Estimates (and controls for) phylogenetic signal through phylogenetic eigenvectors regression (PVR) and phylogenetic signal-representation (PSR) curve, along with some plot utilities.

Compute yield-stability index based on Bayesian methodology, which is useful for analyze multi-environment trials in plant breeding programs. References: Cotes Torres JM, Gonzalez Jaimes EP, and Cotes Torres A (2016) <https://revistas.unimilitar.edu.co/index.php/rfcb/article/view/2037> Seleccion de Genotipos con Alta Respuesta y Estabilidad Fenotipica en Pruebas Regionales: Recuperando el Concepto Biologico.

This package provides functions for 1D and 2D Discrete Cosine Transform (DCT), Discrete Sine Transform (DST) and Discrete Hartley Transform (DHT).

Logistic Factor Analysis (LFA) is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter.

This package supports multiple precision arithmetic (big integers and rationals, prime number tests, matrix computation), "arithmetic without limitations" using the GNU Multiple Precision library.

This package provides functions that wrap popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states.

Li-Ri is a game in which you drive a wooden toy steam locomotive across many levels and collect all the coaches to win.

This package is intended to identify differentially expressed genes driven by Copy Number Alterations from samples with both gene expression and CNA data.

This package provides a thin wrapper around the ajv JSON validation package for JavaScript. See <http://epoberezkin.github.io/ajv/> for details.

C5.0 decision trees and rule-based models for pattern recognition that extend the work of Quinlan (1993, ISBN:1-55860-238-0).

Estimate the severity of a disease and ascertainment of cases, as discussed in Nishiura et al. (2009) <doi:10.1371/journal.pone.0006852>.

Light weight implementation of the standard distribution functions for the chi distribution, wrapping those for the chi-squared distribution in the stats package.

This package performs analysis of categorical-variable with missing values. Implements methods from Schafer, JL, Analysis of Incomplete Multivariate Data, Chapman and Hall.

Generates (half-)normal plots with simulation envelopes using different diagnostics from a range of different fitted models. A few example datasets are included.

This package provides functions to extract joint planes from 3D triangular mesh derived from point cloud and makes data available for structural analysis.

Set of common functions used for manipulating colors, detecting and interacting with RStudio', modeling, formatting, determining users operating system, feature scaling, and more!

This package implements the LPC method of Witten&Tibshirani(Annals of Applied Statistics 2008) for identification of significant genes in a microarray experiment.

This package performs bivariate composite likelihood and full information maximum likelihood estimation for polytomous logit-normit (graded logistic) item response theory (IRT) models.

This package provides a general framework for constructing partial dependence (i.e., marginal effect) plots from various types machine learning models in R.

Analysis of crossover interference in experimental crosses, particularly regarding the gamma model. See, for example, Broman and Weber (2000) <doi:10.1086/302923>.

This package provides cover-tree and kd-tree fast k-nearest neighbor search algorithms. Related applications including KNN classification, regression and information measures are implemented.

This package supports the analysis of count data exhibiting autoregressive properties, using the Autoregressive Conditional Poisson model (ACP(p,q)) proposed by Heinen (2003).

This is a package for computation and visualization of the empirical attainment function (EAF) for the analysis of random sets in multi-criterion optimization.

This package provides tools for Independent Component Analysis (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE).