathematica' Link <https://github.com/NetLogo/Mathematica-Link>.
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2023-06-16 |
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r-rmonad
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public |
A monadic solution to pipeline analysis. All operations -- and the errors, warnings and messages they emit -- are merged into a directed graph. Infix binary operators mediate when values are stored, how exceptions are handled, and where pipelines branch and merge. The resulting structure may be queried for debugging or report generation. 'rmonad' complements, rather than competes with, non-monadic pipeline packages like 'magrittr' or 'pipeR'. This work is funded by the NSF (award number 1546858).
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2023-06-16 |
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r-rmdplugr
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public |
Formats for R Markdown that undo modifications by 'pandoc' and 'rmarkdown' to original 'latex' templates, such as smaller margins, paragraph spacing, and compact titles. In addition, enhancements such as author blocks with affiliations and headers and footers are introduced. All of this functionality is built around plugins that modify the default 'pandoc' template without relying on custom templates.
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2023-06-16 |
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r-rmcorr
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public |
Compute the repeated measures correlation, a statistical technique for determining the overall within-individual relationship among paired measures assessed on two or more occasions, first introduced by Bland and Altman (1995). Includes functions for diagnostics, p-value, effect size with confidence interval including optional bootstrapping, as well as graphing. Also includes several example datasets.
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2023-06-16 |
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r-rjazz
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public |
This is the official 'Jazz' client. 'Jazz' is a lightweight modular data processing framework, including a web server. It provides data persistence and computation capabilities accessible from 'R' and 'Python' and also through a REST API. <https://github.com/bbvadata/Jazz> See ?rjazz::rjazz to get a 'Jazz' server.
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2023-06-16 |
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r-rivervis
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public |
This R package is a flexible and efficient tool to visualise both quantitative and qualitative data from river surveys. It can be used to produce diagrams with the topological structure of the river network.
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2023-06-16 |
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r-rhor
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Rho is used to test the generalization of inter rater reliability (IRR) statistics. Calculating rho starts by generating a large number of simulated, fully-coded data sets: a sizable collection of hypothetical populations, all of which have a kappa value below a given threshold -- which indicates unacceptable agreement. Then kappa is calculated on a sample from each of those sets in the collection to see if it is equal to or higher than the kappa in then real sample. If less than five percent of the distribution of samples from the simulated data sets is greater than actual observed kappa, the null hypothesis is rejected and one can conclude that if the two raters had coded the rest of the data, we would have acceptable agreement (kappa above the threshold).
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2023-06-16 |
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r-rh2
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DBI/RJDBC interface to h2 database. h2 version 1.3.175 is included.
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2023-06-16 |
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r-rgooddata
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public |
Export raw reports from 'GoodData' business intelligence platform (see <http://www.gooddata.com> for more information).
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2023-06-16 |
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r-rfutilities
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public |
Utilities for Random Forest model selection, class balance correction, significance test, cross validation and partial dependency plots.
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2023-06-16 |
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r-reweight
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public |
Adjusts the weights of survey respondents so that the marginal distributions of certain variables fit more closely to those from a more precise source (e.g. Census Bureau's data).
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2023-06-16 |
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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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2023-06-16 |
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r-redmonder
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public |
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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2023-06-16 |
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r-readmzxmldata
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public |
Functions for reading mass spectrometry data in mzXML format.
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2023-06-16 |
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r-rdota2
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public |
An R API Client for Valve's Dota2. RDota2 can be easily used to connect to the Steam API and retrieve data for Valve's popular video game Dota2. You can find out more about Dota2 at <http://store.steampowered.com/app/570/>.
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2023-06-16 |
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r-rcrypt
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public |
Provides easy symmetric file encryption using GPG with cryptographically strong defaults. Only symmetric encryption is supported. GPG is pre-installed with most Linux distributions. Windows users will need to install 'Gpg4win' (http://www.gpg4win.org/). OS X users will need to install 'GPGTools' (https://gpgtools.org/).
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2023-06-16 |
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r-rcppthread
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Provides a C++11-style thread class and thread pool that can safely be interrupted from R; see, Nagler (2018) <arXiv:1811.00450>.
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2023-06-16 |
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r-rclinicalcodes
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public |
R tools for integrating with the www.clinicalcodes.org web repository
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2023-06-16 |
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r-rcites
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public |
A programmatic interface to the Species+ <https://speciesplus.net/> database via the Species+/CITES Checklist API <https://api.speciesplus.net/>.
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2023-06-16 |
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r-rceim
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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.
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2023-06-16 |
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r-rbtt
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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.
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2023-06-16 |
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r-rbmn
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public |
Creation, manipulation, simulation of linear Gaussian Bayesian networks from text files and more...
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2023-06-16 |
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r-rankhazard
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public |
Rank-hazard plots Karvanen and Harrell (2009) <DOI:10.1002/sim.3591> visualize the relative importance of covariates in a proportional hazards model. The key idea is to rank the covariate values and plot the relative hazard as a function of ranks scaled to interval [0,1]. The relative hazard is plotted in respect to the reference hazard, which can bee.g. the hazard related to the median of the covariate.
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2023-06-16 |
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r-randcorr
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Implements the algorithm by Pourahmadi and Wang (2015) <doi:10.1016/j.spl.2015.06.015> for generating a random p x p correlation matrix. Briefly, the idea is to represent the correlation matrix using Cholesky factorization and p(p-1)/2 hyperspherical coordinates (i.e., angles), sample the angles from a particular distribution and then convert to the standard correlation matrix form. The angles are sampled from a distribution with pdf proportional to sin^k(theta) (0 < theta < pi, k >= 1) using the efficient sampling algorithm described in Enes Makalic and Daniel F. Schmidt (2018) <arXiv:1809.05212>.
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2023-06-16 |
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r-r62s3
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public |
After defining an R6 class, R62S3 is used to automatically generate optional S3/S4 generics and methods for dispatch. Also allows piping for R6 objects.
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2023-06-16 |
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r-r0
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public |
Estimation of reproduction numbers for disease outbreak, based on incidence data. The R0 package implements several documented methods. It is therefore possible to compare estimations according to the methods used. Depending on the methods requested by user, basic reproduction number (commonly denoted as R0) or real-time reproduction number (referred to as R(t)) is computed, along with a 95% Confidence Interval. Plotting outputs will give different graphs depending on the methods requested : basic reproductive number estimations will only show the epidemic curve (collected data) and an adjusted model, whereas real-time methods will also show the R(t) variations throughout the outbreak time period. Sensitivity analysis tools are also provided, and allow for investigating effects of varying Generation Time distribution or time window on estimates.
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2023-06-16 |
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r-quietr
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public |
Simplifies output suppression logic in R packages, as it's common to develop some form of it in R. 'quietR' intends to simplify that problem and allow a set of simple toggle functions to be used to suppress console output.
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2023-06-16 |
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r-quantilenpci
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Based on Alan D. Hutson (1999) <doi:10.1080/02664769922458>, "Calculating nonparametric confidence intervals for quantiles using fractional order statistics", Journal of Applied Statistics, 26:3, 343-353.
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2023-06-16 |
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r-quadprogxt
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Extends the quadprog package to solve quadratic programs with absolute value constraints and absolute values in the objective function.
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2023-06-16 |
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r-qrsvm
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public |
Quantile Regression (QR) using Support Vector Machines under the Pinball-Loss. Estimation is based on "Nonparametric Quantile Regression" by I. Takeuchi, Q.V.Le , T. Sears, A.J.Smola (2004). Implementation relies on 'quadprog' package, package 'kernlab' Kernelfunctions and package 'Matrix' nearPD to find next Positive definite Kernelmatrix. Package estimates quantiles individually but an Implementation of non crossing constraints coming soon. Function multqrsvm() now supports parallel backend for faster fitting.
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2023-06-16 |
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r-qqman
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public |
Create Q-Q and manhattan plots for GWAS data from PLINK results.
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2023-06-16 |
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r-pymturkr
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public |
Provides access to the latest 'Amazon Mechanical Turk' ('MTurk') <https://www.mturk.com> Requester API (version '2017–01–17'), replacing the now deprecated 'MTurkR' package.
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2023-06-16 |
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r-pwrab
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Power analysis for AB testing. The calculations are based on the Welch's unequal variances t-test, which is generally preferred over the Student's t-test when sample sizes and variances of the two groups are unequal, which is frequently the case in AB testing. In such situations, the Student's t-test will give biased results due to using the pooled standard deviation, unlike the Welch's t-test.
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2023-06-16 |
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r-pulsar
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Model selection for penalized graphical models using the Stability Approach to Regularization Selection ('StARS'), with options for speed-ups including Bounded StARS (B-StARS), batch computing, and other stability metrics (e.g., graphlet stability G-StARS). Christian L. Müller, Richard Bonneau, Zachary Kurtz (2016) <arXiv:1605.07072>.
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2023-06-16 |
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r-psy
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public |
Kappa, ICC, Cronbach alpha, screeplot, mtmm
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2023-06-16 |
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r-pseval
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Contains the core methods for the evaluation of principal surrogates in a single clinical trial. Provides a flexible interface for defining models for the risk given treatment and the surrogate, the models for integration over the missing counterfactual surrogate responses, and the estimation methods. Estimated maximum likelihood and pseudo-score can be used for estimation, and the bootstrap for inference. A variety of post-estimation summary methods are provided, including print, summary, plot, and testing.
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2023-06-16 |
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r-proscorertools
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Provides a reliable and flexible toolbox to score patient-reported outcome (PRO), Quality of Life (QOL), and other psychometric measures. The guiding philosophy is that scoring errors can be eliminated by using a limited number of well-tested, well-behaved functions to score PRO-like measures. The workhorse of the package is the 'scoreScale' function, which can be used to score most single-scale measures. It can reverse code items that need to be reversed before scoring and pro-rate scores for missing item data. Currently, three different types of scores can be output: summed item scores, mean item scores, and scores scaled to range from 0 to 100. The 'PROscorerTools' functions can be used to write new functions that score more complex measures. In fact, 'PROscorerTools' functions are the building blocks of the scoring functions in the 'PROscorer' package (which is a repository of functions that score specific commonly-used instruments). Users are encouraged to use 'PROscorerTools' to write scoring functions for their favorite PRO-like instruments, and to submit these functions for inclusion in 'PROscorer' (a tutorial vignette will be added soon). The long-term vision for the 'PROscorerTools' and 'PROscorer' packages is to provide an easy-to-use system to facilitate the incorporation of PRO measures into research studies in a scientifically rigorous and reproducible manner. These packages and their vignettes are intended to help establish and promote "best practices" for scoring and describing PRO-like measures in research.
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2023-06-16 |
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r-prettymapr
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Automates the process of creating a scale bar and north arrow in any package that uses base graphics to plot in R. Bounding box tools help find and manipulate extents. Finally, there is a function to automate the process of setting margins, plotting the map, scale bar, and north arrow, and resetting graphic parameters upon completion.
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2023-06-16 |
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r-practools
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Functions and datasets to support Valliant, Dever, and Kreuter, ``Practical Tools for Designing and Weighting Survey Samples'' (2nd edition, 2018). Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example data sets are included.
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2023-06-16 |
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r-powerpkg
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(1) To estimate the power of testing for linkage using an affected sib pair design, as a function of the recurrence risk ratios. We will use analytical power formulae as implemented in R. These are based on a Mathematica notebook created by Martin Farrall. (2) To examine how the power of the transmission disequilibrium test (TDT) depends on the disease allele frequency, the marker allele frequency, the strength of the linkage disequilibrium, and the magnitude of the genetic effect. We will use an R program that implements the power formulae of Abel and Muller-Myhsok (1998). These formulae allow one to quickly compute power of the TDT approach under a variety of different conditions. This R program was modeled on Martin Farrall's Mathematica notebook.
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2023-06-16 |
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r-powercomprisk
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A power analysis tool for jointly testing the cause-1 cause-specific hazard and the any-cause hazard with competing risks data.
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2023-06-16 |
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r-pointdensityp
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The function pointdensity returns a density count and the temporal average for every point in the original list. The dataframe returned includes four columns: lat, lon, count, and date_avg. The "lat" column is the original latitude data; the "lon" column is the original longitude data; the "count" is the density count of the number of points within a radius of radius*grid_size (the neighborhood); and the date_avg column includes the average date of each point in the neighborhood.
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2023-06-16 |
