The r-phylogram package is a tool for for developing phylogenetic trees as deeply-nested lists known as "dendrogram" objects. It provides functions for conversion between "dendrogram" and "phylo" class objects, as well as several tools for command-line tree manipulation and import/export via Newick parenthetic text. This improves accessibility to the comprehensive range of object-specific analytical and tree-visualization functions found across a wide array of bioinformatic R packages.

This package performs optimization in R using C++. A unified wrapper interface is provided to call C functions of the five optimization algorithms (Nelder-Mead, BFGS, CG, L-BFGS-B and SANN) underlying optim().

Subject recruitment for medical research is challenging. Slow patient accrual leads to delay in research. Accrual monitoring during the process of recruitment is critical. Researchers need reliable tools to manage the accrual rate. This package provides an implementation of a Bayesian method that integrates researcher's experience on previous trials and data from the current study, providing reliable prediction on accrual rate for clinical studies. It provides functions for Bayesian accrual prediction which can be easily used by statisticians and clinical researchers.

prospectr provides miscellaneous functions to preprocess spectroscopic data and conduct representative sample selection, or calibration sampling.

This package provides functions for simple fixed and random effects meta-analysis for two-sample comparisons and cumulative meta-analyses. It draws standard summary plots, funnel plots, and computes summaries and tests for association and heterogeneity.

This package provides an interface to the rich display capabilities of Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a running IRkernel session.

This package provides computationally efficient tools related to the multivariate normal and Student's t distributions. The main functionalities are: simulating multivariate random vectors, evaluating multivariate normal or Student's t densities and Mahalanobis distances. These tools are developed using C++ code and of the OpenMP API.

This package provides datasets to accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage.

This package provides a fast dimensionality reduction method scalable to large numbers of samples. Landmark Multi-Dimensional Scaling (LMDS) is an extension of classical Torgerson MDS, but rather than calculating a complete distance matrix between all pairs of samples, only the distances between a set of landmarks and the samples are calculated.

This package provides useful tools for both users and developers of packages for fitting Bayesian models or working with output from Bayesian models. The primary goals of the package are to:

1. Efficiently convert between many different useful formats of draws (samples) from posterior or prior distributions.

2. Provide consistent methods for operations commonly performed on draws, for example, subsetting, binding, or mutating draws.

3. Provide various summaries of draws in convenient formats.

4. Provide lightweight implementations of state of the art posterior inference diagnostics.

This package provides a common interface to specifying clustering models, in the same style as parsnip. It creates a unified interface across different functions and computational engines.

This package provides tools and functions for parsing, rendering and operating on semantic version strings. Semantic versioning is a simple set of rules and requirements that dictate how version numbers are assigned and incremented as outlined at http://semver.org.

Kernel factory is an ensemble method where each base classifier (random forest) is fit on the kernel matrix of a subset of the training data.

This package was designed to find an acceptable Python binary that matches version and feature constraints.

Miscellaneous functions commonly used by YuLab-SMU, such as install_zip_gh to install R packages from Github ZIP files.

This package lets you import Excel files into R. It supports .xls via the embedded libxls C library and .xlsx via the embedded RapidXML C++ library.

Tools to clean and process text. Tools are geared at checking for substrings that are not optimal for analysis and replacing or removing them (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen, Kumar, Ostendorf, & Richards (2001) doi:10.1006/csla.2001.0169) or extracting them into new variables. For example, emoticons are often used in text but not always easily handled by analysis algorithms. The replace_emoticon() function replaces emoticons with word equivalents.

This package provides mosaic plots for the ggplot2 framework. Mosaic plot functionality is provided in a single ggplot2 layer by calling the geom mosaic.

This package provides an R API to the Open Source Geometry Engine (GEOS) library and a vector format with which to efficiently store GEOS geometries. High-performance functions to extract information from, calculate relationships between, and transform geometries are provided. Finally, facilities to import and export geometry vectors to other spatial formats are provided.

This package provides a number of user-level functions to work with grid graphics, notably to arrange multiple grid-based plots on a page, and draw tables.

The first day of any MMWR week is Sunday. MMWR week numbering is sequential beginning with 1 and incrementing with each week to a maximum of 52 or 53. MMWR week #1 of an MMWR year is the first week of the year that has at least four days in the calendar year. This package provides functionality to convert dates to MMWR day, week, and year and the reverse.

Phangorn is a package for phylogenetic analysis in R. It supports estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation.

The spdlog library is a widely-used and very capable header-only C++ library for logging. This package includes its headers as an R package to permit other R packages to deploy it via a simple LinkingTo: RcppSpdlog. As of version 0.0.9, it also provides both simple R logging functions and compiled functions callable by other packages.

The gg.gap function enables you to define segments for the y-axis in a ggplot2 plot.