use "path/dataset", clear

** q5 education, q6 venue-visits, q7 outness; q8 experienced stigma, q9 Knowing testing facilities, q10 condoms received, q12 tested for STI
** q14 tested for HIV in the previous 12 months, q36 satisfied with sex life


** Gen HIVnew2
gen HIVnew2 = HIVnew

*tab q32 q31a if q32 == . & q31a == 2 & hiv_status == 3
replace HIVnew2 = 1 if q32 == . & q31a == 2 & hiv_status == 3 // include 13 from indeterminate HIV status who did not report an HIV test and tested positive in the study sample
replace HIVnew2 = . if HIVnew == 3
lab val HIVnew2 HIVnew_L


tab agerec10um HIVnew2, col
tab Migration_Status HIVnew2, col
tab q5_Rec1 HIVnew2, col
tab q6bR HIVnew2, col
tab q7_Recode_ULI HIVnew2, col
tab q9 HIVnew2, col
tab q10 HIVnew2, col
tab q12 HIVnew2, col
tab q13_total HIVnew2, col
tab q13_bin HIVnew2, col
tab q14 HIVnew2, col
tab partnumsexcat HIVnew2, col
tab partnumuaicat HIVnew2, col
tab	sexrole	HIVnew2,	col
tab GARPR1_12 HIVnew2, col
tab GARPR1_13 HIVnew2, col
tab sexpract HIVnew2, col
tab num_drugs HIVnew2, col
tab anydrug2 HIVnew2, col
tab concord HIVnew2, col
tab serocomm HIVnew2, col
tab q36R HIVnew2, col
tab partner_all HIVnew2, col
tab sexpract HIVnew2, col
tab q26_weight HIVnew2, col
 

gen alcohol = q30a_mi
replace alcohol = 0 if q30a_mi == 2
label define alcohol_L 0 "no alcohol" 1 "alcohol" 
lab val alcohol alcohol_L

gen cannabis = q30e_mi
replace cannabis = 0 if q30e_mi == 2
label define cannabis_L 0 "no cannabis" 1 "cannabis" 
lab val cannabis cannabis_L

gen sps = .
replace sps = 0 if q30b_mi == 2 | q30d_mi == 2
replace sps = 1 if q30b_mi == 1 | q30d_mi == 1
label define sps_L 0 "no sps" 1 "sps" 
lab val sps sps_L

gen chemsex = .
replace chemsex = 0 if (q30h_mi == 2 | q30i1 == 2 | q30i2 == 2 | q30i3 == 2)
replace chemsex = 1 if (q30h_mi == 1 | q30i1 == 1 | q30i2 == 1 | q30i3 == 1)
label define chemsex_L 0 "no chemsex" 1 "chemsex" 
lab val chemsex chemsex_L

gen party_2 = .
replace party_2 = 0 if (q30c_mi == 2 | q30f_mi == 2 | q30g_mi == 2)
replace party_2 = 1 if (q30c_mi == 1 | q30f_mi == 1 | q30g_mi == 1)
label define party_2_L 0 "no party_2" 1 "party_2" 
lab val party_2 party_2_L

gen num_drugs_2 = num_drugs
replace num_drugs_2 = 4 if (num_drugs > 3 & num_drugs != .)
label define num_drugs_2_L 0 "0" 1 "1" 2 "2" 3 "3" 4 "4+"
lab val num_drugs_2 num_drugs_2_L


**********
* RECENCY OF TEST VARIABLE

gen testrec2 = 2
replace testrec2 = 1 if q14 == 1 & q31 ==.
replace testrec2 = 1 if q14 == . & q31 == 2013
replace testrec2 = 1 if q14 == .p & q31 == 2013
replace testrec2 = 1 if q14 == 1 & q31 > 2011
replace testrec2 = 1 if q31 == 2014
replace testrec2 = 1 if q31 == 2013 & q14 == 2 & city != 2 & city != 5 & city != 11 & city != 12



label define testrec2_L 1 "within 12 months" 2 "not within past 12 months"
lab val testrec2 testrec2_L
*label var "HIV Test within the past 12 months"

** create new vars uHIVinc uHIVunk
**************************************************


gen uHIVinc = .
replace uHIVinc = 0 if HIVnew2 == 2 & testrec2 == 1  // 1972 men (neg with HIV test in previous year)
replace uHIVinc = 1 if HIVnew2 == 1 & testrec2 == 1  // 106 men (as yet undiagnosed HIV infection)
replace uHIVinc = . if city == 9  // Sofia does not have test date information
lab var uHIVinc "HIV negative & incident cases"
label define uHIVinc_L 0 "negative with recent test" 1 "pos/incident with recent test"
label val uHIVinc uHIVinc_L


gen uHIVunk = .
replace uHIVunk = 0 if HIVnew2 == 2 & testrec2 == 2 // 1868 men (neg without HIV test in previous year)
replace uHIVunk = 1 if HIVnew2 == 1 & testrec2 == 2  //58 men (as yet undiagnosed HIV infection of unknown duration)
replace uHIVunk = . if city == 9  // Sofia does not have test date information
lab var uHIVunk "HIV negative & previously undiagnosed (yet not incident) cases"
label define uHIVunk_L 0 "negative (but not incident)" 1 "previously undiagnosed (and not incident)"
label val uHIVunk uHIVunk_L





**** Tab1
tab city HIVnew2, row
tab city q14 if HIVnew2 < 3, m row
tab city testrec2 if HIVnew<3, row
tab city uHIVinc
tab city uHIVunk
tab city HIVnew2


***** Tab2
tab q31 uHIVunk, m
tab q31 uHIVinc, m
tab q31 HIVnew2 if city !=9, m


*/ 
*** Tab 3 and 4 for uHIV ***


tab agerec10um HIVnew2, col
tab q5_Rec1 HIVnew2, col
tab Migration_Status HIVnew2, col
tab q6bR HIVnew2, col
tab q7_Recode_ULI HIVnew2, col
*tab q9 HIVnew2, col
*tab q10 HIVnew2, col
tab q12 HIVnew2, col
tab q13_total HIVnew2, col
tab q13_bin HIVnew2, col
tab GARPR1_13 HIVnew2, col
*tab q14 HIVnew2, col
tab partnumsexcat HIVnew2, col
tab partnumuaicat HIVnew2, col
tab partner_all HIVnew2, col
*tab GARPR1_12 HIVnew2, col
tab sexpract HIVnew2, col
tab q26_weight HIVnew2, col
tab	sexrole	HIVnew2,	col
tab serocomm HIVnew2, col
tab num_drugs HIVnew2, col
*tab anydrug2 HIVnew2, col
tab party_2 HIVnew2, col
tab chemsex HIVnew2, col
tab sps HIVnew2, col
tab cannabis HIVnew2, col
tab alcohol HIVnew2, col
tab q36R HIVnew2, col
*tab concord HIVnew2, col

/** city
gen city_p1 = city 
replace city_p1 = 0 if city == 6
lab var city city_L
*/

gen HIVnew2_p1 = HIVnew2
replace HIVnew2_p1 = 0 if HIVnew2 == 2
label define HIVnew2_p1_L 0 "HIV-negative" 1 "undiagnosed" 
lab val HIVnew2_p1 HIVnew2_p1_L

*logit HIVnew2_p1 i.city, or
logit HIVnew2_p1 i.agerec10um, or
logit HIVnew2_p1 i.q5_Rec1, or
logit HIVnew2_p1 i.Migration_Status, or
logit HIVnew2_p1 i.q6bR, or
logit HIVnew2_p1 i.q7_Recode_ULI, or
logit HIVnew2_p1 ib2.q12, or
logit HIVnew2_p1 i.q13_total, or
logit HIVnew2_p1 i.q13_bin, or
*logit HIVnew2_p1 i.GARPR1_11, or
*logit HIVnew2_p1 i.GARPR1_12, or
logit HIVnew2_p1 i.GARPR1_13, or
logit HIVnew2_p1 i.partnumsexcat, or
logit HIVnew2_p1 i.partnumuaicat, or
logit HIVnew2_p1 i.partner_all, or
logit HIVnew2_p1 i.sexpract, or
logit HIVnew2_p1 i.q26_weight, or
logit HIVnew2_p1 i.sexrole, or
logit HIVnew2_p1 i.serocomm, or
logit HIVnew2_p1 i.num_drugs, or
logit HIVnew2_p1 i.party_2, or
logit HIVnew2_p1 i.chemsex, or
logit HIVnew2_p1 i.sps, or
logit HIVnew2_p1 i.cannabis, or
logit HIVnew2_p1 i.alcohol, or
logit HIVnew2_p1 ib1.q36R, or
*******************************************
* START MODELING 
*******************************************



melogit HIVnew2_p1 i.agerec10um, or
estimates store empty


***** add random intercept at city level
melogit HIVnew2_p1 i.agerec10um || city:, or
estimates store emptycity

lrtest empty emptycity, stats dir force

melogit HIVnew2_p1 i.agerec10um ib2.GARPR1_13 || city:, or
estimates store ctq14
testparm ib2.GARPR1_13

lrtest emptycity ctq14, stats dir force

melogit HIVnew2_p1 i.agerec10um ib2.GARPR1_13 i.partnumuaicat || city:, or
estimates store ctq14p_uai
testparm ib2.GARPR1_13
testparm i.partnumuaicat

lrtest ctq14 ctq14p_uai, stats dir force


melogit HIVnew2_p1 i.agerec10um ib2.GARPR1_13 i.partnumuaicat i.sps || city:, or
estimates store ctq14p_uaiq30sps
testparm ib2.GARPR1_13
testparm i.partnumuaicat
testparm i.sps

lrtest ctq14p_uai ctq14p_uaiq30sps, stats dir force


* Final model**
melogit HIVnew2_p1 ib1.agerec10um ib2.GARPR1_13 i.partnumuaicat i.sps ||city:, or


***************************
* separate Analysis for incident undiagnosed infections (last negative HIV test within last 12 months)
* and undiagnosed infection with last negative HIV test longer ago 
**************************************************


/*
gen uHIVun2 = .
replace uHIVun2 = 0 if HIVnew2 == 2 & ((q31 < 2007 | q31 ==.)& age25 == 2) // 
replace uHIVun2 = 1 if HIVnew2 == 1 & ((q31 < 2007 | q31 ==.)& age25 == 2)
replace uHIVun2 = 1 if q32 == . & q31a == 2 & hiv_status == 3 & ((q31 < 2007 | q31 ==.)& age25 == 2) // 13 men without previous test information
replace uHIVun2 = . if city == 9  // Sofia does not have test date information
lab var uHIVun2 "HIV negative & previously undiagnosed (long untested) cases"
label define uHIVun2_L 0 "negative (last test <2007)" 1 "previously undiagnosed (last test <2007)"
label val uHIVun2 uHIVun2_L

tab q31 uHIVun2, m

logit uHIVun2 i.city, or
logit uHIVun2 i.agerec10um, or
logit uHIVun2 i.q5_Rec1, or
logit uHIVun2 i.q6bR, or
logit uHIVun2 i.q7_Recode_ULI, or   // outness
logit uHIVun2 i.q12, or
*logit uHIVun2 i.GARPR1_11, or
*logit uHIVun2 i.GARPR1_12, or
logit uHIVun2 i.GARPR1_13, or
logit uHIVun2 i.q13_total, or
logit uHIVun2 i.q13_bin, or
logit uHIVun2 i.partnumsexcat, or
logit uHIVun2 i.partnumuaicat, or
logit uHIVun2 i.sexrole, or
logit uHIVun2 i.num_drugs, or
logit uHIVun2 i.party_2, or
logit uHIVun2 i.alcohol, or
logit uHIVun2 i.cannabis, or
logit uHIVun2 i.sps, or
logit uHIVun2 i.chemsex, or
logit uHIVun2 i.serocomm, or
logit uHIVun2 i.Migration_Status, or
logit uHIVun2 i.partner_all, or
logit uHIVun2 i.sexpract, or
logit uHIVun2 ib1.q36R, or
logit uHIVun2 i.q26_weight, or

melogit uHIVun2 i.agerec10um i.partnumuaicat i.q12 || city: ,or

*/



**** Tab 3 and 4 for uHIVinc *****


logit uHIVinc i.agerec10um, or
logit uHIVinc i.q5_Rec1, or
logit uHIVinc i.Migration_Status, or
logit uHIVinc i.q6bR, or
logit uHIVinc i.q7_Recode_ULI, or
*logit uHIVinc i.q8aR, or
*logit uHIVinc i.q8bR, or
*logit uHIVinc i.q8cR, or
logit uHIVinc ib2.q12, or
*logit uHIVinc i.GARPR1_11, or
*logit uHIVinc i.GARPR1_12, or
logit uHIVinc i.q13_bin, or
logit uHIVinc i.q13_total, or
*logit uHIVinc i.GARPR1_13, or
logit uHIVinc i.partnumsexcat, or
logit uHIVinc i.partnumuaicat, or
logit uHIVinc i.partner_all, or
logit uHIVinc i.sexpract, or
logit uHIVinc i.q26_weight, or
logit uHIVinc i.sexrole, or
logit uHIVinc i.serocomm, or
logit uHIVinc i.num_drugs, or
logit uHIVinc i.party_2, or
logit uHIVinc i.chemsex, or
logit uHIVinc i.sps, or
logit uHIVinc i.cannabis, or
logit uHIVinc i.alcohol, or
logit uHIVinc ib1.q36R, or


melogit uHIVinc i.agerec10um i.q6bR i.sexrole i.party_2 i.sps ib1.serocomm || city: ,or


melogit uHIVinc i.agerec10um i.sexrole i.party_2 i.sps ib1.serocomm || city: ,or


*** Tab 3 and 4 for uHIVunk *****


*logit uHIVunk i.city, or
logit uHIVunk i.agerec10um, or
logit uHIVunk i.q5_Rec1, or
logit uHIVunk i.Migration_Status, or
logit uHIVunk i.q6bR, or
logit uHIVunk i.q7_Recode_ULI, or   // outness
logit uHIVunk ib2.q12, or
*logit uHIVunk i.GARPR1_11, or
*logit uHIVunk i.GARPR1_12, or
*logit uHIVunk i.GARPR1_13, or
logit uHIVunk i.q13_total, or
logit uHIVunk i.q13_bin, or
logit uHIVunk i.partnumsexcat, or
logit uHIVunk i.partnumuaicat, or
logit uHIVunk i.partner_all, or
logit uHIVunk i.sexpract, or
logit uHIVunk i.q26_weight, or
logit uHIVunk i.sexrole, or
logit uHIVunk i.serocomm, or
logit uHIVunk i.num_drugs, or
logit uHIVunk i.party_2, or
logit uHIVunk i.chemsex, or
logit uHIVunk i.sps, or
logit uHIVunk i.cannabis, or
logit uHIVunk i.alcohol, or
logit uHIVunk ib1.q36R, or


melogit uHIVunk i.agerec10um i.partnumuaicat ib2.q12 || city: ,or