covid19.ontario

Time series of COVID-19 cases and tests in Ontario, Canada,
daily from February 8, 2020 to May 1, 2022.

datasets

Maximum likelihood estimation of nonlinear mixed effects models of
epidemic growth using Template Model Builder ('TMB'). Enables
joint estimation for collections of disease incidence time series,
including time series that describe multiple epidemic waves.
Supports a set of widely used phenomenological models: exponential,
logistic, Richards (generalized logistic), subexponential,
and Gompertz. Provides methods for interrogating model objects
and several auxiliary functions, including one for computing basic
reproduction numbers from fitted values of the initial exponential
growth rate.
Preliminary versions of this software were applied
in Ma et al. (2014) <doi:10.1007/s11538-013-9918-2> and
in Earn et al. (2020) <doi:10.1073/pnas.2004904117>.

Mikael Jagan

epigrowthfit

Nonlinear Mixed Effects Models of Epidemic Growth

Ben Bolker

Jonathan Dushoff

David Earn

Junling Ma

covid19.ontario function

A data frame with 814 rows and 3 variables:<dl>
<dt><code>date</code></dt>
<dd>a <code><a href="/link/Date?package=epigrowthfit&version=0.15.4" data-mini-rdoc="epigrowthfit::Date">Date</a></code> vector.</dd><dt><code>cases</code></dt>
<dd>an integer vector. <code>cases[i]</code> is the number of cases confirmed
 by Ontario public health units prior to <code>date[i]</code>.
 This number includes resolved and fatal cases as well as reinfections.</dd><dt><code>tests</code></dt>
<dd>an integer vector. <code>tests[i]</code> is the number of tests completed
 prior to <code>date[i]</code>. This number includes repeated tests by
 individuals except prior to April 15, 2020, when individuals were
 counted at most once.</dd>
</dl>

Format

COVID-19 in Ontario, Canada — covid19.ontario

A data frame with 814 rows and 3 variables:<dl>
<dt><code>date</code></dt>
<dd>a <code><a href='https://rdrr.io/r/base/Dates.html'>Date</a></code> vector.</dd>

<dt><code>cases</code></dt>
<dd>an integer vector. <code>cases[i]</code> is the number of cases confirmed
 by Ontario public health units prior to <code>date[i]</code>.
 This number includes resolved and fatal cases as well as reinfections.</dd>

<dt><code>tests</code></dt>
<dd>an integer vector. <code>tests[i]</code> is the number of tests completed
 prior to <code>date[i]</code>. This number includes repeated tests by
 individuals except prior to April 15, 2020, when individuals were
 counted at most once.</dd>


</dl>

covid19.ontario: COVID-19 in Ontario, Canada

Description

Usage

Arguments

Format

Examples