Package: incidence 1.7.5
Tim Taylor
incidence: Compute, Handle, Plot and Model Incidence of Dated Events
Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Authors:
incidence_1.7.5.tar.gz
incidence_1.7.5.zip(r-4.5)incidence_1.7.5.zip(r-4.4)incidence_1.7.5.zip(r-4.3)
incidence_1.7.5.tgz(r-4.4-any)incidence_1.7.5.tgz(r-4.3-any)
incidence_1.7.5.tar.gz(r-4.5-noble)incidence_1.7.5.tar.gz(r-4.4-noble)
incidence_1.7.5.tgz(r-4.4-emscripten)incidence_1.7.5.tgz(r-4.3-emscripten)
incidence.pdf |incidence.html✨
incidence/json (API)
NEWS
| # Install 'incidence' in R: |
| install.packages('incidence', repos = c('https://r4epi.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/reconhub/incidence/issues
Last updated 4 months agofrom:42212a2ce0. Checks:OK: 7. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 05 2024 |
| R-4.5-win | OK | Nov 05 2024 |
| R-4.5-linux | OK | Nov 05 2024 |
| R-4.4-win | OK | Nov 05 2024 |
| R-4.4-mac | OK | Nov 05 2024 |
| R-4.3-win | OK | Nov 05 2024 |
| R-4.3-mac | OK | Nov 05 2024 |
Exports:add_incidence_fitas.incidencebootstrapcumulateestimate_peakfind_peakfitfit_optim_splitget_countsget_datesget_fitget_infoget_intervalget_nget_timespangroup_namesgroup_names<-incidenceincidence_pal1incidence_pal1_darkincidence_pal1_lightmake_breakspoolscale_x_incidence
Dependencies:aweekclicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr
Conversions to and from the incidence class
Rendered fromconversions.Rmdusingknitr::rmarkdownon Nov 05 2024.Last update: 2020-11-03
Started: 2017-04-03
Customize plots of incidence
Rendered fromcustomize_plot.Rmdusingknitr::rmarkdownon Nov 05 2024.Last update: 2024-05-15
Started: 2016-10-25
Details of the incidence class
Rendered fromincidence_class.Rmdusingknitr::rmarkdownon Nov 05 2024.Last update: 2020-11-03
Started: 2016-10-25
Details of the incidence_fit class
Rendered fromincidence_fit_class.Rmdusingknitr::rmarkdownon Nov 05 2024.Last update: 2018-11-30
Started: 2018-08-21
Overview of the incidence package
Rendered fromoverview.Rmdusingknitr::rmarkdownon Nov 05 2024.Last update: 2024-05-15
Started: 2016-10-17
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Conversion of incidence objects | as.data.frame.incidence as.incidence as.incidence.data.frame as.incidence.matrix as.incidence.numeric |
| Bootstrap incidence time series | bootstrap |
| Compute cumulative 'incidence' | cumulate cumulate.default cumulate.incidence |
| Access various elements of an incidence object | dim.incidence get_interval get_interval.default get_interval.incidence get_n get_n.default get_n.incidence get_timespan get_timespan.default get_timespan.incidence |
| Estimate the peak date of an incidence curve using bootstrap | estimate_peak |
| Find the peak date of an incidence curve | find_peak |
| Fit exponential models to incidence data | fit fit_optim_split print.incidence_fit print.incidence_fit_list |
| Get counts from an incidence object | get_counts get_counts.incidence |
| Retrieve dates from an incidence object | get_dates get_dates.default get_dates.incidence |
| Accessors for 'incidence_fit' objects | get_fit get_fit.incidence_fit get_fit.incidence_fit_list get_info get_info.incidence_fit get_info.incidence_fit_list |
| extract and set group names | group_names group_names.default group_names.incidence group_names<- group_names<-.default group_names<-.incidence `group_names<-`.default |
| Compute incidence of events from a vector of dates. | incidence incidence.character incidence.Date incidence.default incidence.integer incidence.numeric incidence.POSIXt print.incidence |
| Color palettes used in incidence | incidence_pal1 incidence_pal1_dark incidence_pal1_light palettes |
| Plot function for incidence objects | add_incidence_fit make_breaks plot.incidence plot.incidence_fit plot.incidence_fit_list scale_x_incidence |
| Pool 'incidence' across groups | pool |
| Subsetting 'incidence' objects | "subset.incidence" "[.incidence" subset.incidence [.incidence |
