From ed99cff6bd804dbecfa5330bad6b8c89be103c21 Mon Sep 17 00:00:00 2001
From: Luis Aleixo <luis.aleixo@cern.ch>
Date: Fri, 8 Oct 2021 15:12:21 +0200
Subject: [PATCH] CRemoved unused concepts

---
 .../calculator/templates/userguide.html.j2    | 100 ++++++++++++------
 1 file changed, 66 insertions(+), 34 deletions(-)

diff --git a/cara/apps/calculator/templates/userguide.html.j2 b/cara/apps/calculator/templates/userguide.html.j2
index 3be0ef2a..4d35c32b 100644
--- a/cara/apps/calculator/templates/userguide.html.j2
+++ b/cara/apps/calculator/templates/userguide.html.j2
@@ -22,7 +22,7 @@
         CARA is a risk assessment tool developed to model the concentration of viruses in enclosed spaces, in order to inform space-management decisions.
     </p>
     <p>
-        CARA models the concentration profile of potential infectious viruses in enclosed spaces with clear and intuitive graphs.
+        CARA models the concentration profile of potential virions in enclosed spaces with clear and intuitive graphs.
         The user can set a number of parameters, including room volume, exposure time, activity type, mask-wearing and ventilation.
         The report generated indicates how to avoid exceeding critical concentrations and chains of airborne transmission in spaces such as individual offices, meeting rooms and labs.
     </p>
@@ -50,13 +50,15 @@
     <p>
         CARA has not undergone review, approval or certification by competent authorities, and as a result, it cannot be considered
         as a fully endorsed and reliable tool, namely in the assessment of potential viral emissions from infected hosts to be modelled.
-    </p>  </div>
+    </p>  
+    </div>
 </div>
 
 
 <div class="container container--padding">
 <h1>How to use this tool</h1><br>
-<h3>Simulation Name &amp; Room number</h3><br>
+<h3>Simulation Name &amp; Room number</h3>
+<br>
 <p>In order to be able to trace back the simulations in your workplace risk assessments, performed with the tool, you can give each one a unique name - for example "Office use on Tuesday mornings".
 The simulation name has no bearing on the calculation.</p>
 <p>A room number is included, if you do not wish to use a formal room number any reference will do - for example "57/2-004"</p>
@@ -66,12 +68,12 @@ Changing this setting alters the properties of the virus which are used for the
 This has a significant effect on the probability of infection. 
 The choices are:</p>
 <ul>
-<li><code>SARS-CoV-2 (nominal strain)</code>, covering typical strains and varaints which are not of concern from an epidemiologic point of view of the virus;</li>
+<li><code>SARS-CoV-2 (nominal strain)</code>, covering typical strains and variants which are not of concern from an epidemiologic point of view of the virus;</li>
 <li><code>SARS-CoV-2 (Alpha VOC)</code>, first identified in the UK at the end of 2020 which is found to be approximately 1.5x more transmissible compared to the non-VOCs; </li>
 <li><code>SARS-CoV-2 (Gamma VOC)</code>, first identified in Brazil in January 2021 which is found to be approximately 2.2x more transmissible compared to the non-VOCs.</li>
 <li><code>SARS-CoV-2 (Delta VOC)</code>, first identified in India towards the end of 2020 which is found to be approximately 60% more transmissible compared to the ALPHA VOC.</li>
 </ul>
-<p>The user can base their choice according to the prevalence of the different variants in the local area. Access to this information can be found here:</p>
+<p>The user can modify the selected variant from the default, according to the prevalence of the different variants in the local area. Access to this information can be found here:</p>
 <ul>
 <li>Geneva: <a href="https://www.covid19.admin.ch/fr/epidemiologic/virus-variants?detGeo=GE">https://www.covid19.admin.ch/fr/epidemiologic/virus-variants?detGeo=GE</a></li>
 <li>Ain (France): <a href="https://www.santepubliquefrance.fr/dossiers/coronavirus-covid-19/covid-19-cartographie-des-variants-en-france-donnees-par-region-et-par-departement">https://www.santepubliquefrance.fr/dossiers/coronavirus-covid-19/covid-19-cartographie-des-variants-en-france-donnees-par-region-et-par-departement</a></li>
@@ -80,58 +82,71 @@ The choices are:</p>
 The local population in Manaus had very high levels of Covid-19 antibodies (&gt;67%) in recent months.
 This factor has been taken into account by the authors of the study, via statistical adjustments to the transmission value (i.e. it has been increased, to account for spread in a population with significant acquired Covid-19 immunity).
 However, this value may be revised in the future as more studies of the Gamma VOC transmission in different geographical locations become available.</p>
-<br><h3>Room Data</h3><br>
+<br>
+<h3>Room Data</h3>
+<br>
 <p>Please enter either the room volume (in m³) or both the floor area (m²) and the room height (m).
 This information is available via GIS Portal (<a href="https://gis.cern.ch/gisportal/">https://gis.cern.ch/gisportal/</a>).</p>
-<br><h4>Room heating system</h4><br>
+<br>
+<h4>Room heating system</h4>
+<br>
 <p>The use of central heating (e.g. radiators) reduces relative humidity of the indoor air, which can decrease the decay rate of viral infectivity. If your space is heated with such water radiators, select 'Yes'. If your space does not have such heating, or they are not in use in the period of the simulation (e.g. summer), select 'No'.</p>
-<br><h3>Ventilation type</h3><br>
+<br>
+<h3>Ventilation type</h3>
+<br>
 <p>There are three main options:</p>
-<br><h4>Mechanical ventilation</h4><br>
+<br>
+<h4>Mechanical ventilation</h4>
+<br>
 <p>If the room has mechanical ventilation, suppling fresh air from outside (either a local or centralised system), you should select this option.
 In order to make an accurate calculation you will need to know either the flow rate of fresh air supplied in the room or th total number of air changes per hour with fresh air.</p>
 <p>Please bear in mind that any of the two inputs only consider the supply of fresh air. If a portion of air is recirculated, it shall not be accounted for in the inputs.</p>
-<br><h4>Natural ventilation</h4><br>
+<br>
+<h4>Natural ventilation</h4>
+<br>
 <p>Natural ventilation refers to rooms which have openable windows. 
 There are many possibilities to calculate natural ventilation air flows, for simplification this tool assumes a single-sided natural ventilation scheme which is a conservative approach for the purpose of this tool.</p>
 <p>Please choose the type of window (see illustration below):</p>
 <ul>
 <li>Sliding or side-hung</li>
 <li>Top- or bottom-hung
-    </li>
-    
+<img src="static/images/window_type.PNG" alt="Window type" title="How to determine the window type" width="100%"></li>
 </ul>
-<img src="static/images/window_type.PNG" alt="Window type" title="How to determine the window type" width="100%">
 <p>Please enter the number, height and width and opening distance of the windows (in m).
 If there are multiple windows of different sizes, you should take an average.</p>
 <p>The window opening distance (in m) is:</p>
 <ul>
-<li>In case of Top- or Bottom-Hung, the distance between the fixed frame and the movable glazed part when open.</li>
 <li>In the case of Sliding or Side-Hung option, the length the window is moved open.
 <em>Window opening distance example (image of open window and measuring tape):</em>
-</li>
-
-
+<img src="static/images/window_opening.png" alt="Window Opening Distance" title="How to measure window opening distance" width="70%" style="margin:auto; display:block;"></li>
+<li>In case of Top- or Bottom-Hung, the distance between the fixed frame and the movable glazed part when open.</li>
 </ul>
-<img src="static/images/window_opening.png" alt="Window Opening Distance" title="How to measure window opening distance" width="70%" style="margin:auto; display:block;">
 <p><strong>Notes</strong>: If you are unsure about the opening distance for the window, it is recommended to choose a conservative value (5 cms, 0.05m or 10cms, 0.10m).
 If you open the window at different distances throughout the day, choose an average value.</p>
 <p>When using natural ventilation, the circulation of air is simulated as a function of the difference between the temperature inside the room and the outside air temperature. The average outdoor temperature for each hour of the day has been computed for every month of the year based on historical data for Geneva, Switzerland.
 It is therefore very important to enter the correct time and date in the event data section.
 Finally, you must specify if the windows are open permanently (at all the times), or periodically (in intervals for a certain duration and frequency - both in minutes) - e.g. open the window for 10 minutes (duration) every 60 minutes (frequency).</p>
-<br><h4>No ventilation</h4><br>
+<br>
+<h4>No ventilation</h4>
+<br>
 <p>This option assumes there is neither Mechanical nor Natural ventilation in the simulation.</p>
-<br><h4>HEPA filtration</h4><br>
+<br>
+<h4>HEPA filtration</h4>
+<br>
 <p>A HEPA filter is a high efficiency particulate matter filter, which removes small airborne particles from the air.
 They can be very useful for removing particles with viruses from the air in an enclosed space.
 The calculator allows you to simulate the installation of a HEPA air filter within the room.
 The recommended airflow rate for the HEPA filter should correspond to a total air exchange rate of 3 - 6 ACH (the higher the better, even beyond 6).</p>
-<br><h3>Event Data</h3><br>
+<br>
+<h3>Event Data</h3>
+<br>
 <p>Here we capture the information about the event being simulated.
 First enter the number of occupants in the space, if you have a (small) variation in the number of people, please input the average or consider using the expert tool.
 Within the number of people occupying the space, you should specify how many are infected.</p>
 <p>As an example, for a shared office with 4 people, where one person is infected, we enter 4 occupants and 1 infected person.</p>
-<br><h4>Activity type</h4><br>
+<br>
+<h4>Activity type</h4>
+<br>
 <p>There are a few predefined activities in the tool at present.</p>
 <ul>
 <li><strong>Office </strong> = All persons seated, talking occasionally (1/3rd of the time, with normal breathing the other 2/3rds of the time). Everyone (exposed and infected occupants) is treated the same in this model.</li>
@@ -154,15 +169,20 @@ It is possible to specify a different time for the entry and exit of both the ex
 <br><h4>When is the event?</h4><br>
 <p>This is included for completeness in all simulations, however it is of particular relevance to those using natural ventilation because of variations in outside air temperature.</p>
 <p>Only the month is used by the model to retrieve the average outdoor air temperatures for the Geneva region.</p>
-<br><h3>Breaks</h3><br>
-<h4>Lunch Break</h4><br>
+<br>
+<h3>Breaks</h3>
+<br>
+<h4>Lunch Break</h4>
+<br>
 <p>You have the option to specify a lunch break.
 This will be useful if you plan to simulate a typical full working day.
 During the lunch break it is assumed that all occupants will leave the simulated space (to go eat lunch somewhere else - restaurant or break room).
 If you plan to eat lunch in the same area where you have been working, you should select 'No' even if a lunch break will be taken, since the risk of infection is related to the occupation of the simulated space.
 See 'Split Breaks' if the occupants do not break at the same time.</p>
 <p>It should also be noted that the infection probabilities presented in the report does not take into account any potential exposures during the break times.</p>
-<br><h4>Coffee Breaks</h4><br>
+<br>
+<h4>Coffee Breaks</h4>
+<br>
 <p>You have the option to choose 0(No breaks), 2 or 4 coffee breaks during the simulated period.
 It is assumed that all occupants vacate the space during the break period.
 If coffee breaks are taken in-situ, this option should be set to 'No breaks'.</p>
@@ -172,7 +192,9 @@ The variation of coffee breaks can be altered in 5 minute increments up to 30 mi
 Note that this doesn't necessarily have to be a coffee break, it can represent any period where the simulated space is vacated.
 See 'Split Breaks' if the occupants do not break at the same time.</p>
 <p>It should also be noted that the infection probabilities presented in the report does not take into account any potential exposures during the break times.</p>
-<br><h4>Split breaks</h4><br>
+<br>
+<h4>Split breaks</h4>
+<br>
 <p>You have the option to specify whether the exposed and infected person(s) break at the same time.
 If not, then you can input separate breaks. This is particularly different when specifying coffee breaks as they are spread evenly throughout the activity times specified.</p>
 <p>If we take an example where the exposed person(s) activity time is from 9:00 to 18:00 and the infected person(s) is from 10:00 to 17:00, with both having a lunch break from 13:00 to 14:00 and have 2 coffee breaks each, we can have two different results:</p>
@@ -182,44 +204,54 @@ If not, then you can input separate breaks. This is particularly different when
 <li><p>Specify separate breaks for the infected person(s): in this case the coffee breaks will be calculated based on the different activity times (i.e. exposed from 9:00 to 18:00 and infected from 10:00 to 17:00) - the exposed person(s) will have their first coffee break around 11:00 and the second around 16:00, whereas the infected will have their first coffee break around 11:30 and the second around 15:30.</p>
 </li>
 </ol>
-<br><h3>Face Masks</h3><br>
+<br>
+<h3>Face Masks</h3>
+<br>
 <p>The model allows for a simulation with either a continuous wearing of face masks throughout the duration of the event, or have the removed at all times - i.e. all occupants (infected and exposed alike) wear or not masks for the duration of the simulation. 
 Please bear in mind the user inputs shall be aligned with the current applicable public health &amp; safety instructions. 
 Please check what are the applicable rules, before deciding which assumptions are used for the simulation.</p>
 <p>If you have selected the Training activity type, this equates to the trainer and all participants either wearing masks throughout the training (Yes), or removing them when seated/standing at their socially distanced positions within the training room (No). 
 Please confirm what are the applicable rules, before deciding which assumptions are used for the simulation</p>
 <p>For the time being only the Type 1 surgical and FFP2 masks can be selected.</p>
-<br><h2>Generate Report</h2><br>
+<br>
+<h2>Generate Report</h2>
+<br>
 <p>When you have entered all the necessary information, please click on the Generate Report button to execute the model. With the implementation of Monte Carlo simulations, the browser might take a few secounds to react.</p>
 <br><h1>Report</h1><br>
 <p>The report will open in your web browser.
 It contains a summary of all the input data, which will allow the simulation to be repeated if required in the future as we improve the model.</p>
-<br><h2>Results</h2><br>
+<br>
+<h2>Results</h2>
+<br>
 <p>This part of the report shows the <code>P(I)</code> or probability of one exposed person getting infected.
 It is estimated based on the emission rate of virus into the simulated volume, and the amount which is inhaled by exposed individuals.
 This probability is valid for the simulation duration - i.e. the start and end time.
 If you are using the natural ventilation option, the simulation is only valid for the selected month, because the following or preceding month will have a different average temperature profile.
 The <code>expected number of new cases</code> for the simulation is calculated based on the probability of infection, multiplied by the number of exposed occupants.</p>
-<p>The graph shows the variation in the concentration of infectious viruses within the simulated volume.
+<p>The graph shows the variation in the concentration of virions within the simulated volume.
 It is determined by:</p>
 <ul>
 <li>The presence of the infected person, who emits airborne viruses in the volume.</li>
 <li>The emission rate is related to the type of activity of the infected person (sitting, light exercise), their level of vocalisation (breathing, talking or shouting).</li>
-<li>The accumulation of infectious quanta in the volume, which is driven, among other factors, by ventilation (if applicable).<ul>
+<li>The accumulation of virions in the volume, which is driven, among other factors, by ventilation (if applicable).<ul>
 <li>In a mechanical ventilation scenario, the removal rate is constant, based on fresh airflow supply in and out of the simulated space.</li>
 <li>Under natural ventilation conditions, the effectiveness of ventilation relies upon the hourly temperature difference between the inside and outside air temperature.</li>
-<li>A HEPA filter removes infectious virus from the air at a constant rate and is modelled in the same way as mechanical ventilation, however air passed through a HEPA filter is recycled (i.e. it is not fresh air).</li>
+<li>A HEPA filter removes virions from the air at a constant rate and is modelled in the same way as mechanical ventilation, however air passed through a HEPA filter is recycled (i.e. it is not fresh air).</li>
 </ul>
 </li>
 </ul>
-<br><h3>QR code</h3><br>
+<br>
+<h3>QR code</h3>
+<br>
 <p>At the end of the report you can find a unique QR code / hyperlink for this report. This provides an automatic way to review the calculator form with the corresponding specified parameters.
 This allows for:</p>
 <ul>
 <li>sharing reports by either scanning or clicking on the QR code to obtain a shareable link.</li>
 <li>easily regenerating reports with any new versions of the CARA model released in the future.</li>
 </ul>
-<br><h1>Conclusion</h1><br>
+<br>
+<h1>Conclusion</h1>
+<br>
 <p>This tool provides informative comparisons for COVID-19 (long-range) airborne risk only - see Disclaimer
 If you have any comments on your experience with the app, or feedback for potential improvements, please share them with the development team <a href="mailto:cara-dev@cern.ch">Send email</a>.</p>
 </div>