The YUIMA Project Package for SDEs

Simulation and Inference for SDEs and Other Stochastic Processes.

Simulation-Based Inference for Regression Models

Performs simulation-based inference as an alternative to the delta method for obtaining valid confidence intervals and p-values for regression post-estimation quantities, such as average marginal effects and predictions at representative values. This framework for simulation-based inference is especially useful when the resulting quantity is not normally distributed and the delta method approximation fails. The methodology is described in King, Tomz, and Wittenberg (2000) . 'clarify' is meant to replace some of the functionality of the archived package 'Zelig'; see the vignette "Translating Zelig to clarify" for replicating this functionality.

Compute and Display Tendril Plots

Compute the coordinates to produce a tendril plot. In the tendril plot, each tendril (branch) represents a type of events, and the direction of the tendril is dictated by on which treatment arm the event is occurring. If an event is occurring on the first of the two specified treatment arms, the tendril bends in a clockwise direction. If an event is occurring on the second of the treatment arms, the tendril bends in an anti-clockwise direction. Ref: Karpefors, M and Weatherall, J., "The Tendril Plot - a novel visual summary of the incidence, significance and temporal aspects of adverse events in clinical trials" - JAMIA 2018; 25(8): 1069-1073 .

Social Ranking Solutions for Power Relations on Coalitions

The notion of power index has been widely used in literature to evaluate the influence of individual players (e.g., voters, political parties, nations, stockholders, etc.) involved in a collective decision situation like an electoral system, a parliament, a council, a management board, etc., where players may form coalitions. Traditionally this ranking is determined through numerical evaluation. More often than not however only ordinal data between coalitions is known. The package 'socialranking' offers a set of solutions to rank players based on a transitive ranking between coalitions, including through CP-Majority, ordinal Banzhaf or lexicographic excellence solution summarized by Tahar Allouche, Bruno Escoffier, Stefano Moretti and Meltem Öztürk (2020, ).

Interactively Gate Points

Interactively gate points on a scatter plot. Interactively drawn gates are recorded and can be applied programmatically to reproduce results exactly. Programmatic gating is based on the package gatepoints by Wajid Jawaid (who is also an author of this package).

Knowledge Discovery by Accuracy Maximization

An unsupervised and semi-supervised learning algorithm that performs feature extraction from noisy and high-dimensional data. It facilitates identification of patterns representing underlying groups on all samples in a data set. Based on Cacciatore S, Tenori L, Luchinat C, Bennett PR, MacIntyre DA. (2017) Bioinformatics and Cacciatore S, Luchinat C, Tenori L. (2014) Proc Natl Acad Sci USA .

Tidy Model Visualisation for Generalised Additive Models

Provides functions for visualising generalised additive models and getting predicted values using tidy tools from the 'tidyverse' packages.

Biodiversity Assessment Tools

Includes algorithms to assess alpha and beta diversity in all their dimensions (taxonomic, phylogenetic and functional). It allows performing a number of analyses based on species identities/abundances, phylogenetic/functional distances, trees, convex-hulls or kernel density n-dimensional hypervolumes depicting species relationships. Cardoso et al. (2015) .

Chemical Structural Similarity Analysis

A new pipeline to explore chemical structural similarity across metabolite. It allows to classify metabolites in structurally-related modules and identify common shared functional groups. KODAMA algorithm is used to highlight structural similarity between metabolites. See Cacciatore S, Tenori L, Luchinat C, Bennett PR, MacIntyre DA. (2017) Bioinformatics , Cacciatore S, Luchinat C, Tenori L. (2014) Proc Natl Acad Sci USA , and Abdel-Shafy EA, Melak T, MacIntyre DA, Zadra G, Zerbini LF, Piazza S, Cacciatore S. (2023) Bioinformatics Advances .

Gene-Based Association Tests using the Actual Impurity Reduction (AIR) Variable Importance

Gene-based association tests using the actual impurity reduction (AIR) variable importance. The function aggregates AIR importance measures from a group of SNPs or probes and outputs a p-value for each gene. The procedures builds upon the method described in and will be published soon.