Merge pull request #186 from UCL/ds/ltpinfection

 Long-term partner infection

setup.cfg

@@ -47,7 +47,7 @@ console_scripts =
     run_model = hivpy.cli:run_model
 
 [flake8]
-max-line-length = 120
+max-line-length = 150
 per-file-ignores =
     # Don't complain about unused imports in __init__.py
     */__init__.py: F401

src/hivpy/cli.py

@@ -3,7 +3,7 @@
 
 import yaml
 
-from .experiment import create_experiment, run_experiment
+from hivpy.experiment import create_experiment, run_experiment
 
 
 def run_model():

src/hivpy/column_names.py

@@ -14,6 +14,7 @@
 RISK_DIAGNOSIS = "risk_diagnosis"               # float: risk associated with recent HIV diagnosis
 RISK_PERSONAL = "risk_personal"                 # float: individual risk reduction applied with a certain probability
 RISK_LTP = "risk_long_term_partnered"           # float: risk reduction for people in long term partnerships
+RISK_LTP_INFECTED = "risk_ltp_infected"         # float: risk of infection from infected long term partner
 RISK_ART_ADHERENCE = "risk_art_adherence"       # float: risk reduction associated with low ART adherence
 RISK_INITIAL = "risk_initial"                   # float: initial risk reduction factor
 CIRCUMCISED = "circumcised"                     # bool: True if a man is circumcised
@@ -27,10 +28,18 @@
 SEX_BEHAVIOUR = "sex_behaviour"                 # int: sexual behaviour grouping
 SEX_BEHAVIOUR_CLASS = "sex_class"               # sexual_behaviour.SexBehaviourClass(enum): Men, Young Women, Older Women, or Sex Workers
 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
+LTP_INFECTION_DATE = "ltp_infection_date"       # date: date at which the long term partner gets infected o/w None if not infected
+LTP_DIAGNOSED = "ltp_diagnosed"                 # bool: True if a person's long term partner has been diagnosed, o/w False
+RECENT_LTP_DIAGNOSED = "recent_ltp_diagnosed"   # bool: True if a person's most recent long term partner was diagnosed
+RECENT_LTP_ART = "recent_ltp_art"               # bool: True if a person's most recent long term partner was on ART
+LTP_ART = "ltp_art"                             # bool: True if a person's long term partner is on ART
+LTP_VIRAL_SUPPRESSED = "ltp_viral_suppressed"   # bool: True if a person's long term partner is virally suppressed
 LOW_FERTILITY = "low_fertility"                 # bool: True if a woman is considered to have a 0% chance of pregnancy, o/w False
 PREGNANT = "pregnant"                           # bool: True if a woman is currently pregnant
 LAST_PREGNANCY_DATE = "last_pregnancy_date"     # None | datetime.date: date of most recent pregnancy, o/w None if never pregnant
@@ -41,6 +50,8 @@
 NUM_HIV_CHILDREN = "num_HIV_children"           # int: number of children infected with HIV a woman has
 WANT_NO_CHILDREN = "want_no_children"           # bool: True if a woman does not want any more children
 
+ON_ART = "on_art"                               # bool: True if a person is currently on ART
+
 SEX_WORKER = "sex_worker"                       # bool: True if person is a sex worker, o/w False
 SW_AGE_GROUP = "sw_age_group"                   # int: categorises sex worker behaviour by age
 DATE_STOP_SW = "date_stop_sex_work"             # date: date at which a former sex worker (last) stopped sex work
@@ -62,14 +73,19 @@
 NSTP_LAST_TEST = "nstp_last_test"               # int: number of short term condomless sex partners since last test (DUMMY)
 NP_LAST_TEST = "np_last_test"                   # int: total number of condomless sex partners since last test (DUMMY)
 HIV_STATUS = "HIV_status"                       # bool: True if person is HIV positive, o/w False
+LTP_STATUS = "LTP_status"                       # bool: True if long term partner is HIV positive, o/w False
+RECENT_LTP_STATUS = "recent_LTP_status"         # bool: True if the most recent long term partner was HIV positive
 DATE_HIV_INFECTION = "date_HIV_infection"       # None | date: date of HIV infection if HIV+, o/w None
 IN_PRIMARY_INFECTION = "in_primary_infection"   # bool: True if a person contracted HIV within 3 months of the current date, o/w False
 HIV_INFECTION_GE6M = "HIV_infection_ge6m"       # bool: True is a person has been infected with HIV for 6 months or more (DUMMY)
+LTP_IN_PRIMARY = "ltp_in_primary"               # bool: True if a person's long term partner is in primary infection
 HIV_DIAGNOSED = "HIV_diagnosed"                 # bool: True if individual had a positive HIV test
 HIV_DIAGNOSIS_DATE = "HIV_Diagnosis_Date"       # None | datetime.date: date of HIV diagnosis (to nearest timestep) if HIV+, o/w None
+VIRAL_LOAD_GROUP = "viral_load_group"           # int: value 0-5 placing bounds on viral load for an HIV positive person. [(0, 2.7), (2.7, 3.7), (3.7, 4.7), (4.7, 5.7), > 5.7, primary infection]
 UNDER_CARE = "under_care"                       # bool: True if under care after a positive HIV diagnosis
-VIRAL_LOAD_GROUP = "viral_load_group"           # int: value 0-5 placing bounds on viral load for an HIV positive person
 VIRAL_LOAD = "viral_load"                       # float: viral load for HIV+ person
+VIRAL_SUPPRESSION = "viral suppression"         # bool: True if person is virally suppressed
+RESISTANCE_MUTATIONS = "resistance_mutations"   # integer: total proportion of (people in?) resistance mutations
 CD4 = "cd4"                                     # None | float: CD4 count per cubic millimeter; set to None for people w/o HIV
 MAX_CD4 = "max_cd4"                             # float: maximum CD4 count to which a person can return when on ART
 ART_NAIVE = "art_naive"                         # bool: True if person has never been on antiretroviral therapy

src/hivpy/common.py

@@ -60,6 +60,20 @@ def opposite_sex(sex: SexType):
     return (1 - sex)
 
 
+def sub_pop_ratio(sp1, sp2):
+    if len(sp2) == 0:
+        return 0
+    else:
+        return len(sp1) / len(sp2)
+
+
+def safe_ratio(n1, n2):
+    if n2 == 0:
+        return 0
+    else:
+        return n1/n2
+
+
 class date:
     def __init__(self, year, month=1, day=1):
         self.year = year