Test would always fail for viral load zero

ictr · Oct 9, 2020 · 4e14f9b · 4e14f9b
1 parent b324dcc
commit 4e14f9b
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/covid19_outbreak_simulator/plugins/testing.py b/covid19_outbreak_simulator/plugins/testing.py
@@ -87,7 +87,9 @@ def select(ind, counts=None):
             n_tested += 1
             affected = isinstance(ind.infected, float)
             if affected:
-                lod_sensitivity = ind.test_sensitivity(time, args.sensitivity[1]) if len(args.sensitivity) == 2 else 1
+                test_lod = args.sensitivity[1] if len(args.sensitivity) == 2 else 0
+                lod_sensitivity = ind.test_sensitivity(time, test_lod)
+                #
                 sensitivity = lod_sensitivity * args.sensitivity[0]
                 res = sensitivity == 1 or sensitivity > numpy.random.uniform()
 

diff --git a/covid19_outbreak_simulator/population.py b/covid19_outbreak_simulator/population.py
@@ -436,7 +436,10 @@ def viral_load(self, time):
     def test_sensitivity(self, time, lod):
         # return transmissibility at specified time
         viral_load = self.viral_load(time)
-        if viral_load >= lod:
+        if viral_load == 0.0:
+            # if it is 0, it will already be 0
+            return 0
+        elif viral_load >= lod:
             return 1
         else:
             return viral_load / lod