setup_logging

<a href="https://lifecycle.r-lib.org/articles/stages.html#questioning"><img src="figures/lifecycle-questioning.svg?package=EpiNow2&version=1.7.1" alt="[Questioning]"></a>
Sets up <code>{futile.logger}</code> logging, which is integrated into <code>{EpiNow2}</code>.
See the documentation for <code>{futile.logger}</code> for full details. By default
<code>{EpiNow2}</code> prints all logs at the "INFO" level and returns them to the
console. Usage of logging is currently being explored as the current
setup cannot log stan errors or progress.

Estimates the time-varying reproduction number,
rate of spread, and doubling time using a range of open-source tools
(Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1>), and
current best practices (Gostic et al. (2020)
<doi:10.1101/2020.06.18.20134858>). It aims to help users avoid some
of the limitations of naive implementations in a framework that is
informed by community feedback and is actively supported.

Sebastian Funk

EpiNow2

Estimate Real-Time Case Counts and Time-Varying Epidemiological
Parameters

Sam Abbott

Joel Hellewell

Katharine Sherratt

Katelyn Gostic

Joe Hickson

Hamada S. Badr

Michael DeWitt

James M. Azam

Robin Thompson

Sophie Meakin

James Munday

Nikos Bosse

Paul Mee

Peter Ellis

Pietro Monticone

Lloyd Chapman

Andrew Johnson

Kaitlyn Johnson

EpiForecasts 

setup_logging function

<dl><dt>threshold</dt>
<dd>Character string indicating the logging level see
(?futile.logger for details of the available options). Defaults to "INFO".</dd>
<dt>file</dt>
<dd>Character string indicating the path to save logs to. By default
logs will be written to the console.</dd>
<dt>mirror_to_console</dt>
<dd>Logical, defaults to <code>FALSE</code>. If saving logs to a
file should they also be duplicated in the console.</dd>
<dt>name</dt>
<dd>Character string defaulting to EpiNow2. This indicates the name
of the logger to setup. The default logger for EpiNow2 is called EpiNow2.
Nested options include: Epinow2.epinow which controls all logging for
<code>epinow()</code> and nested functions, EpiNow2.epinow.estimate_infections
(logging in <code>estimate_infections()</code>, and
EpiNow2.epinow.estimate_infections.fit (logging in fitting functions).</dd></dl>

Arguments

<a href='https://lifecycle.r-lib.org/articles/stages.html#questioning'><img src='figures/lifecycle-questioning.svg' alt='[Questioning]' /></a>
Sets up <code>{futile.logger}</code> logging, which is integrated into <code>{EpiNow2}</code>.
See the documentation for <code>{futile.logger}</code> for full details. By default
<code>{EpiNow2}</code> prints all logs at the "INFO" level and returns them to the
console. Usage of logging is currently being explored as the current
setup cannot log stan errors or progress.

Setup Logging — setup_logging

<dl>

<dt>threshold</dt>
<dd>Character string indicating the logging level see
(?futile.logger for details of the available options). Defaults to "INFO".</dd>


<dt>file</dt>
<dd>Character string indicating the path to save logs to. By default
logs will be written to the console.</dd>


<dt>mirror_to_console</dt>
<dd>Logical, defaults to <code>FALSE</code>. If saving logs to a
file should they also be duplicated in the console.</dd>


<dt>name</dt>
<dd>Character string defaulting to EpiNow2. This indicates the name
of the logger to setup. The default logger for EpiNow2 is called EpiNow2.
Nested options include: Epinow2.epinow which controls all logging for
<code>epinow()</code> and nested functions, EpiNow2.epinow.estimate_infections
(logging in <code>estimate_infections()</code>, and
EpiNow2.epinow.estimate_infections.fit (logging in fitting functions).</dd>

</dl>

Setup Logging

setup_logging: Setup Logging

Description

Usage

Value

Arguments