Package Name | Access | Summary | Updated |
---|---|---|---|

r-glm2 | public | Fits generalized linear models using the same model specification as glm in the stats package, but with a modified default fitting method that provides greater stability for models that may fail to converge using glm. | 2019-07-21 |

r-giant | public | Toolbox for various enrichment analysis methods and quantification of uncertainty of gene sets. | 2019-07-21 |

r-ggseqlogo | public | The extensive range of functions provided by this package makes it possible to draw highly versatile sequence logos. Features include, but not limited to, modifying colour schemes and fonts used to draw the logo, generating multiple logo plots, and aiding the visualisation with annotations. Sequence logos can easily be combined with other plots 'ggplot2' plots. | 2019-07-21 |

r-ggm | public | Functions and datasets for maximum likelihood fitting of some classes of graphical Markov models. | 2019-07-21 |

r-ggmuller | public | Create plots that combine a phylogeny and frequency dynamics. Phylogenetic input can be a generic adjacency matrix or a tree of class "phylo". Inspired by similar plots in publications of the labs of RE Lenski and JE Barrick. Named for HJ Muller (who popularised such plots) and H Wickham (whose code this package exploits). | 2019-07-21 |

r-hh | public | Support software for Statistical Analysis and Data Display (Second Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package. | 2019-07-21 |

r-icluster | public | Integrative clustering of multiple genomic data types using a joint latent variable model. | 2019-07-21 |

r-huge | public | Provides a general framework for high-dimensional undirected graph estimation. It integrates data preprocessing, neighborhood screening, graph estimation, and model selection techniques into a pipeline. In preprocessing stage, the nonparanormal(npn) transformation is applied to help relax the normality assumption. In the graph estimation stage, the graph structure is estimated by Meinshausen-Buhlmann graph estimation or the graphical lasso, and both methods can be further accelerated by the lossy screening rule preselecting the neighborhood of each variable by correlation thresholding. We target on high-dimensional data analysis usually d >> n, and the computation is memory-optimized using the sparse matrix output. We also provide a computationally efficient approach, correlation thresholding graph estimation. Three regularization/thresholding parameter selection methods are included in this package: (1)stability approach for regularization selection (2) rotation information criterion (3) extended Bayesian information criterion which is only available for the graphical lasso. | 2019-07-21 |

r-grf | public | A pluggable package for forest-based statistical estimation and inference. GRF currently provides methods for non-parametric least-squares regression, quantile regression, and treatment effect estimation (optionally using instrumental variables). This package is currently in beta, and we expect to make continual improvements to its performance and usability. | 2019-07-21 |

r-hypergea | public | Performs (exact) hypergeometric tests on IxJ and 2x2x2 contingency tables using parallelized C code. | 2019-07-21 |

r-icsnp | public | Tools for multivariate nonparametrics, as location tests based on marginal ranks, spatial median and spatial signs computation, Hotelling's T-test, estimates of shape are implemented. | 2019-07-21 |

r-hashmap | public | Provides a hash table class for fast key-value storage of atomic vector types. | 2019-07-21 |

r-imbalance | public | Class imbalance usually damages the performance of classifiers. Thus, it is important to treat data before applying a classifier algorithm. This package includes recent resampling algorithms in the literature. | 2019-07-21 |

r-hiclimr | public | A tool for Hierarchical Climate Regionalization applicable to any correlation-based clustering. It adds several features and a new clustering method (called, 'regional' linkage) to hierarchical clustering in R ('hclust' function in 'stats' library): data regridding, coarsening spatial resolution, geographic masking, contiguity-constrained clustering, data filtering by mean and/or variance thresholds, data preprocessing (detrending, standardization, and PCA), faster correlation function with preliminary big data support, different clustering methods, hybrid hierarchical clustering, multivariate clustering (MVC), cluster validation, visualization of regionalization results, and exporting region map and mean timeseries into NetCDF-4 file. | 2019-07-21 |

r-hiddenmarkov | public | Contains functions for the analysis of Discrete Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated Poisson Process. It includes functions for simulation, parameter estimation, and the Viterbi algorithm. See the topic "HiddenMarkov" for an introduction to the package, and "Change Log" for a list of recent changes. The algorithms are based of those of Walter Zucchini. | 2019-07-21 |

r-gsmoothr | public | Tools rewritten in C for various smoothing tasks | 2019-07-21 |

r-huxtable | public | Like 'xtable', creates styled tables. Export to HTML, LaTeX, 'Word', 'Excel', 'PowerPoint' and RTF. Simple, modern interface to manipulate borders, size, position, captions, colours, text styles and number formatting. Table cells can span multiple rows and/or columns. Includes a 'huxreg' function for creation of regression tables, and 'quick_*' one-liners to print data to a new document. | 2019-07-21 |

r-ibd | public | A collection of several utility functions related to binary incomplete block designs. The package contains function to generate A- and D-efficient binary incomplete block designs with given numbers of treatments, number of blocks and block size. The package also contains function to generate an incomplete block design with specified concurrence matrix. There are functions to generate balanced treatment incomplete block designs and incomplete block designs for test versus control treatments comparisons with specified concurrence matrix. Package also allows performing analysis of variance of data and computing estimated marginal means of factors from experiments using a connected incomplete block design. Tests of hypothesis of treatment contrasts in incomplete block design set up is supported. | 2019-07-21 |

r-hwriter | public | Easy-to-use and versatile functions to output R objects in HTML format | 2019-07-21 |

r-ic.infer | public | Implements inequality constrained inference. This includes parameter estimation in normal (linear) models under linear equality and inequality constraints, as well as normal likelihood ratio tests involving inequality-constrained hypotheses. For inequality-constrained linear models, averaging over R-squared for different orderings of regressors is also included. | 2019-07-21 |

r-ggraph | public | The grammar of graphics as implemented in ggplot2 is a poor fit for graph and network visualizations due to its reliance on tabular data input. ggraph is an extension of the ggplot2 API tailored to graph visualizations and provides the same flexible approach to building up plots layer by layer. | 2019-07-21 |

r-ic10trainingdata | public | Training datasets for iC10; which implements the classifier described in the paper 'Genome-driven integrated classification of breast cancer validated in over 7,500 samples' (Ali HR et al., Genome Biology 2014). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group. Genomic annotation for the training dataset has been obtained from Mark Dunning's lluminaHumanv3.db package. | 2019-07-21 |

r-iml | public | Interpretability methods to analyze the behavior and predictions of any machine learning model. Implemented methods are: Feature importance described by Fisher et al. (2018) <arXiv:1801.01489>, accumulated local effects plots described by Apley (2018) <arXiv:1612.08468>, partial dependence plots described by Friedman (2001) <http://www.jstor.org/stable/2699986>, individual conditional expectation (ice) plots described by Goldstein et al. (2013) <doi:10.1080/10618600.2014.907095>, local models (variant of lime) described by Ribeiro et. al (2016) <arXiv:1602.04938>, the Shapley Value described by Strumbelj et. al (2014) <doi:10.1007/s10115-013-0679-x>, feature interactions described by Friedman et. al <doi:10.1214/07-AOAS148> and tree surrogate models. | 2019-07-21 |

r-ica | public | Independent Component Analysis (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE). | 2019-07-21 |

r-hrbrthemes | public | A compilation of extra 'ggplot2' themes, scales and utilities, including a spell check function for plot label fields and an overall emphasis on typography. A copy of the 'Google' font 'Roboto Condensed' <https://github.com/google/roboto/> is also included along with a copy of the 'IBM' 'Plex Sans' <https://github.com/IBM/type> and 'Titillium Web' <https://fonts.google.com/specimen/Titillium+Web> fonts are also included to support their respective typography-oriented themes. | 2019-07-21 |

r-glasso | public | Estimation of a sparse inverse covariance matrix using a lasso (L1) penalty. Facilities are provided for estimates along a path of values for the regularization parameter. | 2019-07-21 |

r-highcharter | public | A wrapper for the 'Highcharts' library including shortcut functions to plot R objects. 'Highcharts' <http://www.highcharts.com/> is a charting library offering numerous chart types with a simple configuration syntax. | 2019-07-21 |

r-hive | public | No Summary | 2019-07-21 |

r-heatmaply | public | Create interactive cluster 'heatmaps' that can be saved as a stand- alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical method for visualizing high-dimensional data, in which a table of numbers are encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by 'dendrograms'. 'Heatmaps' are used in many fields for visualizing observations, correlations, missing values patterns, and more. Interactive 'heatmaps' allow the inspection of specific value by hovering the mouse over a cell, as well as zooming into a region of the 'heatmap' by dragging a rectangle around the relevant area. This work is based on the 'ggplot2' and 'plotly.js' engine. It produces similar 'heatmaps' as 'heatmap.2' or 'd3heatmap', with the advantage of speed ('plotly.js' is able to handle larger size matrix), the ability to zoom from the 'dendrogram' panes, and the placing of factor variables in the sides of the 'heatmap'. | 2019-07-21 |

r-howmany | public | When testing multiple hypotheses simultaneously, this package provides functionality to calculate a lower bound for the number of correct rejections (as a function of the number of rejected hypotheses), which holds simultaneously -with high probability- for all possible number of rejections. As a special case, a lower bound for the total number of false null hypotheses can be inferred. Dependent test statistics can be handled for multiple tests of associations. For independent test statistics, it is sufficient to provide a list of p-values. | 2019-07-21 |

r-gwidgetsrgtk2 | public | Port of the gWidgets API to the RGtk2 toolkit. | 2019-07-21 |

r-here | public | Constructs paths to your project's files based on heuristics. | 2019-07-21 |

r-graphtweets | public | Allows building an edge table from data frame of tweets, also provides function to build nodes and another create a temporal graph. | 2019-07-21 |

r-ggiraph | public | Create interactive 'ggplot2' graphics using 'htmlwidgets'. | 2019-07-21 |

r-goric | public | Generalized Order-Restricted Information Criterion (GORIC) value for a set of hypotheses in multivariate linear models and generalised linear models. | 2019-07-21 |

r-googlevis | public | R interface to Google's chart tools, allowing users to create interactive charts based on data frames. Charts are displayed locally via the R HTTP help server. A modern browser with an Internet connection is required and for some charts a Flash player. The data remains local and is not uploaded to Google. | 2019-07-21 |

r-goodpractice | public | Give advice about good practices when building R packages. Advice includes functions and syntax to avoid, package structure, code complexity, code formatting, etc. | 2019-07-21 |

r-googleauthr | public | Create R functions that interact with OAuth2 Google APIs <https://developers.google.com/apis-explorer/> easily, with auto-refresh and Shiny compatibility. | 2019-07-21 |

r-ggresidpanel | public | An R package for creating panels of diagnostic plots for residuals from a model using ggplot2 and plotly to analyze residuals and model assumptions from a variety of viewpoints. It also allows for the creation of interactive diagnostic plots. | 2019-07-21 |

r-ggupset | public | Replace the standard x-axis in 'ggplots' with a combination matrix to visualize complex set overlaps. 'UpSet' has introduced a new way to visualize the overlap of sets as an alternative to Venn diagrams. This package provides a simple way to produce such plots using 'ggplot2'. In addition it can convert any categorical axis into a combination matrix axis. | 2019-07-21 |

r-ggtern | public | Extends the functionality of 'ggplot2', providing the capability to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally, 'ggtern' has implemented several NEW geometries which are unavailable to the standard 'ggplot2' release. For further examples and documentation, please proceed to the 'ggtern' website. | 2019-07-21 |

r-ggspectra | public | Additional annotations, stats, geoms and scales for plotting "light" spectra with 'ggplot2', together with specializations of ggplot() and autoplot() methods for spectral data and waveband definitions stored in objects of classes defined in package 'photobiology'. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>. | 2019-07-21 |

r-ggpmisc | public | Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Specialization of method ggplot(): accept and convert on the fly time series data. Geom: "table", adds tables to plots. Statistics: locate and tag peaks and valleys in 2D plots; count observations in different quadrants of a plot; select observations based on 2D density; label with the equation of a polynomial fitted with lm() or other types of models; labels with P-value, R^2 or adjusted R^2 or information criteria for fitted models; label with ANOVA table for fitted models; label with summary for fitted models. Model fit classes for which suitable methods are provided by package 'broom' are supported. | 2019-07-21 |

r-ggpage | public | Facilitates the creation of page layout visualizations in which words are represented as rectangles with sizes relating to the length of the words. Which then is divided in lines and pages for easy overview of up to quite large texts. | 2019-07-21 |

r-ggparallel | public | Create hammock plots, parallel sets, and common angle plots with 'ggplot2'. | 2019-07-21 |

r-ggnetwork | public | Geometries to plot network objects with 'ggplot2'. | 2019-07-21 |

r-ggmap | public | A collection of functions to visualize spatial data and models on top of static maps from various online sources (e.g Google Maps and Stamen Maps). It includes tools common to those tasks, including functions for geolocation and routing. | 2019-07-21 |

r-ggmcmc | public | Tools for assessing and diagnosing convergence of Markov Chain Monte Carlo simulations, as well as for graphically display results from full MCMC analysis. The package also facilitates the graphical interpretation of models by providing flexible functions to plot the results against observed variables. | 2019-07-21 |

r-ggfocus | public | A 'ggplot2' extension that provides tools for automatically focusing specific factor levels. | 2019-07-21 |

r-ggjoy | public | Joyplots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in 'ggplot2'. | 2019-07-21 |

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