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r-glmgraph
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We propose to use sparse regression model to achieve variable selection while accounting for graph-constraints among coefficients. Different linear combination of a sparsity penalty(L1) and a smoothness(MCP) penalty has been used, which induces both sparsity of the solution and certain smoothness on the linear coefficients.
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2023-06-16 |
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r-spacejam
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This package provides an extension of conditional independence (CIG) and directed acyclic graph (DAG) estimation to the case where conditional relationships are (non-linear) additive models.
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2023-06-16 |
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r-softrandomforest
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Performs random forests for soft decision trees for a classification problem. Current limitations are for a maximum depth of 5 resulting in 16 terminal nodes. Some data cleaning is required before input. Final graphic output requires currently requires exporting to 'Microsoft Excel' for visualization. Method based on Irsoy, Yildiz and Alpaydin (2012, ISBN: 978-4-9906441-1-6).
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2023-06-16 |
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r-sdat
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Test the global null in linear models using marginal approach.
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2023-06-16 |
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r-smds
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Symbolic multidimensional scaling for interval-valued dissimilarities. The hypersphere model and the hyperbox model are available.
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2023-06-16 |
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r-sdnet
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Fitting discrete Bayesian networks using soft-discretized data. Soft-discretization is based on mixture of normal distributions. Also implemented is a supervised Bayesian network learning employing Kullback-Leibler divergence. For more information see Balov (2013) <DOI:10.1186/1755-8794-6-S3-S1>.
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2023-06-16 |
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r-sdde
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Compares the evolution of an original network X to an augmented network Y by counting the number of Shortcuts, Detours, Dead Ends (SDDE), equal paths and disconnected nodes.
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2023-06-16 |
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r-fts
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Fast operations for time series objects.
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2023-06-16 |
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r-soobench
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Collection of different single objective test functions useful for benchmarks and algorithm development.
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2023-06-16 |
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r-snnr
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Solve the problem of over-parameterization in neural networks for genomic selection. Daniel Gianola, Hayrettin OkutEmail, Kent A Weigel and Guilherme JM Rosa (2011) <doi:10.1186/1471-2156-12-87>.
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2023-06-16 |
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r-snappier
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Compression and decompression with 'Snappy'.
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2023-06-16 |
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r-snakecharmr
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Run 'Python' code, make function calls, assign and retrieve variables, etc. from R. A fork from 'rPython' which uses 'jsonlite', 'Rcpp' and has several fixes and improvements.
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2023-06-16 |
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r-securitytxt
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When security risks in web services are discovered by independent security researchers who understand the severity of the risk, they often lack the channels to properly disclose them. As a result, security issues may be left unreported. The 'security.txt' 'Web Security Policies' specification defines an 'IETF' draft standard <https://tools.ietf.org/html/draft-foudil-securitytxt-00> to help organizations define the process for security researchers to securely disclose security vulnerabilities. Tools are provided to help identify and parse 'security.txt' files to enable analysis of the usage and adoption of these policies.
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2023-06-16 |
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r-geocount
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This package provides a variety of functions to analyze and model geostatistical count data with generalized linear spatial models, including 1) simulate and visualize the data; 2) posterior sampling with robust MCMC algorithms (in serial or parallel way); 3) perform prediction for unsampled locations; 4) conduct Bayesian model checking procedure to evaluate the goodness of fitting; 5) conduct transformed residual checking procedure. In the package, seamlessly embedded C++ programs and parallel computing techniques are implemented to speed up the computing processes.
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2023-06-16 |
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r-smoothhazard
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Estimation of two-state (survival) models and irreversible illness- death models with possibly interval-censored,left-truncated and right-censored data. Proportional intensities regression models can be specified to allow for covariates effects separately for each transition. We use either a parametric approach with Weibull baseline intensities or a semi-parametric approach with M-splines approximation of baseline intensities in order to obtain smooth estimates of the hazard functions. Parameter estimates are obtained by maximum likelihood in the parametric approach and by penalized maximum likelihood in the semi-parametric approach.
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2023-06-16 |
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r-rdtq
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Implementation of density tracking by quadrature (DTQ) algorithms for stochastic differential equations (SDEs). DTQ algorithms numerically compute the density function of the solution of an SDE with user-specified drift and diffusion functions. The calculation does not require generation of sample paths, but instead proceeds in a deterministic fashion by repeatedly applying quadrature to the Chapman-Kolmogorov equation associated with a discrete-time approximation of the SDE. The DTQ algorithm is provably convergent. For several practical problems of interest, we have found the DTQ algorithm to be fast, accurate, and easy to use.
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2023-06-16 |
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r-geoops
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Tools for doing calculations and manipulations on 'GeoJSON', a 'geospatial' data interchange format (<https://tools.ietf.org/html/rfc7946>). 'GeoJSON' is also valid 'JSON'.
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2023-06-16 |
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r-galgo
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Build multivariate predictive models from large datasets having far larger number of features than samples such as in functional genomics datasets. Trevino and Falciani (2006) <doi:10.1093/bioinformatics/btl074>.
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2023-06-16 |
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r-smoothsurv
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Contains, as a main contribution, a function to fit a regression model with possibly right, left or interval censored observations and with the error distribution expressed as a mixture of G-splines. Core part of the computation is done in compiled C++ written using the Scythe Statistical Library Version 0.3.
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2023-06-16 |
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r-rcppdl
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This package is based on the C++ code from Yusuke Sugomori, which implements basic machine learning methods with many layers (deep learning), including dA (Denoising Autoencoder), SdA (Stacked Denoising Autoencoder), RBM (Restricted Boltzmann machine) and DBN (Deep Belief Nets).
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2023-06-16 |
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r-rcassandra
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This packages provides a direct interface (without the use of Java) to the most basic functionality of Apache Cassanda such as login, updates and queries.
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2023-06-16 |
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r-gamboost
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This package provides routines for fitting generalized linear and and generalized additive models by likelihood based boosting, using penalized B-splines
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2023-06-16 |
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r-freeknotsplines
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Algorithms for fitting free-knot splines for data with one independent variable and one dependent variable. Four free-knot spline algorithms are provided for the case where the number of knots is known in advance. A knot-search algorithm is provided for the case where the number of knots is not known in advance. In addition, methods are available to compute the fitted values, the residuals, and the coefficients of the splines, and to plot the results, along with a method to summarize the results.
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2023-06-16 |
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r-rcppfaddeeva
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Access to a family of Gauss error functions for arbitrary complex arguments is provided via the 'Faddeeva' package by Steven G. Johnson (see <http://ab-initio.mit.edu/wiki/index.php/Faddeeva_Package> for more information).
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2023-06-16 |
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r-gee4
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Fit joint mean-covariance models for longitudinal data within the framework of (weighted) generalised estimating equations (GEE/WGEE). The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Armadillo' C++ library for numerical linear algebra and 'RcppArmadillo' glue.
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2023-06-16 |
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r-gdmp
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Manage and analyze high-dimensional SNP data from chips with multiple densities.
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2023-06-16 |
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r-gconcord
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Estimates a sparse inverse covariance matrix from a convex pseudo-likelihood function with L1 penalty
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2023-06-16 |
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r-space
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Partial correlation estimation with joint sparse regression model
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2023-06-16 |
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r-sme
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Fit smoothing-splines mixed-effects models to replicated functional data sets and visualise the results.
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2023-06-16 |
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r-sensitivitypstrat
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This package provides functions to perform principal stratification sensitivity analyses on datasets.
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2023-06-16 |
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r-segmentor3isback
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Performs a fast exact segmentation on data and allows for use of various cost functions.
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2023-06-16 |
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r-rapror
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Calculate sketches of a data set reducing the number of observations using random projections. These can be used for Bayesian or frequentist linear regression on large data sets as described in Geppert et. al (2017) <doi:10.1007/s11222-015-9608-z>.
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2023-06-16 |
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r-socialnetworks
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Generates social networks using either of two approaches: using either pairwise distances or territorial area intersections.
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2023-06-16 |
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r-randomfieldsutils
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Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used.
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2023-06-16 |
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r-solverationalmatrixequation
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Given a symmetric positive definite matrix Q and a non-singular matrix L, find symmetric positive definite solution X such that X = Q + L (X inv) L^T. Reference: Benner, P., Faßbender, H. On the Solution of the Rational Matrix Equation. Benner, Faßbender (2007) <doi:10.1155/2007/21850>.
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2023-06-16 |
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r-socialposition
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Provides to sociologists (and related scientists) a toolbox to facilitate the construction of social position indicators from survey data. Social position indicators refer to what is commonly known as social class and social status. There exists in the sociological literature many theoretical conceptualisation and empirical operationalization of social class and social status. This first version of the package offers tools to construct the International Socio-Economic Index of Occupational Status (ISEI) and the Oesch social class schema. It also provides tools to convert several occupational classifications (PCS82, PCS03, and ISCO08) into a common one (ISCO88) to facilitate data harmonisation work, and tools to collapse (i.e. group) modalities of social position indicators.
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2023-06-16 |
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r-snpmaxsel
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This package implements asymptotic methods related to maximally selected statistics, with applications to SNP data.
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2023-06-16 |
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r-sii
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This package calculates ANSI S3.5-1997 Speech Intelligibility Index (SII), a standard method for computing the intelligibility of speech from acoustical measurements of speech, noise, and hearing thresholds. This package includes data frames corresponding to Tables 1 - 4 in the ANSI standard as well as a function utilizing these tables and user-provided hearing threshold and noise level measurements to compute the SII score. The methods implemented here extend the standard computations to allow calculation of SII when the measured frequencies do not match those required by the standard by applying interpolation to obtain values for the required frequencies -- Development of this package was funded by the Center for Bioscience Education and Technology (CBET) of the Rochester Institute of Technology (RIT).
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2023-06-16 |
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r-signmedian.test
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Perform sign test on one-sample data, which is one of the oldest non-parametric statistical methods. Assume that X comes from a continuous distribution with median = v ( unknown ). Test the null hypothesis H0: median of X v = mu ( mu is the location parameter and is given in the test ) v.s. the alternative hypothesis H1: v > mu ( or v < mu or v != mu ) and calculate the p-value. When the sample size is large, perform the asymptotic sign test. In both ways, calculate the R-estimate of location of X and the distribution free confidence interval for mu.
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2023-06-16 |
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r-shinybootstrap2
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Provides Bootstrap 2 web components for use with the Shiny package. With versions of Shiny prior to 0.11, these Bootstrap 2 components were included as part of the package. Later versions of Shiny include Bootstrap 3, so the Bootstrap 2 components have been moved into this package for those uses who rely on features specific to Bootstrap 2.
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2023-06-16 |
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r-session
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Utility functions for interacting with R processes from external programs. This package includes functions to save and restore session information (including loaded packages, and attached data objects), as well as functions to evaluate strings containing R commands and return the printed results or an execution transcript.
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2023-06-16 |
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r-rphylip
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Rphylip provides an R interface for the PHYLIP package. All users of Rphylip will thus first have to install the PHYLIP phylogeny methods program package (Felsenstein 2013). See http://www.phylip.com for more information about installing PHYLIP.
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2023-06-16 |
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r-rop
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Trees Classification and Regression using multivariate nodes calculated by an exhaustive numerical approach. We propose a new concept of decision tree, including multivariate knots and non hierarchical pathway. This package's model uses a multivariate nodes tree that calculates directly a risk score for each observation for the state Y observed. Nguyen JM, Gaultier A, Antonioli D (2015) <doi:10.1016/j.respe.2018.03.088> Castillo JM, Knol AC, Nguyen JM, Khammari A, Saint Jean M, Dreno B (2016) <doi:10.1684/ejd.2016.2826> Vildy S, Nguyen JM, Gaultier A, Khammari A, Dreno B (2017) <doi:10.1684/ejd.2016.2955> Nguyen JM, Gaultier A, Antonioli D (2018) <doi:10.1016/j.respe.2018.03.088>.
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2023-06-16 |
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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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2023-06-16 |
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r-ridit
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An extension of the Kruskal-Wallis Test that allow selection of arbitrary reference group. Also provide Mean Ridit for each group. Mean Ridit of a group is an estimate of probability a random observation from that group will be greater than or equal to a random observation from reference group.
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2023-06-16 |
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r-rga
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Provides functions for accessing and retrieving data from the Google Analytics APIs (https://developers.google.com/analytics/). Supports OAuth 2.0 authorization. Package provides access to the Management, Core Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and Metadata APIs. Access to all the Google Analytics accounts which the user has access to. Auto-pagination to return more than 10,000 rows of the results by combining multiple data requests. Also package provides shiny app to explore the core reporting API dimensions and metrics.
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2023-06-16 |
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r-rcarto
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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.
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2023-06-16 |
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r-qlearn
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Functions to implement Q-learning for estimating optimal dynamic treatment regimes from two stage sequentially randomized trials, and to perform inference via m-out-of-n bootstrap for parameters indexing the optimal regime.
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2023-06-16 |
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r-spiassay
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The SNP Panel Identification Assay (SPIA) is a package that enables an accurate determination of cell line identity from the genotype of single nucleotide polymorphisms (SNPs). The SPIA test allows to discern when two cell lines are close enough to be called similar and when they are not. Details about the method are available at "Demichelis et al. (2008) SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines. Nucleic Acids Res., 3, 2446-2456".
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2023-06-16 |
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r-spar
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This package performs robust nonparametric tests for rare variants association analysis using summation of partition approaches that incorporate gene-gene and gene-environmental interactions
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2023-06-16 |
