Small Helpers and Tricks for Epidemics Analysis

A collection of small functions useful for epidemics analysis and infectious disease modelling. This includes computation of basic reproduction numbers from growth rates, generation of hashed labels to anonymize data, and fitting discretized Gamma distributions.

Monazite Dating for the NiLeDAM Team

Th-U-Pb electron microprobe age dating of monazite, as originally described in .

Estimators of Non-Linear Cross-Validated Risks Optimized for Small Samples

Methods for obtaining improved estimates of non-linear cross-validated risks are obtained using targeted minimum loss-based estimation, estimating equations, and one-step estimation (Benkeser, Petersen, van der Laan (2019), ). Cross-validated area under the receiver operating characteristics curve (LeDell, Petersen, van der Laan (2015), ) and other metrics are included.

Assessing the Integrity and Trustworthiness of Clinical Trials Data

The integrity package implements the IPD Integrity Tool, a structured and transparent framework for evaluating the integrity of individual participant data (IPD) from randomised trials (see Hunter et al. (2024) and ). It supports users to identify potential issues, such as unusual data patterns, implausible values, lack of expected correlations, date violations, and inconsistencies. The package provides reproducible workflows for screening, documenting and summarising integrity concerns, and may be applied by evidence synthesists, editors, and others to determine whether a randomised trial may be considered sufficiently trustworthy to contribute to the evidence base that informs policy and practice.

Analysis of Chronological Patterns from Archaeological Count Data

A toolkit for absolute and relative dating and analysis of chronological patterns. This package includes functions for chronological modeling and dating of archaeological assemblages from count data. It provides methods for matrix seriation. It also allows to compute time point estimates and density estimates of the occupation and duration of an archaeological site.

Continuous Mapping of Genetic Diversity

Generate continuous maps of genetic diversity using moving windows with options for rarefaction, interpolation, and masking as described in Bishop et al. (2023) .

Time Series Artificial Neural Network

The best ANN structure for time series data analysis is a demanding need in the present era. This package will find the best-fitted ANN model based on forecasting accuracy. The optimum size of the hidden layers was also determined after determining the number of lags to be included. This package has been developed using the algorithm of Paul and Garai (2021) .

Estimation of Transmissibility in the Early Stages of a Disease Outbreak

Implements a simple, likelihood-based estimation of the reproduction number (R0) using a branching process with a Poisson likelihood. This model requires knowledge of the serial interval distribution, and dates of symptom onsets. Infectiousness is determined by weighting R0 by the probability mass function of the serial interval on the corresponding day. It is a simplified version of the model introduced by Cori et al. (2013) .

ICS via a Shiny Application

Performs Invariant Coordinate Selection (ICS) (Tyler, Critchley, Duembgen and Oja (2009) ) and especially ICS for multivariate outlier detection with application to quality control (Archimbaud, Nordhausen, Ruiz-Gazen (2018) ) using a shiny app.

Soil Organic Carbon Turnover Modelling with 'C-TOOL'

Provides an 'R' interface to the 'C-TOOL' soil carbon turnover model for simulating soil organic carbon dynamics in agricultural systems. The package supports the definition of carbon inputs, management schedules, soil parameters, and temperature forcing, and includes tools for scenario analysis and calibration of selected model parameters against observed soil organic carbon stocks. The 'C-TOOL' model and related modelling framework are described by Petersen et al. (2002) , Petersen et al. (2005) , Petersen et al. (2013) , and Taghizadeh-Toosi et al. (2014) . Further applications and developments are described by Taghizadeh-Toosi et al. (2016) , Keel et al. (2017) , Taghizadeh-Toosi et al. (2020) , and Taghizadeh-Toosi and Christensen (2021) .