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r-mdw
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Dimension-reduction methods aim at defining a score that maximizes signal diversity. Two approaches, namely maximum entropy weights and maximum variance weights, are provided.
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2023-06-16 |
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r-mdhglm
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Allows various models for multivariate response variables where each response is assumed to follow double hierarchical generalized linear models. In double hierarchical generalized linear models, the mean, dispersion parameters for variance of random effects, and residual variance can be further modeled as random-effect models.
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2023-06-16 |
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r-md
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Selects bandwidth for the kernel density estimator with minimum distance method as proposed by Devroye and Lugosi (1996). The minimum distance method directly selects the optimal kernel density estimator from countably infinite kernel density estimators and indirectly selects the optimal bandwidth. This package selects the optimal bandwidth from finite kernel density estimators.
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2023-06-16 |
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r-mcgibbsit
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'mcgibbsit' provides an implementation of Warnes & Raftery's MCGibbsit run-length diagnostic for a set of (not-necessarily independent) MCMC samplers. It combines the estimate error-bounding approach of the Raftery and Lewis MCMC run length diagnostic with the between verses within chain approach of the Gelman and Rubin MCMC convergence diagnostic.
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2023-06-16 |
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r-matrixnormal
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Computes densities, probabilities, and random deviates of the Matrix Normal (Iranmanesh et al. (2010) <doi:10.7508/ijmsi.2010.02.004>). Also includes simple but useful matrix functions. See the vignette for more information.
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2023-06-16 |
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r-mar
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R functions for multivariate autoregressive analysis
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2023-06-16 |
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r-mangrove
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Methods for performing genetic risk prediction from genotype data. You can use it to perform risk prediction for individuals, or for families with missing data.
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2023-06-16 |
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r-lsm
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When the values of the outcome variable Y are either 0 or 1, the function lsm() calculates the estimation of the log likelihood in the saturated model. This model is characterized by Llinas (2006, ISSN:2389-8976) in section 2.3 through the assumptions 1 and 2. The function LogLik() works (almost perfectly) when the number of independent variables K is high, but for small K it calculates wrong values in some cases. For this reason, when Y is dichotomous and the data are grouped in J populations, it is recommended to use the function lsm() because it works very well for all K.
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2023-06-16 |
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r-lsdinterface
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Interfaces R with LSD. Reads object-oriented data in results files (.res) produced by LSD and creates appropriate multi-dimensional arrays in R. Supports multiple core parallelization of multi-file data reading for increased performance. Also provides functions to extract basic information and statistics from data files. LSD (Laboratory for Simulation Development) is free software developed by Marco Valente (documentation and downloads available at <http://labsimdev.org>).
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2023-06-16 |
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r-lsasim
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Provides functions to simulate data from large-scale educational assessments, including background questionnaire data and cognitive item responses that adhere to a multiple-matrix sampled design.
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2023-06-16 |
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r-lpcm
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Fitting multivariate data patterns with local principal curves, including tools for data compression (projection) and measuring goodness-of-fit; with some additional functions for mean shift clustering.
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2023-06-16 |
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r-lotri
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Provides a simple mechanism to specify a symmetric block diagonal matrices (often used for covariance matrices). This is based on the domain specific language implemented in 'nlmixr' but expanded to create matrices in R generally instead of specifying parts of matrices to estimate.
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2023-06-16 |
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r-logitnorm
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Density, distribution, quantile and random generation function for the logitnormal distribution. Estimation of the mode and the first two moments. Estimation of distribution parameters.
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2023-06-16 |
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r-lncpath
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Identifies pathways synergisticly regulated by the interested lncRNA(long non-coding RNA) sets based on a lncRNA-mRNA(messenger RNA) interaction network. 1) The lncRNA-mRNA interaction network was built from the protein-protein interactions and the lncRNA-mRNA co-expression relationships in 28 RNA-Seq data sets. 2) The interested lncRNAs can be mapped into networks as seed nodes and a random walk strategy will be performed to evaluate the rate of each coding genes influenced by the seed lncRNAs. 3) Pathways regulated by the lncRNA set will be evaluated by a weighted Kolmogorov-Smirnov statistic as an ES Score. 4) The p value and false discovery rate value will also be calculated through a permutation analysis. 5) The running score of each pathway can be plotted and the heat map of each pathway can also be plotted if an expression profile is provided. 6) The rank and scores of the gene list of each pathway can be printed.
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2023-06-16 |
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r-lmf
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This R package provide methods for estimation and statistical inference on directional and fluctuating selection in age-structured populations.
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2023-06-16 |
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r-lindenmayer
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L-systems or Lindenmayer systems are parallel rewriting systems which can be used to simulate biological forms and certain kinds of fractals. Briefly, in an L-system a series of symbols in a string are replaced iteratively according to rules to give a more complex string. Eventually, the symbols are translated into turtle graphics for plotting. Wikipedia has a very good introduction: en.wikipedia.org/wiki/L-system This package provides basic functions for exploring L-systems.
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2023-06-16 |
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r-leiden
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Implements the 'Python leidenalg' module to be called in R. Enables clustering using the leiden algorithm for partition a graph into communities. See the 'Python' repository for more details: <https://github.com/vtraag/leidenalg> Traag et al (2018) From Louvain to Leiden: guaranteeing well-connected communities. <arXiv:1810.08473>.
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2023-06-16 |
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r-leafstar
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Implementation of trigonometric functions to calculate the exposure of flat, tilted surfaces, such as leaves and slopes, to direct solar radiation. It implements the equations in A.G. Escribano-Rocafort, A. Ventre-Lespiaucq, C. Granado-Yela, et al. (2014) <doi:10.1111/2041-210X.12141> in a few user-friendly R functions. All functions handle data obtained with 'Ahmes' 1.0 for Android, as well as more traditional data sources (compass, protractor, inclinometer). The main function (star()) calculates the potential exposure of flat, tilted surfaces to direct solar radiation (silhouette to area ratio, STAR). It is equivalent to the ratio of the leaf projected area to total leaf area, but instead of using area data it uses spatial position angles, such as pitch, roll and course, and information on the geographical coordinates, hour, and date. The package includes additional functions to recalculate STAR with custom settings of location and time, to calculate the tilt angle of a surface, and the minimum angle between two non-orthogonal planes.
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2023-06-16 |
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r-leaflet.providers
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Contains third-party map tile provider information from 'Leaflet.js', <https://github.com/leaflet-extras/leaflet-providers>, to be used with the 'leaflet' R package. Additionally, 'leaflet.providers' enables users to retrieve up-to-date provider information between package updates.
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2023-06-16 |
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r-leafarea
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An interface for the image processing program 'ImageJ', which allows a rapid digital image analysis for particle sizes. This package includes function to write an 'ImageJ' macro which is optimized for a leaf area analysis by default.
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2023-06-16 |
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r-nlmeode
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This package combines the odesolve and nlme packages for mixed-effects modelling using differential equations.
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2023-06-16 |
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r-nipals
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Principal Components Analysis of a matrix using Non-linear Iterative Partial Least Squares with Gram-Schmidt orthogonalization of the scores and loadings. Optimized for speed. See Andrecut (2009) <doi:10.1089/cmb.2008.0221>.
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2023-06-16 |
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r-neverhpfilter
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In the working paper titled "Why You Should Never Use the Hodrick-Prescott Filter", James D. Hamilton proposes an interesting new alternative to economic time series filtering. The neverhpfilter package provides functions for implementing his solution. Hamilton (2017) <doi:10.3386/w23429>.
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2023-06-16 |
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r-netswan
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A set of functions for studying network robustness, resilience and vulnerability.
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2023-06-16 |
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r-needy
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needy is a small utility library designed to make testing function inputs less difficult. R is a dynamically typed language, but larger projects need input checking for scalabity. needy offers a single function, require_a( ), which lets you specify the traits an input object should have, such as class, size, numerical properties or number of parameters, while reducing boilerplate code and aiding debugging.
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2023-06-16 |
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r-mwridge
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A two stage moving-window Ridge method for coefficients estimation and model prediction. In the first stage, moving-window penalty and L1 penalty are applied. In the second stage, ridge regression is applied.
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2023-06-16 |
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r-mvntest
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Routines for assessing multivariate normality. Implements three Wald's type chi-squared tests; non-parametric Anderson-Darling and Cramer-von Mises tests; Doornik-Hansen test, Royston test and Henze-Zirkler test.
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2023-06-16 |
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r-mvcwt
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Computes the continuous wavelet transform of irregularly sampled time series.
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2023-06-16 |
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r-multiplencc
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Fit Cox proportional hazard models with a weighted partial likelihood. It handles one or multiple endpoints, additional matching and makes it possible to reuse controls for other endpoints.
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2023-06-16 |
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r-multicoll
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The detection of worrying approximate collinearity in a multiple linear regression model is a problem addressed in all existing statistical packages. However, we have detected deficits regarding to the incorrect treatment of qualitative independent variables and the role of the intercept of the model. The objective of this package is to correct these deficits. In this package will be available detection and treatment techniques traditionally used as the recently developed. D.A. Belsley (1982) <doi:10.1016/0304-4076(82)90020-3>. D. A. Belsley (1991, ISBN: 978-0471528890). C. Garcia, R. Salmeron and C.B. Garcia (2019) <doi:10.1080/00949655.2018.1543423>. R. Salmeron, C.B. Garcia and J. Garcia (2018) <doi:10.1080/00949655.2018.1463376>. G.W. Stewart (1987) <doi:10.1214/ss/1177013444>.
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2023-06-16 |
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r-mstr
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Generation of response patterns under dichotomous and polytomous computerized multistage testing (MST) framework. It holds various item response theory (IRT) and score-based methods to select the next module and estimate ability levels (Magis, Yan and von Davier (2017, ISBN:978-3-319-69218-0)).
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2023-06-16 |
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r-ms.sev
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Calculates ARMSS (age related multiple sclerosis severity), and both local and global MSSS (multiple sclerosis severity score).
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2023-06-16 |
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r-mreg
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Implements the methods described in Bond S, Farewell V, 2006, Exact Likelihood Estimation for a Negative Binomial Regression Model with Missing Outcomes, Biometrics
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2023-06-16 |
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r-mpsychor
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Supplementary materials and datasets for the book "Modern Psychometrics With R" (Mair, 2018, Springer useR! series).
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2023-06-16 |
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r-mpinet
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(1) Our system provides a network-based strategies for metabolite pathway identification.(2) The MPINet can support the identification of pathways using Hypergeometric test based on metabolite set. (3)MPINet can support pathways from multiple databases.
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2023-06-16 |
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r-moult
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Functions to estimate start and duration of moult from moult data, based on models developed in Underhill and Zucchini (1988, 1990).
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2023-06-16 |
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r-mopsocd
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A multi-objective optimization solver based on particle swarm optimization with crowding distance.
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2023-06-16 |
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r-monte.carlo.se
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Computes Monte Carlo standard errors for summaries of Monte Carlo output. Summaries and their standard errors are based on columns of Monte Carlo simulation output. Dennis D. Boos and Jason A. Osborne (2015) <doi:10.1111/insr.12087>.
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2023-06-16 |
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r-momtrunc
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It computes the raw moments for the truncated and folded multivariate normal, Skew-normal (SN), Extended skew normal (ESN) and Student's t-distribution. It also offers specific functions to compute the mean and variance-covariance matrix as well as the cumulative distribution function (cdf) for the folded normal, SN, ESN, and folded t-distribution. Density and random deviates are offered for the ESN (SN as particular case) distribution. Most algorithms are extensions based on Kan, R., & Robotti, C. (2017) <doi:10.1080/10618600.2017.1322092>.
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2023-06-16 |
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r-mogavs
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Functions for exploring the best subsets in regression with a genetic algorithm. The package is much faster than methods relying on complete enumeration, and is suitable for data sets with large number of variables. For more information, see Sinha, Malo & Kuosmanen (2015) <doi:10.1080/10618600.2014.899236>.
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2023-06-16 |
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r-modules
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Provides modules as an organizational unit for source code. Modules enforce to be more rigorous when defining dependencies and have a local search path. They can be used as a sub unit within packages or in scripts.
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2023-06-16 |
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r-mmms
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The package implements a multi-marker molecular signature (MMMS) approach for treatment-specific subgroup identification.
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2023-06-16 |
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r-mmac
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Contains the data sets for the textbook "Mathematical Modeling and Applied Calculus" by Joel Kilty and Alex M. McAllister. The book will be published by Oxford University Press in 2018 with ISBN-13: 978-019882472.
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2023-06-16 |
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r-missmech
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To test whether the missing data mechanism, in a set of incompletely observed data, is one of missing completely at random (MCAR). For detailed description see Jamshidian, M. Jalal, S., and Jansen, C. (2014). "MissMech: An R Package for Testing Homoscedasticity, Multivariate Normality, and Missing Completely at Random (MCAR)," Journal of Statistical Software, 56(6), 1-31. URL http://www.jstatsoft.org/v56/i06/.
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2023-06-16 |
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r-mise
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Clears the workspace. Useful for the beginnings of R scripts, to avoid potential problems with accidentally using information from variables or functions from previous script evaluations, too many figure windows open at the same time, packages that you don't need any more, or a cluttered console. Uses code from various StackOverflow users. See help(mise) for pointers to the relevant StackOverflow pages.
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2023-06-16 |
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r-minirand
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Randomization schedules are generated in the schemes with k (k>=2) treatment groups and any allocation ratios by minimization algorithms.
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2023-06-16 |
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r-milc
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The MILC package is designed to predict individual trajectories using the continuous time microsimulation model MILC, that describes the natural history of lung cancer.
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2023-06-16 |
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r-michelrodange
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Michel Rodange was a Luxembourguish writer and poet who lived in the 19th century. His most notable work is Rodange (1872, ISBN:1166177424), ("Renert oder de Fuuß am Frack an a Ma'nsgrëßt"), but he also wrote many more works, including Rodange, Tockert (1928) <https://www.autorenlexikon.lu/page/document/361/3614/1/FRE/index.html> ("D'Léierchen - Dem Léiweckerche säi Lidd") and Rodange, Welter (1929) <https://www.autorenlexikon.lu/page/document/361/3615/1/FRE/index.html> ("Dem Grow Sigfrid seng Goldkuommer"). This package contains three datasets, each made from the plain text versions of his works available on <https://data.public.lu/fr/datasets/the-works-in-luxembourguish-of-michel-rodange/>.
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2023-06-16 |
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r-mhadaptive
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Performs general Metropolis-Hastings Markov Chain Monte Carlo sampling of a user defined function which returns the un-normalized value (likelihood times prior) of a Bayesian model. The proposal variance-covariance structure is updated adaptively for efficient mixing when the structure of the target distribution is unknown. The package also provides some functions for Bayesian inference including Bayesian Credible Intervals (BCI) and Deviance Information Criterion (DIC) calculation.
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2023-06-16 |
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r-mfp
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Fractional polynomials are used to represent curvature in regression models. A key reference is Royston and Altman, 1994.
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2023-06-16 |
