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r-comp2roc
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public |
Comparison of two ROC curves through the methodology proposed by Ana C. Braga.
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2024-01-16 |
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r-commonjavajars
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public |
Useful libraries for building a Java based GUI under R are provided.
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2024-01-16 |
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r-comics
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public |
Provided are Computational methods for Immune Cell-type Subsets, including:(1) DCQ (Digital Cell Quantifier) to infer global dynamic changes in immune cell quantities within a complex tissue; and (2) VoCAL (Variation of Cell-type Abundance Loci) a deconvolution-based method that utilizes transcriptome data to infer the quantities of immune-cell types, and then uses these quantitative traits to uncover the underlying DNA loci.
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2024-01-16 |
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r-colourpicker
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public |
A colour picker that can be used as an input in 'Shiny' apps or Rmarkdown documents. The colour picker supports alpha opacity, custom colour palettes, and many more options. A Plot Colour Helper tool is available as an 'RStudio' Addin, which helps you pick colours to use in your plots. A more generic Colour Picker 'RStudio' Addin is also provided to let you select colours to use in your R code.
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2024-01-16 |
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r-comf
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public |
Calculation of various common and less common comfort indices such as predicted mean vote or the two node model. Converts physical variables such as relative to absolute humidity and evaluates the performance of comfort indices.
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2024-01-16 |
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r-comclim
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public |
Computes community climate statistics for volume and mismatch using species' climate niches either unscaled or scaled relative to a regional species pool. These statistics can be used to describe biogeographic patterns and infer community assembly processes. Includes a vignette outlining usage.
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2024-01-16 |
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r-cols4all
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public |
Color palettes for all people, including those with color vision deficiency. Popular color palette series have been organized by type and have been scored on several properties such as color-blind-friendliness and fairness (i.e. do colors stand out equally?). Own palettes can also be loaded and analysed. Besides the common palette types (categorical, sequential, and diverging) it also includes bivariate color palettes. Furthermore, a color for missing values is assigned to each palette.
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2024-01-16 |
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r-combins
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public |
Series of partially balanced incomplete block designs (PBIB) based on the combinatory method (S) introduced in (Imane Rezgui et al, 2014) <doi:10.3844/jmssp.2014.45.48>; and it gives their associated U-type design.
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2024-01-16 |
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r-combinat
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public |
routines for combinatorics
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2024-01-16 |
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r-combineportfolio
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public |
Estimation of optimal portfolio weights as combination of simple portfolio strategies, like the tangency, global minimum variance (GMV) or naive (1/N) portfolio. It is based on a utility maximizing 8-fund rule. Popular special cases like the Kan-Zhou(2007) 2-fund and 3-fund rule or the Tu-Zhou(2011) estimator are nested.
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2024-01-16 |
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r-colt
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public |
A collection of command-line color styles based on the 'crayon' package. 'Colt' styles are defined in themes that can easily be switched, to ensure command line output looks nice on dark as well as light consoles.
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2024-01-16 |
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r-combat
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public |
Genome-wide association studies (GWAS) have been widely used for identifying common variants associated with complex diseases. Due to the small effect sizes of common variants, the power to detect individual risk variants is generally low. Complementary to SNP-level analysis, a variety of gene-based association tests have been proposed. However, the power of existing gene-based tests is often dependent on the underlying genetic models, and it is not known a priori which test is optimal. Here we proposed COMBined Association Test (COMBAT) to incorporate strengths from multiple existing gene-based tests, including VEGAS, GATES and simpleM. Compared to individual tests, COMBAT shows higher overall performance and robustness across a wide range of genetic models. The algorithm behind this method is described in Wang et al (2017) <doi:10.1534/genetics.117.300257>.
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2024-01-16 |
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r-colorscience
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public |
Methods and data for color science - color conversions by observer, illuminant, and gamma. Color matching functions and chromaticity diagrams. Color indices, color differences, and spectral data conversion/analysis.
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2024-01-16 |
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r-coloc
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public |
Performs the colocalisation tests described in Giambartolomei et al (2013) <doi:10.1371/journal.pgen.1004383>, Wallace (2020) <doi:10.1371/journal.pgen.1008720>, Wallace (2021) <doi:10.1371/journal.pgen.1009440>.
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2024-01-16 |
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r-colourlovers
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public |
Provides access to the COLOURlovers <https://www.colourlovers.com/> API, which offers color inspiration and color palettes.
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2024-01-16 |
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r-colorblindness
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public |
Provide the safe color set for color blindness, the simulator of protanopia, deuteranopia. The color sets are collected from: Wong, B. (2011) <doi:10.1038/nmeth.1618>, and <http://mkweb.bcgsc.ca/biovis2012/>. The simulations of the appearance of the colors to color-deficient viewers were based on algorithms in Vienot, F., Brettel, H. and Mollon, J.D. (1999) <doi:10.1002/(SICI)1520-6378(199908)24:4%3C243::AID-COL5%3E3.0.CO;2-3>. The cvdPlot() function to generate 'ggplot' grobs of simulations were modified from <https://github.com/clauswilke/colorblindr>.
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2024-01-16 |
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r-collapsibletree
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public |
Interactive Reingold-Tilford tree diagrams created using 'D3.js', where every node can be expanded and collapsed by clicking on it. Tooltips and color gradients can be mapped to nodes using a numeric column in the source data frame. See 'collapsibleTree' website for more information and examples.
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2024-01-16 |
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r-colorramps
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public |
Builds gradient color maps.
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2024-01-16 |
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r-colorr
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public |
Color palettes for EPL, MLB, NBA, NHL, and NFL teams.
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2024-01-16 |
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r-colorhcplot
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public |
Build dendrograms with sample groups highlighted by different colors. Visualize results of hierarchical clustering analyses as dendrograms whose leaves and labels are colored according to sample grouping. Assess whether data point grouping aligns to naturally occurring clusters.
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2024-01-16 |
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r-coefplot
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public |
Plots the coefficients from model objects. This very quickly shows the user the point estimates and confidence intervals for fitted models.
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2024-01-16 |
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r-codalm
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public |
Implements the expectation-maximization (EM) algorithm as described in Fiksel et al. (2021) <doi:10.1111/biom.13465> for transformation-free linear regression for compositional outcomes and predictors.
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2024-01-16 |
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r-colmozzie
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public |
Weekly notified dengue cases and climate variables in Colombo district Sri Lanka from 2008/ week-52 to 2014/ week-21.
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2024-01-16 |
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r-codingmatrices
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public |
A collection of coding functions as alternatives to the standard functions in the stats package, which have names starting with 'contr.'. Their main advantage is that they provide a consistent method for defining marginal effects in factorial models. In a simple one-way ANOVA model the intercept term is always the simple average of the class means.
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2024-01-16 |
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r-cointreg
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public |
Cointegration methods are widely used in empirical macroeconomics and empirical finance. It is well known that in a cointegrating regression the ordinary least squares (OLS) estimator of the parameters is super-consistent, i.e. converges at rate equal to the sample size T. When the regressors are endogenous, the limiting distribution of the OLS estimator is contaminated by so-called second order bias terms, see e.g. Phillips and Hansen (1990) <DOI:10.2307/2297545>. The presence of these bias terms renders inference difficult. Consequently, several modifications to OLS that lead to zero mean Gaussian mixture limiting distributions have been proposed, which in turn make standard asymptotic inference feasible. These methods include the fully modified OLS (FM-OLS) approach of Phillips and Hansen (1990) <DOI:10.2307/2297545>, the dynamic OLS (D-OLS) approach of Phillips and Loretan (1991) <DOI:10.2307/2298004>, Saikkonen (1991) <DOI:10.1017/S0266466600004217> and Stock and Watson (1993) <DOI:10.2307/2951763> and the new estimation approach called integrated modified OLS (IM-OLS) of Vogelsang and Wagner (2014) <DOI:10.1016/j.jeconom.2013.10.015>. The latter is based on an augmented partial sum (integration) transformation of the regression model. IM-OLS is similar in spirit to the FM- and D-OLS approaches, with the key difference that it does not require estimation of long run variance matrices and avoids the need to choose tuning parameters (kernels, bandwidths, lags). However, inference does require that a long run variance be scaled out. This package provides functions for the parameter estimation and inference with all three modified OLS approaches. That includes the automatic bandwidth selection approaches of Andrews (1991) <DOI:10.2307/2938229> and of Newey and West (1994) <DOI:10.2307/2297912> as well as the calculation of the long run variance.
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2024-01-16 |
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r-cointmonitor
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public |
We propose a consistent monitoring procedure to detect a structural change from a cointegrating relationship to a spurious relationship. The procedure is based on residuals from modified least squares estimation, using either Fully Modified, Dynamic or Integrated Modified OLS. It is inspired by Chu et al. (1996) <DOI:10.2307/2171955> in that it is based on parameter estimation on a pre-break "calibration" period only, rather than being based on sequential estimation over the full sample. See the discussion paper <DOI:10.2139/ssrn.2624657> for further information. This package provides the monitoring procedures for both the cointegration and the stationarity case (while the latter is just a special case of the former one) as well as printing and plotting methods for a clear presentation of the results.
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2024-01-16 |
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r-cofra
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public |
Calculates complete functional regulation analysis and visualize the results in a single heatmap. The provided example data is for biological data but the methodology can be used for large data sets to compare quantitative entities that can be grouped. For example, a store might divide entities into cloth, food, car products etc and want to see how sales changes in the groups after some event. The theoretical background for the calculations are provided in New insights into functional regulation in MS-based drug profiling, Ana Sofia Carvalho, Henrik Molina & Rune Matthiesen, Scientific Reports <doi:10.1038/srep18826>.
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2024-01-16 |
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r-cofad
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public |
Contrast analysis for factorial designs is an alternative to the classical ANOVA approach with the advantage of testing focused hypothesis. The method is mainly based on Rosenthal, Rosnow and Rubin (2000, ISBN:978-0521659802) and Sedlmeier and Renkewitz (2018, ISBN:978-3868943214).
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2024-01-16 |
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r-coenocliner
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public |
Simulate species occurrence and abundances (counts) along gradients.
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2024-01-16 |
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r-codetools
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None |
Code analysis tools for R.
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2024-01-16 |
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r-codina
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public |
Categorize links and nodes from multiple networks in 3 categories: Common links (alpha) specific links (gamma), and different links (beta). Also categorizes the links into sub-categories and groups. The package includes a visualization tool for the networks. More information about the methodology can be found at: Gysi et. al., 2018 <arXiv:1802.00828>.
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2024-01-16 |
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r-code
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public |
Generates all necessary C functions allowing the user to work with the compiled-code interface of ode() and bvptwp(). The implementation supports "forcings" and "events". Also provides functions to symbolically compute Jacobians, sensitivity equations and adjoint sensitivities being the basis for sensitivity analysis.
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2024-01-16 |
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r-codatags
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public |
Computes genomic breeding values using external information on the markers. The package fits a linear mixed model with heteroscedastic random effects, where the random effect variance is fitted using a linear predictor and a log link. The method is described in Mouresan, Selle and Ronnegard (2019) <doi:10.1101/636746>.
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2024-01-16 |
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r-cobalt
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public |
Generate balance tables and plots for covariates of groups preprocessed through matching, weighting or subclassification, for example, using propensity scores. Includes integration with 'MatchIt', 'twang', 'Matching', 'optmatch', 'CBPS', 'ebal', 'WeightIt', 'cem', 'sbw', and 'designmatch' for assessing balance on the output of their preprocessing functions. Users can also specify data for balance assessment not generated through the above packages. Also included are methods for assessing balance in clustered or multiply imputed data sets or data sets with multi-category, continuous, or longitudinal treatments.
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2024-01-16 |
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r-coda
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None |
Provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain.
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2024-01-16 |
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r-coarsedatatools
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public |
Functions to analyze coarse data. Specifically, it contains functions to (1) fit parametric accelerated failure time models to interval-censored survival time data, and (2) estimate the case-fatality ratio in scenarios with under-reporting. This package's development was motivated by applications to infectious disease: in particular, problems with estimating the incubation period and the case fatality ratio of a given disease. Sample data files are included in the package. See Reich et al. (2009) <doi:10.1002/sim.3659>, Reich et al. (2012) <doi:10.1111/j.1541-0420.2011.01709.x>, and Lessler et al. (2009) <doi:10.1016/S1473-3099(09)70069-6>.
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2024-01-16 |
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r-cocron
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public |
Statistical tests for the comparison between two or more alpha coefficients based on either dependent or independent groups of individuals. A web interface is available at http://comparingcronbachalphas.org. A plugin for the R GUI and IDE RKWard is included. Please install RKWard from https:// rkward.kde.org to use this feature. The respective R package 'rkward' cannot be installed directly from a repository, as it is a part of RKWard.
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2024-01-16 |
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r-coconut
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public |
Allows for pooled analysis of microarray data by batch-correcting control samples, and then applying the derived correction parameters to non-control samples to obtain bias-free, inter-dataset corrected data.
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2024-01-16 |
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r-cocor
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public |
Statistical tests for the comparison between two correlations based on either independent or dependent groups. Dependent correlations can either be overlapping or nonoverlapping. A web interface is available on the website <http://comparingcorrelations.org>. A plugin for the R GUI and IDE RKWard is included. Please install RKWard from <https://rkward.kde.org> to use this feature. The respective R package 'rkward' cannot be installed directly from a repository, as it is a part of RKWard.
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2024-01-16 |
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r-clustree
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public |
Deciding what resolution to use can be a difficult question when approaching a clustering analysis. One way to approach this problem is to look at how samples move as the number of clusters increases. This package allows you to produce clustering trees, a visualisation for interrogating clusterings as resolution increases.
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2024-01-16 |
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r-coclust
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public |
A copula based clustering algorithm that finds clusters according to the complex multivariate dependence structure of the data generating process. The updated version of the algorithm is described in Di Lascio, F.M.L. and Giannerini, S. (2016). "Clustering dependent observations with copula functions". Statistical Papers, p.1-17. <doi:10.1007/s00362-016-0822-3>.
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2024-01-16 |
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r-cobiclust
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public |
Implementation of a probabilistic method for biclustering adapted to overdispersed count data. It is a Gamma-Poisson Latent Block Model. It also implements two selection criteria in order to select the number of biclusters.
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2024-01-16 |
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r-cnorm
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public |
Conventional methods for producing standard scores or percentiles in psychometrics or biometrics are often plagued with 'jumps' or 'gaps' (i.e., discontinuities) in norm tables and low confidence for assessing extreme scores. The continuous norming method introduced by A. Lenhard et al. (2016, <doi:10.1177/1073191116656437>; 2019, <doi:10.1371/journal.pone.0222279>; 2021 <doi: 10.1177/0013164420928457>) estimates percentile development (e. g. over age) and generates continuous test norm scores on the basis of the raw data from standardization samples, without requiring assumptions about the distribution of the raw data: Norm scores are directly established from raw data by modeling the latter ones as a function of both percentile scores and an explanatory variable (e.g., age). The method minimizes bias arising from sampling and measurement error, while handling marked deviations from normality, addressing bottom or ceiling effects and capturing almost all of the variance in the original norm data sample. It includes procedures for post stratification of norm samples to overcome bias in data collection and to mitigate violations of representativeness. An online demonstration is available via <https://cnorm.shinyapps.io/cNORM/>.
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2024-01-16 |
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r-cmvnorm
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public |
Various utilities for the complex multivariate Gaussian distribution and complex Gaussian processes.
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2024-01-16 |
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r-cmrutils
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public |
A collection of useful helper routines developed by students of the Center for Mathematical Research, Stankin, Moscow.
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2024-01-16 |
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r-cmplot
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public |
Manhattan plot, a type of scatter plot, was widely used to display the association results. However, it is usually time-consuming and laborious for a non-specialist user to write scripts and adjust parameters of an elaborate plot. Moreover, the ever-growing traits measured have necessitated the integration of results from different Genome-wide association study researches. Circle Manhattan Plot is the first open R package that can lay out. Genome-wide association study P-value results in both traditional rectangular patterns, QQ-plot and novel circular ones. United in only one bull's eye style plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals. Additional functions include: highlight signals, a group of SNPs, chromosome visualization and candidate genes around SNPs.
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2024-01-16 |
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r-cmocean
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public |
Perceptually uniform palettes for commonly used variables in oceanography as functions taking an integer and producing character vectors of colours. See Thyng, K.M., Greene, C.A., Hetland, R.D., Zimmerle, H.M. and S.F. DiMarco (2016) <doi:10.5670/oceanog.2016.66> for the guidelines adhered to when creating the palettes.
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2024-01-16 |
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r-cmna
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public |
Provides the source and examples for James P. Howard, II, "Computational Methods for Numerical Analysis with R," <https://jameshoward.us/cmna/>, a book on numerical methods in R.
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2024-01-16 |
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r-cmaesr
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public |
Pure R implementation of the Covariance Matrix Adaptation - Evolution Strategy (CMA-ES) with optional restarts (IPOP-CMA-ES).
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2024-01-16 |
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r-cmm
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public |
Quite extensive package for maximum likelihood estimation and weighted least squares estimation of categorical marginal models (CMMs; e.g., Bergsma and Rudas, 2002, <http://www.jstor.org/stable/2700006?; Bergsma, Croon and Hagenaars, 2009, <DOI:10.1007/b12532>.
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2024-01-16 |
