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r-oomisc
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public |
Includes miscellaneous functions.
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2023-06-16 |
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r-pcit
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Apply Partial Correlation coefficient with Information Theory (PCIT) to a correlation matrix. The PCIT algorithm identifies meaningful correlations to define edges in a weighted network. The algorithm can be applied to any correlation-based network including but not limited to gene co-expression networks. To reduce compute time by making use of multiple compute cores, simply run PCIT on a computer with has multiple cores and also has the Rmpi package installed. PCIT will then auto-detect the multicore environment and run in parallel mode without the need to rewrite your scripts. This makes scripts, using PCIT, portable across single core (or no Rmpi package installed) computers which will run in serial mode and multicore (with Rmpi package installed) computers which will run in parallel mode.
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2023-06-16 |
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r-pacbo
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A function for clustering online datasets. The number of cells is data-driven which need not to be chosen in advance by the user. The method is introduced and fully described in Le Li, Benjamin Guedj and Sebastien Loustau (2016), "PAC-Bayesian Online Clustering" (arXiv preprint: <https://arxiv.org/abs/1602.00522>).
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2023-06-16 |
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r-ormdr
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public |
Odds ratio based multifactor-dimensionality reduction method for detecting gene-gene interactions
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2023-06-16 |
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r-obliclus
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public |
This package conducts factor rotation techniques which intentd to identify a simple and well-clustered structure in a factor loading matrix.
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2023-06-16 |
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r-pbdncdf4
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This package adds collective parallel read and write capability to the R package ncdf4 version 1.8. Typical use is as a parallel NetCDF4 file reader in SPMD style programming. Each R process reads and writes its own data in a synchronized collective mode, resulting in faster parallel performance. Performance improvement is conditional on a parallel file system.
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2023-06-16 |
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r-nsrfa
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public |
A collection of statistical tools for objective (non-supervised) applications of the Regional Frequency Analysis methods in hydrology. The package refers to the index-value method and, more precisely, helps the hydrologist to: (1) regionalize the index-value; (2) form homogeneous regions with similar growth curves; (3) fit distribution functions to the empirical regional growth curves. Most of the methods are those described in the Flood Estimation Handbook (Centre for Ecology & Hydrology, 1999, ISBN:9781906698003). Homogeneity tests from Hosking and Wallis (1993) <doi:10.1029/92WR01980> and Viglione et al. (2007) <doi:10.1029/2006WR005095> are available.
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2023-06-16 |
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r-npst
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Package 'npst' generalizes Hewitt's (1971) test for seasonality and Rogerson's (1996) extension based on Monte-Carlo simulation.
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2023-06-16 |
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r-nonpmodelcheck
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Provides tests of significance for covariates (or groups of covariates) in a fully nonparametric regression model and a variable (or group) selection procedure based on False Discovery Rate. In addition, it provides a function for local polynomial regression for any number of dimensions, using a bandwidth specified by the user or automatically chosen by cross validation or an adaptive procedure.
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2023-06-16 |
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r-nmfgpu4r
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Wrapper package for the nmfgpu library, which implements several Non-negative Matrix Factorization (NMF) algorithms for CUDA platforms. By using the acceleration of GPGPU computing, the NMF can be used for real-world problems inside the R environment. All CUDA devices starting with Kepler architecture are supported by the library.
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2023-06-16 |
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r-parallelsvm
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By sampling your data, running the Support-Vector-Machine algorithm on these samples in parallel on your own machine and letting your models vote on a prediction, we return much faster predictions than the regular Support-Vector-Machine and possibly even more accurate predictions.
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2023-06-16 |
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r-parallelize.dynamic
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Passing a given function name or a call to the parallelize/parallelize_call functions analyses and executes the code, if possible in parallel. Parallel code execution can be performed locally or on remote batch queuing systems.
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2023-06-16 |
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r-nutshell.audioscrobbler
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This package contains the Audio Scrobbler data set used as an example in the book "R in a Nutshell" from O'Reilly Media. For more information about this book, see http://shop.oreilly.com/product/0636920022008.do
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2023-06-16 |
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r-npsimex
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This package contains a collection of functions to to perform nonparametric deconvolution using simulation extrapolation (SIMEX). We propose an estimator that adopts the SIMEX idea but bypasses the simulation step in the original SIMEX algorithm. There is no bandwidth parameter and the estimate is determined by appropriately selecting "design points". See details in: Wang, X.F., Sun, J. and Fan, Z. (2011). Deconvolution density estimation with heteroscedastic errors using SIMEX.
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2023-06-16 |
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r-parsetools
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Tools and utilities for dealing with parse data. Parse data represents the parse tree as data with location and type information. This package provides functions for navigating the parse tree as a data frame.
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2023-06-16 |
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r-paneldata
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Linear models for panel data: the fixed effect model and the random effect model
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2023-06-16 |
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r-pairheatmap
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A tool to compare two heatmaps and discover patterns within and across groups. In the context of biology, group can be defined based on gene ontology.
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2023-06-16 |
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r-packs4
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Illustration of the book "Petit Manuel de Programmation Orientee Objet sous R". The english version "A (Not so) Short Introduction to S4" is on CRAN, 'Contributed documentation'.
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2023-06-16 |
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r-obs.agree
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The package includes two functions for measuring agreement. Raw Agreement Indices (RAI) to categorical data and Information-Based Measure of Disagreement (IBMD) to continuous data. It can be used for multiple raters and multiple readings cases.
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2023-06-16 |
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r-pawls
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Efficient algorithms for fitting weighted least squares regression with \eqn{L_{1}}{L1} regularization on both the coefficients and weight vectors, which is able to perform simultaneous variable selection and outliers detection efficiently.
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2023-06-16 |
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r-nnlm
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This is a package for Non-Negative Linear Models (NNLM). It implements fast sequential coordinate descent algorithms for non-negative linear regression and non-negative matrix factorization (NMF). It supports mean square error and Kullback-Leibler divergence loss. Many other features are also implemented, including missing value imputation, domain knowledge integration, designable W and H matrices and multiple forms of regularizations.
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2023-06-16 |
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r-netcomp
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This package contains functions to carry out high throughput data analysis and to conduct data set comparisons. Similarity matrices from high throughput phenotypic data containing uninformative (e.g. wild type) or missing data can be calculated to report similarity of response. A suite of graph comparisons using an adjacency or correlation matrix format are included to facilitate quick network analysis.
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2023-06-16 |
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r-netcoh
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Model fitting procedures for regression with network cohesion effects, when a network connecting sample individuals is available in a regression problem. In the future, other commonly used statistical models will be added, such as gaussian graphical model.
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2023-06-16 |
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r-pbdrpc
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A very light implementation yet secure for remote procedure calls with unified interface via ssh (OpenSSH) or plink/plink.exe (PuTTY).
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2023-06-16 |
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r-optgs
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Functions to find near-optimal multi-stage designs for continuous outcomes.
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2023-06-16 |
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r-nvennr
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Provides an interface for the "nVenn"" algorithm (Perez-Silva, Araujo-Voces and Quesada (2018), <doi:10.1093/bioinformatics/bty109>). This algorithm works for any number of sets, and usually yields pleasing and informative Venn diagrams with proportionality information. However, representing more than six sets takes a long time and is hard to interpret, unless many of the regions are empty. If you cannot make sense of the result, you may want to consider 'UpSetR'.
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2023-06-16 |
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r-paleobiodb
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Includes 19 functions to wrap each endpoint of the PaleobioDB API, plus 8 functions to visualize and process the fossil data. The API documentation for the Paleobiology Database can be found in <http://paleobiodb.org/data1.1/>.
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2023-06-16 |
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r-p2distance
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The welfare's synthetic indicator provides an ideal tool for measuring multi-dimensional concepts such as welfare, development, living standards, etc. It enables information from the various indicators to be aggregated into a single synthetic measure.
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2023-06-16 |
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r-nws
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Provides coordination and parallel execution facilities, as well as limited cross-language data exchange, using the netWorkSpaces server developed by REvolution Computing
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2023-06-16 |
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r-nsgp
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A Gaussian process regression using a Gaussian kernel for both one-sample and two-sample cases. Includes non-stationary Gaussian kernel (exponential decay function) and several likelihood ratio tests for differential testing along target points.
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2023-06-16 |
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r-yummlyr
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Yummly.com is one of the world's largest and most powerful recipe search sites and this package aims to provide R bindings for publicly available Yummly.com Recipe API (https://developer.yummly.com/).
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2023-06-16 |
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r-wmdb
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Distance discriminant analysis method is one of classification methods according to multiindex performance parameters.However,the traditional Mahalanobis distance discriminant method treats with the importance of all parameters equally,and exaggerates the role of parameters which changes a little.The weighted Mahalanobis distance is used in discriminant analysis method to distinguish the importance of each parameter.In the concrete application,firstly based on the principal component analysis scheme,a new group of parameters and their corresponding percent contributions of the parameters are calculated ,and the weighted matrix is regarded as the diagonal matrix of the contributions rates.Setting data to standardization,then the weighted Mahalanobis distance can be calculated.Besides the methods metioned above,bayes method is also given.
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2023-06-16 |
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r-wvtool
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This tool, wood vision tool, is intended to facilitate preprocessing and analyzing 2-dimensional wood images toward automated recognition. The former includes some basics such as functions to RGB to grayscale, gray to binary, cropping, rotation(bilinear), median/mean/Gaussian filter, and Canny/Sobel edge detection. The latter includes gray level co-occurrence matrix (GLCM), Haralick parameters, local binary pattern (LBP), higher order local autocorrelation (HLAC), Fourier transform (radial and azimuthal integration), and Gabor filtering. The functions are intended to read data using 'readTIFF(x,info=T)' from 'tiff' package. The functions in this packages basically assumes the grayscale images as input data, thus the color images should be subjected to the function rgb2gray() before used for some other functions.
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2023-06-16 |
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r-worms
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Retrieves taxonomic information from <http://www.marinespecies.org> using WoRMS' RESTful Webservice. Utility functions aim at taxonomic consistency.
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2023-06-16 |
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r-wilcoxcv
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This package provides functions to perform fast variable selection based on the Wilcoxon rank sum test in the cross-validation or Monte-Carlo cross-validation settings, for use in microarray-based binary classification.
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2023-06-16 |
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r-wavefunction
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Real probability distributions can be represented as the square of an orthogonal sum in the Hermite basis. This representation is formally similar to the representation of quantum mechanical states as wave functions, whose squared modulus is a probability density. This is described in more detail in "Wave function representation of probability distributions," by Madeleine B. Thompson <arXiv:1712.07764>. This package provides a reference implementation of the technique.
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2023-06-16 |
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r-zen4r
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Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API, including management of depositions, attribution of DOIs by 'Zenodo' and upload of files.
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2023-06-16 |
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r-wsvm
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We propose weighted SVM methods with penalization form. By adding weights to loss term, we can build up weighted SVM easily and examine classification algorithm properties under weighted SVM. Through comparing each of test error rates, we conclude that our Weighted SVM with boosting has predominant properties than the standard SVM have, as a whole.
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2023-06-16 |
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r-wikipediar
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Provides an interface to the Wikipedia web application programming interface (API), using internet connexion.Three functions provide details for a specific Wikipedia page : all links that are present, all pages that link to, all the contributions (revisions for main pages, and discussions for talk pages). Two functions provide details for a specific user : all contributions, and general information (as name, gender, rights or groups). It provides additional information compared to others packages, as WikipediR. It does not need login. The multiplex network that can be constructed from the results of the functions of WikipediaR can be modeled as Stochastic Block Model as in Barbillon P., Donnet, S., Lazega E., and Bar-Hen A. : Stochastic Block Models for Multiplex networks: an application to networks of researchers, ArXiv 1501.06444, http://arxiv.org/abs/1501.06444.
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2023-06-16 |
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r-xltabr
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Writes beautifully formatted cross tabulations to Excel using 'openxlsx'. It has been developed to help automate the process of publishing Official Statistics. The user provides a dataframe, which is outputted to Excel with various types of rich formatting which are automatically detected from the structure of the cross tabulation. Documentation can be found at the following url <https://github.com/moj-analytical-services/xltabr>.
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2023-06-16 |
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r-xhwe
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Conduct the likelihood ratio tests for Hardy-Weinberg equilibrium at marker loci on the X chromosome.
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2023-06-16 |
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r-xgobi
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Interface to the XGobi and XGvis programs for graphical data analysis.
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2023-06-16 |
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r-zoomgrid
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Provides the grid search algorithm with a zoom. The grid search algorithm with a zoom aims to help solving difficult optimization problem where there are many local optima inside the domain of the target function. It offers suitable initial or starting value for the following optimization procedure, provided that the global optimum exists in the neighbourhood of the initial or starting value. The grid search algorithm with a zoom saves time tremendously in cases with high-dimensional arguments.
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2023-06-16 |
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r-whoapi
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Retrieve data from the 'Whoapi' (https://whoapi.com) store of domain information, including a domain's geographic location, registration status and search prominence.
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2023-06-16 |
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r-xyloplot
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A method for creating vertical histograms sharing a y-axis using base graphics.
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2023-06-16 |
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r-xlsimple
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Provides a simple wrapper for some 'XLConnect' functions. 'XLConnect' is a package that allows for reading, writing, and manipulating Microsoft Excel files. This package, 'xlsimple', adds some documentation and pre-defined formatting to the outputted Excel file. Individual sheets can include a description on the first row to remind user what is in the data set. Auto filters and freeze rows are turned on. A brief readme file is created that provides a summary listing of the created sheets and, where provided, the description.
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2023-06-16 |
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r-wee
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Secondary analysis of case-control studies using a weighted estimating equation (WEE) approach: logistic regression for binary secondary outcomes, linear regression and quantile regression for continuous secondary outcomes.
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2023-06-16 |
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r-webddx
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Freely available online differential-diagnosis generating tools are changing clinical medicine and biomedical research. With webddx, useRs can generate differential diagnosis lists given a set of symptoms. The web tools would likely be directly used in clinical practice, but programmatic interaction and data manipulation can sharply increase efficiency and reproducibility of research in clinical informatics. Relevant visualizations can also be created with webddx.
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2023-06-16 |
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r-wordmatch
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Matches words in one file with words in another file and shows index(row number) for the matches
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2023-06-16 |
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r-wcq
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The package contains the WCQ method for detection of QTL effects in a small mapping population. It also contains implementation of the Chen-Qin two-sample and one-sample test of means.
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2023-06-16 |
