No packages match

multigroup.vaccine - Analyze Outbreak Models of Multi-Group Populations with Vaccination

Model infectious disease dynamics in populations with multiple subgroups having different vaccination rates, transmission characteristics, and contact patterns. Calculate final and intermediate outbreak sizes, form age-structured contact models with automatic fetching of U.S. census data, and explore vaccination scenarios with an interactive 'shiny' dashboard for a model with two subgroups, as described in Nguyen et al. (2024) <doi:10.1016/j.jval.2024.03.039> and Duong et al. (2026) <doi:10.1093/ofid/ofaf695.217>.

Last updated

cpp

6.92 score 2 stars 20 scripts 224 downloads

rbranding - Manage Branding and Accessibility of R Projects

A tool for building projects that are visually consistent, accessible, and easy to maintain. It provides functions for managing branding assets, applying organization-wide themes using 'brand.yml', and setting up new projects with accessibility features and correct branding. It supports 'quarto', 'shiny', and 'rmarkdown' projects, and integrates with 'ggplot2'. The accessibility features are based on the Web Content Accessibility Guidelines <https://www.w3.org/WAI/WCAG22/quickref/?versions=2.1> and Accessible Rich Internet Applications (ARIA) specifications <https://www.w3.org/WAI/ARIA/apg/>. The branding framework implements the 'brand.yml' specification <https://posit-dev.github.io/brand-yml/>.

Last updated

6.73 score 4 stars 8 scripts 120 downloads

linkeR - Link Interactive Plots and Tables in 'shiny' Applications

Build powerful, linked-view dashboards in 'shiny' applications. With a declarative, one-line setup, you can create bidirectional links between interactive components. When a user interacts with one element (e.g., clicking a map marker), all linked components (such as 'DT' tables or other charts) instantly update. Supports 'leaflet' maps, 'DT' tables, 'plotly' charts, and spatial data via 'sf' objects out-of-the-box, with an extensible API for custom components.

Last updated

6.48 score 4 stars 21 scripts 137 downloads

epitraxr - 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.

Last updated

5.95 score 3 stars 8 scripts 455 downloads

bayestransmission - Bayesian Transmission Models

Provides Bayesian inference methods for infectious disease transmission models in healthcare settings. Implements Markov Chain Monte Carlo (MCMC) algorithms for estimating transmission parameters from patient-level data including admission, discharge, and testing events as described in Thomas et al. (2015) <doi:10.1093/imammb/dqt021>.

Last updated

openblascpp

5.11 score 3 stars 32 scripts 2 downloads

facilityepimath - Analyze Mathematical Models of Healthcare Facility Transmission

Calculate useful quantities for a user-defined differential equation model of infectious disease transmission among individuals in a healthcare facility. Input rates of transition between states of individuals with and without the disease-causing organism, distributions of states at facility admission, relative infectivity of transmissible states, and the facility length of stay distribution. Calculate the model equilibrium and the basic facility reproduction number, as described in Toth et al. (2025) <doi:10.1371/journal.pcbi.1013577>.

Last updated

4.88 score 1 stars 9 scripts 203 downloads

branchingprocess - Calculate Outbreak Probabilities for a Branching Process Model

Quantify outbreak risk posed by individual importers of a transmissible pathogen. Input parameters of negative binomial offspring distributions for the number of transmissions from each infected individual and initial number of infected. Calculate probabilities of final outbreak size and generations of transmission, as described in Toth et al. (2015) <doi:10.3201/eid2108.150170> and Toth et al. (2016) <doi:10.1016/j.epidem.2016.04.002>.

Last updated

4.18 score 3 scripts 528 downloads

quadkeyr - Generate Raster Images from QuadKey-Identified Datasets

A set of functions of increasing complexity allows users to (1) convert QuadKey-identified datasets, based on 'Microsoft's Bing Maps Tile System', into Simple Features data frames, (2) transform Simple Features data frames into rasters, and (3) process multiple 'Meta' ('Facebook') QuadKey-identified human mobility files directly into raster files. For more details, see D’Andrea et al. (2024) <doi:10.21105/joss.06500>.

Last updated

3.26 score 1 stars 12 scripts 308 downloads

summrt - What the Package Does (One Line, Title Case)

What the package does (one paragraph).

Last updated

epidemiologyreproduction-numberrt

2.48 score 1 stars 7 scripts