What does it do? | Functions at a glance | Basic Usage | Computing incidence from a linelist | Computing incidence from pre-aggregated data | Plotting in style of European Programme for Intervention Epidemiology Training (EPIET) | Support for tidy-select semantics | Working with incidence objects | regroup() | complete_dates() | keep_first(), keep_last() and keep_peaks() | Bootstrapping and estimating peaks | cumulate() | Building on incidence2 | Class preservation | Accessing variable information | Grouping aware methods | Example fitting a poisson model | Example - Adding a rolling average
Package: incidence2 2.6.4.9000
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.
Authors:
incidence2_2.6.4.9000.tar.gz
incidence2_2.6.4.9000.zip(r-4.7-any)incidence2_2.6.4.9000.zip(r-4.6-any)incidence2_2.6.4.9000.zip(r-4.5-any)
incidence2_2.6.4.9000.tgz(r-4.6-any)incidence2_2.6.4.9000.tgz(r-4.5-any)
incidence2_2.6.4.9000.tar.gz(r-4.7-any)incidence2_2.6.4.9000.tar.gz(r-4.6-any)
incidence2_2.6.4.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
incidence2/json (API)
| # Install 'incidence2' in R: |
| install.packages('incidence2', repos = c('https://reconverse.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/reconverse/incidence2/issues
Datasets:
- covidregionaldataUK - Regional data for COVID-19 cases in the UK
Last updated from:443fd4c0d0. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 147 | ||
| source / vignettes | OK | 191 | ||
| linux-release | OK | 168 | ||
| macos-release | OK | 117 | ||
| macos-oldrel | OK | 89 | ||
| windows-devel | OK | 73 | ||
| windows-release | OK | 89 | ||
| windows-oldrel | OK | 98 | ||
| wasm-release | OK | 125 |
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_interval_durationget_timespanincidenceincidence_keep_firstkeep_lastkeep_peaksmutatemutednestnew_incidenceregroupregroup_selectsummariseunnestunpackvalidate_incidencevibrant
Dependencies:clicpp11data.tabledplyrfastymdgenericsgluegrateslifecyclemagrittrpillarpkgconfigpurrrR6rlangstringistringrtibbletidyrtidyselectutf8vctrswithrympes
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 and from an incidence object | as as.data.frame.incidence2 as.data.table.incidence2 as_incidence as_incidence.default as_incidence.incidence2 as_tibble.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 |
| dplyr and tidyr verbs | dplyr-verbs mutate.incidence2 nest.incidence2 summarise.incidence2 |
| Estimate the peak date of an incidence curve | estimate_peak estimate_peaks |
| Days covered by the date index of an incidence object | get_interval_duration.incidence2 |
| Compute the incidence of events | incidence incidence_ |
| Keep first, last and peak occurences | first_peak keep keep_first keep_last keep_peaks |
| Plot an incidence object | plot.incidence2 |
| Regroup 'incidence' objects | regroup regroup_ |
| Divide an incidence2 object in to it's implicit groupings | split.incidence2 |
| Summary of an incidence object | summary.incidence2 |
| Color palettes used in incidence | muted palettes vibrant |