From d966e911538039f2cb23b36aba146db967563c0d Mon Sep 17 00:00:00 2001
From: Luis Aleixo <luis.aleixo@cern.ch>
Date: Wed, 10 Nov 2021 16:59:02 +0100
Subject: [PATCH] Updated references throughout the code

---
 cara/models.py                              | 8 +++++---
 cara/monte_carlo/data.py                    | 6 +++---
 cara/tests/test_predefined_distributions.py | 6 +++---
 3 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/cara/models.py b/cara/models.py
index 6d484be4..26cbf548 100644
--- a/cara/models.py
+++ b/cara/models.py
@@ -788,14 +788,16 @@ class ConcentrationModel:
         if (isinstance(self.infected, InfectedPopulation)
             and isinstance(self.infected.expiration, Expiration)):
             d = self.infected.expiration.diameter * self.evaporation_factor
-            vg = 1.88e-4 * (d / 2.5)**2 # see CERN-OPEN-2021-04
+            vg = 1.88e-4 * (d / 2.5)**2 
+            # see https://doi.org/10.1101/2021.10.14.21264988
             # (velocity of 1.88e-4 corresponds to diameter of 2.5 microns)
         else:
             # model is not evaluated for specific values of aerosol
             # diameters - we choose a single velocity value
             # corresponding to that obtained with a diameter of 2.5 microns
             # (geometric average of the breathing expiration distribution,
-            # taking evaporation into account, see CERN-OPEN-2021-04)
+            # taking evaporation into account, see 
+            # https://doi.org/10.1101/2021.10.14.21264988)
             vg = 1.88e-4
         # Height of the emission source to the floor - i.e. mouth/nose (m)
         h = 1.5
@@ -983,7 +985,7 @@ class ExposureModel:
                 and isinstance(self.concentration_model.infected.expiration,Expiration)):
             # model is not evaluated for specific values of aerosol
             # diameters - we choose a single "average" deposition factor,
-            # as in CERN-OPEN-2021-04.
+            # as in https://doi.org/10.1101/2021.10.14.21264988.
             fdep = 0.6
         else:
             # deposition factor depends on aerosol particle diameter.
diff --git a/cara/monte_carlo/data.py b/cara/monte_carlo/data.py
index 6d4dded6..ea4977b1 100644
--- a/cara/monte_carlo/data.py
+++ b/cara/monte_carlo/data.py
@@ -65,7 +65,7 @@ class BLOmodel:
         return result
 
 
-# From CERN-OPEN-2021-04 and refererences therein
+# From https://doi.org/10.1101/2021.10.14.21264988 and refererences therein
 activity_distributions = {
     'Seated': mc.Activity(LogNormal(-0.6872121723362303, 0.10498338229297108),
                           LogNormal(-0.6872121723362303, 0.10498338229297108)),
@@ -84,7 +84,7 @@ activity_distributions = {
 }
 
 
-# From CERN-OPEN-2021-04 and refererences therein
+# From https://doi.org/10.1101/2021.10.14.21264988 and refererences therein
 symptomatic_vl_frequencies = LogCustomKernel(
     np.array((2.46032, 2.67431, 2.85434, 3.06155, 3.25856, 3.47256, 3.66957, 3.85979, 4.09927, 4.27081,
      4.47631, 4.66653, 4.87204, 5.10302, 5.27456, 5.46478, 5.6533, 5.88428, 6.07281, 6.30549,
@@ -105,7 +105,7 @@ viable_to_RNA_ratio_distribution = Uniform(0.15, 0.45)
 # From discussion with virologists
 infectious_dose_distribution = Uniform(10., 100.)
 
-# From CERN-OPEN-2021-04 and refererences therein
+# From https://doi.org/10.1101/2021.10.14.21264988 and refererences therein
 virus_distributions = {
     'SARS_CoV_2': mc.SARSCoV2(
                 viral_load_in_sputum=symptomatic_vl_frequencies,
diff --git a/cara/tests/test_predefined_distributions.py b/cara/tests/test_predefined_distributions.py
index 524cfcfe..b576b7e3 100644
--- a/cara/tests/test_predefined_distributions.py
+++ b/cara/tests/test_predefined_distributions.py
@@ -8,7 +8,7 @@ from cara.monte_carlo.data import activity_distributions, virus_distributions
 np.random.seed(2000)
 
 
-# mean & std deviations from CERN-OPEN-2021-04 (Table 4)
+# mean & std deviations from https://doi.org/10.1101/2021.10.14.21264988 (Table 3)
 # NOTE: a mistake was corrected for the std deviation of the
 # "Moderate exercise" case (0.37 in the report, but should be 0.34)
 @pytest.mark.parametrize(
@@ -30,8 +30,8 @@ def test_activity_distributions(distribution, mean, std):
     npt.assert_allclose(activity.inhalation_rate.std(), std, atol=0.01)
 
 
-# mean & std deviations from CERN-OPEN-2021-04 (Table 4) - with a refined
-# precision on the values
+# mean & std deviations from https://doi.org/10.1101/2021.10.14.21264988 (Table 3) 
+# - with a refined precision on the values
 @pytest.mark.parametrize(
     "distribution, mean, std",[
         ['SARS_CoV_2', 6.59, 1.74],