This package adds indicators (spinner, progress bar, gif) that you can use in your Shiny applications to show the user that the server is busy. It also provides other tools to let your users know something is happening (send notifications, reports, ...).

Blaze is an open-source, high-performance C++ math library for dense and sparse arithmetic. With its state-of-the-art Smart Expression Template implementation Blaze combines the elegance and ease of use of a domain-specific language with HPC-grade performance, making it one of the most intuitive and fastest C++ math libraries available. The RcppBlaze package includes the header files from the Blaze library with disabling some functionalities related to link to the thread and system libraries which make RcppBlaze be a header-only library. Therefore, users do not need to install Blaze'.

This package provides tools for optimal subset matching of treated units and control units in observational studies, with support for refined covariate balance constraints, (including fine and near-fine balance as special cases). A close relative is the rcbalance package. See Pimentel, et al.(2015) <doi:10.1080/01621459.2014.997879> and Pimentel and Kelz (2020) <doi:10.1080/01621459.2020.1720693>. The rrelaxiv package, which provides an alternative solver for the underlying network flow problems, carries an academic license and is not available on CRAN, but may be downloaded from Github at <https://github.com/josherrickson/rrelaxiv/>.

This package provides unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis. The package offers a single plotting interface for these analysis results and plots in a unified style using the ggplot2 package.

This package provides tools to download the climatic data of the Spanish Meteorological Agency (AEMET) directly from R using their API and create scientific graphs (climate charts, trend analysis of climate time series, temperature and precipitation anomalies maps, warming stripes graphics, climatograms, etc.).

The method may be conceptualised as a test of overall significance in regression analysis, where the response variable is overdispersed and the number of explanatory variables exceeds the sample size. Useful for testing for association between RNA-Seq and high-dimensional data.

Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR.

Record asciicast screen casts from R scripts. Convert them to animated SVG images, to be used in README files, or blog posts. Includes asciinema-player as an HTML widget, and an asciicast knitr engine, to embed ascii screen casts in Rmarkdown documents.

This is a port of the WTC MATLAB package written by Aslak Grinsted and the wavelet program written by Christopher Torrence and Gibert P. Compo. This package can be used to perform univariate and bivariate (cross-wavelet, wavelet coherence, wavelet clustering) analyses.

Interface to a high-performance implementation of k-medoids clustering described in Tiwari, Zhang, Mayclin, Thrun, Piech and Shomorony (2020) "BanditPAM: Almost Linear Time k-medoids Clustering via Multi-Armed Bandits" <https://proceedings.neurips.cc/paper/2020/file/73b817090081cef1bca77232f4532c5d-Paper.pdf>.

Convolute probabilistic distributions using the random generator function of each distribution. A new random number generator function is created that perform the mathematical operation on the individual random samples from the random generator function of each distribution. See the documentation for examples.

Allows users to seamlessly query several CDC PLACES APIs (<https://data.cdc.gov/browse?q=PLACES%20&sortBy=relevance>) by geography, state, measure, and release year. This package also contains a function to explore the available measures for each release year.

Compute the certainty equivalents and premium risks as tools for risk-efficiency analysis. For more technical information, please refer to: Hardaker, Richardson, Lien, & Schumann (2004) <doi:10.1111/j.1467-8489.2004.00239.x>, and Richardson, & Outlaw (2008) <doi:10.2495/RISK080231>.

Efficient Global Optimization (EGO) algorithm as described in "Roustant et al. (2012)" <doi:10.18637/jss.v051.i01> and adaptations for problems with noise ("Picheny and Ginsbourger, 2012") <doi:10.1016/j.csda.2013.03.018>, parallel infill, and problems with constraints.

Rare variant association test integrating variant position information. It aims to identify the presence of clusters of disease-risk variants in specific gene regions. For more details, please read the publication from Persyn et al. (2017) <doi:10.1371/journal.pone.0179364>.

Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>. entropart provides functions to calculate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity. Estimation-bias corrections are available.

This package implements Escalation With Overdose Control trial designs using two drug combinations described by this paper <doi:10.1002/sim.6961>(Tighiouart et al., 2016). It calculates the recommended dose for next cohorts and perform simulations to obtain operating characteristics.

Calculate cutoff values for model fit measures used in structural equation modeling (SEM) by simulating and testing data sets (cf. Hu & Bentler, 1999 <doi:10.1080/10705519909540118>) with the same parameters (population model, number of observations, etc.) as the model under consideration.

It enables detailed interpretation of complex classification and regression models through Shapley analysis including data-driven characterization of subgroups of individuals. Furthermore, it facilitates multi-measure model evaluation, model fairness, and decision curve analysis. Additionally, it offers enhanced visualizations with interactive elements.

The ggplot2 package provides simple functions for visualizing contours of 2-d kernel density estimates. ggdensity implements several additional density estimators as well as more interpretable visualizations based on highest density regions instead of the traditional height of the estimated density surface.

Haplotype and covariate relative risks in case-control data are estimated by weighted logistic regression. Diplotype probabilities, which are estimated by EM computation with progressive insertion of loci, are utilized as weights. French et al. (2006) <doi:10.1002/gepi.20161>.

It performs maximum likelihood estimation for the Heckman selection model (Normal, Student-t or Contaminated normal) using an EM-algorithm <doi:10.1016/j.jmva.2021.104737>. It also performs influence diagnostic through global and local influence for four possible perturbation schema.

This package implements a procedure to automatically generate 2D masks for clusters on dimensional reduction plots from methods like t-SNE (t-distributed stochastic neighbor embedding) or UMAP (uniform manifold approximation and projection), with a focus on single-cell RNA-sequencing data.

The MetAlyzer S4 object provides methods to read and reformat metabolomics data for convenient data handling, statistics and downstream analysis. The resulting format corresponds to input data of the Shiny app MetaboExtract (<https://www.metaboextract.shiny.dkfz.de/MetaboExtract/>).