Package: incidence 1.7.4

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_1.7.4.tar.gz
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incidence.pdf |incidence.html
incidence/json (API)
NEWS

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

Peer review:

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

On CRAN:

outbreak

24 exports 58 stars 4.11 score 29 dependencies 10 dependents 2.5k downloads

Last updated 1 months agofrom:7f3b5576a91d4637e2392e16ff1f5462c0303cbc

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 Jun 14 2024.

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

Customize plots of incidence

Rendered fromcustomize_plot.Rmdusingknitr::rmarkdownon Jun 14 2024.

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

Details of the incidence class

Rendered fromincidence_class.Rmdusingknitr::rmarkdownon Jun 14 2024.

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

Details of the incidence_fit class

Rendered fromincidence_fit_class.Rmdusingknitr::rmarkdownon Jun 14 2024.

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

Overview of the incidence package

Rendered fromoverview.Rmdusingknitr::rmarkdownon Jun 14 2024.

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

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