Adjusted CD4 calculation ordering to make sense.

Author: pineapple-cat

src/hivpy/resistance_mutations.py

@@ -343,15 +343,18 @@ def calc_cd4_delta(self, age, sex, active_drugs, cont_on_art, adherence, adheren
 
         # calculate change in cd4
         cd4_delta = base_cd4_recovery_on_art + cd4_recovery_on_art * x
-        cd4 = max(0, cd4_tm1 + cd4_delta)
-
-        # changes for people on PrEP/ART
+        # changes for people on antiretroviral drugs
         if on_prep or on_art:
-            # adjust cd4 delta for higher cd4 levels
+            # adjust cd4 delta for higher previous cd4 levels
             if 100 < cd4_tm1 <= 200:
                 cd4_delta *= 0.85
             elif cd4_tm1 > 200:
                 cd4_delta *= 0.7
+
+        # calculate current cd4 levels
+        cd4 = max(0, cd4_tm1 + cd4_delta)
+        # changes for people on antiretroviral drugs
+        if on_prep or on_art:
             # add cd4 variability
             cd4 = np.sqrt(cd4) + self.cd4_stdev_on_art * rng.normal() ** 2
             # adjust cd4 according to max value

src/tests/test_resistance_mutations.py

@@ -103,10 +103,10 @@ def test_calc_cd4_delta():
 
     # check adjustments on ARV
     # 6 + 0.2 * 6 = 12 >> 12 * 0.85 = 10.2
-    # 150 + 12 = 162 >> sqrt(162) + cd4_stdev_on_art * rng.normal() ** 2
+    # 150 + 10.2 = 160.2 >> sqrt(160.2) + cd4_stdev_on_art * rng.normal() ** 2
     cd4, delta = res.calc_cd4_delta(20, SexType.Male, 3, timedelta(months=6), 0.8, 0.8,
                                     False, False, False, False, False, False, 150, 0.2, 200, True, False)
-    assert sqrt(162) - res.cd4_stdev_on_art * 3 <= cd4 <= sqrt(162) + res.cd4_stdev_on_art * 3
+    assert sqrt(160.2) - res.cd4_stdev_on_art * 3 <= cd4 <= sqrt(160.2) + res.cd4_stdev_on_art * 3
     assert isclose(delta, 10.2)
 
     # check max cd4 cap on ARV