Epidemiological Report

Drafting an epidemiological report in 'Microsoft Word' format for a given disease, similar to the Annual Epidemiological Reports published by the European Centre for Disease Prevention and Control. Through standalone functions, it is specifically designed to generate each disease specific output presented in these reports and includes: - Table with the distribution of cases by Member State over the last five years; - Seasonality plot with the distribution of cases at the European Union / European Economic Area level, by month, over the past five years; - Trend plot with the trend and number of cases at the European Union / European Economic Area level, by month, over the past five years; - Age and gender bar graph with the distribution of cases at the European Union / European Economic Area level. Two types of datasets can be used: - The default dataset of dengue 2015-2019 data; - Any dataset specified as described in the vignette.

Database of Epidemiological Parameters

A data package containing a database of epidemiological parameters. It stores the data for the 'epiparameter' R package. Epidemiological parameter estimates are extracted from the literature.

Causal Modeling in Epidemiology

Create causal models for use in epidemiological studies, including sufficient-component cause models as introduced by Rothman (1976) .

Tidy Epidemiological Rates

Compute age-adjusted rates by direct and indirect methods and other epidemiological indicators in a tidy way, wrapping functions from the 'epitools' package.

Variational Techniques in Epidemiology

Using variational techniques we address some epidemiological problems as the incidence curve decomposition by inverting the renewal equation as described in Alvarez et al. (2021) and Alvarez et al. (2022) or the estimation of the functional relationship between epidemiological indicators. We also propose a learning method for the short time forecast of the trend incidence curve as described in Morel et al. (2022) .

Epidemiological Data Analysis

This is a tool for epidemiologist, medical data analyst, medical or public health professionals. It contains three domains of functions: 1) data management, 2) statistical analysis and 3) calculating epidemiological measures.

Landscape Epidemiology and Evolution

A stochastic, spatially-explicit, demo-genetic model simulating the spread and evolution of a plant pathogen in a heterogeneous landscape to assess resistance deployment strategies. It is based on a spatial geometry for describing the landscape and allocation of different cultivars, a dispersal kernel for the dissemination of the pathogen, and a SEIR ('Susceptible-Exposed-Infectious-Removed’) structure with a discrete time step. It provides a useful tool to assess the performance of a wide range of deployment options with respect to their epidemiological, evolutionary and economic outcomes. Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G Barrett, Peter H Thrall (2018) .

Dynamic Models in Epidemiology

Mathematical models of infectious diseases in humans and animals. Both, deterministic and stochastic models can be simulated and plotted.

Power and Sample Size Calculation for Survival Analysis of Epidemiological Studies

Functions to calculate power and sample size for testing main effect or interaction effect in the survival analysis of epidemiological studies (non-randomized studies), taking into account the correlation between the covariate of the interest and other covariates. Some calculations also take into account the competing risks and stratified analysis. This package also includes a set of functions to calculate power and sample size for testing main effect in the survival analysis of randomized clinical trials and conditional logistic regression for nested case-control study.

Epidemiological Tool for Contact Tracing

Routines for epidemiological contact tracing and visualisation of network of contacts.