Package: ern 2.0.0
David Champredon
ern: Effective Reproduction Number Estimation
Estimate the effective reproduction number from wastewater and clinical data sources.
Authors:
ern_2.0.0.tar.gz
ern_2.0.0.tar.gz(r-4.5-noble)ern_2.0.0.tar.gz(r-4.4-noble)
ern_2.0.0.tgz(r-4.4-emscripten)ern_2.0.0.tgz(r-4.3-emscripten)
ern.pdf |ern.html✨
ern/json (API)
| # Install 'ern' in R: |
| install.packages('ern', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 6 months agofrom:a5ac4c4213. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 20 2024 |
| R-4.5-linux | OK | Sep 20 2024 |
Exports:agg_to_dailydef_distestimate_R_clestimate_R_wwget_discrete_distplot_diagnostic_clplot_diagnostic_wwplot_dist
Dependencies:assertthataweekclicoarseDataToolscodacolorspacecpp11dplyrEpiEstimfansifarverfitdistrplusgenericsggplot2gluegridExtragtableincidenceisobandlabelinglatticelifecyclelubridatemagrittrMASSMatrixMatrixModelsmcmcMCMCpackmgcvmunsellnlmepatchworkpillarpkgconfigplyrpurrrquantregR6RColorBrewerRcppreshape2rjagsrlangrunjagsscalesSparseMstringistringrsurvivaltibbletidyrtidyselecttimechangeutf8vctrsviridisLitewithrzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Infer daily counts from aggregates | agg_to_daily |
| Sample of aggregated clinical reports | cl.data |
| Define a family of distributions. | def_dist |
| Estimate the effective reproduction from clinical report data | estimate_R_cl |
| Estimate the effective reproduction from wastewater concentration data. | estimate_R_ww |
| Extract MCMC chains from a JAGS object | extract_mcmc_values |
| Get a discretized, truncated version of a distribution | get_discrete_dist |
| Daily incidence from linear interpolation | linear_int_daily |
| Diagnostic plot for R estimation from clinical report data | plot_diagnostic_cl |
| Diagnostic plot for R estimation from wastewater data | plot_diagnostic_ww |
| Plot a distribution | plot_dist |
| Plot the Gelman Rubin statistic for all parameters. | plot_gelman_rubin |
| Plot MCMC traces | plot_traces |
| Sample of wastewater concentration | ww.data |
