Package: R0 1.3-0
Thomas Obadia
R0: Estimation of R0 and Real-Time Reproduction Number from Epidemics
Estimation of reproduction numbers for disease outbreak, based on incidence data. The R0 package implements several documented methods. It is therefore possible to compare estimations according to the methods used. Depending on the methods requested by user, basic reproduction number (commonly denoted as R0) or real-time reproduction number (referred to as R(t)) is computed, along with a 95% Confidence Interval. Plotting outputs will give different graphs depending on the methods requested : basic reproductive number estimations will only show the epidemic curve (collected data) and an adjusted model, whereas real-time methods will also show the R(t) variations throughout the outbreak time period. Sensitivity analysis tools are also provided, and allow for investigating effects of varying Generation Time distribution or time window on estimates.
Authors:
R0_1.3-0.tar.gz
R0_1.3-0.zip(r-4.7-any)R0_1.3-0.zip(r-4.6-any)R0_1.3-0.zip(r-4.5-any)
R0_1.3-0.tgz(r-4.6-any)R0_1.3-0.tgz(r-4.5-any)
R0_1.3-0.tar.gz(r-4.7-any)R0_1.3-0.tar.gz(r-4.6-any)
R0_1.3-0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
R0/json (API)
| # Install 'R0' in R: |
| install.packages('R0', repos = c('https://epiverse-connect.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tobadia/r0/issues
- Germany.1918 - Germany 1918 dataset
- GT.chld.hsld - 2009 A/H1N1 observed generation time distribution
- H1N1.serial.interval - H1N1 serial interval
Last updated from:f13028dbe1. Checks:7 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | NOTE | 124 | ||
| source / vignettes | OK | 221 | ||
| linux-release | NOTE | 119 | ||
| macos-release | NOTE | 94 | ||
| macos-oldrel | NOTE | 109 | ||
| windows-devel | NOTE | 70 | ||
| windows-release | NOTE | 68 | ||
| windows-oldrel | NOTE | 83 | ||
| wasm-release | OK | 94 |
Exports:check.incidest.GTest.R0.ARest.R0.EGest.R0.MLest.R0.SBest.R0.TDestimate.Rgeneration.timeimpute.incidinspect.dataintegrity.checksplotfitsa.GTsa.timesensitivity.analysissim.epidsmooth.Rt
Dependencies:MASS
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Estimate generation time distribution | est.GT |
| Estimate reproduction number (R0 or Rt) for one incidence dataset using available methods | estimate.R |
| Generation Time distribution | generation.time |
| Germany 1918 dataset | Germany.1918 |
| 2009 A/H1N1 observed generation time distribution | GT.chld.hsld |
| H1N1 serial interval | H1N1.serial.interval |
| Optimiziation routine for incidence imputation | impute.incid |
| Audit input data for common issues | inspect.data |
| Integrity checks for input parameters | integrity.checks |
| Sensitivity of R0 to varying generation time distributions | sa.GT |
| Sensitivity of R0 to time estimation windows | sa.time |
| Sensitivity analysis of basic reproduction ratio to begin/end dates | sensitivity.analysis |
| Epidemic outbreak simulation | sim.epid |
| Influenza-like illness simulation (individual-based model) | sim.epid.indiv |
| Smooth real-time reproduction number over larger time periods | smooth.Rt |