Project Future Case Incidence

Provides functions and graphics for projecting daily incidence based on past incidence, and estimates of the serial interval and reproduction number. Projections are based on a branching process using a Poisson-distributed number of new cases per day, similar to the model used for estimating R in 'EpiEstim' or in 'earlyR', and described by Nouvellet et al. (2017) . The package provides the S3 class 'projections' which extends 'matrix', with accessors and additional helpers for handling, subsetting, merging, or adding these objects, as well as dedicated printing and plotting methods.


News

projections 0.3.1

  • get_dates() now inherits the generic get_dates() from incidence

projections 0.3.0

New features

This is a big release! Plenty of new features have been added, including:

  • projections can now be subsetted like matrices using x[i,j], or using the function subset

  • new function cumulate to compute cumulative incidence for projections objects, akin to the similar function in the incidence package

  • much improved graphics; plot now call upons add_projections, which implements many options for plotting projections, including quantiles lines, ribbon, and boxplots; add_projections can also be used to add such plots to an existing incidence plot

  • build_projections can be used to build a projections object from an input matrix and optional dates

projections 0.1.1

New features

  • project can now use a Negative Binomial model as an alternative to the original Poisson model to account for over-dispersion in new cases / super-spreading.

Bug fixes

Fixed the calls to sample, which has a rather irrational behaviour when passing a first argument of length 1 (i.e. not bootstrapping from the vector).

projections 0.0.1

First release of the package!

New features

  • project: a function generating projections from an existing incidence object, a serial interval distribution, and a set of plausible reproduction numbers ($R$); returns a projections object.

  • plot/print: plotting and printing methods for projections objects.

  • get_dates: accessors for projections objects.

  • as.data.frame: conversion from projections objects to data.frame.

Reference manual

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install.packages("projections")

0.5.1 by Thibaut Jombart, 3 months ago


http://www.repidemicsconsortium.org/projections


Report a bug at http://github.com/reconhub/projections/issues


Browse source code at https://github.com/cran/projections


Authors: Thibaut Jombart [aut, cre] , Pierre Nouvellet [aut] , Sangeeta Bhatia [ctb] , Zhian N. Kamvar [ctb] , Tim Taylor [ctb] , Stephane Ghozzi [ctb]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports stats, utils, incidence, ggplot2, methods

Suggests testthat, vdiffr, roxygen2, knitr, rmarkdown, outbreaks, magrittr, distcrete


See at CRAN