Plots, Summary Statistics and Tools for Arena Simulation Users

Reads Arena < https://www.arenasimulation.com/> CSV output files and generates nice tables and plots. The package contains a Shiny App that can be used to interactively visualize Arena's results.

Validation of Arguments and Objects in User-Defined Functions

Utility functions that implement and automate common sets of validation tasks. These functions are particularly useful to validate inputs, intermediate objects and output values in user-defined functions, resulting in tidier and less verbose functions.

Doubly Robust Difference-in-Differences Estimators

Implements the locally efficient doubly robust difference-in-differences (DiD) estimators for the average treatment effect proposed by Sant'Anna and Zhao (2020) . The estimator combines inverse probability weighting and outcome regression estimators (also implemented in the package) to form estimators with more attractive statistical properties. Two different estimation methods can be used to estimate the nuisance functions.

Computational Tools for Economics

Implements solutions to canonical models of Economics such as Monopoly Profit Maximization, Cournot's Duopoly, Solow (1956, ) growth model and Mankiw, Romer and Weil (1992, ) growth model.

Infer Gene Probabilistic Boolean Networks from Single-Cell Data

Given a gene regulatory boolean network and a RNA-seq dataset, this package computes protein activity normalised enrichment scores using 'VIPER', and then produces a probabilistic network using the scores as probabilities for fixed node activation or deactivation, in addition to the original Boolean functions. For more information, refer to the preprint: Victori and Buffa (2022) .

Bayes Linear Estimators for Finite Population

Allows the user to apply the Bayes Linear approach to finite population with the Simple Random Sampling - BLE_SRS() - and the Stratified Simple Random Sampling design - BLE_SSRS() - (both without replacement), to the Ratio estimator (using auxiliary information) - BLE_Ratio() - and to categorical data - BLE_Categorical(). The Bayes linear estimation approach is applied to a general linear regression model for finite population prediction in BLE_Reg() and it is also possible to achieve the design based estimators using vague prior distributions. Based on Gonçalves, K.C.M, Moura, F.A.S and Migon, H.S.(2014) < https://www150.statcan.gc.ca/n1/en/catalogue/12-001-X201400111886>.

Selecting Variable Subsets

A collection of functions which (i) assess the quality of variable subsets as surrogates for a full data set, in either an exploratory data analysis or in the context of a multivariate linear model, and (ii) search for subsets which are optimal under various criteria. Theoretical support for the heuristic search methods and exploratory data analysis criteria is in Cadima, Cerdeira, Minhoto (2003, ). Theoretical support for the leap and bounds algorithm and the criteria for the general multivariate linear model is in Duarte Silva (2001, ). There is a package vignette "subselect", which includes additional references.

Efficient Outlier Detection for Large Time Series Databases

Programs for detecting and cleaning outliers in single time series and in time series from homogeneous and heterogeneous databases using an Orthogonal Greedy Algorithm (OGA) for saturated linear regression models. The programs implement the procedures presented in the paper entitled "Efficient Outlier Detection for Large Time Series Databases" by Pedro Galeano, Daniel Peña and Ruey S. Tsay (2026), working paper, Universidad Carlos III de Madrid. Version 1.1.2 fixes one bug.

Aggregate Multiple ROC Curves into One Global ROC

Aggregates multiple Receiver Operating Characteristic (ROC) curves obtained from different sources into one global ROC. Additionally, it’s also possible to calculate the aggregated precision-recall (PR) curve.

Helper Functions for Species Delimitation Analysis

Helpers functions to process, analyse, and visualize the output of single locus species delimitation methods. For full functionality, please install suggested software at < https://legallab.github.io/delimtools/articles/install.html>.