build_projections

This function builds a valid <code>projections</code> object from some input
simulations and dates.

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) <doi:10.1016/j.epidem.2017.02.012>. 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.

Thibaut Jombart

projections

Project Future Case Incidence

Pierre Nouvellet

Sangeeta Bhatia

Zhian N. Kamvar

Tim Taylor

Stephane Ghozzi

build_projections function

<dl><dt>x</dt>
<dd>A <code>matrix</code> of simulated incidence stored as integers, where
rows correspond to dates and columns to simulations.</dd>
<dt>dates</dt>
<dd>A vector of dates containing one value per row in <code>x</code>;
acceptable formats are: <code>integer</code>, <code>Date</code>, and <code>POSIXct</code>; if
NULL, the time steps will be counted, with the first dates corresponding to
0.</dd>
<dt>cumulative</dt>
<dd>A logical indicating if data represent cumulative
incidence; defaults to <code>FALSE</code>.</dd>
<dt>order_dates</dt>
<dd>A logical indicating whether the dates should be ordered,
from the oldest to the most recent one; <code>TRUE</code> by default.</dd></dl>

Arguments

Thibaut Jombart <a href="/link/thibautjombart%40gmail.com?package=projections&version=0.6.0" data-mini-rdoc="projections::thibautjombart@gmail.com">thibautjombart@gmail.com</a>

Author

Constructor for projections objects — build_projections

<dl>

<dt>x</dt>
<dd>A <code>matrix</code> of simulated incidence stored as integers, where
rows correspond to dates and columns to simulations.</dd>


<dt>dates</dt>
<dd>A vector of dates containing one value per row in <code>x</code>;
acceptable formats are: <code>integer</code>, <code>Date</code>, and <code>POSIXct</code>; if
NULL, the time steps will be counted, with the first dates corresponding to
0.</dd>


<dt>cumulative</dt>
<dd>A logical indicating if data represent cumulative
incidence; defaults to <code>FALSE</code>.</dd>


<dt>order_dates</dt>
<dd>A logical indicating whether the dates should be ordered,
from the oldest to the most recent one; <code>TRUE</code> by default.</dd>

</dl>

Thibaut Jombart <a href='mailto:thibautjombart@gmail.com'>thibautjombart@gmail.com</a>

build_projections: Constructor for projections objects

Description

Usage

Arguments

Author

See Also