Package: incidence 1.7.6

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:Thibaut Jombart [aut], Zhian N. Kamvar [aut], Rich FitzJohn [aut], Tim Taylor [cre], Jun Cai [ctb], Sangeeta Bhatia [ctb], Jakob Schumacher [ctb], Juliet R.C. Pulliam [ctb]

incidence_1.7.6.tar.gz
incidence_1.7.6.zip(r-4.7)incidence_1.7.6.zip(r-4.6)incidence_1.7.6.zip(r-4.5)
incidence_1.7.6.tgz(r-4.6-any)incidence_1.7.6.tgz(r-4.5-any)
incidence_1.7.6.tar.gz(r-4.7-any)incidence_1.7.6.tar.gz(r-4.6-any)
incidence_1.7.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
incidence/json (API)

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

Bug tracker:https://github.com/reconhub/incidence/issues

Pkgdown/docs site:https://www.repidemicsconsortium.org

On CRAN:

Conda:

outbreak

11.45 score 57 stars 11 packages 542 scripts 1.4k downloads 9 mentions 24 exports 18 dependencies

Last updated from:bda31a524a. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK119
source / vignettesOK234
linux-release-x86_64OK132
macos-release-arm64OK124
macos-oldrel-arm64OK77
windows-develOK86
windows-releaseOK123
windows-oldrelOK102
wasm-releaseOK104

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:aweekclicpp11farverggplot2gluegtableisobandlabelinglifecycleR6RColorBrewerrlangS7scalesvctrsviridisLitewithr

Customize plots of incidence
Example data: simulated Ebola outbreak | The plot.incidence function | Default behaviour | Changing colors | The default palette | Using different palettes | Specifying colors manually | Example 1: changing a single color | Example 2: changing several colors (note that naming colors is optional) | Example 3: using color to highlight specific groups | Useful ggplot2 tweaks | Changing dates on the x-axis | Changing date format | Changing the grid | Handling non-ISO weeks | Labelling every bin | Changing the legend | Applying the style of European Programme for Intervention Epidemiology Training (EPIET) | Display individual cases
Rendered fromcustomize_plot.Rmdusingknitr::rmarkdown

Last update: 2024-05-15
Started: 2016-10-25

Overview of the incidence package
Installing the package | What does it do? | Worked example: simulated Ebola outbreak | Loading the data | Computing and plotting incidence | Handling incidence objects | Modelling incidence
Rendered fromoverview.Rmdusingknitr::rmarkdown

Last update: 2024-05-15
Started: 2016-10-17

Conversions to and from the incidence class
Exporting results | Importing pre-computed incidence
Rendered fromconversions.Rmdusingknitr::rmarkdown

Last update: 2020-11-03
Started: 2017-04-03

Details of the incidence class
Structure of an incidence object. | $dates | $counts | $timespan | $interval | $n | $weeks
Rendered fromincidence_class.Rmdusingknitr::rmarkdown

Last update: 2020-11-03
Started: 2016-10-25

Details of the incidence_fit class
Structure of an incidence_fit object | Building an incidence_fit object from scratch | Step 1: create the model | Step 2: creation of the $info list: | Step 3: combine lists and create object | Structure of an incidence_fit_list object | Example: A tale of two fits | Example: Nested incidence_fit
Rendered fromincidence_fit_class.Rmdusingknitr::rmarkdown

Last update: 2018-11-30
Started: 2018-08-21

Readme and manuals

Help Manual

Help pageTopics
Conversion of incidence objectsas.data.frame.incidence as.incidence as.incidence.data.frame as.incidence.matrix as.incidence.numeric
Bootstrap incidence time seriesbootstrap
Compute cumulative 'incidence'cumulate cumulate.default cumulate.incidence
Access various elements of an incidence objectdim.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 bootstrapestimate_peak
Find the peak date of an incidence curvefind_peak
Fit exponential models to incidence datafit fit_optim_split print.incidence_fit print.incidence_fit_list
Get counts from an incidence objectget_counts get_counts.incidence
Retrieve dates from an incidence objectget_dates get_dates.default get_dates.incidence
Accessors for 'incidence_fit' objectsget_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 namesgroup_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 incidenceincidence_pal1 incidence_pal1_dark incidence_pal1_light palettes
Plot function for incidence objectsadd_incidence_fit make_breaks plot.incidence plot.incidence_fit plot.incidence_fit_list scale_x_incidence
Pool 'incidence' across groupspool
Subsetting 'incidence' objects"subset.incidence" "[.incidence" subset.incidence [.incidence