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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.

Functions (16)

accessors

Access various elements of an incidence object

bootstrap

Bootstrap incidence time series

conversions

Conversion of incidence objects

cumulate

Compute cumulative 'incidence'

estimate_peak

Estimate the peak date of an incidence curve using bootstrap

find_peak

Find the peak date of an incidence curve

fit

Fit exponential models to incidence data

get_counts

Get counts from an incidence object

get_dates

Retrieve dates from an incidence object

get_fit

Accessors for incidence_fit objects

group_names

extract and set group names

incidence

Compute incidence of events from a vector of dates.

palettes

Color palettes used in incidence

plot.incidence

Plot function for incidence objects

pool

Pool 'incidence' across groups

subset

Subsetting 'incidence' objects

incidence

Compute, Handle, Plot and Model Incidence of Dated Events

v1.7.3

MIT + file LICENSE

Authors

Thibaut Jombart [aut], Zhian N. Kamvar [aut] (<https://orcid.org/0000-0003-1458-7108>), Rich FitzJohn [aut], Tim Taylor [cre] (<https://orcid.org/0000-0002-8587-7113>), Jun Cai [ctb] (<https://orcid.org/0000-0001-9495-1226>), Sangeeta Bhatia [ctb], Jakob Schumacher [ctb], Juliet R.C. Pulliam [ctb] (<https://orcid.org/0000-0003-3314-8223>)

Initial release

incidence

Functions (16)

incidence

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