This package provides a significant pattern mining-based toolbox for region-based genome-wide association studies and higher-order epistasis analyses, implementing the methods described in Llinares-López et al. (2017) <doi:10.1093/bioinformatics/btx071>.

Process Digital Cover Photography images of tree canopies to get canopy attributes like Foliage Cover and Leaf Area Index. Detailed description of the methods in Chianucci et al. (2022) <doi:10.1007/s00468-018-1666-3>.

Convex Clustering methods, including K-means algorithm, On-line Update algorithm (Hard Competitive Learning) and Neural Gas algorithm (Soft Competitive Learning), and calculation of several indexes for finding the number of clusters in a data set.

Work with data on Venetian doges and dogaresse and the noble families of the Republic of Venice, and use it for social network analysis, as used in Merelo (2022) <doi:10.48550/arXiv.2209.07334>.

Decodes meshes and point cloud data encoded by the Draco mesh compression library from Google. Note that this is only designed for basic decoding and not intended as a full scale wrapping of the Draco library.

Datasets and functions to accompany the book Analisis de datos con el programa estadistico R: una introduccion aplicada by Salas-Eljatib (2021, ISBN: 9789566086109). The package helps carry out data management, exploratory analyses, and model fitting.

Visualize one-factor data frame. Beads plot consists of diamonds of each factor of each data series. A diamond indicates average and range. Look over a data frame with many numeric columns and a factor column.

This package implements a fast, flexible method for simulating continuous variables with specified rank correlations using the Imanâ Conover transformation (Iman & Conover, 1982 <doi:10.1080/03610918208812265>) and back-ranking. Includes plotting tools and error-diagnostics.

Fits Weibull or sigmoidal models to percent loss conductivity (plc) curves as a function of plant water potential, computes confidence intervals of parameter estimates and predictions with bootstrap or parametric methods, and provides convenient plotting methods.

This package provides a plain Rcpp wrapper for MeCab that can segment Chinese, Japanese, and Korean text into tokens. The main goal of this package is to provide an alternative to tidytext using morphological analysis.

This package implements several extensions of the elastic net regularization scheme. These extensions include individual feature penalties for the L1 term, feature-feature penalties for the L2 term, as well as translation coefficients for the latter.

This package provides utility functions for, and drawing on, the data.table package. The package also collates useful miscellaneous functions extending base R not available elsewhere. The name is a portmanteau of utils and the author.

Uses the Jaccard similarity index to account for population structure in sequencing studies. This method was specifically designed to detect population stratification based on rare variants, hence it will be especially useful in rare variant analysis.

This package provides tools to use API such as e-Stat (<https://www.e-stat.go.jp/>), the portal site for Japanese government statistics, and RESAS (Regional Economy and Society Analyzing System, <https://resas.go.jp>).

This package provides a new practical method to evaluate whether relationships between two sets of high-dimensional variables are different or not across two conditions. Song, H. and Wu, M.C. (2023) <arXiv:2307.15268>.

This package provides a set of functions, classes and methods for performing ABC and ABC/XYZ analyses, identifying overperforming, underperforming and constantly performing items, and plotting, analyzing as well as predicting the temporal development of items.

This package provides a fast, flexible machine learning library, written in C++, that aims to provide fast, extensible implementations of cutting-edge machine learning algorithms. See also Curtin et al. (2023) <doi:10.21105/joss.05026>.

User-friendly Shiny apps for designing and evaluating phase I cancer clinical trials, with the aim to estimate the maximum tolerated dose (MTD) of a novel drug, using a Bayesian decision procedure based on logistic regression.

Co-Expression Network Analysis by adopting network embedding technique. Song W.-M., Zhang B. (2015) Multiscale Embedded Gene Co-expression Network Analysis. PLoS Comput Biol 11(11): e1004574. <doi: 10.1371/journal.pcbi.1004574>.

Package computes popular and widely used multicollinearity diagnostic measures <doi:10.17576/jsm-2019-4809-26> and <doi:10.32614/RJ-2016-062> . Package also indicates which regressors may be the reason of collinearity among regressors.

Obtain and evaluate various optimal designs for the 3, 4, and 5-parameter logistic models. The optimal designs are obtained based on the numerical algorithm in Hyun, Wong, Yang (2018) <doi:10.18637/jss.v083.i05>.

Simulation of continuous, correlated high-dimensional data with time to event or binary response, and parallelized functions for Lasso, Ridge, and Elastic Net penalized regression with repeated starts and two-dimensional tuning of the Elastic Net.

Implementation of assumption-lean and data-adaptive post-prediction inference (POPInf), for valid and efficient statistical inference based on data predicted by machine learning. See Miao, Miao, Wu, Zhao, and Lu (2023) <arXiv:2311.14220>.

This package provides tools to show and draw image pixels using HTML widgets and Shiny applications. It can be used to visualize the MNIST dataset for handwritten digit recognition or to create new image recognition datasets.