This package provides a function for the estimation of mixture of longitudinal factor analysis models using the iterative expectation-maximization algorithm (Ounajim, Slaoui, Louis, Billot, Frasca, Rigoard (2023) <doi:10.1002/sim.9804>) and several tools for visualizing and interpreting the models parameters.

This package provides functions to estimate the kinship matrix of individuals from a large set of biallelic SNPs, and extract inbreeding coefficients and the generalized FST (Wright's fixation index). Method described in Ochoa and Storey (2021) <doi:10.1371/journal.pgen.1009241>.

Integrates the 13C nuclear magnetic resonance spectra using different integration ranges. Output depends on the method chosen. For the Molecular Mixing Model, a measurement of the fitting quality is given by its R-factor. For more details see: <doi:10.5281/zenodo.10137768>.

Builds, evaluates and validates a nomogram with survey data and right-censored outcomes. As described in Capanu (2015) <doi:10.18637/jss.v064.c01>, the package contains functions to create the nomogram, validate it using bootstrap, as well as produce the calibration plots.

Implementation for sparse logistic functional principal component analysis (SLFPCA). SLFPCA is specifically developed for functional binary data, and the estimated eigenfunction can be strictly zero on some sub-intervals, which is helpful for interpretation. The crucial function of this package is SLFPCA().

Fit a threshold regression model for Interval Censored Data based on the first-hitting-time of a boundary by the sample path of a Wiener diffusion process. The threshold regression methodology is well suited to applications involving survival and time-to-event data.

This package provides functions to design phase 1 trials using an isotonic regression based design incorporating time-to-event information. Simulation and design functions are available, which incorporate information about followup and DLTs, and apply isotonic regression to devise estimates of DLT probability.

This package provides a collection of statistical tests for martingale difference hypothesis, including automatic portmanteau test (Escansiano and Lobato, 2009) <doi:10.1016/j.jeconom.2009.03.001> and automatic variance ratio test (Kim, 2009) <doi:10.1016/j.frl.2009.04.003>.

It shows the connections between selected clusters from the latest time point and the clusters from all the previous time points. The transition matrices between time point t and t+1 are obtained from Waddington-OT analysis <https://github.com/ScialdoneLab/WOTPLY>.

The package implements MBASED algorithm for detecting allele-specific gene expression from RNA count data, where allele counts at individual loci (SNVs) are integrated into a gene-specific measure of ASE, and utilizes simulations to appropriately assess the statistical significance of observed ASE.

This package contains the resample and windowfilter command line utilities. The resample command allows changing the sampling rate of a sound file, while the windowfilter command allows designing Finite Impulse Response (FIR) filters using the so-called window method.

This package generates interactive visualisations for analysis of RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an HTML page. The interactions are built on top of the popular static representations of analysis results in order to provide additional information.

This package implements the Python leidenalg module to be called in R. It enables clustering using the Leiden algorithm for partitioning a graph into communities. See also Traag et al (2018) "From Louvain to Leiden: guaranteeing well-connected communities." <arXiv:1810.08473>.

This package provides bindings to libsodium: a library for encryption, decryption, signatures, password hashing and more. Sodium uses curve25519, a Diffie-Hellman function by Daniel Bernstein, which has become very popular after it was discovered that the NSA had backdoored Dual EC DRBG.

This package provides miscellaneous functions for SciViews or general use, including tools to manage a temporary environment attached to the search path for temporary variables you do not want to save() or load(); test the current platform; showing progress bars, etc.

This package provides a set of Shiny apps for effective communication and understanding in statistics. The current version includes properties of normal distribution, properties of sampling distribution, one-sample z and t tests, two samples independent (unpaired) t test and analysis of variance.

Quality Ensured Demonstrations (QED) is a test framework for Test Driven Development (TDD) and Behaviour Driven Development (BDD) utilizing Literate Programming techniques. QED sits somewhere between lower-level testing tools like Test::Unit and requirement specifications systems like Cucumber.

Multivariate optimal allocation for different domains in one and two stages stratified sample design. R2BEAT extends the Neyman (1934) â Tschuprow (1923) allocation method to the case of several variables, adopting a generalization of the Bethelâ s proposal (1989). R2BEAT develops this methodology but, moreover, it allows to determine the sample allocation in the multivariate and multi-domains case of estimates for two-stage stratified samples. It also allows to perform both Primary Stage Units and Secondary Stage Units selection. This package requires the availability of ReGenesees', that can be installed from <https://github.com/DiegoZardetto/ReGenesees>.

Generates data for challenging machine learning models in Arena <https://arena.drwhy.ai> - an interactive web application. You can start the server with XAI (Explainable Artificial Intelligence) plots to be generated on-demand or precalculate and auto-upload data file beside shareable Arena URL.

The tools in this package are intended to help researchers assess multiple treatment-covariate interactions with data from a parallel-group randomized controlled clinical trial. The methods implemented in the package were proposed in Kovalchik, Varadhan and Weiss (2013) <doi: 10.1002/sim.5881>.

This package provides data import and offers 3 daily snapshot functions from securities of varying prices traded on the Bolivian Securities Exchange, website <https://www.bbv.com.bo/>. The snapshots include a detailed list, scatter plot correlation, and descriptive statistics table for the securities.

Extract, visualize and summarize aerial movements of birds and insects from weather radar data. See Dokter, A. M. et al. (2018) "bioRad: biological analysis and visualization of weather radar data" <doi:10.1111/ecog.04028> for a software paper describing package and methodologies.

This package provides functions to perform Bayesian nonparametric univariate and multivariate density estimation and clustering, by means of Pitman-Yor mixtures, and dependent Dirichlet process mixtures for partially exchangeable data. See Corradin et al. (2021) <doi:10.18637/jss.v100.i15> for more details.

An implementation of Jon Kleinberg's burst detection algorithm (Kleinberg (2003) <doi:10.1023/A:1024940629314>). Uses an infinite Markov model to detect periods of increased activity in a series of discrete events with known times, and provides a simple visualization of the results.