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r-metaboqc
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public |
Takes QC signal for each day and normalize metabolomic data that has been acquired in a certain period of time. At least three QC per day are required.
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2023-06-16 |
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r-measures
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public |
Provides the biggest amount of statistical measures in the whole R world. Includes measures of regression, (multiclass) classification and multilabel classification. The measures come mainly from the 'mlr' package and were programed by several 'mlr' developers.
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2023-06-16 |
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r-mbir
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Allows practitioners and researchers a wholesale approach for deriving magnitude-based inferences from raw data. A major goal of 'mbir' is to programmatically detect appropriate statistical tests to run in lieu of relying on practitioners to determine correct stepwise procedures independently.
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2023-06-16 |
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r-mbcluster.seq
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Cluster genes based on Poisson or Negative-Binomial model for RNA-Seq or other digital gene expression (DGE) data
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2023-06-16 |
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r-mathgraph
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Simple tools for constructing and manipulating objects of class mathgraph from the book "S Poetry", available at <http://www.burns-stat.com/pages/spoetry.html>.
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2023-06-16 |
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r-mancie
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High-dimensional data integration is a critical but difficult problem in genomics research because of potential biases from high-throughput experiments. We present MANCIE, a computational method for integrating two genomic data sets with homogenous dimensions from different sources based on a PCA procedure as an approximation to a Bayesian approach.
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2023-06-16 |
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r-longroc
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Time-dependent Receiver Operating Characteristic curves, Area Under the Curve, and Net Reclassification Indexes for repeated measures. It is based on methods in Barbati and Farcomeni (2017) <doi:10.1007/s10260-017-0410-2>.
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2023-06-16 |
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r-logofgamma
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Uses approximations to compute the natural logarithm of the Gamma function for large values.
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2023-06-16 |
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r-logger
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Inspired by the the 'futile.logger' R package and 'logging' Python module, this utility provides a flexible and extensible way of formatting and delivering log messages with low overhead.
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2023-06-16 |
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r-locfdr
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Computation of local false discovery rates.
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2023-06-16 |
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r-lllcrc
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Applies local log-linear capture-recapture models (LLLMs) for closed populations, as described in the doctoral thesis of Zachary Kurtz. The method is relevant when there are 3-5 capture occasions, with auxiliary covariates available for all capture occasions. As part of estimating the number of missing population units, the method estimates the "rate of missingness" as it varies over the covariate space. In addition, user-friendly functions are provided to recreate (approximately) the method of Zwane and van der Heijden (2004), which applied the VGAM package in a way that is closely related to LLLMs.
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2023-06-16 |
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r-listest
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Tests for independence between X and Y computed from a paired sample (x1,y1),...(xn,yn) of (X,Y), using one of the following statistics (a) the Longest Increasing Subsequence (Ln), (b) JLn, a Jackknife version of Ln or (c) JLMn, a Jackknife version of the longest monotonic subsequence. This family of tests can be applied under the assumption of continuity of X and Y.
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2023-06-16 |
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r-linreginteractive
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Interactive visualization of effects, response functions and marginal effects for different kinds of regression models. In this version linear regression models, generalized linear models, generalized additive models and linear mixed-effects models are supported. Major features are the interactive approach and the handling of the effects of categorical covariates: if two or more factors are used as covariates every combination of the levels of each factor is treated separately. The automatic calculation of marginal effects and a number of possibilities to customize the graphical output are useful features as well.
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2023-06-16 |
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r-legocolors
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Provides a dataset containing several color naming conventions established by multiple sources, along with associated color metadata. The package also provides related helper functions for mapping among the different Lego color naming conventions and between Lego colors, hex colors, and 'R' color names, making it easy to convert any color palette to one based on existing Lego colors while keeping as close to the original color palette as possible. The functions use nearest color matching based on Euclidean distance in RGB space. Naming conventions for color mapping include those from 'BrickLink' (<https://www.bricklink.com>), 'The Lego Group' (<https://www.lego.com>), 'LDraw' (<https://www.ldraw.org/>), and 'Peeron' (<http://www.peeron.com/>).
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2023-06-16 |
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r-learningr
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Crabs in the English channel, deer skulls, English monarchs, half-caste Manga characters, Jamaican cities, Shakespeare's The Tempest, drugged up cyclists and sexually transmitted diseases.
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2023-06-16 |
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r-leapfrog
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Contains LEAPFrOG Gradient Optimisation and Expectation Maximisation functions for inferring parental admixture proportions from an offspring with SNP genotypes.
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2023-06-16 |
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r-nna
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Calculates spatial pattern analysis using a T-square sample procedure. This method is based on two measures "x" and "y". "x" - Distance from the random point to the nearest individual. "y" - Distance from individual to its nearest neighbor. This is a methodology commonly used in phytosociology or marine benthos ecology to analyze the species' distribution (random, uniform or clumped patterns). Ludwig & Reynolds (1988, ISBN:0471832359).
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2023-06-16 |
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r-nmainla
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Performs network meta-analysis using integrated nested Laplace approximations ('INLA'). Includes methods to assess the heterogeneity and inconsistency in the network. Contains more than ten different network meta-analysis data. 'INLA' package can be obtained from <http://www.r-inla.org>. We recommend the testing version.
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2023-06-16 |
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r-nlstools
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Several tools for assessing the quality of fit of a gaussian nonlinear model are provided.
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2023-06-16 |
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r-nlsmsn
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Fit univariate non-linear scale mixture of skew-normal(NL-SMSN) regression.
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2023-06-16 |
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r-nhds
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The National Hospital Discharge Survey (2010) summarizes the state of patients at the end of their hospital admissions. The US CDC publishes the data in the public domain, and describes it as follows: The National Hospital Discharge Survey (NHDS) is a continuing nationwide sample survey of short-stay hospitals in the United States. The scope of NHDS encompasses patients discharged from noninstitutional hospitals, exclusive of military and Department of Veterans Affairs hospitals, located in the 50 States and the District of Columbia. Only hospitals having six or more beds for in-patient use are included in the survey. See <https://www.cdc.gov/nchs/nhds> for more information.
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2023-06-16 |
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r-nbc4va
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An implementation of the Naive Bayes Classifier (NBC) algorithm used for Verbal Autopsy (VA) built on code from Miasnikof et al (2015) <DOI:10.1186/s12916-015-0521-2>.
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2023-06-16 |
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r-nat.utils
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Utility functions that may be of general interest but are specifically required by the 'NeuroAnatomy Toolbox' ('nat'). Includes functions to provide a basic make style system to update files based on timestamp information, file locking and 'touch' utility. Convenience functions for working with file paths include 'abs2rel', 'split_path' and 'common_path'. Finally there are utility functions for working with 'zip' and 'gzip' files including integrity tests.
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2023-06-16 |
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r-myepisodes
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Useful functions for accessing MyEpisodes feeds and episode information as well as other tv episode related actions through www.myepisodes.com
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2023-06-16 |
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r-mwright
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Implements random number generation, plotting, and estimation algorithms for the two-parameter one-sided and two-sided M-Wright (Mainardi-Wright) family. The M-Wright distributions naturally generalize the widely used one-sided (Airy and half-normal or half-Gaussian) and symmetric (Airy and Gaussian or normal) models. These are widely studied in time-fractional differential equations. References: Cahoy and Minkabo (2017) <doi:10.3233/MAS-170388>; Cahoy (2012) <doi:10.1007/s00180-011-0269-x>; Cahoy (2012) <doi:10.1080/03610926.2010.543299>; Cahoy (2011); Mainardi, Mura, and Pagnini (2010) <doi:10.1155/2010/104505>.
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2023-06-16 |
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r-multiord
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A method for multivariate ordinal data generation given marginal distributions and correlation matrix based on the methodology proposed by Demirtas (2006).
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2023-06-16 |
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r-mthapower
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Calculate Sample Size and Power for Association Studies Involving Mitochondrial DNA Haplogroups. Based on formulae by Samuels et al. AJHG, 2006. 78(4):713-720. <DOI:10.1086/502682>.
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2023-06-16 |
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r-mssqlr
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Can be used to query data from data from Microsoft SQL Server (MSSQL, see <http://www.microsoft.com/sqlserver/> for more information). Based on the concepts of Entity Framework, the package allows querying data from MSSQL Database.
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2023-06-16 |
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r-msma
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Several functions can be used to analyze multiblock multivariable data. If the input is a single matrix, then principal components analysis (PCA) is implemented. If the input is a list of matrices, then multiblock PCA is implemented. If the input is two matrices, for exploratory and objective variables, then partial least squares (PLS) analysis is implemented. If the input is two lists of matrices, for exploratory and objective variables, then multiblock PLS analysis is implemented. Additionally, if an extra outcome variable is specified, then a supervised version of the methods above is implemented. For each method, sparse modeling is also incorporated. Functions for selecting the number of components and regularized parameters are also provided.
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2023-06-16 |
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r-mpt
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Fitting and testing multinomial processing tree (MPT) models, a class of nonlinear models for categorical data. The parameters are the link probabilities of a tree-like graph and represent the latent cognitive processing steps executed to arrive at observable response categories (Batchelder & Riefer, 1999 <doi:10.3758/bf03210812>; Erdfelder et al., 2009 <doi:10.1027/0044-3409.217.3.108>; Riefer & Batchelder, 1988 <doi:10.1037/0033-295x.95.3.318>).
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2023-06-16 |
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r-mountainplot
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Lattice functions for drawing folded empirical cumulative distribution plots, or mountain plots. A mountain plot is similar to an empirical CDF plot, except that the curve increases from 0 to 0.5, then decreases from 0.5 to 1 using an inverted scale at the right side.
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2023-06-16 |
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r-mondrian
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The unique function of this package allows representing in a single graph the relative occurrence and co-occurrence of events measured in a sample. As examples, the package was applied to describe the occurrence and co-occurrence of different species of bacterial or viral symbionts infecting arthropods at the individual level. The graphics allows determining the prevalence of each symbiont and the patterns of multiple infections (i.e. how different symbionts share or not the same individual hosts). We named the package after the famous painter as the graphical output recalls Mondrian’s paintings.
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2023-06-16 |
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r-modelwordcloud
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Makes a word cloud of text, sized by the frequency of the word, and colored either by user-specified colors or colored by the strength of the coefficient of that text derived from a regression model.
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2023-06-16 |
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r-mockery
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The two main functionalities of this package are creating mock objects (functions) and selectively intercepting calls to a given function that originate in some other function. It can be used with any testing framework available for R. Mock objects can be injected with either this package's own stub() function or a similar with_mock() facility present in the 'testthat' package.
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2023-06-16 |
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r-mmpp
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public |
Compute similarities and distances between marked point processes.
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2023-06-16 |
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r-mlbstats
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Computational functions for player metrics in major league baseball including batting, pitching, fielding, base-running, and overall player statistics. This package is actively maintained with new metrics being added as they are developed.
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2023-06-16 |
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r-mkssd
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mkssd is a package that generates efficient balanced non-aliased multi-level k-circulant supersaturated designs by interchanging the elements of the generator vector. The package tries to generate a supersaturated design that has chisquare efficiency more than user specified efficiency level (mef). The package also displays the progress of generation of an efficient multi-level k-circulant design through a progress bar. The progress of 100% means that one full round of interchange is completed. More than one full round (typically 4-5 rounds) of interchange may be required for larger designs.
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2023-06-16 |
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r-mixtureinf
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Functions for computing the penalized maximum likelihood estimate (PMLE) or maximum likelihood estimate (MLE), testing the order of a finite mixture model using EM-test, drawing histogram of observations and the fitted density or probability mass function of the mixture model.
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2023-06-16 |
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r-mhg
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Runs a minimum-hypergeometric (mHG) test as described in: Eden, E. (2007). Discovering Motifs in Ranked Lists of DNA Sequences. Haifa.
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2023-06-16 |
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r-mglm
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Provides functions that (1) fit multivariate discrete distributions, (2) generate random numbers from multivariate discrete distributions, and (3) run regression and penalized regression on the multivariate categorical response data. Implemented models include: multinomial logit model, Dirichlet multinomial model, generalized Dirichlet multinomial model, and negative multinomial model. Making the best of the minorization-maximization (MM) algorithm and Newton-Raphson method, we derive and implement stable and efficient algorithms to find the maximum likelihood estimates. On a multi-core machine, multi-threading is supported.
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2023-06-16 |
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r-mfilter
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The mFilter package implements several time series filters useful for smoothing and extracting trend and cyclical components of a time series. The routines are commonly used in economics and finance, however they should also be interest to other areas. Currently, Christiano-Fitzgerald, Baxter-King, Hodrick-Prescott, Butterworth, and trigonometric regression filters are included in the package.
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2023-06-16 |
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r-metasubtract
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If results from a meta-GWAS are used for validation in one of the cohorts that was included in the meta-analysis, this will yield biased (i.e. too optimistic) results. The validation cohort needs to be independent from the meta-Genome-Wide-Association-Study (meta-GWAS) results. 'MetaSubtract' will subtract the results of the respective cohort from the meta-GWAS results analytically without having to redo the meta-GWAS analysis using the leave-one-out methodology. It can handle different meta-analyses methods and takes into account if single or double genomic control correction was applied to the original meta-analysis. It can also handle different meta-analysis methods. It can be used for whole GWAS, but also for a limited set of genetic markers.
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2023-06-16 |
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r-mctest
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Package computes popular and widely used multicollinearity diagnostic measures. Package also indicates which regressors may be the reason of collinearity among regressors.
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2023-06-16 |
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r-mcparalleldo
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Provides a function that wraps mcparallel() and mccollect() from 'parallel' with temporary variables and a task handler. Wrapped in this way the results of an mcparallel() call can be returned to the R session when the fork is complete without explicitly issuing a specific mccollect() to retrieve the value. Outside of top-level tasks, multiple mcparallel() jobs can be retrieved with a single call to mcparallelDoCheck().
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2023-06-16 |
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r-mattools
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This package in includes functions for receiver operating characteristic (ROC) analyses as well as Monte Carlo simulation. It includes specific graphical functions for interpreting the output of these techniques.
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2023-06-16 |
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r-matrixtests
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Functions to perform fast statistical hypothesis tests on rows/columns of matrices. The main goals are: 1) speed via vectorization, 2) output that is detailed and easy to use, 3) compatibility with tests implemented in R (like those available in the 'stats' package).
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2023-06-16 |
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r-matrixeqtl
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Matrix eQTL is designed for fast eQTL analysis on large datasets. Matrix eQTL can test for association between genotype and gene expression using linear regression with either additive or ANOVA genotype effects. The models can include covariates to account for factors as population stratification, gender, and clinical variables. It also supports models with heteroscedastic and/or correlated errors, false discovery rate estimation and separate treatment of local (cis) and distant (trans) eQTLs.
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2023-06-16 |
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r-matrixcalc
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A collection of functions to support matrix calculations for probability, econometric and numerical analysis. There are additional functions that are comparable to APL functions which are useful for actuarial models such as pension mathematics. This package is used for teaching and research purposes at the Department of Finance and Risk Engineering, New York University, Polytechnic Institute, Brooklyn, NY 11201.
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2023-06-16 |
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r-markmyassignment
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Automatic marking of R assignments for students and teachers based on 'testthat' test suites.
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2023-06-16 |
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r-mareymap
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Local recombination rates are graphically estimated across a genome using Marey maps.
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2023-06-16 |
