This package provides a toolkit for making antigenic maps from immunological assay data, in order to quantify and visualize antigenic differences between different pathogen strains as described in Smith et al. (2004) <doi:10.1126/science.1097211> and used in the World Health Organization influenza vaccine strain selection process. Additional functions allow for the diagnostic evaluation of antigenic maps and an interactive viewer is provided to explore antigenic relationships amongst several strains and incorporate the visualization of associated genetic information.

This package wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering results.

This package provides methods for cluster analysis. It is a much extended version of the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".

This R package contains examples from the book Regression for Categorical Data, Tutz 2012, Cambridge University Press. The names of the examples refer to the chapter and the data set that is used.

This package implements list environments. List environments are environments that have list-like properties. For instance, the elements of a list environment are ordered and can be accessed and iterated over using index subsetting.

Currently there are many functions in S-PLUS that are missing in R. To facilitate the conversion of S-PLUS packages to R packages, this package provides some missing S-PLUS functionality in R.

Create and customize interactive maps using the Leaflet JavaScript library and the htmlwidgets package. These maps can be used directly from the R console, from RStudio, in Shiny applications and R Markdown documents.

This package simulates the process of installing a package and then attaching it. This is a key part of the devtools package as it allows you to rapidly iterate while developing a package.

blame outputs an annotated revision from each RCS file. An annotated RCS file describes the revision and date in which each line was added to the file, and the author of each line.

Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained parameters can be interpreted to infer the clonal structure of the tumor.

This package provides a general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as described in Pounds et. al. (2009) Bioinformatics 25: 2013-2019.

This includes a set of convenience functions for working with the SummarizedExperiment class. Note that plotting functions historically in this package have been moved to the sechm package (see vignette for details).

This package implements a parametric semi-supervised mixture model. The permutation test detects markers with main or interactive effects, without distinguishing them. Possible applications include genome-wide association analysis and differential expression analysis.

Point-scale variogram deconvolution from irregular/regular spatial support according to Goovaerts, P., (2008) <doi: 10.1007/s11004-007-9129-1>; ordinary area-to-area (co)Kriging and area-to-point (co)Kriging.

Whitening is the first step of almost all blind source separation (BSS) methods. A fast implementation of whitening for BSS is implemented to serve as a lightweight dependency for packages providing BSS methods.

Implementation of the d/p/q/r family of functions for a continuous analog to the standard discrete beta-binomial with continuous size parameter and continuous support with x in [0, size + 1].

An interactive document on the topic of confusion matrix analysis using rmarkdown and shiny packages. Runtime examples are provided in the package function as well as at <https://predanalyticssessions1.shinyapps.io/ConfusionMatrixShiny/>.

This package implements the instruments for complex-valued modelling, including time series analysis and forecasting. This is based on the monograph by Svetunkov & Svetunkov (2024) <doi: 10.1007/978-3-031-62608-1>.

This package contains the adaptation of bubblebath from MATLAB (Danz, 2020: <https://www.mathworks.com/matlabcentral/fileexchange/70348>) and the tools to transform a dataframe of radii and points to plot-able paths.

Solves quadratic programming problems using Richard L. Dykstra's cyclic projection algorithm. Routine allows for a combination of equality and inequality constraints. See Dykstra (1983) <doi:10.1080/01621459.1983.10477029> for details.

Geodesic distance between phylogenetic trees and associated functions. The theoretical background of distory is published in Billera et al. (2001) "Geometry of the space of phylogenetic trees." <doi:10.1006/aama.2001.0759>.

The df2yaml aims to simplify the process of converting dataframe to YAML <https://yaml.org/>. The dataframe with multiple key columns and one value column will be converted to the multi-level hierarchy.

This package provides methods for estimating multi-stage optimal dynamic treatment regimes for survival outcomes with dependent censoring. Cho, H., Holloway, S. T., and Kosorok, M. R. (2022) <doi:10.1093/biomet/asac047>.

This dataset contains population estimates of all European cities with at least 10,000 inhabitants during the period 1500-1800. These data are adapted from Jan De Vries, "European Urbanization, 1500-1800" (1984).