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r-metaheuristicfpa
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A nature-inspired metaheuristics algorithm based on the pollination process of flowers. This R package makes it easy to implement the standard flower pollination algorithm for every user. The algorithm was first developed by Xin-She Yang in 2012 (<DOI:10.1007/978-3-642-32894-7_27>).
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2025-04-22 |
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r-metafolio
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A tool to simulate salmon metapopulations and apply financial portfolio optimization concepts. The package accompanies the paper Anderson et al. (2015) <doi:10.1101/2022.03.24.485545>.
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2025-04-22 |
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r-metadynminer
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Metadynamics is a state of the art biomolecular simulation technique. 'Plumed' Tribello, G.A. et al. (2014) <doi:10.1016/j.cpc.2013.09.018> program makes it possible to perform metadynamics using various simulation codes. The results of metadynamics done in 'Plumed' can be analyzed by 'metadynminer'. The package 'metadynminer' reads 1D and 2D metadynamics hills files from 'Plumed' package. It uses a fast algorithm by Hosek, P. and Spiwok, V. (2016) <doi:10.1016/j.cpc.2015.08.037> to calculate a free energy surface from hills. Minima can be located and plotted on the free energy surface. Transition states can be analyzed by Nudged Elastic Band method by Henkelman, G. and Jonsson, H. (2000) <doi:10.1063/1.1323224>. Free energy surfaces, minima and transition paths can be plotted to produce publication quality images.
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2025-04-22 |
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r-mergetrees
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Aggregates a set of trees with the same leaves to create a consensus tree. The trees are typically obtained via hierarchical clustering, hence the hclust format is used to encode both the aggregated trees and the final consensus tree. The method is exact and proven to be O(nqlog(n)), n being the individuals and q being the number of trees to aggregate.
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2025-04-22 |
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r-memuse
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How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is your current R session using? How much ram do you even have? Learn the scintillating answer to these and many more such questions with the 'memuse' package.
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2025-04-22 |
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r-memo
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A simple in-memory, LRU cache that can be wrapped around any function to memoize it. The cache is keyed on a hash of the input data (using 'digest') or on pointer equivalence.
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2025-04-22 |
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r-memnet
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Efficient implementations of network science tools to facilitate research into human (semantic) memory. In its current version, the package contains several methods to infer networks from verbal fluency data, various network growth models, diverse (switcher-) random walk processes, and tools to analyze and visualize networks. To deliver maximum performance the majority of the code is written in C++. For an application see: Wulff, D. U., Hills, T., & Mata, R. (2018) <doi:10.31234/osf.io/s73dp>.
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2025-04-22 |
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r-mediak
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Calculates MeDiA_K (means Mean Distance Association by K-nearest neighbor) in order to detect nonlinear associations.
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2025-04-22 |
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r-v8
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An R interface to V8 <https://v8.dev>: Google's open source JavaScript and WebAssembly engine. This package can be compiled either with V8 version 6 and up or NodeJS when built as a shared library.
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2025-04-22 |
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r-weco
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Western Electric Company Rules (WECO) have been widely used for Shewhart control charts in order to increase the sensitivity of detecting assignable causes of process change. This package implements eight commonly used WECO rules and allow to apply the combination of these individual rules for detecting the deviation from a stable process. The package also provides a web-based graphical user interface to help users conduct the analysis.
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2025-04-22 |
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r-webutils
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Parses http request data in application/json, multipart/form-data, or application/x-www-form-urlencoded format. Includes example of hosting and parsing html form data in R using either 'httpuv' or 'Rhttpd'.
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2025-04-22 |
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r-websocket
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Provides a 'WebSocket' client interface for R. 'WebSocket' is a protocol for low-overhead real-time communication: <https://en.wikipedia.org/wiki/WebSocket>.
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2025-04-22 |
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r-webp
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Lossless webp images are 26% smaller in size compared to PNG. Lossy webp images are 25-34% smaller in size compared to JPEG. This package reads and writes webp images into a 3 (rgb) or 4 (rgba) channel bitmap array using conventions from the 'jpeg' and 'png' packages.
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2025-04-22 |
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r-wdm
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Provides efficient implementations of weighted dependence measures and related asymptotic tests for independence. Implemented measures are the Pearson correlation, Spearman's rho, Kendall's tau, Blomqvist's beta, and Hoeffding's D; see, e.g., Nelsen (2006) <doi:10.1007/0-387-28678-0> and Hollander et al. (2015, ISBN:9780470387375).
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2025-04-22 |
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r-wcorr
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Calculates Pearson, Spearman, polychoric, and polyserial correlation coefficients, in weighted or unweighted form. The package implements tetrachoric correlation as a special case of the polychoric and biserial correlation as a specific case of the polyserial.
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2025-04-22 |
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r-wbs
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Provides efficient implementation of the Wild Binary Segmentation and Binary Segmentation algorithms for estimation of the number and locations of multiple change-points in the piecewise constant function plus Gaussian noise model.
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2025-04-22 |
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r-wavethresh
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Performs 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.
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2025-04-22 |
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r-waveslim
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Basic wavelet routines for time series (1D), image (2D) and array (3D) analysis. The code provided here is based on wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002). All figures in chapters 4-7 of GSW (2001) are reproducible using this package and R code available at the book website(s) below.
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2025-04-22 |
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r-wavelets
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Contains functions for computing and plotting discrete wavelet transforms (DWT) and maximal overlap discrete wavelet transforms (MODWT), as well as their inverses. Additionally, it contains functionality for computing and plotting wavelet transform filters that are used in the above decompositions as well as multiresolution analyses.
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2025-04-22 |
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r-waffect
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waffect (pronounced 'double-u affect' for 'weighted affectation') is a package to simulate phenotypic (case or control) datasets under a disease model H1 such that the total number of cases is constant across all the simulations (the constrain in the title). The package also makes it possible to generate phenotypes in the case of more than two classes, so that the number of phenotypes belonging to each class is constant across all the simulations. waffect is used to assess empirically the statistical power of Genome Wide Association studies.
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2025-04-22 |
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r-volesti
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Provides an R interface for 'volesti' C++ package. 'volesti' computes estimations of volume of polytopes given by (i) a set of points, (ii) linear inequalities or (iii) Minkowski sum of segments (a.k.a. zonotopes). There are three algorithms for volume estimation as well as algorithms for sampling, rounding and rotating polytopes. Moreover, 'volesti' provides algorithms for estimating copulas useful in computational finance. Methods implemented in 'volesti' are described in A. Chalkis and V. Fisikopoulos (2022) <doi:10.32614/RJ-2021-077> and references therein.
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2025-04-22 |
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r-vnm
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Provide tools for finding multiple-objective optimal designs for estimating the shape of dose-response, the ED50 (the dose producing an effect midway between the expected responses at the extreme doses) and the MED (the minimum effective dose level) for the 2,3,4-parameter logistic models and for evaluating its efficiencies for the three objectives. The acronym VNM stands for V-algorithm using Newton Raphson method to search multiple-objective optimal design.
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2025-04-22 |
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r-vlmc
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Functions, Classes & Methods for estimation, prediction, and simulation (bootstrap) of Variable Length Markov Chain ('VLMC') Models.
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2025-04-22 |
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r-vlad
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Contains functions to set up risk-adjusted quality control charts in health care. For the variable life adjusted display (VLAD) proposed by Lovegrove et al. (1997) <doi:10.1016/S0140-6736(97)06507-0> signaling rules derived in Wittenberg et al. (2018) <doi:10.1002/sim.7647> are implemented. Additionally, for the risk-adjusted cumulative sum chart based on log-likelihood ratio statistic introduced by Steiner et al. (2000) <doi:10.1093/biostatistics/1.4.441> average run length and control limits can be computed with fast and accurate Markov chain approximations developed in Knoth et al. (2019) <doi:10.1002/sim.8104>.
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2025-04-22 |
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r-vita
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Implements the novel testing approach by Janitza et al.(2015) <http://nbn-resolving.de/urn/resolver.pl?urn=nbn:de:bvb:19-epub-25587-4> for the permutation variable importance measure in a random forest and the PIMP-algorithm by Altmann et al.(2010) <doi:10.1093/bioinformatics/btq134>. Janitza et al.(2015) <http://nbn-resolving.de/urn/resolver.pl?urn=nbn:de:bvb:19-epub-25587-4> do not use the "standard" permutation variable importance but the cross-validated permutation variable importance for the novel test approach. The cross-validated permutation variable importance is not based on the out-of-bag observations but uses a similar strategy which is inspired by the cross-validation procedure. The novel test approach can be applied for classification trees as well as for regression trees. However, the use of the novel testing approach has not been tested for regression trees so far, so this routine is meant for the expert user only and its current state is rather experimental.
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2025-04-22 |
