Package: incidence2 2.6.0
Tim Taylor
incidence2: Compute, Handle and Plot 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 'incidence2' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis (<https://www.reconverse.org>).
Authors:
incidence2_2.6.0.tar.gz
incidence2_2.6.0.zip(r-4.5)incidence2_2.6.0.zip(r-4.4)incidence2_2.6.0.zip(r-4.3)
incidence2_2.6.0.tgz(r-4.4-any)incidence2_2.6.0.tgz(r-4.3-any)
incidence2_2.6.0.tar.gz(r-4.5-noble)incidence2_2.6.0.tar.gz(r-4.4-noble)
incidence2_2.6.0.tgz(r-4.4-emscripten)incidence2_2.6.0.tgz(r-4.3-emscripten)
incidence2.pdf |incidence2.html✨
incidence2/json (API)
NEWS
| # Install 'incidence2' in R: |
| install.packages('incidence2', repos = c('https://epiverse-connect.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/reconverse/incidence2/issues
- covidregionaldataUK - Regional data for COVID-19 cases in the UK
Last updated 3 days agofrom:1b032127dd. Checks:OK: 7. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 22 2024 |
| R-4.5-win | OK | Nov 22 2024 |
| R-4.5-linux | OK | Nov 22 2024 |
| R-4.4-win | OK | Nov 22 2024 |
| R-4.4-mac | OK | Nov 22 2024 |
| R-4.3-win | OK | Nov 22 2024 |
| R-4.3-mac | OK | Nov 22 2024 |
Exports:as_incidenceas_tibbleas.data.tablebootstrap_incidencebuild_incidencecomplete_datescumulateestimate_peakfacet_plotfirst_peakget_count_valueget_count_value_nameget_count_variableget_count_variable_nameget_date_indexget_date_index_nameget_datesget_dates_nameget_group_namesget_groupsget_intervalget_timespanincidenceincidence_keep_firstkeep_lastkeep_peaksmutatemutednestnew_incidenceregroupregroup_selectsummariseunnestunpackvalidate_incidencevibrant
Dependencies:clicpp11data.tabledplyrfansigenericsgluegrateslifecyclemagrittrpillarpkgconfigpurrrR6rlangstringistringrtibbletidyrtidyselectutf8vctrswithrympes
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Access various elements of an incidence object | accessors get_count_value get_count_value.default get_count_value.incidence2 get_count_value_name get_count_value_name.default get_count_value_name.incidence2 get_count_variable get_count_variable.default get_count_variable.incidence2 get_count_variable_name get_count_variable_name.default get_count_variable_name.incidence2 get_dates get_dates_name get_date_index get_date_index.default get_date_index.incidence2 get_date_index_name get_date_index_name.default get_date_index_name.incidence2 get_groups get_groups.default get_groups.incidence2 get_group_names get_group_names.default get_group_names.incidence2 |
| Coerce to an incidence object | as_incidence as_incidence.default as_incidence.incidence2 |
| Coerce to a tibble | as_tibble.incidence2 |
| Convert incident object to a data frame | as.data.frame.incidence2 |
| Coerce to a data.table | as.data.table.incidence2 |
| Bootstrap incidence time series | bootstrap_incidence |
| Complete dates for all group combinations | complete_dates |
| Regional data for COVID-19 cases in the UK | covidregionaldataUK |
| Compute cumulative 'incidence' | cumulate |
| Estimate the peak date of an incidence curve | estimate_peak estimate_peaks |
| Compute the incidence of events | incidence |
| Compute the incidence of events (tidyselect compatible) | incidence_ |
| Keep first, last and peak occurences | first_peak keep keep_first keep_last keep_peaks |
| Create, modify, and delete incidence2 columns | mutate.incidence2 |
| Nest rows into a list-column of data frames | nest.incidence2 |
| Plot an incidence object | plot.incidence2 |
| Regroup 'incidence' objects | regroup |
| Regroup 'incidence' objects (tidyselect compatible) | regroup_ |
| Divide an incidence2 object in to it's implicit groupings | split.incidence2 |
| Summarise each grouping down to one row | summarise.incidence2 |
| Summary of an incidence object | summary.incidence2 |
| Color palettes used in incidence | muted palettes vibrant |
