<h1>Welcome to the Rnaught web application</h1>
<p>
  Rnaught is an R package and web application for estimating the
  <a href="https://en.wikipedia.org/wiki/Basic_reproduction_number" target="_blank">basic reproduction number</a>
  of infectious diseases. 
  We note that the estimators included in this web application are applied to diseases directly transmitted between the
  same host-type (i.e., they are not applicable to vector-borne diseases).
  For information about using this application, view the
  <span class="fw-bold text-primary">Help <span class="glyphicon glyphicon-question-sign"></span></span> tab.
  To learn more about the package, visit the online
  <a href="https://MI2YorkU.github.io/Rnaught" target="_blank">documentation</a> or
  <a href="https://github.com/MI2YorkU/Rnaught" target="_blank">GitHub</a> repository.
  Technical details about the estimators featured in this project can be found in the reference
  <a href="https://doi.org/10.1371/journal.pone.0269306" target="_blank">article</a>. 
  This application is pre-loaded with publicly available COVID-19 case counts for Canada, 
  sourced from the <a href="https://github.com/ccodwg/CovidTimelineCanada" target="_blank">CovidTimelineCanada</a> dataset on GitHub.
</p>
<h4>What is the basic reproduction number?</h4>
<p>
  The basic reproduction number, denoted <em>R</em><sub>0</sub>, is defined as the expected number of infections caused
  by a single infectious individual when introduced into a totally susceptible population. It assumes that all
  individuals in a given population are susceptible to the disease, and that no preventive measures (such as lockdowns
  or vaccinations) have been enforced. It is a useful indicator of the transmissibility of an infectious disease during
  the early stages of its spread and detection.
</p>
<p>
  If <em>R</em><sub>0</sub> &lt; 1, the disease will eventually die out. On the other hand, if
  <em>R</em><sub>0</sub> &gt; 1, the disease will spread (the higher the <em>R</em><sub>0</sub>, the faster this will
  happen). Due to uncertainty of known data about the disease, it is difficult to determine <em>R</em><sub>0</sub>
  precisely. Therefore, many estimation methods exist, each based on different assumptions and yielding different
  estimates. It is the responsibility of users to employ the most appropriate estimator (or suite of estimators) given
  the situation at hand.
</p>
