Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework as described in Muñoz-Pajares (2013) <doi:10.1111/2041-210X.12118>.

Tree Ring Analysis of Disturbance Events in R (TRADER) package provides functions for disturbance reconstruction from tree-ring data, e.g. boundary line, absolute increase, growth averaging methods.

This package provides functions for interacting directly with the Taiwan Economic Journal API to offer data in R. For more information go to <https://api.tej.com.tw>.

This package provides a suite of statistics for identifying areas of the genome under selective pressure. See Jacobs, Sluckin and Kivisild (2016) <doi:10.1534/genetics.115.185900>.

Some basic features of MUMPS are wrapped in a class whose methods can be used for sequentially solving a sparse linear system (symmetric or not) with one or many right hand sides (dense or sparse). There is a possibility to do separately symbolic analysis, LU (or LDL^t) factorization and system solving. Third part ordering libraries are included and can be used: PORD, METIS, SCOTCH.

An implementation of functionalities to transform directed graphs that are bound to a set of known forbidden paths. There are several transformations, following the rules provided by Villeneuve and Desaulniers (2005) <doi: 10.1016/j.ejor.2004.01.032>, and Hsu et al. (2009) <doi: 10.1007/978-3-642-03095-6_60>. The resulting graph is generated in a data-frame format. See rsppfp website for more information, documentation an examples.

This package provides methods and algorithms for discrete optimization, e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and Hooke-Jeeves minimization, and some (evolutionary) global optimization functions.

This package lets you plot model surfaces for a wide variety of models using partial dependence plots and other techniques. Also plot model residuals and other information on the model.

This package provides Gaussian finite mixture models fitted via EM algorithm for model-based clustering, classification, and density estimation, including Bayesian regularization, dimension reduction for visualisation, and resampling-based inference.

This package provides an all relevant feature selection wrapper algorithm. It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies (shadows).

This package provides tools for exploratory data analysis and data visualization of biological sequence (DNA and protein) data. It also includes utilities for sequence data management under the ACNUC system.

The aim of vidger is to rapidly generate information-rich visualizations for the interpretation of differential gene expression results from three widely-used tools: Cuffdiff, DESeq2, and edgeR.

View and analyze data where bunching is expected. Estimate counter- factual distributions. For earnings data, estimate the compensated elasticity of earnings w.r.t. the net-of-tax rate.

Generating multiple binary and normal variables simultaneously given marginal characteristics and association structure based on the methodology proposed by Demirtas and Doganay (2012) <DOI:10.1080/10543406.2010.521874>.

This package provides a framework for building interactive dashboards and document-based reports. Underlying data manipulation and visualization is possible using a web-based point and click user interface.

This package provides high-level modeling functions to define and train models using the torch R package. Models include linear, logistic, and multinomial regression as well as multilayer perceptrons.

Implementation of Tobit type I and type II families for censored regression using the mgcv package, based on methods detailed in Woods (2016) <doi:10.1080/01621459.2016.1180986>.

Broken adaptive ridge estimator for censored data is used to select variables and estimate their coefficients in the semi-parametric accelerated failure time model for right-censored survival data.

This package provides functions to generate ensembles of generalized linear models using competing proximal gradients. The optimal sparsity and diversity tuning parameters are selected via an alternating grid search.

Fits hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>.

It is devoted to Cramer-von Mises goodness-of-fit tests. It implements three statistical methods based on Cramer-von Mises statistics to estimate and test a regression model.

With the development of new cross-cultural methods this package is intended to combine multiple functions automating and simplifying functions providing a unified analysis approach for commonly employed methods.

This package provides a graphical user interface (GUI) to the functions implemented in the R package DQAstats'. Publication: Mang et al. (2021) <doi:10.1186/s12911-022-01961-z>.

Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. (2015) <doi:10.1111/ele.12461>.