Included Data: florida_vaccine_coverage | Core Concepts: Smart Defaults | Modeling a Custom Disease | Visualization Functions | plot_coverage_history() | plot_risk_curve() | Saving Plot Data
Package: vaxineR 0.1.0
vaxineR: Vaccine Coverage and Outbreak Risk Analysis
Provides tools to analyze vaccine coverage data and simulate potential disease outbreak scenarios. It allows users to calculate key epidemiological metrics such as the effective reproduction number (Re), outbreak probabilities, and expected infection counts based on county-level vaccination rates, disease characteristics, and vaccine effectiveness. The package includes historical kindergarten vaccination data for Florida counties and offers functions for generating summary tables, visualizations, and exporting the underlying plot data.
Authors:
vaxineR_0.1.0.tar.gz
vaxineR_0.1.0.zip(r-4.7-any)vaxineR_0.1.0.zip(r-4.6-any)vaxineR_0.1.0.zip(r-4.5-any)
vaxineR_0.1.0.tgz(r-4.6-any)vaxineR_0.1.0.tgz(r-4.5-any)
vaxineR_0.1.0.tar.gz(r-4.7-any)vaxineR_0.1.0.tar.gz(r-4.6-any)
vaxineR_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
vaxineR/json (API)
| # Install 'vaxineR' in R: |
| install.packages('vaxineR', repos = c('https://peiyuliu-biostats.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/peiyuliu-biostats/vaxiner/issues
Datasets:
- florida_vaccine_coverage - Kindergarten Vaccination Coverage for Florida Counties
Last updated from:3e386406d2. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 112 | ||
| source / vignettes | OK | 186 | ||
| linux-release | OK | 127 | ||
| macos-release | OK | 147 | ||
| macos-oldrel | OK | 140 | ||
| windows-devel | OK | 87 | ||
| windows-release | OK | 83 | ||
| windows-oldrel | OK | 85 | ||
| wasm-release | OK | 102 |
Exports:calc_expected_infectionscalc_replot_coverage_historyplot_outbreak_probplot_risk_curveprob_major_outbreakprob_sec_casesummary_coveragesummary_infection_risk
Dependencies:clicpp11dplyrfarvergenericsggplot2gluegtableisobandlabelinglifecyclemagrittropenxlsxpillarpkgconfigpurrrR6RColorBrewerRcpprlangS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithrzip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate the expected number of infections in a cohort | calc_expected_infections |
| Calculate the effective reproduction number (Re) | calc_re |
| Kindergarten Vaccination Coverage for Florida Counties | florida_vaccine_coverage |
| Plot Historical Vaccination Coverage Rate | plot_coverage_history |
| Plot Outbreak Probability vs. Coverage | plot_outbreak_prob |
| Plot the Risk Curve of Expected Infections | plot_risk_curve |
| Calculate the probability of a major outbreak | prob_major_outbreak |
| Calculate the probability of at least one secondary infection | prob_sec_case |
| Summarize Vaccination Coverage for a Given Year | summary_coverage |
| Generate an Outbreak Risk Simulation Table | summary_infection_risk |