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r-rocwogs
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public |
Function to estimate the ROC Curve of a continuous-scaled diagnostic test with the help of a second imperfect diagnostic test with binary responses.
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2025-03-25 |
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r-rocnit
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Non-inferiority test and diagnostic test are very important in clinical trails. This package is to get a p value from the non-inferiority test for ROC curves from diagnostic test.
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2025-03-25 |
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r-rocit
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Sensitivity (or recall or true positive rate), false positive rate, specificity, precision (or positive predictive value), negative predictive value, misclassification rate, accuracy, F-score- these are popular metrics for assessing performance of binary classifier for certain threshold. These metrics are calculated at certain threshold values. Receiver operating characteristic (ROC) curve is a common tool for assessing overall diagnostic ability of the binary classifier. Unlike depending on a certain threshold, area under ROC curve (also known as AUC), is a summary statistic about how well a binary classifier performs overall for the classification task. ROCit package provides flexibility to easily evaluate threshold-bound metrics. Also, ROC curve, along with AUC, can be obtained using different methods, such as empirical, binormal and non-parametric. ROCit encompasses a wide variety of methods for constructing confidence interval of ROC curve and AUC. ROCit also features the option of constructing empirical gains table, which is a handy tool for direct marketing. The package offers options for commonly used visualization, such as, ROC curve, KS plot, lift plot. Along with in-built default graphics setting, there are rooms for manual tweak by providing the necessary values as function arguments. ROCit is a powerful tool offering a range of things, yet it is very easy to use.
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2025-03-25 |
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r-roccv
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Cross validate large genetic data while specifying clinical variables that should always be in the model using the function cv(). An ROC plot from the cross validation data with AUC can be obtained using rocplot(), which also can be used to compare different models. Framework was built to handle genetic data, but works for any data.
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2025-03-25 |
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r-rocc
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Functions for a classification method based on receiver operating characteristics (ROC). Briefly, features are selected according to their ranked AUC value in the training set. The selected features are merged by the mean value to form a meta-gene. The samples are ranked by their meta-gene value and the meta-gene threshold that has the highest accuracy in splitting the training samples is determined. A new sample is classified by its meta-gene value relative to the threshold. In the first place, the package is aimed at two class problems in gene expression data, but might also apply to other problems.
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2025-03-25 |
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r-robustx
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Robustness -- 'eXperimental', 'eXtraneous', or 'eXtraordinary' Functionality for Robust Statistics. Hence methods which are not well established, often related to methods in package 'robustbase'. Amazingly, 'BACON()', originally by Billor, Hadi, and Velleman (2000) <doi:10.1016/S0167-9473(99)00101-2> has become established in places. The "barrow wheel" `rbwheel()` is from Stahel and Mächler (2009) <doi:10.1111/j.1467-9868.2009.00706.x>.
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2025-03-25 |
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r-robustrankaggreg
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Methods for aggregating ranked lists, especially lists of genes. It implements the Robust Rank Aggregation Kolde et al (2012) <doi:10.1093/bioinformatics/btr709> and some other simple algorithms for the task. RRA method uses a probabilistic model for aggregation that is robust to noise and also facilitates the calculation of significance probabilities for all the elements in the final ranking.
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2025-03-25 |
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r-robumeta
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Functions for conducting robust variance estimation (RVE) meta-regression using both large and small sample RVE estimators under various weighting schemes. These methods are distribution free and provide valid point estimates, standard errors and hypothesis tests even when the degree and structure of dependence between effect sizes is unknown. Also included are functions for conducting sensitivity analyses under correlated effects weighting and producing RVE-based forest plots.
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2025-03-25 |
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r-robrsvd
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This package provides the function to calculate SVD, regularized SVD, robust SVD and robust regularized SVD method. The robust SVD methods use alternating iteratively reweighted least squares methods. The regularized SVD uses generalized cross validation to choose the optimal smoothing parameters.
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2025-03-25 |
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r-robcor
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Robust pairwise correlations based on estimates of scale, particularly on "FastQn" one-step M-estimate.
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2025-03-25 |
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r-robastrda
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public |
Includes 'sysdata.rda' file for packages of the 'RobASt' - family of packages; is currently used by package 'RobExtremes' only.
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2025-03-25 |
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r-roauth
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public |
Provides an interface to the OAuth 1.0 specification allowing users to authenticate via OAuth to the server of their choice.
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2025-03-25 |
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r-rnumerai
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public |
Routines to interact with the Numerai Machine Learning Tournament API <https://numer.ai>. The functionality includes the ability to automatically download the current tournament data, submit predictions, and to get information for your user.
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2025-03-25 |
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r-rnr
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Apply sensitivity analysis for offline policy evaluation, as implemented in Jung et al. (2017) <arXiv:1702.04690> based on Rosenbaum and Rubin (1983) <http://www.jstor.org/stable/2345524>.
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2025-03-25 |
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r-rnpn
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public |
Programmatic interface to the Web Service methods provided by the National 'Phenology' Network (<https://usanpn.org/>), which includes data on various life history events that occur at specific times.
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2025-03-25 |
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r-rngforgpd
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Generation of univariate and multivariate data that follow the generalized Poisson distribution. The details of the univariate part are explained in Demirtas (2017) <doi: 10.1080/03610918.2014.968725>, and the multivariate part is an extension of the correlated Poisson data generation routine that was introduced in Yahav and Shmueli (2012) <doi: 10.1002/asmb.901>.
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2025-03-25 |
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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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2025-03-25 |
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r-rneos
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Within this package the XML-RPC API to NEOS <https://neos-server.org/neos/> is implemented. This enables the user to pass optimization problems to NEOS and retrieve results within R.
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2025-03-25 |
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r-rnentropy
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An implementation of a method based on information theory devised for the identification of genes showing a significant variation of expression across multiple conditions. Given expression estimates from any number of RNA-Seq samples and conditions it identifies genes or transcripts with a significant variation of expression across all the conditions studied, together with the samples in which they are over- or under-expressed. Zambelli et al. (2018) <doi:10.1093/nar/gky055>.
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2025-03-25 |
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r-rndtexexams
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Using as input a 'LaTeX' file with a multiple choice exam, this package will produce several versions with randomized contents of the same exam. Functions for grading are also available.
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2025-03-25 |
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r-rnd
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Extract the implied risk neutral density from options using various methods.
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2025-03-25 |
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r-rncbieutilslibs
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public |
Provides the libraries of the EUtils operations for the RNCBI package.
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2025-03-25 |
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r-rnbp
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public |
Use the <http://api.nbp.pl/> API through R. Retrieve currency exchange rates and gold prices data published by the National Bank of Poland in form of convenient R objects.
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2025-03-25 |
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r-rnavicell
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Provides a set of functions to access a data visualization web service. For more information and a tutorial on how to use it, see https://navicell.curie.fr/pages/nav_web_service.html and https://github.com/sysbio-curie/RNaviCell.
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2025-03-25 |
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r-rnavgraphimagedata
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Image data used as examples in the loon R package.
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2025-03-25 |
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r-rnaturalearthdata
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Vector map data from <http://www.naturalearthdata.com/>. Access functions are provided in the accompanying package 'rnaturalearth'.
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2025-03-25 |
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r-rnassqs
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Interface to access data via the United States Department of Agriculture's National Agricultural Statistical Service (NASS) 'Quick Stats' web API <https://quickstats.nass.usda.gov/api>. Convenience functions facilitate building queries based on available parameters and valid parameter values. This product uses the NASS API but is not endorsed or certified by NASS.
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2025-03-25 |
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r-rnaseqwrapper
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This package is designed to streamline several of the common steps for RNA-seq analysis, including differential expression and variant discovery. For the development build, or to contribute changes to this package, please see our repository at https://bitbucket.org/petersmp/rnaseqwrapper/
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2025-03-25 |
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r-rmtstat
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Functions for working with the Tracy-Widom laws and other distributions related to the eigenvalues of large Wishart matrices. The tables for computing the Tracy-Widom densities and distribution functions were computed by functions were computed by Momar Dieng's MATLAB package "RMLab". This package is part of a collaboration between Iain Johnstone, Zongming Ma, Patrick Perry, and Morteza Shahram.
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2025-03-25 |
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r-rmtl
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Efficient solvers for 10 regularized multi-task learning algorithms applicable for regression, classification, joint feature selection, task clustering, low-rank learning, sparse learning and network incorporation. Based on the accelerated gradient descent method, the algorithms feature a state-of-art computational complexity O(1/k^2). Sparse model structure is induced by the solving the proximal operator. The detail of the package is described in the paper of Han Cao and Emanuel Schwarz (2018) <doi:10.1093/bioinformatics/bty831>.
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2025-03-25 |
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r-rmthreshold
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An algorithm which can be used to determine an objective threshold for signal-noise separation in large random matrices (correlation matrices, mutual information matrices, network adjacency matrices) is provided. The package makes use of the results of Random Matrix Theory (RMT). The algorithm increments a suppositional threshold monotonically, thereby recording the eigenvalue spacing distribution of the matrix. According to RMT, that distribution undergoes a characteristic change when the threshold properly separates signal from noise. By using the algorithm, the modular structure of a matrix - or of the corresponding network - can be unraveled.
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2025-03-25 |
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r-rms.gof
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This package can be used to test any simple null hypothesis using the root-mean-square goodness of fit test. Monte Carlo estimation is used to calculate the associated P-value.
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2025-03-25 |
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r-rmsfact
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Display a randomly selected quote about Richard M. Stallman based on the collection in the 'GNU Octave' function 'fact()' which was aggregated by Jordi Gutiérrez Hermoso based on the (now defunct) site stallmanfacts.com (which is accessible only via <http://archive.org>).
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2025-03-25 |
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r-rmr
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Analysis of oxygen consumption data generated by Loligo (R) Systems respirometry equipment. The package includes a function for loading data output by Loligo's 'AutoResp' software (get.witrox.data()), functions for calculating metabolic rates over user-specified time intervals, extracting critical points from data using broken stick regressions based on Yeager and Ultsch (<DOI:10.1086/physzool.62.4.30157935>), and easy functions for converting between different units of barometric pressure.
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2025-03-25 |
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r-rmpw
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We implement causal mediation analysis using the methods proposed by Hong (2010) and Hong, Deutsch & Hill (2015) <doi:10.3102/1076998615583902>. It allows the estimation and hypothesis testing of causal mediation effects through ratio of mediator probability weights (RMPW). This strategy conveniently relaxes the assumption of no treatment-by-mediator interaction while greatly simplifying the outcome model specification without invoking strong distributional assumptions. We also implement a sensitivity analysis by extending the RMPW method to assess potential bias in the presence of omitted pretreatment or posttreatment covariates. The sensitivity analysis strategy was proposed by Hong, Qin, and Yang (2018) <doi:10.3102/1076998617749561>.
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2025-03-25 |
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r-rmosek
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This is a meta-package designed to support the installation of Rmosek (>= 6.0) and bring the optimization facilities of MOSEK (>= 6.0) to the R-language. The interface supports large-scale optimization of many kinds: Mixed-integer and continuous linear, second-order cone, exponential cone and power cone optimization, as well as continuous semidefinite optimization. Rmosek and the R-language are open-source projects. MOSEK is a proprietary product, but unrestricted trial and academic licenses are available.
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2025-03-25 |
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r-rmonad
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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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2025-03-25 |
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r-rmoajars
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External jars required for package RMOA. RMOA is a framework to build data stream models on top of MOA (Massive Online Analysis - <https://moa.cms.waikato.ac.nz/>). The jar files are put in this R package, the modelling logic can be found in the RMOA package.
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2025-03-25 |
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r-rmixpanel
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Provides an interface to many endpoints of Mixpanel's Data Export, Engage and JQL API. The R functions allow for event and profile data export as well as for segmentation, retention, funnel and addiction analysis. Results are always parsed into convenient R objects. Furthermore it is possible to load and update profiles.
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2025-03-25 |
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r-rmisc
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Contains many functions useful for data analysis and utility operations.
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2025-03-25 |
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r-rmio
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Provides header files of 'mio', a cross-platform C++11 header-only library for memory mapped file IO <https://github.com/mandreyel/mio>.
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2025-03-25 |
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r-rmeta
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Functions for simple fixed and random effects meta-analysis for two-sample comparisons and cumulative meta-analyses. Draws standard summary plots, funnel plots, and computes summaries and tests for association and heterogeneity.
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2025-03-25 |
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r-rmediation
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We provide functions to compute confidence intervals for a well-defined nonlinear function of the model parameters (e.g., product of k coefficients) in single--level and multilevel structural equation models. It also computes a chi-square test statistic for a function of indirect effects. 'Tofighi', D. and 'MacKinnon', D. P. (2011). 'RMediation' An R package for mediation analysis confidence intervals. Behavior Research Methods, 43, 692--700. <doi:10.3758/s13428-011-0076-x>. 'Tofighi', D. (2020). Bootstrap Model-Based Constrained Optimization Tests of Indirect Effects. Frontiers in Psychology, 10, 2989. <doi:10.3389/fpsyg.2019.02989>.
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2025-03-25 |
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r-rmea
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A suite of tools useful to read, visualize and export bivariate motion energy time-series. Lagged synchrony between subjects can be analyzed through windowed cross-correlation. Surrogate data generation allows an estimation of pseudosynchrony that helps to estimate the effect size of the observed synchronization. Kleinbub, J. R., & Ramseyer, F. T. (2020). rMEA: An R package to assess nonverbal synchronization in motion energy analysis time-series. Psychotherapy research, 1-14. <doi:10.1080/10503307.2020.1844334>.
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2025-03-25 |
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r-rmdshower
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'R' 'Markdown' format for 'shower' presentations, see <https://github.com/shower/shower>.
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2025-03-25 |
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r-rmdplugr
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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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2025-03-25 |
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r-rmdfiltr
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A collection of 'Lua' filters that extend the functionality of R Markdown templates (e.g., count words or post-process citations).
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2025-03-25 |
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r-rmcorr
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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. For more details, see the web documentation <https://lmarusich.github.io/rmcorr/index.html> and the original paper: Bakdash and Marusich (2017) <doi:10.3389/fpsyg.2017.00456>.
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2025-03-25 |
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r-rmawgen
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S3 and S4 functions are implemented for spatial multi-site stochastic generation of daily time series of temperature and precipitation. These tools make use of Vector AutoRegressive models (VARs). The weather generator model is then saved as an object and is calibrated by daily instrumental "Gaussianized" time series through the 'vars' package tools. Once obtained this model, it can it can be used for weather generations and be adapted to work with several climatic monthly time series.
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2025-03-25 |
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r-r.matlab
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Methods readMat() and writeMat() for reading and writing MAT files. For user with MATLAB v6 or newer installed (either locally or on a remote host), the package also provides methods for controlling MATLAB (trademark) via R and sending and retrieving data between R and MATLAB.
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2025-03-25 |
