Package: cfr 0.1.1.9000
Adam Kucharski
cfr: Estimate Disease Severity and Case Ascertainment
Estimate the severity of a disease and ascertainment of cases, as discussed in Nishiura et al. (2009) <doi:10.1371/journal.pone.0006852>.
Authors:
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cfr.pdf |cfr.html✨
cfr/json (API)
NEWS
| # Install 'cfr' in R: |
| install.packages('cfr', repos = c('https://epiverse-trace.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/epiverse-trace/cfr/issues
- covid_data - Daily Covid-19 case and death data for countries with 100,000 or more deaths
- ebola1976 - Ebola 1976 outbreak case data
case-fatality-rateepidemic-modellingepidemiologyepiversehealth-outcomesoutbreak-analysissdg-3
Last updated 2 months agofrom:29ee12aa9b. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 15 2024 |
| R-4.5-win | OK | Sep 15 2024 |
| R-4.5-linux | OK | Sep 15 2024 |
| R-4.4-win | OK | Sep 15 2024 |
| R-4.4-mac | OK | Sep 15 2024 |
| R-4.3-win | OK | Sep 15 2024 |
| R-4.3-mac | OK | Sep 15 2024 |
Exports:cfr_rollingcfr_staticcfr_time_varyingestimate_ascertainmentestimate_outcomesprepare_data
A primer on working with delay distributions
Rendered fromdelay_distributions.Rmdusingknitr::rmarkdownon Sep 15 2024.Last update: 2024-07-17
Started: 2023-10-26
Calculating a static, delay-adjusted estimate of disease severity
Rendered fromestimate_static_severity.Rmdusingknitr::rmarkdownon Sep 15 2024.Last update: 2024-07-17
Started: 2023-05-15
Estimating disease severity while correcting for reporting delays
Rendered fromcfr.Rmdusingknitr::rmarkdownon Sep 15 2024.Last update: 2024-07-17
Started: 2023-07-13
Estimating how disease severity varies over the course of an outbreak
Rendered fromestimate_time_varying_severity.Rmdusingknitr::rmarkdownon Sep 15 2024.Last update: 2024-07-17
Started: 2023-05-15
Estimating the proportion of cases that are ascertained during an outbreak
Rendered fromestimate_ascertainment.Rmdusingknitr::rmarkdownon Sep 15 2024.Last update: 2024-07-17
Started: 2023-05-15
Handling data from {incidence2}
Rendered fromdata_from_incidence2.Rmdusingknitr::rmarkdownon Sep 15 2024.Last update: 2024-07-17
Started: 2023-06-22
Software permissions and regulations
Rendered fromsoftware-permissions.Rmdusingknitr::rmarkdownon Sep 15 2024.Last update: 2024-02-19
Started: 2024-02-19
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Estimate static severity for an expanding time series | cfr_rolling |
| Estimate a static disease severity measure | cfr_static |
| Estimate a severity measure that varies over time | cfr_time_varying |
| Daily Covid-19 case and death data for countries with 100,000 or more deaths | covid_data |
| Ebola 1976 outbreak case data | ebola1976 |
| Estimate the ascertainment ratio of a disease | estimate_ascertainment |
| Estimate known outcomes of cases using a delay distribution | estimate_outcomes |
| Prepare common epidemiological data formats for CFR estimation | prepare_data prepare_data.incidence2 |
