This package provides a collection of tools for building RAxML supermatrix using PHYLIP or aligned FASTA files. These functions will be useful for building large phylogenies using multiple markers.

The ammeter gem makes it easy to write specs for Rails generators. An existing user is rspec-rails, which uses ammeter to spec its own generators.

Promise is a Ruby implementation of the Promises/A+ specification. It provides 100% mutation coverage, tested on MRI 1.9, 2.0, 2.1, 2.2, Rubinius, and JRuby.

omicsPrint provides functionality for cross omic genetic fingerprinting, for example, to verify sample relationships between multiple omics data types, i.e. genomic, transcriptomic and epigenetic (DNA methylation).

This package provides functions to compute summary scores (besides proprietary ones) reported in the tabulated data resource that is released by the Adolescent Brain Cognitive Development (ABCD) study.

This package provides tools for sampling from the PolyaGamma distribution based on Polson, Scott, and Windle (2013) <doi:10.1080/01621459.2013.829001>. Useful for logistic regression.

Generate Rd markup to list methods for a generic function. Makes it easier to document S3, S4, and S7 generics by automatically finding and linking to method documentation.

This package provides functions for demographic analysis including lifetable calculations; Lee-Carter modelling; functional data analysis of mortality rates, fertility rates, net migration numbers; and stochastic population forecasting.

This package provides functions for fitting data to a quiescent growth model, i.e. a growth process that involves members of the population who stop dividing or propagating.

This package provides a ggplot2 grammar for circular, axial and directional data, including rose diagrams, circular densities, mean directions, confidence arcs, theoretical circular distributions and movement data visualizations.

Genotype plus genotype-by-environment (GGE) biplots rendered using ggplot2'. Provides a command line interface to all of the functionality contained within the archived package GGEBiplotGUI'.

This package contains functions to construct high-dimensional orthogonal maximin distance designs in two, four, eight, and sixteen levels from rotating the Kronecker product of sub-Hadamard matrices.

Tool for generating quality reports from cruncher outputs (and calculating series scores). The latest version of the cruncher can be downloaded here: <https://github.com/jdemetra/jwsacruncher/releases>.

This package provides extensions to the leaflet package to customize legends with images, text styling, orientation, sizing, and symbology and functions to create symbols to plot on maps.

This package provides helper functions, metadata utilities, and workflows for administering and managing databases on the Motherduck cloud platform. Some features require a Motherduck account (<https://motherduck.com/>).

This package contains a sample of the 2005 Grade 8 Mathematics data from the National Assessment of Educational Progress (NAEP). This data set is called the NAEP Primer.

Exports an enhanced version of the tools::parseLatex() function to handle LaTeX syntax more accurately. Also includes numerous functions for searching and modifying LaTeX source.

For a multivariate dataset with independent Poisson measurement error, calculates principal components of transformed latent Poisson means. T. Kenney, T. Huang, H. Gu (2019) <arXiv:1904.11745>.

An interactive Shiny application to perform fast parameter inference on dynamical systems (described by ordinary differential equations) using gradient matching. Please see the project page for more details.

This package provides an XY pad input for the Shiny framework. An XY pad is like a bivariate slider. It allows to pick up a pair of numbers.

Data filtering module for teal applications. Allows for interactive filtering of data stored in data.frame and MultiAssayExperiment objects. Also displays filtered and unfiltered observation counts.

Tabu search algorithm for binary configurations. A basic version of the algorithm as described by Fouskakis and Draper (2007) <doi:10.1111/j.1751-5823.2002.tb00174.x>.

Interface to TensorFlow Datasets, a high-level library for building complex input pipelines from simple, re-usable pieces. See <https://www.tensorflow.org/guide> for additional details.

This package provides a set of custom R Markdown templates for documents and presentations with the University of Illinois at Urbana-Champaign (UIUC) color scheme and identity standards.