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r-multivariance
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Distance multivariance is a measure of dependence which can be used to detect and quantify dependence of arbitrarily many random vectors. The necessary functions are implemented in this packages and examples are given. It includes: distance multivariance, distance multicorrelation, dependence structure detection, tests of independence and copula versions of distance multivariance based on the Monte Carlo empirical transform. Detailed references are given in the package description, as starting point for the theoretic background we refer to: B. Böttcher, Dependence and Dependence Structures: Estimation and Visualization Using the Unifying Concept of Distance Multivariance. Open Statistics, Vol. 1, No. 1 (2020), <doi:10.1515/stat-2020-0001>.
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2025-03-25 |
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r-multitaper
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Implements multitaper spectral analysis using discrete prolate spheroidal sequences (Slepians) and sine tapers. It includes an adaptive weighted multitaper spectral estimate, a coherence estimate, Thomson's Harmonic F-test, and complex demodulation. The Slepians sequences are generated efficiently using a tridiagonal matrix solution, and jackknifed confidence intervals are available for most estimates. This package is an implementation of the method described in D.J. Thomson (1982) "Spectrum estimation and harmonic analysis" <doi:10.1109/PROC.1982.12433>.
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2025-03-25 |
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r-multispatialccm
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The multispatial convergent cross mapping algorithm can be used as a test for causal associations between pairs of processes represented by time series. This is a combination of convergent cross mapping (CCM), described in Sugihara et al., 2012, Science, 338, 496-500, and dew-drop regression, described in Hsieh et al., 2008, American Naturalist, 171, 71–80. The algorithm allows CCM to be implemented on data that are not from a single long time series. Instead, data can come from many short time series, which are stitched together using bootstrapping.
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2025-03-25 |
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r-multinet
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Functions for the creation/generation and analysis of multilayer social networks <doi:10.18637/jss.v098.i08>.
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2025-03-25 |
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r-multifit
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Test for independence of two random vectors, learn and report the dependency structure. For more information, see Gorsky, Shai and Li Ma, Multiscale Fisher's Independence Test for Multivariate Dependence, Biometrika, accepted, January 2022.
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2025-03-25 |
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r-multicool
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A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix Shifts. SODA 2009, Symposium on Discrete Algorithms, New York, United States. The permutation code is distributed without restrictions. The code for stable and efficient computation of multinomial coefficients comes from Dave Barber. The code can be download from <http://tamivox.org/dave/multinomial/index.html> and is distributed without conditions. The package also generates the integer partitions of a positive, non-zero integer n. The C++ code for this is based on Python code from Jerome Kelleher which can be found here <https://jeromekelleher.net/category/combinatorics.html>. The C++ code and Python code are distributed without conditions.
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2025-03-25 |
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r-multicnvdetect
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This package provides a tool for analysis of multiple CNV.
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2025-03-25 |
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r-muhaz
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Produces a smooth estimate of the hazard function for censored data.
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2025-03-25 |
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r-mudens
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Compute a density estimate from a vector of right-censored survival time using kernel functions.
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2025-03-25 |
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r-muchpoint
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Nonparametric approach to estimate the location of block boundaries (change-points) of non-overlapping blocks in a random symmetric matrix which consists of random variables whose distribution changes from block to block. BRAULT Vincent, OUADAH Sarah, SANSONNET Laure and LEVY-LEDUC Celine (2017) <doi:10.1016/j.jmva.2017.12.005>.
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2025-03-25 |
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r-mts
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Multivariate Time Series (MTS) is a general package for analyzing multivariate linear time series and estimating multivariate volatility models. It also handles factor models, constrained factor models, asymptotic principal component analysis commonly used in finance and econometrics, and principal volatility component analysis. (a) For the multivariate linear time series analysis, the package performs model specification, estimation, model checking, and prediction for many widely used models, including vector AR models, vector MA models, vector ARMA models, seasonal vector ARMA models, VAR models with exogenous variables, multivariate regression models with time series errors, augmented VAR models, and Error-correction VAR models for co-integrated time series. For model specification, the package performs structural specification to overcome the difficulties of identifiability of VARMA models. The methods used for structural specification include Kronecker indices and Scalar Component Models. (b) For multivariate volatility modeling, the MTS package handles several commonly used models, including multivariate exponentially weighted moving-average volatility, Cholesky decomposition volatility models, dynamic conditional correlation (DCC) models, copula-based volatility models, and low-dimensional BEKK models. The package also considers multiple tests for conditional heteroscedasticity, including rank-based statistics. (c) Finally, the MTS package also performs forecasting using diffusion index , transfer function analysis, Bayesian estimation of VAR models, and multivariate time series analysis with missing values.Users can also use the package to simulate VARMA models, to compute impulse response functions of a fitted VARMA model, and to calculate theoretical cross-covariance matrices of a given VARMA model.
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2025-03-25 |
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r-mtlr
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An implementation of Multi-Task Logistic Regression (MTLR) for R. This package is based on the method proposed by Yu et al. (2011) which utilized MTLR for generating individual survival curves by learning feature weights which vary across time. This model was further extended to account for left and interval censored data.
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2025-03-25 |
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r-mstate
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Contains functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models, see Putter, Fiocco, Geskus (2007) <doi:10.1002/sim.2712>.
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2025-03-25 |
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r-mssm
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Provides methods to perform parameter estimation and make analysis of multivariate observed outcomes through time which depends on a latent state variable. All methods scale well in the dimension of the observed outcomes at each time point. The package contains an implementation of a Laplace approximation, particle filters like suggested by Lin, Zhang, Cheng, & Chen (2005) <doi:10.1198/016214505000000349>, and the gradient and observed information matrix approximation suggested by Poyiadjis, Doucet, & Singh (2011) <doi:10.1093/biomet/asq062>.
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2025-03-25 |
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r-msimcc
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Micro simulation model to reproduce natural history of cervical cancer and cost-effectiveness evaluation of prevention strategies. See Georgalis L, de Sanjose S, Esnaola M, Bosch F X, Diaz M (2016) <doi:10.1097/CEJ.0000000000000202> for more details.
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2025-03-25 |
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r-msgps
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Computes the degrees of freedom of the lasso, elastic net, generalized elastic net and adaptive lasso based on the generalized path seeking algorithm. The optimal model can be selected by model selection criteria including Mallows' Cp, bias-corrected AIC (AICc), generalized cross validation (GCV) and BIC.
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2025-03-25 |
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r-msglasso
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For fitting multivariate response and multiple predictor linear regressions with an arbitrary group structure assigned on the regression coefficient matrix, using the multivariate sparse group lasso and the mixed coordinate descent algorithm.
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2025-03-25 |
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r-msde
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Implements an MCMC sampler for the posterior distribution of arbitrary time-homogeneous multivariate stochastic differential equation (SDE) models with possibly latent components. The package provides a simple entry point to integrate user-defined models directly with the sampler's C++ code, and parallelizes large portions of the calculations when compiled with 'OpenMP'.
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2025-03-25 |
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r-msda
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Efficient procedures for computing a new Multi-Class Sparse Discriminant Analysis method that estimates all discriminant directions simultaneously. It is an implementation of the work proposed by Mai, Q., Yang, Y., and Zou, H. (2019) <doi:10.5705/ss.202016.0117>.
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2025-03-25 |
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r-msbp
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Performs Bayesian nonparametric multiscale density estimation and multiscale testing of group differences with multiscale Bernstein polynomials (msBP) mixtures as in Canale and Dunson (2016).
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2025-03-25 |
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r-mrs
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An implementation of the MRS algorithm for comparison across distributions, as described in Jacopo Soriano, Li Ma (2016) <doi:10.1111/rssb.12180>. The model is based on a nonparametric process taking the form of a Markov model that transitions between a "null" and an "alternative" state on a multi-resolution partition tree of the sample space. MRS effectively detects and characterizes a variety of underlying differences. These differences can be visualized using several plotting functions.
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2025-03-25 |
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r-mrmre
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Computes mutual information matrices from continuous, categorical and survival variables, as well as feature selection with minimum redundancy, maximum relevance (mRMR) and a new ensemble mRMR technique. Published in De Jay et al. (2013) <doi:10.1093/bioinformatics/btt383>.
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2025-03-25 |
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r-mrm
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Conditional maximum likelihood estimation via the EM algorithm and information-criterion-based model selection in binary mixed Rasch models.
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2025-03-25 |
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r-mrfse
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Three algorithms for estimating a Markov random field structure.Two of them are an exact version and a simulated annealing version of a penalized maximum conditional likelihood method similar to the Bayesian Information Criterion. These algorithm are described in Frondana (2016) <doi:10.11606/T.45.2018.tde-02022018-151123>.The third one is a greedy algorithm, described in Bresler (2015) <doi:10.1145/2746539.2746631).
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2025-03-25 |
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r-mra
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Accomplishes mark-recapture analysis with covariates. Models available include the Cormack-Jolly-Seber open population (Cormack (1972) <doi:10.2307/2556151>; Jolly (1965) <doi:10.2307/2333826>; Seber (1965) <doi:10.2307/2333827>) and Huggin's (1989) <doi:10.2307/2336377> closed population. Link functions include logit, sine, and hazard. Model selection, model averaging, plot, and simulation routines included. Open population size by the Horvitz-Thompson (1959) <doi:10.2307/2280784> estimator.
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2025-03-25 |
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r-mptinr
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Provides a user-friendly way for the analysis of multinomial processing tree (MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the measurement of cognitive processes. Psychological Review, 95, 318-339) for single and multiple datasets. The main functions perform model fitting and model selection. Model selection can be done using AIC, BIC, or the Fisher Information Approximation (FIA) a measure based on the Minimum Description Length (MDL) framework. The model and restrictions can be specified in external files or within an R script in an intuitive syntax or using the context-free language for MPTs. The 'classical' .EQN file format for model files is also supported. Besides MPTs, this package can fit a wide variety of other cognitive models such as SDT models (see fit.model). It also supports multicore fitting and FIA calculation (using the snowfall package), can generate or bootstrap data for simulations, and plot predicted versus observed data.
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2025-03-25 |
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r-mpsem
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Computational tools to represent phylogenetic signals using adapted eigenvector maps.
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2025-03-25 |
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r-mpmi
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Uses a kernel smoothing approach to calculate Mutual Information for comparisons between all types of variables including continuous vs continuous, continuous vs discrete and discrete vs discrete. Uses a nonparametric bias correction giving Bias Corrected Mutual Information (BCMI). Implemented efficiently in Fortran 95 with OpenMP and suited to large genomic datasets.
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2025-03-25 |
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r-mp
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Multidimensional projection techniques are used to create two dimensional representations of multidimensional data sets.
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2025-03-25 |
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r-monreg
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Estimates monotone regression and variance functions in a nonparametric model, based on Dette, Holger, Neumeyer, and Pilz (2006) <doi:10.3150/bj/1151525131>.
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2025-03-25 |
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r-monopoly
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Functions for fitting monotone polynomials to data. Detailed discussion of the methodologies used can be found in Murray, Mueller and Turlach (2013) <doi:10.1007/s00180-012-0390-5> and Murray, Mueller and Turlach (2016) <doi:10.1080/00949655.2016.1139582>.
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2025-03-25 |
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r-monomvn
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Estimation of multivariate normal (MVN) and student-t data of arbitrary dimension where the pattern of missing data is monotone. See Pantaleo and Gramacy (2010) <arXiv:0907.2135>. Through the use of parsimonious/shrinkage regressions (plsr, pcr, lasso, ridge, etc.), where standard regressions fail, the package can handle a nearly arbitrary amount of missing data. The current version supports maximum likelihood inference and a full Bayesian approach employing scale-mixtures for Gibbs sampling. Monotone data augmentation extends this Bayesian approach to arbitrary missingness patterns. A fully functional standalone interface to the Bayesian lasso (from Park & Casella), Normal-Gamma (from Griffin & Brown), Horseshoe (from Carvalho, Polson, & Scott), and ridge regression with model selection via Reversible Jump, and student-t errors (from Geweke) is also provided.
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2025-03-25 |
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r-monetdb.r
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Allows to pull data from MonetDB into R.
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2025-03-25 |
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r-modelltest
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An implementation of the cross-validated difference in means (CVDM) test by Desmarais and Harden (2014) <doi:10.1007/s11135-013-9884-7> (see also Harden and Desmarais, 2011 <doi:10.1177/1532440011408929>) and the cross-validated median fit (CVMF) test by Desmarais and Harden (2012) <doi:10.1093/pan/mpr042>. These tests use leave-one-out cross-validated log-likelihoods to assist in selecting among model estimations. You can also utilize data from Golder (2010) <doi:10.1177/0010414009341714> and Joshi & Mason (2008) <doi:10.1177/0022343308096155> that are included to facilitate examples from real-world analysis.
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2025-03-25 |
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r-modelgood
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Bootstrap cross-validation for ROC, AUC and Brier score to assess and compare predictions of binary status responses.
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2025-03-25 |
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r-moc
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Fits and vizualize user defined finite mixture models for multivariate observations using maximum likelihood. (McLachlan, G., Peel, D. (2000) Finite Mixture Models. Wiley-Interscience.)
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2025-03-25 |
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r-mnp
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Fits the Bayesian multinomial probit model via Markov chain Monte Carlo. The multinomial probit model is often used to analyze the discrete choices made by individuals recorded in survey data. Examples where the multinomial probit model may be useful include the analysis of product choice by consumers in market research and the analysis of candidate or party choice by voters in electoral studies. The MNP package can also fit the model with different choice sets for each individual, and complete or partial individual choice orderings of the available alternatives from the choice set. The estimation is based on the efficient marginal data augmentation algorithm that is developed by Imai and van Dyk (2005). "A Bayesian Analysis of the Multinomial Probit Model Using the Data Augmentation." Journal of Econometrics, Vol. 124, No. 2 (February), pp. 311-334. <doi:10.1016/j.jeconom.2004.02.002> Detailed examples are given in Imai and van Dyk (2005). "MNP: R Package for Fitting the Multinomial Probit Model." Journal of Statistical Software, Vol. 14, No. 3 (May), pp. 1-32. <doi:10.18637/jss.v014.i03>.
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2025-03-25 |
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r-mnormpow
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Computes integral of f(x)*x_i^k on a product of intervals, where f is the density of a gaussian law. This a is small alteration of the mnormt code from A. Genz and A. Azzalini.
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2025-03-25 |
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r-mmsample
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Subset a control group to match an intervention group on a set of features using multivariate matching and propensity score calipers. Based on methods in Rosenbaum and Rubin (1985).
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2025-03-25 |
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r-mmeta
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Multiple 2 by 2 tables often arise in meta-analysis which combines statistical evidence from multiple studies. Two risks within the same study are possibly correlated because they share some common factors such as environment and population structure. This package implements a set of novel Bayesian approaches for multivariate meta analysis when the risks within the same study are independent or correlated. The exact posterior inference of odds ratio, relative risk, and risk difference given either a single 2 by 2 table or multiple 2 by 2 tables is provided. Luo, Chen, Su, Chu, (2014) <doi:10.18637/jss.v056.i11>, Chen, Luo, (2011) <doi:10.1002/sim.4248>, Chen, Chu, Luo, Nie, Chen, (2015) <doi:10.1177/0962280211430889>, Chen, Luo, Chu, Su, Nie, (2014) <doi:10.1080/03610926.2012.700379>, Chen, Luo, Chu, Wei, (2013) <doi:10.1080/19466315.2013.791483>.
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2025-03-25 |
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r-mmap
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R interface to POSIX mmap and Window's MapViewOfFile.
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2025-03-25 |
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r-mmand
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Provides tools for performing mathematical morphology operations, such as erosion and dilation, on data of arbitrary dimensionality. Can also be used for finding connected components, resampling, filtering, smoothing and other image processing-style operations.
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2025-03-25 |
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r-mm4lmm
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The main function MMEst() performs (Restricted) Maximum Likelihood in a variance component mixed models using a Min-Max (MM) algorithm (Laporte, F., Charcosset, A. & Mary-Huard, T. (2022) <doi:10.1371/journal.pcbi.1009659>).
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2025-03-25 |
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r-mlr3misc
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Frequently used helper functions and assertions used in 'mlr3' and its companion packages. Comes with helper functions for functional programming, for printing, to work with 'data.table', as well as some generally useful 'R6' classes. This package also supersedes the package 'BBmisc'.
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2025-03-25 |
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r-mlmmm
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Computational strategies for multivariate linear mixed-effects models with missing values, Schafer and Yucel (2002), Journal of Computational and Graphical Statistics, 11, 421-442.
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2025-03-25 |
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r-mlegp
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Maximum likelihood Gaussian process modeling for univariate and multi-dimensional outputs with diagnostic plots following Santner et al (2003) <doi:10.1007/978-1-4757-3799-8>. Contact the maintainer for a package version that includes sensitivity analysis.
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2025-03-25 |
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r-mlecens
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We provide functions to compute the nonparametric maximum likelihood estimator (MLE) for the bivariate distribution of (X,Y), when realizations of (X,Y) cannot be observed directly. To be more precise, we consider the situation where we observe a set of rectangles in R^2 that are known to contain the unobservable realizations of (X,Y). We compute the MLE based on such a set of rectangles. The methods can also be used for univariate censored data (see data set 'cosmesis'), and for censored data with competing risks (see data set 'menopause'). We also provide functions to visualize the observed data and the MLE.
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2025-03-25 |
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r-mlbench
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A collection of artificial and real-world machine learning benchmark problems, including, e.g., several data sets from the UCI repository.
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2025-03-25 |
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r-mkde
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Provides functions to compute and visualize movement-based kernel density estimates (MKDEs) for animal utilization distributions in 2 or 3 spatial dimensions.
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2025-03-25 |
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r-mixtureregltic
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Fit mixture regression models with nonsusceptibility/cure for left-truncated and interval-censored (LTIC) data (see Chen et al. (2013) <doi:10.1002/sim.5845>). This package also provides the nonparametric maximum likelihood estimator (NPMLE) for the survival/event curves with LTIC data.
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2025-03-25 |
