# HIV and Polygamy

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; 6/30/10 - added simple birth and death rates ; 6/30/10 - added plots ; 8/10/10 - more plots ; - % on treatment (total; < 200; 200 - 350; 350 - 500) ; - Incidence (total; due to acute; due to chronic) ; - % infected (total; acute; chronic) ; - more inputs ; - treatment threshold (CD4 count) ; - entry rate ; - acute duration ; - initial percent infected ; - initial percent acute ; - proportion on treatment undirected-link-breed [ non-spousal-links non-spousal-link ] undirected-link-breed [ spousal-links spousal-link ] globals [ Pyramid f-add-prob ; item i of f-add-prob applies when node in state item i of R ; item i is a list [a b c] where a is the probability of not adding any links, b of a spousal link, and c of a non-spousal link m-add-prob ; similar for males P_m ;Transition Probability Matrix P_f ;Transition Probability Matrix R ;List of possible relationship combinations MtoF-ratio male-remarry-pos-odds ;odds and ever-married? infected will have a new relationship female-remarry-pos-odds sero-sorting-odds ;odds one chooses partner with same sero-status (is everything symmetric???) ever-married-pos-choose-polygamous-odds ; odds that ever-married HIV+/- women choose a husband who already has a partner ever-married-neg-choose-polygamous-odds F+M-divorce-odds ;relative risk of a discordant couple disolving F-M+divorce-odds relative-coital-freq number-of-female-nodes male-proportion-spousal female-proportion-spousal male-proportion-0 male-proportion-1 male-proportion-2 male-proportion-3 male-proportion-4 female-proportion-0 female-proportion-1 female-proportion-2 female-proportion-3 female-proportion-4 entry-rate-m ;ignored here entry-rate-f spousal-change-rate non-spousal-change-rate t-hat t-hat-probs m15 m16 m17 m18 m19 m20 m21 m22 m23 m24 m25 m26 m27 m28 m29 m30 m31 m32 m33 m34 m35 m36 m37 m38 m39 m40 m41 m42 m43 m44 m45 m46 m47 m48 m49 f15 f16 f17 f18 f19 f20 f21 f22 f23 f24 f25 f26 f27 f28 f29 f30 f31 f32 f33 f34 f35 f36 f37 f38 f39 f40 f41 f42 f43 f44 f45 f46 f47 f48 f49 total-deaths curr-component-size ; for recursion component-size ; list of component sizes (one per component) outside-death-rate current-yearly-incidence current-yearly-incidence-acute current-yearly-incidence-chronic current-yearly-incidence-final current-yearly-incidence->1-partner current-yearly-incidence-1-partner current-yearly-incidence-non-spousal current-yearly-incidence-spousal cum-infections cum-infections-acute run-number ] to startup carefully [ file-open "default.txt" while [not file-at-end?] [ run file-read-line ] file-close ] [print error-message] set male-proportion-4 0 set female-proportion-4 0 end turtles-own [ randnum num-partners num-non-spousal-partners num-spousal-partners num-non-spousal-missing num-spousal-missing num-non-spousal-requests num-spousal-requests ever-married? ;actually both types of relationships age-years age-months female? infected? explored? ; HIV Variables stage-3-indicator months-since-infected months-left-to-live infectivity HIV-stage CD4-count-original CD4-count-present CD4-at-treatment CD4-decline-rate-no-treatment on-treatment? eligible-for-treatment? failed-treatment? time-on-treatment HAART-supp-death-rate ] to go age deaths-births progress-disease put-on-treatment spread-HIV change-relationships find-all-components plot-statistics tick ;if ticks = 120 [ stop ] ;if current-incidence != current-incidence-acute + current-incidence-chronic [ stop ] end to setup-keep setup set run-number run-number + 1 end to setup-clear clear-drawing clear-all-plots clear-output call-globals setup set run-number 1 end to setup clear-patches ask patches [set pcolor white] ; turns world white auto-plot-on set-default-shape turtles "person" ; let tuned-prob-file (word scenario "T.txt") ; ifelse (file-exists? tuned-prob-file) [ ; file-open tuned-prob-file ; while [not file-at-end?] [ run file-read-line ] ; file-close ; ] [ ;otherwise tune probabilities and write them to file clear-turtles reset-ticks setup-nodes initialize-HIV-population put-on-treatment ask non-spousal-links [set color black] ask spousal-links [set color red] ask turtles [set size 10 ] repeat 120 [ age deaths-births progress-disease put-on-treatment spread-HIV change-relationships tweak-probs tick ] ; file-open tuned-prob-file ; file-print (word "set m-add-prob " m-add-prob) ; file-print (word "set f-add-prob " f-add-prob) ; file-close ; ] clear-turtles reset-ticks setup-nodes initialize-HIV-population put-on-treatment ask non-spousal-links [set color black] ask spousal-links [set color red] ask turtles [set size 10 ] set cum-infections 0 set cum-infections-acute 0 find-all-components end ; tweaks the new relationship probabilities to better match the desired distribution ; uses simulation optimization to tweak-probs let m-props (list male-proportion-0 male-proportion-1 male-proportion-2 male-proportion-3) let f-props (list female-proportion-0 female-proportion-1 female-proportion-2 female-proportion-3) let f-curr-probs (n-values 4 [count turtles with [female? and num-partners = ?] / count turtles with [female?]]) let m-curr-probs (n-values 4 [count turtles with [not female? and num-partners = ?] / count turtles with [not female?]]) let f-ratio (map [(?2 + 1) / (?1 + 1)] f-props f-curr-probs) let m-ratio (map [(?2 + 1) / (?1 + 1)] m-props m-curr-probs) let new-m-add-prob [] let new-f-add-prob [] (foreach R m-add-prob f-add-prob [ let partner-num (sum ?1) let f-ratio-num (item partner-num f-ratio) let m-ratio-num (item partner-num m-ratio) let m-prob-1 ((item 1 ?2) * m-ratio-num) let m-prob-2 ((item 2 ?2) * m-ratio-num) let f-prob-1 ((item 1 ?3) * f-ratio-num) let f-prob-2 ((item 2 ?3) * f-ratio-num) let m-prob (list (1 - m-prob-1 - m-prob-2) m-prob-1 m-prob-2) let f-prob (list (1 - f-prob-1 - f-prob-2) f-prob-1 f-prob-2) set new-m-add-prob (lput m-prob new-m-add-prob) set new-f-add-prob (lput f-prob new-f-add-prob) ]) set m-add-prob new-m-add-prob set f-add-prob new-f-add-prob end to ignore [stuff] end to call-globals file-open (word scenario "P.txt") ignore file-read-line set P_f file-read ignore file-read-line set P_m file-read file-close ; let Pyramid [] ; carefully [ ; file-open "default.txt" ; while [not file-at-end?] [ ; run file-read-line ; ] ; file-close ; ] [print error-message] file-open (word scenario ".txt") while [not file-at-end?] [ run file-read-line ] file-close foreach Pyramid [ let lower item 0 ? let upper item 1 ? let m item 2 ? let f item 3 ? ;show lower show upper show m show f (foreach (n-values (upper - lower + 1) [word "m" (? + lower)]) (n-values (upper - lower + 1) [word "f" (? + lower)]) [ run ((word "set " ?1 word " " (m / (upper - lower + 1)))) run ((word "set " ?2 word " " (f / (upper - lower + 1)))) ]) ] ; create m-add-prob and f-add-prob here (should probably be done in matlab and in the P files) set m-add-prob [] set f-add-prob [] (foreach R P_m P_f [ ; R entry is current state let new-state-1 (position (list ((item 0 ?1) + 1) (item 1 ?1)) R) ; index into R with extra spouse let new-state-2 (position (list (item 0 ?1) ((item 1 ?1) + 1)) R) ; index into R with extra non-spouse let m-prob-1 0 let f-prob-1 0 let m-prob-2 0 let f-prob-2 0 if new-state-1 != false [ set m-prob-1 (item new-state-1 ?2) set f-prob-1 (item new-state-1 ?3) ] if new-state-2 != false [ set m-prob-2 (item new-state-2 ?2) set f-prob-2 (item new-state-2 ?3) ] let m-prob (list (1 - m-prob-1 - m-prob-2) m-prob-1 m-prob-2) let f-prob (list (1 - f-prob-1 - f-prob-2) f-prob-1 f-prob-2) set m-add-prob (lput m-prob m-add-prob) set f-add-prob (lput f-prob f-add-prob) ]) set current-yearly-incidence 0 set current-yearly-incidence-acute 0 set current-yearly-incidence-chronic 0 end to turtles-own-default set ever-married? (any? my-links) set infected? false ;; HIV Variables set months-since-infected 0 set months-left-to-live 0 set infectivity 0 set HIV-stage 0 set on-treatment? false set eligible-for-treatment? false set failed-treatment? false set time-on-treatment 0 set HAART-supp-death-rate 0 ;; Set CD4-count-present set CD4-count-original exp ((ln 1116) + ((random-normal 0 1) * .303)) set CD4-count-present CD4-count-original set CD4-decline-rate-no-treatment 0 set stage-3-indicator 0 end to make-male setxy (random-xcor * .95) (random-ycor * .95) set color blue set female? false end to make-female setxy (random-xcor * .95) (random-ycor * .95) set color pink set female? true end to setup-nodes crt number-of-male-nodes [ make-male ] ask turtles [ set num-partners 0 set num-non-spousal-partners 0 set num-spousal-partners 0 ] let last-cut-off 0 let current-cut-off round(male-proportion-0 * number-of-male-nodes) (foreach (list (male-proportion-1) (male-proportion-2) (male-proportion-3) (male-proportion-4)) ([1 2 3 4]) [ set last-cut-off current-cut-off set current-cut-off (last-cut-off + round(number-of-male-nodes * (?1 / (1 - male-proportion-0)) * (1 - male-proportion-spousal - male-proportion-0))) ;show (word last-cut-off " " current-cut-off) ask turtles with [who + 1 > last-cut-off and who + 1 <= current-cut-off] [ set num-partners ?2 set num-non-spousal-partners ?2 set num-spousal-partners 0 ] ]) (foreach (list (male-proportion-1) (male-proportion-2) (male-proportion-3) (male-proportion-4)) ([0 1 2 3]) [ set last-cut-off current-cut-off set current-cut-off (last-cut-off + round(number-of-male-nodes * (?1 / (1 - male-proportion-0)) * male-proportion-spousal)) ;show (word last-cut-off " " current-cut-off) ask turtles with [who + 1 > last-cut-off and who + 1 <= current-cut-off] [ set num-partners ?2 + 1 set num-non-spousal-partners ?2 set num-spousal-partners 1 ] ]) ; create female turtles to match number of links of male turtles let number-of-male-links (count turtles with [not female? and num-partners = 1]) + 2 * (count turtles with [not female? and num-partners = 2]) + 3 * (count turtles with [not female? and num-partners = 3]) + 4 * (count turtles with [not female? and num-partners = 4]) set number-of-female-nodes round(number-of-male-links / ((female-proportion-1 + 2 * female-proportion-2 + 3 * female-proportion-3 + 4 * female-proportion-4))) ; define female-proportion-spousal set female-proportion-spousal ((number-of-male-nodes * male-proportion-spousal) / number-of-female-nodes) crt number-of-female-nodes [ make-female ] ask turtles with [female?] [ set num-partners 0 set num-non-spousal-partners 0 set num-spousal-partners 0 ] set last-cut-off 0 set current-cut-off round(female-proportion-0 * number-of-female-nodes) (foreach (list (female-proportion-1) (female-proportion-2) (female-proportion-3) (female-proportion-4)) ([1 2 3 4]) [ set last-cut-off current-cut-off set current-cut-off (last-cut-off + round(number-of-female-nodes * (?1 / (1 - female-proportion-0)) * (1 - female-proportion-spousal - female-proportion-0))) ;show (word last-cut-off " " current-cut-off) ask turtles with [who + 1 - number-of-male-nodes > last-cut-off and who + 1 - number-of-male-nodes <= current-cut-off] [ set num-partners ?2 set num-non-spousal-partners ?2 set num-spousal-partners 0 ] ]) (foreach (list (female-proportion-1) (female-proportion-2) (female-proportion-3) (female-proportion-4)) ([0 1 2 3]) [ set last-cut-off current-cut-off set current-cut-off (last-cut-off + round(number-of-female-nodes * (?1 / (1 - female-proportion-0)) * female-proportion-spousal)) ;show (word last-cut-off " " current-cut-off) ask turtles with [who + 1 - number-of-male-nodes > last-cut-off and who + 1 - number-of-male-nodes <= current-cut-off] [ set num-partners ?2 + 1 set num-non-spousal-partners ?2 set num-spousal-partners 1 ] ]) ask turtles [ set num-non-spousal-missing num-non-spousal-partners set num-spousal-missing num-spousal-partners set age-years -1 set age-months -1 ] let number-of-female-links (count turtles with [female? and num-partners = 1]) + 2 * (count turtles with [female? and num-partners = 2]) + 3 * (count turtles with [female? and num-partners = 3]) + 4 * (count turtles with [female? and num-partners = 4]) ;show (word number-of-female-links " " number-of-male-links) ask turtles with [num-non-spousal-missing > 0 or num-spousal-missing > 0] [ while [num-spousal-missing > 0 and (any? other turtles with [(female? = not ([female?] of myself)) and num-spousal-missing > 0 and (link-neighbor? myself = false)])] [ ask one-of turtles with [(female? = not ([female?] of myself)) and num-spousal-missing > 0] [ create-spousal-link-with myself [ ask both-ends [set num-spousal-missing num-spousal-missing - 1] ] ] ] while [num-non-spousal-missing > 0 and (any? other turtles with [(female? = not ([female?] of myself)) and num-non-spousal-missing > 0 and (link-neighbor? myself = false)])] [ ask one-of turtles with [(female? = not ([female?] of myself)) and num-non-spousal-missing > 0] [ create-non-spousal-link-with myself [ ask both-ends [set num-non-spousal-missing num-non-spousal-missing - 1] ] ] ] ] ask turtles with [num-non-spousal-missing > 0] [ set num-partners num-partners - num-non-spousal-missing set num-non-spousal-partners num-non-spousal-partners - num-non-spousal-missing set num-spousal-missing 0 ] ask turtles with [num-spousal-missing > 0] [ set num-partners num-partners - num-spousal-missing set num-spousal-partners num-spousal-partners - num-spousal-missing set num-non-spousal-missing 0 ] (foreach (n-values 35 [runresult (word "m" (? + 15))]) (n-values 35 [? + 15]) [ ask n-of (min (list (round(number-of-male-nodes * ?1)) (count turtles with [age-years = -1 and not female?]))) turtles with [age-years = -1 and not female?] [ set age-months (?2 * 12 + (random 12)) set age-years (age-months / 12) ] ]) (foreach (n-values 35 [runresult (word "f" (? + 15))]) (n-values 35 [? + 15]) [ ask n-of (min (list (round(number-of-female-nodes * ?1)) (count turtles with [age-years = -1 and female?]))) turtles with [age-years = -1 and female?] [ set age-months (?2 * 12 + (random 12)) set age-years (age-months / 12) ] ]) ask non-spousal-links [set color black] ask spousal-links [set color red] ;; Initialize turtles with default turtles-own values ask turtles [ turtles-own-default ] end to change-relationships ; setup book keeping ask turtles [ set num-spousal-requests false set num-non-spousal-requests false ] ;deleting links ask non-spousal-links [ let multiplier 1 if (any? both-ends with [infected? and female?]) and (any? both-ends with [not infected? and not female?]) [ set multiplier F+M-divorce-odds ] if (any? both-ends with [not infected? and female?]) and (any? both-ends with [infected? and not female?]) [ set multiplier F-M+divorce-odds ] if ((random-float 1) < non-spousal-change-rate * multiplier) [ die ] ] ask spousal-links [ let multiplier 1 if (any? both-ends with [infected? and female?]) and (any? both-ends with [not infected? and not female?]) [ set multiplier F+M-divorce-odds ] if (any? both-ends with [not infected? and female?]) and (any? both-ends with [infected? and not female?]) [ set multiplier F-M+divorce-odds ] if ((random-float 1) < spousal-change-rate * multiplier) [ die ] ] ; creating requests for new links ask turtles [ let rownum (position (list num-spousal-partners num-non-spousal-partners) R) let pmf [] ifelse female? [ set pmf (item rownum f-add-prob) ] [ set pmf (item rownum m-add-prob) ] if ever-married? [ let multiplier 1 if infected? [ifelse female? [set multiplier female-remarry-pos-odds] [set multiplier male-remarry-pos-odds]] let p0 (item 0 pmf) set p0 (p0 / ((1 - p0) * multiplier + p0)) let p1 0 if p0 < 1 [set p1 ((1 - p0) * ((item 1 pmf) / (1 - (item 0 pmf))))] set pmf (list p0 p1 (1 - p0 - p1)) ] let change (random-discrete pmf) if change = 1 [ set num-spousal-requests true ] if change = 2 [ set num-non-spousal-requests true ] ] ; create links ask turtles with [ num-spousal-requests or num-non-spousal-requests ] [ if num-spousal-requests [ set num-spousal-requests false let eligible turtles with [ (female? = not [female?] of myself) ; opposite gender and num-spousal-requests and (link-neighbor? myself = false)] if any? eligible [ if female? and ever-married? [set eligible (ever-married-filter eligible)] set eligible (sero-sorting-filter eligible) ask one-of eligible [ create-spousal-link-with myself set num-spousal-requests false ] ] ] if num-non-spousal-requests [ set num-non-spousal-requests false let eligible turtles with [ (female? = not [female?] of myself) ; opposite gender and num-non-spousal-requests and (link-neighbor? myself = false)] if any? eligible [ if female? and ever-married? [set eligible (ever-married-filter eligible)] set eligible (sero-sorting-filter eligible) ask one-of eligible [ create-non-spousal-link-with myself set num-non-spousal-requests false ] ] ] ] ; update book keeping ask turtles [ set num-partners (count my-links) set num-spousal-partners (count my-spousal-links) set num-non-spousal-partners (count my-non-spousal-links) set ever-married? (ever-married? or num-partners >= 1) ] ask non-spousal-links [set color black] ask spousal-links [set color red] end to initialize-HIV-population ; This is the acute infection population let initial-percent-acute (item 0 t-hat-probs) * (acute-duration / 12) set t-hat-probs replace-item 0 t-hat-probs ((item 0 t-hat-probs) - initial-percent-acute) let adjustment-factor sum t-hat-probs (foreach (n-values acute-duration [?]) [ ask n-of round ((initial-percent-acute / acute-duration) * ((initial-percent-infected) * (count turtles))) turtles [ set months-since-infected ?1 become-infected set months-left-to-live (random-weibull 10.9522 2.25) + (acute-duration - ?1) set stage-3-indicator (months-left-to-live - acute-duration + ?1) * .1 set CD4-decline-rate-no-treatment (CD4-count-present * .75) / (months-left-to-live - acute-duration + ?1) set CD4-count-present CD4-count-present - (?1 * ((CD4-count-original * .25) / acute-duration)) ] ]) ; Now, we'll infect those in the chronic/final stages of HIV by... ; Determining how long ago when they seroconverted ; Determining how much longer they have to live ; Then determining the rate of CD4 decline and starting CD4 value by ; how much longer they are scheduled to live ask n-of ((initial-percent-infected * count turtles) - count turtles with [infected?]) turtles with [not infected?] [ become-infected let lower 0 let upper 0 set randnum random-float adjustment-factor (foreach t-hat-probs t-hat [ set lower upper set upper upper + ?1 if randnum < upper and randnum >= lower [ set months-since-infected ?2 * 12 set months-left-to-live (12 * 10.5922 * ((((?2 / 10.5922) ^ (2.25)) - ln (1 - random-float 1)) ^ (1 / 2.25))) - (?2 * 12) set CD4-decline-rate-no-treatment (CD4-count-original * .75) / (months-since-infected + months-left-to-live) set CD4-count-present (CD4-count-original * .75) - (CD4-decline-rate-no-treatment * months-since-infected) set stage-3-indicator .1 * (months-left-to-live + (?2 * 12)) ] ]) ] end to age ask turtles [ set age-months age-months + 1 set age-years age-months / 12 ] end to deaths-births let num-deaths 0 ask turtles [ ;; Note: deaths are not age/gender specific ; (not any? link-neighbors) and ; if ((random-float 1 < outside-death-rate + HAART-supp-death-rate) or (CD4-count-present <= 0) or (age-years >= 50)) [ ask my-links [ die ] set num-deaths (num-deaths + 1) set age-months 15 * 12 set age-years 15 turtles-own-default ] ] ;; Remember to reset num-partners, etc. after links disappear (this needs to be in separate block ;; since (ask turtles) performs code for each turtle and not in unison ask turtles [ set num-partners (count my-links) set num-spousal-partners (count my-spousal-links) set num-non-spousal-partners (count my-non-spousal-links) ] set total-deaths (total-deaths + num-deaths) set-current-plot "births and deaths" plot num-deaths end to progress-disease ask turtles with [infected?] [ determine-HIV-stage determine-CD4-count determine-infectivity determine-supp-death-rates set months-since-infected months-since-infected + 1 set months-left-to-live months-left-to-live - 1 ] end to determine-HIV-stage if (months-since-infected < acute-duration) [ set HIV-stage 1 ] if (months-since-infected >= acute-duration) [ if months-left-to-live < stage-3-indicator [ set HIV-stage 3 ] if months-left-to-live >= stage-3-indicator [ set HIV-stage 2 ] ] end to determine-infectivity ifelse (on-treatment?) [ set infectivity chronic-infectivity * treatment-infectivity-ratio ] [ if (HIV-stage = 1) [ set infectivity chronic-infectivity * acute-infectivity-ratio ] if (HIV-stage = 2) [ set infectivity chronic-infectivity ] if (HIV-stage = 3) [ set infectivity chronic-infectivity * final-infectivity-ratio ] ] if (num-partners > 1) [ set infectivity infectivity * (item (num-partners - 2) relative-coital-freq) ] if (not female?) [ set infectivity infectivity * MtoF-ratio ] end to determine-supp-death-rates ask turtles with [infected?] [ ifelse (on-treatment?) [ if CD4-at-treatment <= 25 [ set HAART-supp-death-rate .175 / 12 ] if CD4-at-treatment > 25 and CD4-at-treatment <= 50 [ set HAART-supp-death-rate .121 / 12 ] if CD4-at-treatment > 50 and CD4-at-treatment <= 100 [ set HAART-supp-death-rate .738 / 12 ] if CD4-at-treatment > 100 and CD4-at-treatment <= 200 [ set HAART-supp-death-rate .483 / 12 ] if CD4-at-treatment > 200 and CD4-at-treatment <= 250 [ set HAART-supp-death-rate .05 / 12 ] if CD4-at-treatment > 250 and CD4-at-treatment <= 350 [ set HAART-supp-death-rate .05 / 12 ] if CD4-at-treatment > 350 and CD4-at-treatment <= 500 [ set HAART-supp-death-rate .03 / 12 ] if CD4-at-treatment > 500 [ set HAART-supp-death-rate .015 / 12 ] ] [ set HAART-supp-death-rate 0 ] ] end to determine-CD4-count ifelse (on-treatment?) [ ifelse (failed-treatment?) [ set CD4-count-present CD4-count-present - CD4-decline-rate-no-treatment ] [ set CD4-count-present CD4-count-present ] ] [ ifelse (HIV-stage = 1) [ set CD4-count-present CD4-count-present - ((CD4-count-original * .25) / acute-duration) ] [ set CD4-count-present CD4-count-present - CD4-decline-rate-no-treatment ] ] end to spread-HIV if ((ticks mod 12) = 0) [ set current-yearly-incidence-acute 0 set current-yearly-incidence-chronic 0 set current-yearly-incidence-final 0 set current-yearly-incidence->1-partner 0 set current-yearly-incidence-1-partner 0 set current-yearly-incidence-non-spousal 0 set current-yearly-incidence-spousal 0 set current-yearly-incidence 0 ] ask turtles with [infected? = true] [ ask link-neighbors with [infected? = false] [ if random-float 1 < ([infectivity] of myself) [ become-infected set months-left-to-live (random-weibull 10.9522 2.25) + acute-duration set stage-3-indicator (months-left-to-live - acute-duration) * .1 set CD4-decline-rate-no-treatment (CD4-count-present * .75) / (months-left-to-live - acute-duration) set cum-infections cum-infections + 1 if (([HIV-stage] of myself) = 1) [ set current-yearly-incidence-acute current-yearly-incidence-acute + 1 set cum-infections-acute cum-infections-acute + 1 ] if (([HIV-stage] of myself) = 2) [ set current-yearly-incidence-chronic current-yearly-incidence-chronic + 1 ] if (([HIV-stage] of myself) = 3) [ set current-yearly-incidence-final current-yearly-incidence-final + 1 ] if (([num-partners] of myself) > 1) [ set current-yearly-incidence->1-partner current-yearly-incidence->1-partner + 1 ] if (([num-partners] of myself) = 1) [ set current-yearly-incidence-1-partner current-yearly-incidence-1-partner + 1 ] if (non-spousal-link-neighbor? myself) [ set current-yearly-incidence-non-spousal current-yearly-incidence-non-spousal + 1 ] if (spousal-link-neighbor? myself) [ set current-yearly-incidence-spousal current-yearly-incidence-spousal + 1 ] ] ] ] ;; Calculate Incidence set current-yearly-incidence current-yearly-incidence + (count turtles with [infected? and months-since-infected = 0]) end to become-infected set infected? true if female? = true [set color pink - 2] if female? = false [set color blue - 2] end to put-on-treatment ; tick time-on-treatment variable for those on treatment ask turtles with [on-treatment?] [ set time-on-treatment time-on-treatment + 1 ; determine if the treatment has failed ;if (not failed-treatment?) [ ; if (random-float 1 < treatment-failure-rate) [ ; set failed-treatment? true ; set months-left-to-live CD4-count-present / CD4-decline-rate-no-treatment ; ] ;] ] ask turtles with [infected? and months-left-to-live > 0 and (CD4-count-present < treatment-threshold) and (not failed-treatment?)] [ set eligible-for-treatment? true ] ;; a constant (maximum) fraction of the population will be on treatment if (any? turtles with [eligible-for-treatment?]) [ while [(count turtles with [on-treatment?] / count turtles with [eligible-for-treatment?]) < (proportion-on-treatment)] [ ask one-of turtles with [eligible-for-treatment? and (not on-treatment?)] [ set on-treatment? true set CD4-at-treatment CD4-count-present ] ] ] end to make-prettier ask links [set color white] ask turtles [set size 3] repeat 10 [ layout-spring turtles links .8 (world-width / (sqrt count turtles)) 4 ] end to set-plot-pen [plot-pen keep?] if keep? [ create-temporary-plot-pen word plot-pen run-number set-plot-pen-color black ] if (not keep?) [ set-current-plot-pen plot-pen if ticks = 0 [ plot-pen-reset ] ] end to plot-statistics set-current-plot "Women / Men" set-current-plot-pen "overall" plot count turtles with [female?] / count turtles with [not female?] set-current-plot-pen "prevalence" plot count turtles with [female? and infected?] / count turtles with [not female? and infected?] set-current-plot "Prevalence" set-plot-pen "All-HIV-Positive" true ;set-current-plot-pen "All-HIV-Positive" if (not draw-all-HIV-positives?) [ plot-pen-up ] if any? turtles with [infected?] [ plot count turtles with [infected?] / count turtles ] set-plot-pen "Acute" false if (not draw-acute?) [ plot-pen-up ] ifelse any? turtles with [HIV-stage = 1 and infected?] [ plot count turtles with [HIV-stage = 1 and infected?] / count turtles ] [ plot 0 ] set-plot-pen "Chronic" false if (not draw-chronic?) [ plot-pen-up ] ifelse any? turtles with [HIV-stage = 2 and infected?] [ plot count turtles with [HIV-stage = 2 and infected?] / count turtles ] [ plot 0 ] set-plot-pen "Final" false if (not draw-final?) [ plot-pen-up ] ifelse any? turtles with [HIV-stage = 3 and infected?] [ plot count turtles with [HIV-stage = 3 and infected?] / count turtles ] [ plot 0 ] if (ticks mod 12 = 0) [ set-current-plot "Incidence" set-plot-y-range 0 precision ((current-yearly-incidence / count turtles) + .05) 2 set-plot-pen "Incidence" false plot (current-yearly-incidence / count turtles) set-current-plot "Proportion of Incidence Due to HIV Stages" set-plot-pen "Acute" false ifelse current-yearly-incidence != 0 [plot current-yearly-incidence-acute / current-yearly-incidence] [plot 0] set-plot-pen "Chronic" false ifelse current-yearly-incidence != 0 [plot current-yearly-incidence-chronic / current-yearly-incidence] [plot 0] set-plot-pen "Final" false ifelse current-yearly-incidence != 0 [plot current-yearly-incidence-final / current-yearly-incidence] [plot 0] set-current-plot "Proporition of Incidence Due to Types of Partnerships" set-plot-pen "Non-Spousal" false ifelse current-yearly-incidence != 0 [plot current-yearly-incidence-non-spousal / current-yearly-incidence] [plot 0] set-plot-pen "Spousal" false ifelse current-yearly-incidence != 0 [plot current-yearly-incidence-spousal / current-yearly-incidence] [plot 0] set-current-plot "Proportion of Incidence Due to Concurrent Partnerships" set-plot-pen ">1 Partner" false ifelse current-yearly-incidence != 0 [plot current-yearly-incidence->1-partner / current-yearly-incidence] [plot 0] set-plot-pen "1 Partner" false ifelse current-yearly-incidence != 0 [plot current-yearly-incidence-1-partner / current-yearly-incidence] [plot 0] ] set-current-plot "Male Partnership Distribution" foreach n-values 4 [?] [ set-plot-pen (word ? " Partners") false plot count turtles with [(not female?) and (count my-links = ?)] / count turtles with [(not female?)] ] set-current-plot "Female Partnership Distribution" foreach n-values 4 [?] [ set-plot-pen (word ? " Partners") false plot count turtles with [(female?) and (count my-links = ?)] / count turtles with [(female?)] ] set-current-plot "Histogram of Years Left to Live" histogram [months-left-to-live / 12] of turtles with [infected?] set-current-plot "Histogram of Years Since Infected" histogram [months-since-infected / 12] of turtles with [infected?] set-current-plot "Mean CD4 Count at Treatment Initiation" set-plot-pen "CD4-count" false ifelse not any? turtles with [infected? and on-treatment?] [ plot 0 ] [ plot mean [CD4-at-treatment] of turtles with [infected? and on-treatment?] ] end to-report random-weibull [a b] report (a * ((- ln (1 - random-float 1)) ^ (1 / b)) * 12) end to-report random-discrete [pmf] ;returns discrete random variable with given pmf (0-based) let itemnum 0 let lower 0 let upper 0 let randval random-float 1 foreach pmf [ set upper upper + ? if (randval < upper and randval >= lower) [ report itemnum ] set lower upper set itemnum (itemnum + 1) ] end to-report ever-married-filter [eligible] ;we assume eligible is a non-empty agentset ;guaranteed to return a non-empty subset of eligible let withpartner eligible with [num-partners >= 1] let nopartner eligible with [num-partners = 0] let prob 0 ifelse infected? [ set prob ((count nopartner) / (ever-married-pos-choose-polygamous-odds * (count withpartner) + (count nopartner)))] [ set prob ((count nopartner) / (ever-married-neg-choose-polygamous-odds * (count withpartner) + (count nopartner)))] ifelse ((random-float 1) >= prob) [report withpartner] [report nopartner] end to-report sero-sorting-filter [eligible] ;we assume eligible is a non-empty agentset ;guaranteed to return a non-empty subset of eligible let same eligible with [infected? = [infected?] of myself] let diff eligible with [infected? = not [infected?] of myself] let prob ((count diff) / (sero-sorting-odds * (count same) + (count diff))) ifelse ((random-float 1) >= prob) [report same] [report diff] end ; based on Giant Component code from model library ;; to find all the connected components in the network, their sizes and starting turtles to find-all-components set component-size [] ask turtles [ set explored? false ] ;; keep exploring till all turtles get explored loop [ ;; pick a node that has not yet been explored let start one-of turtles with [ not explored? ] if start = nobody [ stop ] ;; reset the number of turtles found to 0 ;; this variable is updated each time we explore an ;; unexplored node. set curr-component-size 0 ask start [ explore ] set component-size (lput curr-component-size component-size) ] end ;; Finds all turtles reachable from this node to explore ;; node procedure if explored? [ stop ] set explored? true set curr-component-size curr-component-size + 1 ask link-neighbors [ explore ] end

There are 2 versions of this model.

## Attached files

File | Type | Description | Last updated | |
---|---|---|---|---|

default.txt | data | default parameters | over 5 years ago, by Benjamin Armbruster | Download |

HIV and Polygamy.png | preview | Preview for 'HIV and Polygamy' | over 5 years ago, by Benjamin Armbruster | Download |

scenarios.zip | data | Scenarios for paper | over 5 years ago, by Benjamin Armbruster | Download |

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