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:Pratik R. Gupte [aut, cph], Adam Kucharski [aut, cph, cre], Tim Russell [aut, cph], Joshua W. Lambert [rev], Hugo Gruson [rev], Tim Taylor [rev], James M. Azam [rev], Abdoelnaser M. Degoot [rev], Sebastian Funk [rev]

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cfr.pdf |cfr.html
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NEWS

# Install 'cfr' in R:
install.packages('cfr', repos = c('https://epiverse-trace.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/epiverse-trace/cfr/issues

Datasets:
  • covid_data - Daily Covid-19 case and death data for countries with 100,000 or more deaths
  • ebola1976 - Ebola 1976 outbreak case data

On CRAN:

case-fatality-rateepidemic-modellingepidemiologyepiversehealth-outcomesoutbreak-analysissdg-3

6 exports 13 stars 8.10 score 2 dependencies 23 scripts 855 downloads

Last updated 3 months agofrom:29ee12aa9b. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 15 2024
R-4.5-winOKSep 15 2024
R-4.5-linuxOKSep 15 2024
R-4.4-winOKSep 15 2024
R-4.4-macOKSep 15 2024
R-4.3-winOKSep 15 2024
R-4.3-macOKSep 15 2024

Exports:cfr_rollingcfr_staticcfr_time_varyingestimate_ascertainmentestimate_outcomesprepare_data

Dependencies:backportscheckmate

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