setup_logging

<a href="https://lifecycle.r-lib.org/articles/stages.html#questioning"><img src="figures/lifecycle-questioning.svg?package=EpiNow2&version=1.3.4" 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.

Sam Abbott 

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

Robin Thompson

Sophie Meakin

James Munday

Nikos Bosse

Paul Mee

Peter Ellis

Pietro Monticone

Lloyd Chapman

EpiForecasts 

Sebastian Funk

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