Replace LTP_HIV_STATUS dummy column with LTP_STATUS column

UCL · Nov 26, 2024 · 872c9c5 · 872c9c5
1 parent 0319779
commit 872c9c5
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 5 deletions.
diff --git a/src/hivpy/column_names.py b/src/hivpy/column_names.py
@@ -30,7 +30,6 @@
 LONG_TERM_PARTNER = "long_term_partner"         # bool: True if the subject has a long term condomless partner
 LTP_NEW = "ltp_new"                             # bool: True if condomless sex with ltp is new this timestep
 LTP_LONGEVITY = "ltp_longevity"                 # int: categorises longevity of long term partnerships (higher => more stable)
-LTP_HIV_STATUS = "ltp_HIV_status"               # bool: True if an individual's long term partner is infected with HIV (DUMMY)
 LTP_HIV_DIAGNOSED = "ltp_HIV_diagnosed"         # bool: True if an individual's long term partner is diagnosed with HIV (DUMMY)
 LTP_ON_ART = "ltp_on_art"                       # bool: True if an individual's long term partner is on ART (DUMMY)
 LTP_MONOGAMOUS = "ltp_monogamous"               # bool: True if a person's long term partner has no short term partners o/w False

diff --git a/src/hivpy/prep.py b/src/hivpy/prep.py
@@ -90,7 +90,6 @@ def init_prep_variables(self, pop: Population):
         pop.init_variable(col.PREP_CAB_TESTED, False)
         pop.init_variable(col.PREP_LEN_TESTED, False)
         pop.init_variable(col.PREP_VR_TESTED, False)
-        pop.init_variable(col.LTP_HIV_STATUS, False)
         pop.init_variable(col.LTP_HIV_DIAGNOSED, False)
         pop.init_variable(col.LTP_ON_ART, False)
 
@@ -117,7 +116,7 @@ def get_risk_informed_pop(self, pop: Population, prob_risk_informed_prep):
         """
         return pop.get_sub_pop(AND(COND(col.LONG_TERM_PARTNER, op.eq, True),
                                    COND(col.LTP_ON_ART, op.eq, False),
-                                   COND(col.LTP_HIV_STATUS, op.eq, False),
+                                   COND(col.LTP_STATUS, op.eq, False),
                                    COND(col.R_PREP, op.lt, prob_risk_informed_prep)))
 
     def get_suspect_risk_pop(self, pop: Population):
@@ -127,7 +126,7 @@ def get_suspect_risk_pop(self, pop: Population):
         """
         return pop.get_sub_pop(AND(COND(col.LONG_TERM_PARTNER, op.eq, True),
                                    COND(col.LTP_ON_ART, op.eq, False),
-                                   COND(col.LTP_HIV_STATUS, op.eq, True),
+                                   COND(col.LTP_STATUS, op.eq, True),
                                    COND(col.R_PREP, op.lt, self.prob_suspect_risk_prep)))
 
     # FIXME: this function may be removed if there are no issues with
@@ -398,7 +397,7 @@ def prep_eligibility(self, pop: Population):
                                                   COND(col.AGE, op.lt, 50),
                                                   OR(COND(col.R_PREP, op.lt, 0.01),  # (alt) risk informed
                                                      AND(COND(col.R_PREP, op.lt, self.prob_suspect_risk_prep),
-                                                         COND(col.LTP_HIV_STATUS, op.eq, True)))))  # (alt) suspect risk
+                                                         COND(col.LTP_STATUS, op.eq, True)))))  # (alt) suspect risk
                 at_risk_ltp_pop = pop.get_sub_pop(AND(COND(col.HIV_DIAGNOSED, op.eq, False),
                                                       COND(col.LTP_HIV_DIAGNOSED, op.eq, True),
                                                       COND(col.LTP_ON_ART, op.eq, False)))