Overview | Example - synthetic dataset | Quick start | Cross Validation | Uneven Reporting Frequency | Changing degree of difference operator | Example - Canadian Covid-19 cases | Approximate confidence bands
Package: rtestim 1.0.2.9001
rtestim: Estimate the Effective Reproductive Number with Trend Filtering
Use trend filtering, a type of regularized nonparametric regression, to estimate the instantaneous reproduction number, also called Rt. This value roughly says how many new infections will result from each new infection today. Values larger than 1 indicate that an epidemic is growing while those less than 1 indicate decline. For more details about this methodology, see Liu, Cai, Gustafson, and McDonald (2024) <doi:10.1371/journal.pcbi.1012324>.
Authors:
rtestim_1.0.2.9001.tar.gz
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rtestim_1.0.2.9001.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rtestim/json (API)
| # Install 'rtestim' in R: |
| install.packages('rtestim', repos = c('https://dajmcdon.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/dajmcdon/rtestim/issues
Pkgdown/docs site:https://dajmcdon.github.io
Datasets:
- cancovid - Canadian Incident COVID-19 Cases
Last updated from:fa078efe99. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 156 | ||
| linux-devel-x86_64 | OK | 243 | ||
| source / vignettes | OK | 256 | ||
| linux-release-arm64 | OK | 169 | ||
| linux-release-x86_64 | OK | 174 | ||
| macos-release-arm64 | OK | 162 | ||
| macos-release-x86_64 | OK | 327 | ||
| macos-oldrel-arm64 | OK | 163 | ||
| macos-oldrel-x86_64 | OK | 230 | ||
| windows-devel | OK | 177 | ||
| windows-release | OK | 149 | ||
| windows-oldrel | OK | 156 | ||
| wasm-release | OK | 155 |
Exports:confbandconfigure_rt_admmcv_estimate_rtdelay_calculatordiscretize_gammaestimate_rtinterpolate_rt
Dependencies:backportsBHbriocallrcheckmateclicpp11crayondescdiffobjdsplineevaluatefarverfsggplot2gluegtableisobandjsonlitelabelinglatticelifecyclemagrittrMatrixotelpillarpkgbuildpkgconfigpkgloadpraiseprocessxpsR6RColorBrewerRcppRcppEigenrlangrprojrootS7scalestestthattibbletvdenoisingutf8vctrsviridisLitewaldowithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Canadian Incident COVID-19 Cases | cancovid |
| Add confidence bands to estimated Rt or incidence curves | confband |
| Rt estimation algorithm configuration | configure_rt_admm |
| Leave-kth-out cross validation for choosing a optimal parameter lambda | cv_estimate_rt |
| Calculate the total infectiousness at each observed time point. | delay_calculator |
| Compute the discretized density function for gamma distribution | discretize_gamma |
| Estimate Rt using smoothness-penalized Poisson likelihood | estimate_rt |
| Fitted cv_poisson_rt | fitted.cv_poisson_rt |
| Interpolate (or extrapolate) Rt estimates to intermediate design points | interpolate_rt interpolate_rt.cv_poisson_rt interpolate_rt.poisson_rt |
| Plot cv_poisson_rt | plot.cv_poisson_rt |
| Plot estimated Rt values from a 'poisson_rt' object | plot.poisson_rt |
| Plot estimated confidence bands for an estimate of Rt | plot.rt_confidence_band |
| Predict observed data using estimated Rt | predict.cv_poisson_rt |
| Predict observed data using estimated Rt | predict.poisson_rt |
