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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.
Tables for Epidemiological Analysis
Produces tables for descriptive epidemiological analysis. These tables include attack rates, case fatality ratios, and mortality rates (with appropriate confidence intervals), with additional functionality to calculate Mantel-Haenszel odds, risk, and incidence rate ratios. The methods implemented follow standard epidemiological approaches described in Rothman et al. (2008, ISBN:978-0-19-513554-2). This package is part of the 'R4EPIs' project < https://R4EPI.github.io/sitrep/>.
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)
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.
Measles Epidemiological Models
A specialized collection of measles epidemiological models built on the 'epiworldR' framework. This package is a spinoff from 'epiworldR' focusing specifically on measles transmission dynamics. It includes models for school settings with quarantine and isolation policies, mixing models with population groups, and risk-based quarantine strategies. The models use Agent-Based Models (ABM) with a fast 'C++' backend from the 'epiworld' library. Ideal for studying measles outbreaks, vaccination strategies, and intervention policies.
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.