Create resistance mutations module

src/hivpy/column_names.py

@@ -48,8 +48,6 @@
 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
@@ -82,26 +80,27 @@
 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 = "viral_load"                       # float: viral load for HIV+ person
+MAX_VIRAL_LOAD = "max_viral_load"               # float: maximum viral load for a given time step? (DUMMY)
 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
+CD4_DELTA = "cd4_delta"                         # float: change in CD4 count since the last time step
 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
+CD4_RECOVERY_ON_ART = "cd4_recovery_on_art"     # float: individual propensity for immune recovery given viral suppression
 X4_VIRUS = "x4_virus"                           # bool: True if X4 virus is present in person, False otherwise
 
-WHO3_EVENT = "who3_event"                       # Bool: True if who3 disease occurs this timestep in HIV positive person
-NON_TB_WHO3 = "non_tb_who3"                     # Bool: True if non-tb who3 disease occurs this timestep in HIV positive person
-TB = "tb"                                       # Bool: True if tb occurs this timestep in HIV positive person
-TB_DIAGNOSED = "tb_diagnosed"                   # Bool: True if TB is diagnosed this timestep
+WHO3_EVENT = "who3_event"                       # bool: True if who3 disease occurs this timestep in HIV positive person
+NON_TB_WHO3 = "non_tb_who3"                     # bool: True if non-tb who3 disease occurs this timestep in HIV positive person
+TB = "tb"                                       # bool: True if tb occurs this timestep in HIV positive person
+TB_DIAGNOSED = "tb_diagnosed"                   # bool: True if TB is diagnosed this timestep
 TB_INFECTION_DATE = "tb_infection_date"         # date: Date of start of most recent TB infection
-TB_INITIAL_INFECTION = "tb_initial_infection"   # Bool: True if TB infection began this timestep
-C_MENINGITIS = "c_meningitis"                       # Bool: True if cryptococcal meningitis occurs this timestep
-C_MENINGITIS_DIAGNOSED = "c_meningitis_diagnosed"   # Bool: True if cryptococcal meningitis diagnosed this timestep
-SBI = "serious_bacterial_infection"             # Bool: True if serious bacterial infection this time step
-SBI_DIAGNOSED = "sbi_diagnosed"                 # Bool: True if SBI diagnosed this time step
-WHO4_OTHER = "who4_other"                       # Bool: True if other WHO4 disease occurs this timestep
-WHO4_OTHER_DIAGNOSED = "who4_other_diagnosed"   # Bool: True if other WHO4 disease diagnosed this timestep
-ADC = "AIDS_defining_condition"                 # Bool: presence of AIDS defining condition (any WHO4)
+TB_INITIAL_INFECTION = "tb_initial_infection"   # bool: True if TB infection began this timestep
+C_MENINGITIS = "c_meningitis"                       # bool: True if cryptococcal meningitis occurs this timestep
+C_MENINGITIS_DIAGNOSED = "c_meningitis_diagnosed"   # bool: True if cryptococcal meningitis diagnosed this timestep
+SBI = "serious_bacterial_infection"             # bool: True if serious bacterial infection this time step
+SBI_DIAGNOSED = "sbi_diagnosed"                 # bool: True if SBI diagnosed this time step
+WHO4_OTHER = "who4_other"                       # bool: True if other WHO4 disease occurs this timestep
+WHO4_OTHER_DIAGNOSED = "who4_other_diagnosed"   # bool: True if other WHO4 disease diagnosed this timestep
+ADC = "AIDS_defining_condition"                 # bool: presence of AIDS defining condition (any WHO4)
 
 R_PREP = "r_prep"                               # float: a semi-permanent random personal variable that determines whether someone is risk informed or suspects they are at risk enough to take PrEP
 PREP_ORAL_PREF = "prep_oral_pref"               # float: a value that determines and individual's preference for oral PrEP
@@ -112,29 +111,29 @@
 PREP_CAB_RANK = "prep_cab_rank"                 # int: an individual's preference ranking for injectable Cabotegravir PrEP
 PREP_LEN_RANK = "prep_len_rank"                 # int: an individual's preference ranking for injectable Lenacapavir PrEP
 PREP_VR_RANK = "prep_vr_rank"                   # int: an individual's preference ranking for vaginal ring PrEP
-PREP_ORAL_WILLING = "prep_oral_willing"         # Bool: True if an individual is willing to use oral PrEP
-PREP_CAB_WILLING = "prep_cab_willing"           # Bool: True if an individual is willing to use injectable Cabotegravir PrEP
-PREP_LEN_WILLING = "prep_len_willing"           # Bool: True if an individual is willing to use injectable Lenacapavir PrEP
-PREP_VR_WILLING = "prep_vr_willing"             # Bool: True if an individual is willing to use vaginal ring PrEP
-PREP_ANY_WILLING = "prep_any_willing"           # Bool: True if an individual is willing to use at least one type of PrEP
-FAVOURED_PREP_TYPE = "favoured_prep_type"       # None | prep.PrEPType(enum): PrEP type with highest preference an individual is willing to take that is also currently available, o/w None
-PREP_ELIGIBLE = "prep_eligible"                 # Bool: True if an individual is eligible for PrEP usage
-PREP_ORAL_TESTED = "prep_oral_tested"           # Bool: True if an individual has tested explicitly to start oral PrEP (DUMMY)
-PREP_CAB_TESTED = "prep_cab_tested"             # Bool: True if an individual has tested explicitly to start injectable Cab PrEP (DUMMY)
-PREP_LEN_TESTED = "prep_len_tested"             # Bool: True if an individual has tested explicitly to start injectable Len PrEP (DUMMY)
-PREP_VR_TESTED = "prep_vr_tested"               # Bool: True if an individual has tested explicitly to start vaginal ring PrEP (DUMMY)
-PREP_TYPE = "prep_type"                         # None | prep.PrEPType(enum): Oral, Cabotegravir, Lenacapavir, or VaginalRing if PrEP is being used, o/w None
-EVER_PREP = "ever_prep"                         # Bool: True if an individual has ever been on PrEP
+PREP_ORAL_WILLING = "prep_oral_willing"         # bool: True if an individual is willing to use oral PrEP
+PREP_CAB_WILLING = "prep_cab_willing"           # bool: True if an individual is willing to use injectable Cabotegravir PrEP
+PREP_LEN_WILLING = "prep_len_willing"           # bool: True if an individual is willing to use injectable Lenacapavir PrEP
+PREP_VR_WILLING = "prep_vr_willing"             # bool: True if an individual is willing to use vaginal ring PrEP
+PREP_ANY_WILLING = "prep_any_willing"           # bool: True if an individual is willing to use at least one type of PrEP
+FAVOURED_PREP_TYPE = "favoured_prep_type"       # prep.PrEPType(enum): PrEP type with highest preference an individual is willing to take that is also currently available, o/w NoPrEP
+PREP_ELIGIBLE = "prep_eligible"                 # bool: True if an individual is eligible for PrEP usage
+PREP_ORAL_TESTED = "prep_oral_tested"           # bool: True if an individual has tested explicitly to start oral PrEP (DUMMY)
+PREP_CAB_TESTED = "prep_cab_tested"             # bool: True if an individual has tested explicitly to start injectable Cab PrEP (DUMMY)
+PREP_LEN_TESTED = "prep_len_tested"             # bool: True if an individual has tested explicitly to start injectable Len PrEP (DUMMY)
+PREP_VR_TESTED = "prep_vr_tested"               # bool: True if an individual has tested explicitly to start vaginal ring PrEP (DUMMY)
+PREP_TYPE = "prep_type"                         # prep.PrEPType(enum): Oral, Cabotegravir, Lenacapavir, or VaginalRing if PrEP is being used, o/w NoPrEP
+EVER_PREP = "ever_prep"                         # bool: True if an individual has ever been on PrEP
 FIRST_ORAL_START_DATE = "first_oral_start_date"     # None | date: start date of first ever oral PrEP usage
 FIRST_CAB_START_DATE = "first_cab_start_date"       # None | date: start date of first ever injectable Cab PrEP usage
 FIRST_LEN_START_DATE = "first_len_start_date"       # None | date: start date of first ever injectable Len PrEP usage
 FIRST_VR_START_DATE = "first_vr_start_date"         # None | date: start date of first ever vaginal ring PrEP usage
 LAST_PREP_START_DATE = "last_prep_start_date"   # None | date: start date of most recent PrEP usage
-PREP_JUST_STARTED = "prep_just_started"         # Bool: True if PrEP usage began this time step
+PREP_JUST_STARTED = "prep_just_started"         # bool: True if PrEP usage began this time step
 LAST_PREP_USE_DATE = "last_prep_use_date"       # None | date: most recent date of PrEP usage
 LAST_PREP_STOP_DATE = "last_prep_stop_date"     # None | date: stop date of most recent PrEP usage
-PREP_PAUSED = "prep_paused"                     # Bool: True if PrEP usage is paused this time step due to ineligibility
-ON_PREP = "on_prep"                             # Bool: True if an individual is currently on PrEP this time step
+PREP_PAUSED = "prep_paused"                     # bool: True if PrEP usage is paused this time step due to ineligibility
+ON_PREP = "on_prep"                             # bool: True if an individual is currently on PrEP this time step
 CONT_ON_PREP = "cont_on_prep"                   # None | timedelta: total length of continuous usage of current PrEP based on user intention (breaks due to ineligibility do not count against continuity - this value will not be reset during an ineligibility break)
 CONT_INTENT_ON_PREP = "cont_intent_on_prep"     # None | timedelta: total length of continuous usage of current PrEP based on user intention, including pauses (will continue to increment even during ineligibility breaks)
 CONT_ACTIVE_ON_PREP = "cont_active_on_prep"     # None | timedelta: actual total length of continuous usage of current PrEP
@@ -143,28 +142,49 @@
 CUMULATIVE_PREP_LEN = "cumulative_prep_len"     # None | timedelta: total length of cumulative injectable Len PrEP usage
 CUMULATIVE_PREP_VR = "cumulative_prep_vr"       # None | timedelta: total length of cumulative injectable vaginal ring PrEP usage
 
-ART_ADHERENCE = "art_adherence"                 # None | Float: percentage of ART intake that is adhered to
-TA_MUTATION = "tam"                             # X_MUTATION: drug resistance cols (TODO: all 24 currently DUMMIED)
-M184_MUTATION = "m184m"
-K65_MUTATION = "k65m"
-Q151_MUTATION = "q151m"
-K103_MUTATION = "k103m"
-Y181_MUTATION = "y181m"
-G190_MUTATION = "g190m"
-P32_MUTATION = "p32m"
-P33_MUTATION = "p33m"
-P46_MUTATION = "p46m"
-P47_MUTATION = "p47m"
-P50L_MUTATION = "p50lm"
-P50V_MUTATION = "p50vm"
-P54_MUTATION = "p54m"
-P76_MUTATION = "p76m"
-P82_MUTATION = "p82m"
-P84_MUTATION = "p84m"
-P88_MUTATION = "p88m"
-P90_MUTATION = "p90m"
-IN118_MUTATION = "in118m"
-IN140_MUTATION = "in140m"
-IN148_MUTATION = "in148m"
-IN155_MUTATION = "in155m"
-IN263_MUTATION = "in263m"
+ART_NAIVE = "art_naive"                         # bool: True if person has never been on antiretroviral therapy
+ON_ART = "on_art"                               # bool: True if a person is currently on ART
+CONT_ON_ART = "cont_on_art"                     # None | timedelta: total length of continuous time on current line of ART
+CONT_ON_ARV = "cont_on_arv"                     # None | timedelta: total length of continuous time on antiretroviral drugs (PrEP or ART)
+ART_ADHERENCE = "art_adherence"                 # None | float: percentage of ART intake that is adhered to
+NUM_ACTIVE_DRUGS = "num_active_drugs"           # int: number of active drugs in an individual's regimen
+
+ON_ZDV = "on_zdv"                               # ON_X: True if individual is on a particular antiretroviral drug (TODO: all currently DUMMIED)
+ON_3TC = "on_3tc"
+ON_TEN = "on_ten"
+ON_NEV = "on_nev"
+ON_DAR = "on_dar"
+ON_EFA = "on_efa"
+ON_LPR = "on_lpr"
+ON_TAZ = "on_taz"
+ON_DOL = "on_dol"
+ON_CAB = "on_cab"
+ON_LEN = "on_len"
+ON_OLE = "on_ole"
+ON_ISL = "on_isl"
+
+RESISTANCE_MUTATIONS = "resistance_mutations"   # int: total number of resistance mutations in an individual
+RTTA_MUTATIONS = "rttams"                       # int: number of RT (reverse transcriptase) gene TA mutations
+RT184_MUTATION = "rt184m"                       # bool: True if an individual has the RT gene M184 mutation
+RT65_MUTATION = "rt65m"                         # bool: True if an individual has the RT gene K65 mutation
+RT151_MUTATION = "rt151m"                       # bool: True if an individual has the RT gene Q151 mutation
+RT103_MUTATION = "rt103m"                       # bool: True if an individual has the RT gene K103 mutation
+RT181_MUTATION = "rt181m"                       # bool: True if an individual has the RT gene Y181 mutation
+RT190_MUTATION = "rt190m"                       # bool: True if an individual has the RT gene G190 mutation
+PR32_MUTATION = "pr32m"                         # bool: True if an individual has the PR (protease) gene P32 mutation
+PR33_MUTATION = "pr33m"                         # bool: True if an individual has the PR gene P33 mutation
+PR46_MUTATION = "pr46m"                         # bool: True if an individual has the PR gene P46 mutation
+PR47_MUTATION = "pr47m"                         # bool: True if an individual has the PR gene P47 mutation
+PR50L_MUTATION = "pr50lm"                       # bool: True if an individual has the PR gene P50L mutation
+PR50V_MUTATION = "pr50vm"                       # bool: True if an individual has the PR gene P50V mutation
+PR54_MUTATION = "pr54m"                         # bool: True if an individual has the PR gene P54 mutation
+PR76_MUTATION = "pr76m"                         # bool: True if an individual has the PR gene P76 mutation
+PR82_MUTATION = "pr82m"                         # bool: True if an individual has the PR gene P82 mutation
+PR84_MUTATION = "pr84m"                         # bool: True if an individual has the PR gene P84 mutation
+PR88_MUTATION = "pr88m"                         # bool: True if an individual has the PR gene P88 mutation
+PR90_MUTATION = "pr90m"                         # bool: True if an individual has the PR gene P90 mutation
+IN118_MUTATION = "in118m"                       # bool: True if an individual has the integrase inhibitor IN118 mutation
+IN140_MUTATION = "in140m"                       # bool: True if an individual has the integrase inhibitor IN140 mutation
+IN148_MUTATION = "in148m"                       # bool: True if an individual has the integrase inhibitor IN148 mutation
+IN155_MUTATION = "in155m"                       # bool: True if an individual has the integrase inhibitor IN155 mutation
+IN263_MUTATION = "in263m"                       # bool: True if an individual has the integrase inhibitor IN263 mutation