From dcc1dac1d4e46034da26763ba442d3c846e31386 Mon Sep 17 00:00:00 2001
From: jdevine <james.dilwyn.devine@cern.ch>
Date: Mon, 16 Nov 2020 16:08:08 +0100
Subject: [PATCH 1/5] Modified activity parameters and updated calculator
 scenarios

---
 cara/apps/calculator/README.md                        |  2 +-
 cara/apps/calculator/model_generator.py               | 11 +++++++----
 .../apps/calculator/templates/calculator.form.html.j2 |  6 +++---
 cara/apps/calculator/templates/report.html.j2         |  4 ++--
 cara/models.py                                        |  4 ++--
 5 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/cara/apps/calculator/README.md b/cara/apps/calculator/README.md
index 77393c1c..43b46337 100644
--- a/cara/apps/calculator/README.md
+++ b/cara/apps/calculator/README.md
@@ -103,7 +103,7 @@ There are three predefined activities in the tool at present.
 
 **Call Centre** = All persons seated, all talking simultaneously, all the time. This is a conservative profile (i.e. will show in increased ``P(i)`` compared to office/meeting) if used for office activity.
 
-**Workshop** = Based on a mechanical assembly workshop, all persons are doing light exercise (standing, moving around, using tools) and talking. Everyone (occupants and infected occupants) is treated the same in this model.
+**Workshop** = Based on a mechanical assembly workshop, all persons are standing and talking 50% of the time. Everyone (occupants and infected occupants) is treated the same in this model.
 
 **Training** = Based on a typical training course scenario.
 One individual (the trainer) is doing light exercise (standing) and talking, with all other individuals seated and talking quietly (whispering).
diff --git a/cara/apps/calculator/model_generator.py b/cara/apps/calculator/model_generator.py
index 9ee7bd20..be46e37b 100644
--- a/cara/apps/calculator/model_generator.py
+++ b/cara/apps/calculator/model_generator.py
@@ -185,8 +185,11 @@ class FormData:
                 {'Talking': 1, 'Breathing': self.total_people - 1}
             ),
             'callcentre': ('Seated', 'Talking'),
-            'training': ('Light exercise', 'Talking'),
-            'workshop': ('Light exercise', 'Talking'),
+            'training': ('Standing', 'Talking'),
+            'workshop': (
+                'Standing',
+                #Model 1/2 of time spent talking in a workshop.
+                {'Talking': 1, 'Breathing': 1})
         }
 
         [activity_defn, expiration_defn] = scenario_activity_and_expiration[self.activity_type]
@@ -210,8 +213,8 @@ class FormData:
             'office': 'Seated',
             'meeting': 'Seated',
             'callcentre': 'Seated',
-            'training': 'Light exercise',
-            'workshop': 'Light exercise',
+            'training': 'Seated',
+            'workshop': 'Standing',
         }
 
         activity_defn = scenario_activity[self.activity_type]
diff --git a/cara/apps/calculator/templates/calculator.form.html.j2 b/cara/apps/calculator/templates/calculator.form.html.j2
index 682dce11..cfebb470 100644
--- a/cara/apps/calculator/templates/calculator.form.html.j2
+++ b/cara/apps/calculator/templates/calculator.form.html.j2
@@ -196,7 +196,7 @@
   <b>Ventilation data:</b> <br>
   <ul>
     <li>Mechanical ventilation = check the rates with a specialist.</li>
-    <li>Natural ventilation = the window opening distance is between the fixed frame and movable part when open.</li> 
+    <li>Natural ventilation = the window opening distance is between the fixed frame and movable part when open.</li>
     <li>HEPA filtration = the air flow of the device. The following values are based on the different fan velocities of a specific commercial device proposed by the HSE Unit:</li>
     <ul>
         <li>Level 6 (max) = 430 m^3/h (noisy)</li>
@@ -209,8 +209,8 @@
   The type of activity that includes both the infected and exposed persons:
   <ul>
     <li>Office = typical scenario all persons seated, in conversation (talking 33% of the time, otherwise breathing normally).</li>
-    <li>Meeting = typical scenario all persons seated, in conversation.</li>
-    <li>Workshop = assembly workshop environment, all persons doing light exercise, talking.</li>
+    <li>Meeting = typical scenario all persons seated, in conversation (talking time is shared equally between all persons).</li>
+    <li>Workshop = assembly workshop environment, all persons standing, talking (50% of the time spent talking).</li>
     <li>Call Centre = A conservative assumption for office spaces, assumes all occupants are seated and talking continuously.</li>
     <li>Training = one person (the trainer) standing, talking, all others seated, talking quietly (whispering). It is assumed the trainer is the infected person, for the worst case scenario.</li>
   </ul>
diff --git a/cara/apps/calculator/templates/report.html.j2 b/cara/apps/calculator/templates/report.html.j2
index 87c0dab5..203569b0 100644
--- a/cara/apps/calculator/templates/report.html.j2
+++ b/cara/apps/calculator/templates/report.html.j2
@@ -70,13 +70,13 @@
 		<li><p class="data_text">
 		Activity type:
 		{% if form.activity_type == "office" %}
-		Office – typical scenario with all persons seated, talking occasionally.
+		Office – typical scenario with all persons seated, talking occasionally (talking assumed for 1/3rd of the time).
 		{% elif form.activity_type == "meeting" %}
 		Meeting – typical scenario with all persons seated, one person talking at a time.
 		{% elif form.activity_type == "callcentre" %}
 		Call Centre = typical office scenario with all persons seated, all talking continuously.
 		{% elif form.activity_type == "workshop" %}
-		Workshop = assembly workshop environment, all persons doing light exercise, talking.
+		Workshop = assembly workshop environment, all persons standing, talking 50% of the time.
 		{% elif form.activity_type == "training" %}
 		Training – one person (the trainer) standing, talking, all others seated, talking quietly (whispering). It is assumed the trainer is the infected person, for the worst case scenario.
 		{% endif %}
diff --git a/cara/models.py b/cara/models.py
index a1bcb574..4bfe8ece 100644
--- a/cara/models.py
+++ b/cara/models.py
@@ -390,8 +390,8 @@ class Activity:
 
 
 Activity.types = {
-    'Resting': Activity(0.49, 0.49),
-    'Seated': Activity(0.54, 0.54),
+    'Seated': Activity(0.51, 0.51),
+    'Standing': Activity(0.57, 0.57),
     'Light exercise': Activity(1.38, 1.38),
     'Moderate exercise': Activity(2.35, 2.35),
     'Heavy exercise': Activity(3.30, 3.30),

From b6403690e78c22d99aca172241553fa80525a15d Mon Sep 17 00:00:00 2001
From: jdevine <james.dilwyn.devine@cern.ch>
Date: Tue, 17 Nov 2020 19:15:33 +0100
Subject: [PATCH 2/5] Updated activity types and profiles. Documentation
 updated as well.

---
 cara/apps/calculator/README.md                    | 10 +++++++---
 cara/apps/calculator/model_generator.py           | 15 +++++++++++----
 .../calculator/templates/calculator.form.html.j2  | 14 +++++++++-----
 cara/apps/calculator/templates/report.html.j2     |  6 +++++-
 cara/apps/expert.py                               |  4 ++--
 cara/models.py                                    |  4 ++--
 cara/tests/test_known_quantities.py               | 10 +++++-----
 7 files changed, 41 insertions(+), 22 deletions(-)

diff --git a/cara/apps/calculator/README.md b/cara/apps/calculator/README.md
index 43b46337..8450d166 100644
--- a/cara/apps/calculator/README.md
+++ b/cara/apps/calculator/README.md
@@ -103,12 +103,16 @@ There are three predefined activities in the tool at present.
 
 **Call Centre** = All persons seated, all talking simultaneously, all the time. This is a conservative profile (i.e. will show in increased ``P(i)`` compared to office/meeting) if used for office activity.
 
-**Workshop** = Based on a mechanical assembly workshop, all persons are standing and talking 50% of the time. Everyone (occupants and infected occupants) is treated the same in this model.
+**Lab** = Based on a typical lab or technical working area, all persons are doing light activity and talking 50% of the time. Everyone (occupants and infected occupants) is treated the same in this model.
+
+**Workshop** = Based on a mechanical assembly workshop or equipment installation scenario, all persons are doing moderate activity and talking 50% of the time. Everyone (occupants and infected occupants) is treated the same in this model. This model is equally applicable to bicycling, or walking on a gradient, in the LHC tunnels.
 
 **Training** = Based on a typical training course scenario.
-One individual (the trainer) is doing light exercise (standing) and talking, with all other individuals seated and talking quietly (whispering).
-In this case it is assumed that the infected person is the trainer, because this is the worst case in terms of viral sheeding.
+One individual (the trainer) is standing and talking, with all other individuals seated and talking quietly (whispering).
+In this case it is assumed that the infected person is the trainer, because this is the worst case in terms of viral sheding.
  
+**Gym** = Included for comparison purposes only, all persons are doing heavy exercise and breathing (no talking). Everyone (occupants and infected occupants) is treated the same in this model.
+
 
 ### Timings
 
diff --git a/cara/apps/calculator/model_generator.py b/cara/apps/calculator/model_generator.py
index be46e37b..57f1301a 100644
--- a/cara/apps/calculator/model_generator.py
+++ b/cara/apps/calculator/model_generator.py
@@ -186,10 +186,15 @@ class FormData:
             ),
             'callcentre': ('Seated', 'Talking'),
             'training': ('Standing', 'Talking'),
+            'lab': (
+                'Light activity',
+                #Model 1/2 of time spent talking in a lab.
+                {'Talking': 1, 'Breathing': 1}),
             'workshop': (
-                'Standing',
+                'Moderate activity',
                 #Model 1/2 of time spent talking in a workshop.
-                {'Talking': 1, 'Breathing': 1})
+                {'Talking': 1, 'Breathing': 1}),
+            'gym':('Heavy exercise', 'Breathing'),
         }
 
         [activity_defn, expiration_defn] = scenario_activity_and_expiration[self.activity_type]
@@ -214,7 +219,9 @@ class FormData:
             'meeting': 'Seated',
             'callcentre': 'Seated',
             'training': 'Seated',
-            'workshop': 'Standing',
+            'workshop': 'Moderate activity',
+            'lab':'Light activity',
+            'gym':'Heavy exercise',
         }
 
         activity_defn = scenario_activity[self.activity_type]
@@ -391,7 +398,7 @@ def baseline_raw_form_data():
     }
 
 
-ACTIVITY_TYPES = {'office', 'meeting', 'training', 'callcentre', 'workshop'}
+ACTIVITY_TYPES = {'office', 'meeting', 'training', 'callcentre', 'workshop', 'lab', 'gym'}
 EVENT_TYPES = {'single_event', 'recurrent_event'}
 MECHANICAL_VENTILATION_TYPES = {'air_changes', 'air_supply', 'not-applicable'}
 MASK_TYPES = {'Type I', 'FFP2'}
diff --git a/cara/apps/calculator/templates/calculator.form.html.j2 b/cara/apps/calculator/templates/calculator.form.html.j2
index cfebb470..a28fb5a8 100644
--- a/cara/apps/calculator/templates/calculator.form.html.j2
+++ b/cara/apps/calculator/templates/calculator.form.html.j2
@@ -113,9 +113,11 @@
                     <option value="office">Office</option>
                     <option value="meeting">Meeting</option>
                     <option value="callcentre">Call Centre</option>
+                    <option value="lab">Laboratory</option>
                     <option value="workshop">Workshop</option>
                     <option value="training">Training</option>
-                   </select><br>
+                    <option value="gym">Gym</option>
+                  </select><br>
     Start: <input type="time" id="activity_start" class="start_time" name="activity_start" value="09:00" required> &nbsp;&nbsp;
     Finish: <input type="time" id="activity_finish" class="finish_time" name="activity_finish" value="18:00" required>
     <span id="activity_time_error" class="red_text" hidden>Finish time must be after start</span><br>
@@ -208,11 +210,13 @@
   <b>Activity types:</b><br>
   The type of activity that includes both the infected and exposed persons:
   <ul>
-    <li>Office = typical scenario all persons seated, in conversation (talking 33% of the time, otherwise breathing normally).</li>
-    <li>Meeting = typical scenario all persons seated, in conversation (talking time is shared equally between all persons).</li>
-    <li>Workshop = assembly workshop environment, all persons standing, talking (50% of the time spent talking).</li>
+    <li>Office = Typical office scenario with all persons seated, in conversation (talking 33% of the time, otherwise breathing normally).</li>
+    <li>Meeting = Typical meeting scenario with all persons seated, in conversation (talking time is shared equally between all persons).</li>
     <li>Call Centre = A conservative assumption for office spaces, assumes all occupants are seated and talking continuously.</li>
-    <li>Training = one person (the trainer) standing, talking, all others seated, talking quietly (whispering). It is assumed the trainer is the infected person, for the worst case scenario.</li>
+    <li>Laboratory =  Typical lab scenario with all persons doing light physical activity and talking 50% of the time.</li>
+    <li>Workshop = Typical mechanical assembly workshop or equipment installation scenario with all persons doing moderate activity and talking 50% of the time.</li>
+    <li>Training = Training course scenario. One person (Trainer) standing, talking, all others seated, talking quietly (whispering). It is assumed the Trainer is the infected person, for the worst case scenario.</li>
+    <li>Gym = Included for comparison purposes only, all persons are doing heavy exercise and breathing (no talking).</li>
   </ul>
   <b>Activity breaks:</b><br>
   <ul>
diff --git a/cara/apps/calculator/templates/report.html.j2 b/cara/apps/calculator/templates/report.html.j2
index 203569b0..61d3d606 100644
--- a/cara/apps/calculator/templates/report.html.j2
+++ b/cara/apps/calculator/templates/report.html.j2
@@ -76,9 +76,13 @@
 		{% elif form.activity_type == "callcentre" %}
 		Call Centre = typical office scenario with all persons seated, all talking continuously.
 		{% elif form.activity_type == "workshop" %}
-		Workshop = assembly workshop environment, all persons standing, talking 50% of the time.
+		Workshop = assembly workshop environment, all persons doing moderate physical activity, talking 50% of the time.
 		{% elif form.activity_type == "training" %}
 		Training – one person (the trainer) standing, talking, all others seated, talking quietly (whispering). It is assumed the trainer is the infected person, for the worst case scenario.
+		{% elif form.activity_type == "lab" %}
+		Laboratory = Lab or technical environment, all persons doing light physical activity, talking 50% of the time.
+		{% elif form.activity_type == "gym" %}
+		Gym = For comparison only, all persons doing heavy physical exercise, breathing and not talking.
 		{% endif %}
 		</p></li>
 			<ul>
diff --git a/cara/apps/expert.py b/cara/apps/expert.py
index 60fcfee9..410e9127 100644
--- a/cara/apps/expert.py
+++ b/cara/apps/expert.py
@@ -369,14 +369,14 @@ baseline_model = models.ExposureModel(
             virus=models.Virus.types['SARS_CoV_2'],
             presence=models.SpecificInterval(((8, 12), (13, 17))),
             mask=models.Mask.types['No mask'],
-            activity=models.Activity.types['Light exercise'],
+            activity=models.Activity.types['Light activity'],
             expiration=models.Expiration.types['Unmodulated Vocalization'],
         ),
     ),
     exposed=models.Population(
         number=10,
         presence=models.SpecificInterval(((8, 12), (13, 17))),
-        activity=models.Activity.types['Light exercise'],
+        activity=models.Activity.types['Light activity'],
         mask=models.Mask.types['No mask'],
     ),
 )
diff --git a/cara/models.py b/cara/models.py
index 4bfe8ece..232cbb5a 100644
--- a/cara/models.py
+++ b/cara/models.py
@@ -392,8 +392,8 @@ class Activity:
 Activity.types = {
     'Seated': Activity(0.51, 0.51),
     'Standing': Activity(0.57, 0.57),
-    'Light exercise': Activity(1.38, 1.38),
-    'Moderate exercise': Activity(2.35, 2.35),
+    'Light activity': Activity(1.25, 1.25),
+    'Moderate activity': Activity(1.78, 1.78),
     'Heavy exercise': Activity(3.30, 3.30),
 }
 
diff --git a/cara/tests/test_known_quantities.py b/cara/tests/test_known_quantities.py
index 7118897b..3c40f902 100644
--- a/cara/tests/test_known_quantities.py
+++ b/cara/tests/test_known_quantities.py
@@ -79,7 +79,7 @@ def build_model(interval_duration):
             virus=models.Virus.types['SARS_CoV_2'],
             presence=models.SpecificInterval(((0, 4), (5, 8))),
             mask=models.Mask.types['No mask'],
-            activity=models.Activity.types['Light exercise'],
+            activity=models.Activity.types['Light activity'],
             expiration=models.Expiration.types['Unmodulated Vocalization'],
         ),
     )
@@ -300,7 +300,7 @@ def build_hourly_dependent_model(month, intervals_open=((7.5, 8.5),),
             virus=models.Virus.types['SARS_CoV_2'],
             presence=models.SpecificInterval(intervals_presence_infected),
             mask=models.Mask.types['No mask'],
-            activity=models.Activity.types['Light exercise'],
+            activity=models.Activity.types['Light activity'],
             expiration=models.Expiration.types['Unmodulated Vocalization'],
         ),
     )
@@ -321,7 +321,7 @@ def build_constant_temp_model(outside_temp, intervals_open=((7.5, 8.5),)):
             virus=models.Virus.types['SARS_CoV_2'],
             presence=models.SpecificInterval(((0, 4), (5, 7.5))),
             mask=models.Mask.types['No mask'],
-            activity=models.Activity.types['Light exercise'],
+            activity=models.Activity.types['Light activity'],
             expiration=models.Expiration.types['Unmodulated Vocalization'],
         ),
     )
@@ -348,7 +348,7 @@ def build_hourly_dependent_model_multipleventilation(month, intervals_open=((7.5
             virus=models.Virus.types['SARS_CoV_2'],
             presence=models.SpecificInterval(((0, 4), (5, 7.5))),
             mask=models.Mask.types['No mask'],
-            activity=models.Activity.types['Light exercise'],
+            activity=models.Activity.types['Light activity'],
             expiration=models.Expiration.types['Unmodulated Vocalization'],
         ),
     )
@@ -364,7 +364,7 @@ def build_hourly_dependent_model_multipleventilation(month, intervals_open=((7.5
     [0.5, 1.2, 2., 3.5, 5., 6.5, 7.5, 7.9, 8.],
 )
 def test_concentrations_hourly_dep_temp_vs_constant(month, temperatures, time):
-    # The concentrations should be the same up to 8 AM (time when the 
+    # The concentrations should be the same up to 8 AM (time when the
     # temperature changes DURING the window opening).
     m1 = build_hourly_dependent_model(month)
     m2 = build_constant_temp_model(temperatures[7]+273.15)

From 8f10706d3ed934f0fadeccf453836ef6c22d3fb5 Mon Sep 17 00:00:00 2001
From: jdevine <james.dilwyn.devine@cern.ch>
Date: Tue, 17 Nov 2020 19:24:07 +0100
Subject: [PATCH 3/5] Updated tests a little

---
 cara/tests/conftest.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cara/tests/conftest.py b/cara/tests/conftest.py
index e50cdea8..59dbe826 100644
--- a/cara/tests/conftest.py
+++ b/cara/tests/conftest.py
@@ -18,7 +18,7 @@ def baseline_model():
             virus=models.Virus.types['SARS_CoV_2'],
             presence=models.SpecificInterval(((0, 4), (5, 8))),
             mask=models.Mask.types['No mask'],
-            activity=models.Activity.types['Light exercise'],
+            activity=models.Activity.types['Light activity'],
             expiration=models.Expiration.types['Unmodulated Vocalization'],
         ),
     )

From d3af776951255d5ea1fd0ac2e38dd735f99a70c5 Mon Sep 17 00:00:00 2001
From: jdevine <james.dilwyn.devine@cern.ch>
Date: Tue, 17 Nov 2020 19:38:47 +0100
Subject: [PATCH 4/5] Changed test results to match new values

---
 cara/tests/test_known_quantities.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/cara/tests/test_known_quantities.py b/cara/tests/test_known_quantities.py
index 3c40f902..34521c78 100644
--- a/cara/tests/test_known_quantities.py
+++ b/cara/tests/test_known_quantities.py
@@ -16,7 +16,7 @@ def test_no_mask_aerosols(baseline_model):
 
 
 def test_no_mask_emission_rate(baseline_model):
-    rate = 167.74011998223307
+    rate = 151.938514
     npt.assert_allclose(
         [baseline_model.infected.emission_rate(t) for t in [0, 1, 4, 4.5, 5, 8, 9]],
         [0, rate, rate, 0, 0, rate, 0],
@@ -52,7 +52,7 @@ def test_concentrations(baseline_model):
     concentrations = [baseline_model.concentration(t) for t in ts]
     npt.assert_allclose(
         concentrations,
-        [0.000000e+00, 2.891970e-01, 1.266287e-04, 2.891969e-01, 5.544607e-08],
+        [0.000000e+00, 2.619538e-01, 1.156999e-04, 2.619537e-01, 5.022289e-08],
         rtol=1e-5
     )
 
@@ -97,7 +97,7 @@ def test_concentrations_startup(baseline_model):
 
 def test_r0(baseline_exposure_model):
     p = baseline_exposure_model.infection_probability()
-    npt.assert_allclose(p, 93.196908)
+    npt.assert_allclose(p, 88.977694)
 
 
 def test_periodic_window(baseline_periodic_window, baseline_room):

From 7cc38af9c2cf3e290175bf6c597f6091b3a26a6e Mon Sep 17 00:00:00 2001
From: jdevine <james.dilwyn.devine@cern.ch>
Date: Tue, 17 Nov 2020 19:44:46 +0100
Subject: [PATCH 5/5] Changed test results to match new values, take 2

---
 cara/tests/test_known_quantities.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/cara/tests/test_known_quantities.py b/cara/tests/test_known_quantities.py
index 34521c78..ddceed02 100644
--- a/cara/tests/test_known_quantities.py
+++ b/cara/tests/test_known_quantities.py
@@ -52,7 +52,7 @@ def test_concentrations(baseline_model):
     concentrations = [baseline_model.concentration(t) for t in ts]
     npt.assert_allclose(
         concentrations,
-        [0.000000e+00, 2.619538e-01, 1.156999e-04, 2.619537e-01, 5.022289e-08],
+        [0.000000e+00, 2.619538e-01, 1.146999e-04, 2.619537e-01, 5.022289e-08],
         rtol=1e-5
     )
 
@@ -435,8 +435,8 @@ def build_exposure_model(concentration_model):
 @pytest.mark.parametrize(
     "month, expected_r0",
     [
-        ['Jan', 91.06953],
-        ['Jun', 99.995335],
+        ['Jan', 86.220749],
+        ['Jun', 99.972046],
     ],
 )
 def test_r0_hourly_dep(month,expected_r0):
@@ -453,8 +453,8 @@ def test_r0_hourly_dep(month,expected_r0):
 @pytest.mark.parametrize(
     "month, expected_r0",
     [
-        ['Jan', 91.19912],
-        ['Jun', 99.997324],
+        ['Jan', 86.385018],
+        ['Jun', 99.982281],
     ],
 )
 def test_r0_hourly_dep_refined(month,expected_r0):