Functions, Classes & Methods for estimation, prediction, and simulation (bootstrap) of Variable Length Markov Chain ('VLMC') Models.

This package provides a shiny app for accurate estimation of vaccine induced immunogenicity with bivariate linear modeling. Method is detailed in: Lhomme, Hejblum, Lacabaratz, Wiedemann, Lelievre, Levy, Thiebaut & Richert (2020). Journal of Immunological Methods, 477:112711. <doi:10.1016/j.jim.2019.112711>.

The "Vertical and Horizontal Inheritance Consistence Analysis" method is described in the following publication: "VHICA: a new method to discriminate between vertical and horizontal transposon transfer: application to the mariner family within Drosophila" by G. Wallau. et al. (2016) <DOI:10.1093/molbev/msv341>. The purpose of the method is to detect horizontal transfers of transposable elements, by contrasting the divergence of transposable element sequences with that of regular genes.

Automatically selects and visualises statistical hypothesis tests between two vectors, based on their class, distribution, sample size, and a user-defined confidence level (conf.level). Visual outputs - including box plots, bar charts, regression lines with confidence bands, mosaic plots, residual plots, and Q-Q plots - are annotated with relevant test statistics, assumption checks, and post-hoc analyses where applicable. The algorithmic workflow helps the user focus on the interpretation of test results rather than test selection. It is particularly suited for quick data analysis, e.g., in statistical consulting projects or educational settings. The test selection algorithm proceeds as follows: Input vectors of class numeric or integer are considered numerical; those of class factor are considered categorical. Assumptions of residual normality and homogeneity of variances are considered met if the corresponding test yields a p-value greater than the significance level alpha = 1 - conf.level. (1) When the response vector is numerical and the predictor vector is categorical, a test of central tendencies is selected. If the categorical predictor has exactly two levels, t.test() is applied when group sizes exceed 30 (Lumley et al. (2002) <doi:10.1146/annurev.publhealth.23.100901.140546>). For smaller samples, normality of residuals is tested using shapiro.test(); if met, t.test() is used; otherwise, wilcox.test(). If the predictor is categorical with more than two levels, an aov() is initially fitted. Residual normality is evaluated using both shapiro.test() and ad.test(); residuals are considered approximately normal if at least one test yields a p-value above alpha. If this assumption is met, bartlett.test() assesses variance homogeneity. If variances are homogeneous, aov() is used; otherwise oneway.test(). Both tests are followed by TukeyHSD(). If residual normality cannot be assumed, kruskal.test() is followed by pairwise.wilcox.test(). (2) When both the response and predictor vectors are numerical, a simple linear regression model is fitted using lm(). (3) When both vectors are categorical, Cochran's rule (Cochran (1954) <doi:10.2307/3001666>) is applied to test independence either by chisq.test() or fisher.test().

The goal of the package is to equip the jmcm package (current version 0.2.1) with estimations of the covariance of estimated parameters. Two methods are provided. The first method is to use the inverse of estimated Fisher's information matrix, see M. Pourahmadi (2000) <doi:10.1093/biomet/87.2.425>, M. Maadooliat, M. Pourahmadi and J. Z. Huang (2013) <doi:10.1007/s11222-011-9284-6>, and W. Zhang, C. Leng, C. Tang (2015) <doi:10.1111/rssb.12065>. The second method is bootstrap based, see Liu, R.Y. (1988) <doi:10.1214/aos/1176351062> for reference.

Realization of published methods to analyze visual field (VF) progression. Introduction to the plotting methods (designed by author TE) for VF output visualization. A sample dataset for two eyes, each with 10 follow-ups is included. The VF analysis methods could be found in -- Musch et al. (1999) <doi:10.1016/S0161-6420(99)90147-1>, Nouri-Mahdavi et at. (2012) <doi:10.1167/iovs.11-9021>, Schell et at. (2014) <doi:10.1016/j.ophtha.2014.02.021>, Aptel et al. (2015) <doi:10.1111/aos.12788>.

Estimates the type of variables in non-quality controlled data. The prediction is based on a random forest model, trained on over 5000 medical variables with accuracy of 99%. The accuracy can hardy depend on type and coding style of data.

This package provides R functions to draw lines and curves with the width of the curve allowed to vary along the length of the curve.

Vega and Vega-Lite parse text in JSON notation to render chart-specifications into HTML'. This package is used to facilitate the rendering. It also provides a means to interact with signals, events, and datasets in a Vega chart using JavaScript or Shiny'.

This package implements a maximum likelihood estimation (MLE) method for estimation and prediction of Gaussian process-based spatially varying coefficient (SVC) models (Dambon et al. (2021a) <doi:10.1016/j.spasta.2020.100470>). Covariance tapering (Furrer et al. (2006) <doi:10.1198/106186006X132178>) can be applied such that the method scales to large data. Further, it implements a joint variable selection of the fixed and random effects (Dambon et al. (2021b) <doi:10.1080/13658816.2022.2097684>). The package and its capabilities are described in (Dambon et al. (2021c) <doi:10.48550/arXiv.2106.02364>).

Import and handling data from vegetation-plot databases, especially data stored in Turboveg 2 (<https://www.synbiosys.alterra.nl/turboveg/>). Also import/export routines for exchange of data with Juice (<https://www.sci.muni.cz/botany/juice/>) are implemented.

This is a package for creating and running Agent Based Models (ABM). It provides a set of base classes with core functionality to allow bootstrapped models. For more intensive modeling, the supplied classes can be extended to fit researcher needs.

Declarative template-based framework for verifying that objects meet structural requirements, and auto-composing error messages when they do not.

Mainly data sets to accompany the VGAM package and the book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) <DOI:10.1007/978-1-4939-2818-7>. These are used to illustrate vector generalized linear and additive models (VGLMs/VGAMs), and associated models (Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column Interaction Models, and constrained and unconstrained ordination models in ecology). This package now contains some old VGAM family functions which have been replaced by newer ones (often because they are now special cases).

Generates interactive plots for analysing and visualising three-class high dimensional data. It is particularly suited to visualising differences in continuous attributes such as gene/protein/biomarker expression levels between three groups. Differential gene/biomarker expression analysis between two classes is typically shown as a volcano plot. However, with three groups this type of visualisation is particularly difficult to interpret. This package generates 3D volcano plots and 3-way polar plots for easier interpretation of three-class data.

This package provides an easy to calculate local variable importance measure based on Ceteris Paribus profile and global variable importance measure based on Partial Dependence Profiles.

This package provides a Shiny application for the interactive visualisation and analysis of networks that also provides a web interface for collecting social media data using vosonSML'.

Calculate point estimates of and valid confidence intervals for nonparametric, algorithm-agnostic variable importance measures in high and low dimensions, using flexible estimators of the underlying regression functions. For more information about the methods, please see Williamson et al. (Biometrics, 2020), Williamson et al. (JASA, 2021), and Williamson and Feng (ICML, 2020).

This package produces violin plots with optional nonparametric (Mann-Whitney test) and parametric (Tukey's honest significant difference) mean comparison and linear regression. This package aims to be a simple and quick visualization tool for comparing means and assessing trends of categorical factors.

This package provides a binding for the valection program which offers various ways to sample the outputs of competing algorithms or parameterizations, and fairly assess their performance against each other. The valection C library is required to use this package and can be downloaded from: <http://labs.oicr.on.ca/boutros-lab/software/valection>. Cooper CI, et al; Valection: Design Optimization for Validation and Verification Studies; Biorxiv 2018; <doi:10.1101/254839>.

This package implements wild bootstrap tests for autocorrelation in Vector Autoregressive (VAR) models based on Ahlgren and Catani (2016) <doi:10.1007/s00362-016-0744-0>, a combined Lagrange Multiplier (LM) test for Autoregressive Conditional Heteroskedasticity (ARCH) in VAR models from Catani and Ahlgren (2016) <doi:10.1016/j.ecosta.2016.10.006>, and bootstrap-based methods for determining the cointegration rank from Cavaliere, Rahbek, and Taylor (2012) <doi:10.3982/ECTA9099> and Cavaliere, Rahbek, and Taylor (2014) <doi:10.1080/07474938.2013.825175>.

This package provides an interface to the VK API <https://vk.com/dev/methods>. VK <https://vk.com/> is the largest European online social networking service, based in Russia.

Offers a wide range of functions for reading and writing data in various file formats, including CSV, RDS, Excel and ZIP files. Additionally, it provides functions for retrieving metadata associated with files, such as file size and creation date, making it easy to manage and organize large data sets. This package is designed to simplify data import and export tasks, and provide users with a comprehensive set of tools to work with different types of data files.

An R client for the vatcheckapi.com VAT number validation API. The API requires registration of an API key. Basic features are free, some require a paid subscription. You can find the full API documentation at <https://vatcheckapi.com/docs> .