Social Contact Matrices for 177 Countries

Data package for the supplementary data in Prem et al. (2017) and Prem et al. . Provides easy access to contact data for 177 countries, for use in epidemiological, demographic or social sciences research.

Simulate Disease Outbreak Line List and Contacts Data

Tools to simulate realistic raw case data for an epidemic in the form of line lists and contacts using a branching process. Simulated outbreaks are parameterised with epidemiological parameters and can have age-structured populations, age-stratified hospitalisation and death risk and time-varying case fatality risk.

Bootstrapped Confidence Intervals for (Negative) Likelihood Ratio Tests

Computes appropriate confidence intervals for the likelihood ratio tests commonly used in medicine/epidemiology, using the method of Marill et al. (2015) . It is particularly useful when the sensitivity or specificity in the sample is 100%. Note that this does not perform the test on nested models--for that, see 'epicalc::lrtest'.

Gene‐based Association Tests of Zero‐inflated Count Phenotype for Rare Variants

Gene‐based association tests to model count data with excessive zeros and rare variants using zero-inflated Poisson/zero-inflated negative Binomial regression framework. This method was originally described by Fan, Sun, and Li in Genetic Epidemiology 46(1):73-86 .

Efficient Estimation of Clustered Current Status Data

Current status data abounds in the field of epidemiology and public health, where the only observable data for a subject is the random inspection time and the event status at inspection. Motivated by such a current status data from a periodontal study where data are inherently clustered, we propose a unified methodology to analyze such complex data.

Manipulate 'EpiTrax' Data and Generate Reports

A fast, flexible tool for generating disease surveillance reports from data exported from 'EpiTrax', a central repository for epidemiological data used by public health officials. It provides functions to manipulate 'EpiTrax' datasets, tailor reports to internal or public use, and export reports in CSV, Excel 'xlsx', or PDF formats.

Work with Two-by-Two Tables

A collection of functions for data analysis with two-by-two contingency tables. The package provides tools to compute measures of effect (odds ratio, risk ratio, and risk difference), calculate impact numbers and attributable fractions, and perform hypothesis testing. Statistical analysis methods are oriented towards epidemiological investigation of relationships between exposures and outcomes.

Color Palettes for Mycobacterium Tuberculosis Data Visualization

Colour palettes and helper functions for visualising Mycobacterium tuberculosis genomic and epidemiological data with 'ggplot2' and 'ggtree'. The package provides predefined palettes, scale functions, tree/cladogram helpers, and convenient preview tools to ensure consistent branding in pathogen-omics visualisations. The palettes were developed as part of the 'mycolorsTB' project < https://github.com/PathoGenOmics-Lab/mycolorsTB>.

Predicting Disease Spread from Flow Data

Provides functions and classes designed to handle and visualise epidemiological flows between locations. Also contains a statistical method for predicting disease spread from flow data initially described in Dorigatti et al. (2017) . This package is part of the RECON (< https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.

Working with Healthcare Databases

A system for identifying diseases or events from healthcare databases and preparing data for epidemiological studies. It includes capabilities not supported by 'SQL', such as matching strings by 'stringr' style regular expressions, and can compute comorbidity scores (Quan et al. (2005) ) directly on a database server. The implementation is based on 'dbplyr' with full 'tidyverse' compatibility.