Examples: visualization, C++, networks, data cleaning, html widgets, ropensci.

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RcppClassicExamples — by Dirk Eddelbuettel, 10 months ago

Examples using 'RcppClassic' to Interface R and C++

The 'Rcpp' package contains a C++ library that facilitates the integration of R and C++ in various ways via a rich API. This API was preceded by an earlier version which has been deprecated since 2010 (but is still supported to provide backwards compatibility in the package 'RcppClassic'). This package 'RcppClassicExamples' provides usage examples for the older, deprecated API. There is also a corresponding package 'RcppExamples' with examples for the newer, current API which we strongly recommend as the basis for all new development.

permGPU — by Ivo D. Shterev, 3 years ago

Using GPUs in Statistical Genomics

Can be used to carry out permutation resampling inference in the context of RNA microarray studies.

ads — by Philippe Verley, 10 months ago

Spatial Point Patterns Analysis

Perform first- and second-order multi-scale analyses derived from Ripley K-function, for univariate, multivariate and marked mapped data in rectangular, circular or irregular shaped sampling windows, with tests of statistical significance based on Monte Carlo simulations.

wmlf — by Francois Semecurbe, 4 years ago

Wavelet Leaders in Multifractal Analysis

Analyzing the texture of an image from a multifractal wavelet leader analysis.

mregions — by Scott Chamberlain, a year ago

Marine Regions Data from 'Marineregions.org'

Tools to get marine regions data from < http://www.marineregions.org/>. Includes tools to get region metadata, as well as data in 'GeoJSON' format, as well as Shape files. Use cases include using data downstream to visualize 'geospatial' data by marine region, mapping variation among different regions, and more.

mixOmics — by Kim-Anh Le Cao, 8 months ago

Omics Data Integration Project

Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.

ChoR — by Matthieu Herrmann, 8 months ago

Chordalysis R Package

Learning the structure of graphical models from datasets with thousands of variables. More information about the research papers detailing the theory behind Chordalysis is available at < http://www.francois-petitjean.com/Research> (KDD 2016, SDM 2015, ICDM 2014, ICDM 2013). The R package development site is < https://github.com/HerrmannM/Monash-ChoR>.

NPflow — by Boris P. Hejblum, a year ago

Bayesian Nonparametrics for Automatic Gating of Flow-Cytometry Data

Dirichlet process mixture of multivariate normal, skew normal or skew t-distributions modeling oriented towards flow-cytometry data preprocessing applications.

RcppClassic — by Dirk Eddelbuettel, 6 months ago

Deprecated 'classic' 'Rcpp' 'API'

The 'RcppClassic' package provides a deprecated C++ library which facilitates the integration of R and C++. New projects should use the new 'Rcpp' 'API' in the 'Rcpp' package.

phylosignal — by ORPHANED, a day ago

Exploring the Phylogenetic Signal in Continuous Traits

A collection of tools to explore the phylogenetic signal in univariate and multivariate data. The package provides functions to plot traits data against a phylogenetic tree, different measures and tests for the phylogenetic signal, methods to describe where the signal is located and a phylogenetic clustering method.