ABM_HPV

extensions [nw]
;extensions [r]


globals [
  infection-chance  ;; The chance out of 100 that an infected person will pass on
                    ;;   infection during one week of couplehood.
  symptoms-show     ;; How long a person will be infected before symptoms occur
                    ;;   which may cause the person to get tested.
  slider-check-1    ;; Temporary variables for slider values, so that if sliders
  slider-check-2    ;;   are changed on the fly, the model will notice and
;  slider-check-3    ;;   change people's tendencies appropriately.
  slider-check-4
  initial-people
  vaccine-rate
  vaccine-type
  recruitment-rate
  natural-death-rate
  cc-death-rate
  time              ;; time in weeks
  year
  infected
  population
  n
  num
  ]

breed [women woman]
breed [men man]

turtles-own [
  infected?          ;; If true, the person is infected.  It may be known or unknown.
  known?             ;; If true, the infection is known (and infected? must also be true).
  sane?
  vaccinated?
  cancer?
  virus-type         ;; Stands for virus type 1,2,3 or 4 depending on what family pf hpv does it goes alpha 11 , 7, 6, 5 respectively
  infection-length   ;; How long the person has been infected.
  coupled?           ;; If true, the person is in a sexually active couple.
  couple-length      ;; How long the person has been in a couple.
  ;; the next four values are controlled by sliders
  commitment         ;; How long the person will stay in a couple-relationship.
  coupling-tendency  ;; How likely the person is to join a couple.
  test-frequency     ;; Number of times a person will get tested per year.
  partner            ;; The person that is our current partner in a couple.
  promiscuity        ;; It measures roughly in a scale of 0 to 1, meaning 0 is monogamous and 1 poligamous (completely promiscuous)
  coupling-efectivity ;;Based on the principle that "el que liga más, liga más"
  age
  stage
  vaccine-lenght
]

;;;
;;; SETUP PROCEDURES
;;;

to setup
  clear-all
  setup-globals
  setup-people
  reset-ticks
end 

to setup-globals
  set infection-chance 80    ;;hay que revisar la probabilidad de infección en la literatura
  set symptoms-show 200.0    ;; lo mismo para el tiempo de infeccion
  set slider-check-1 average-commitment
  set slider-check-2 average-coupling-tendency
  set slider-check-4 average-test-frequency
  set vaccine-rate vr
  set vaccine-type vaccine
  set time 0
  set recruitment-rate 0.75
  set natural-death-rate 0.524
  set cc-death-rate 0.0012
  set year 0
  set population (initial-men + initial-women)
end 

to setup-people
  set initial-people  initial-women + initial-men
  create-women initial-women
  ask women [ifelse version ="people"[set shape "person righty"][set shape "triangle"]]
  create-men initial-men
  ask men [ifelse version ="people"[set shape "person lefty" ][set shape "circle"]]
  ask turtles [set vaccinated? false set infected? false set sane? true set cancer? false]
  ask n-of (floor(initial-women * vaccine-rate)) women [set vaccinated? true]
  ask n-of (floor((count turtles with [vaccinated? = false]) * random-float 1)) turtles with [vaccinated? = false][set infected? true]
  ask turtles[ setxy random-xcor random-ycor
      set known? false
      set coupled? false
      set partner nobody
      set promiscuity random-float 1
      set coupling-efectivity random-float 1
      set age 13 + random 47
      if vaccinated? = true [set vaccine-lenght random 5]
      if infected? = true  [ set virus-type random 4   set infection-length random-float symptoms-show ]
      assign-commitment
      assign-coupling-tendency
      assign-test-frequency]
ask women [assign-woman-color]
ask men [assign-man-color
   if vaccine-type = "vac3"[ask n-of (initial-men * vaccine-rate) men [set vaccinated? true ]]]
end 

;; Different people are displayed in 4 different colors depending on health
;; green is not infected
;; blue is infected but doesn't know it
;; red is infected and knows it
;; grey is vaccinated

to assign-man-color  ;; turtle procedure
  ask men [ifelse infected? = true [ifelse known? = true[ set color red + 2  ][set color blue + 2]][ set color green + 2]]
;  ask men [ifelse infected? = true and Known? = true[ set color red + 0.2  ][set color green + 0.2]]
 ; ask men[if infected? = true and known? = false [ set color blue + 0.2] ]
end 

to assign-woman-color  ;; turtle procedure
  ask women [ifelse infected? = true [ifelse known? = true[ set color red - 2  ][set color blue - 2]][ set color green - 2]]
;  ask women [if sane? = true ]
;;  ask women[ if infected? = true and known? = false  ]
end 

to getSick
 if infected? = true [set stage 1]
 if infection-length >  50 and random 12 < 6 [set stage 2]
 if infection-length > 150 and random 12 = 11[set stage 3]
 if stage = 3 and random 12 < 11 [set cancer? true]
 if cancer? = true and random 12 = 11[die set pcolor black]
end 


;; The following four procedures assign core turtle variables.  They use
;; the helper procedure RANDOM-NEAR so that the turtle variables have an
;; approximately "normal" distribution around the average values set by
;; the sliders.

to assign-commitment  ;; turtle procedure
  set commitment random-near average-commitment
end 

to assign-coupling-tendency  ;; turtle procedure
  set coupling-tendency random-near average-coupling-tendency
end 

;to assign-condom-use  ;; turtle procedure
;  set condom-use random-near average-condom-use
;end

to assign-test-frequency  ;; turtle procedure
  set test-frequency random-near average-test-frequency
end 

to-report random-near [center]  ;; turtle procedure
  let result 0
  repeat 40
    [ set result (result + random-float center) ]
  report result / 20
end 

;; Recruitment hay que cambiar como se hace el reclutamiento,debe asignarse a estas tortugas las variables

to new-year
  if time = 52 [cp set time 0  set year year + 1 ask n-of (floor(natural-death-rate * population)) turtles [die set pcolor black]
    create-women 0.51 * initial-people * recruitment-rate  create-men 0.49 * initial-people * recruitment-rate
  ask women with  [xcor = 0 and ycor = 0 ][ifelse version ="people"[set shape "person righty"][set shape "triangle"]]
  ask men with [xcor = 0 and ycor = 0 ][ifelse version ="people"[set shape "person lefty"][set shape "circle"]]
  ask turtles with [xcor = 0 and ycor = 0 ][set vaccinated? false set infected? false set sane? true set cancer? false]
  ask n-of (floor((count women with [xcor = 0 and ycor = 0]) * vaccine-rate)) women with [xcor = 0 and ycor = 0 ] [set vaccinated? true]
;  ask n-of (floor(initial-women * vaccine-rate)) women [set vaccinated? true]
  ask n-of (floor((count turtles with [xcor = 0 and ycor = 0 and vaccinated? = false]) * random-float 1)) turtles with [xcor = 0 and ycor = 0 and vaccinated? = false][set infected? true]
  ask turtles with [xcor = 0 and ycor = 0 ][ setxy random-xcor random-ycor
      set known? false
      set coupled? false
      set partner nobody
      set promiscuity random-float 1
      set coupling-efectivity random-float 1
      set age 13 + random 47
      if vaccinated? = true [set vaccine-lenght random 5]
      if infected? = true  [ set virus-type random 4   set infection-length random-float symptoms-show ]
      assign-commitment
      assign-coupling-tendency
 ;     assign-condom-use
      assign-test-frequency]
ask women [assign-woman-color]
ask men [assign-man-color
   if vaccine-type = "vac3"[ask n-of (initial-men * vaccine-rate) men [set vaccinated? true ]]]]
end 


;;;
;;; GO PROCEDURES
;;;

to go
   if all? turtles [known? = true]
    [ stop ]
  check-sliders
  ask patches[if turtles-here = 0 [set pcolor black]]
  ask turtles
    [ if infected? = true
        [ set infection-length infection-length + 1 ]
      if coupled? = true
        [ set couple-length couple-length + 1 ] ]
  ask turtles
    [ if coupled? = false
        [ move ] ]
  ;; Righties are always the ones to initiate mating.  This is purely
  ;; arbitrary choice which makes the coding easier.
  ask women
    [ if coupled? = false and (random-float 10.0 < coupling-tendency)
        [ couple ] ]
  ask turtles [ uncouple ]
  ask turtles [ infect ]
  ask turtles [ test ]
  ask turtles [getSick]
  ask men [ assign-man-color ]
  ask women [ assign-woman-color ]
  ;file-open "red_contactos.txt"
  nw:set-context turtles links
  ;ask women [ file-write  map sort nw:get-context ]
  tick
  set time time + 1
  new-year
  ask turtles [set age age + year]
  set population (count turtles)
  ask turtles with [coupled? = true][if partner = nobody[set coupled? false]]
  set n  random 100
  set num (word n)
  if time = 50 [nw:save-matrix (word "matriz"  num  ".txt")]
end 

;; Each tick a check is made to see if sliders have been changed.
;; If one has been, the corresponding turtle variable is adjusted

to check-sliders
  if (slider-check-1 != average-commitment)
    [ ask turtles [ assign-commitment ]
      set slider-check-1 average-commitment ]
  if (slider-check-2 != average-coupling-tendency)
    [ ask turtles [ assign-coupling-tendency ]
      set slider-check-2 average-coupling-tendency ]
  if (slider-check-4 != average-test-frequency )
    [ ask turtles [ assign-test-frequency ]
      set slider-check-4 average-test-frequency ]
end 

;; People move about at random.

to move  ;; turtle procedure
  ifelse version = "people" [rt random-float 360  fd 1] [fd 1]
end 

;; People have a chance to couple depending on their tendency to have sex and
;; if they meet.  To better show that coupling has occurred, the patches below
;; the couple turn gray.

to couple  ;; turtle procedure -- righties only!
  let potential-partner one-of (men-at -1 0)
                          with [coupled? = false]
  if potential-partner != nobody
    [ if random-float 10.0 < [coupling-tendency] of potential-partner and coupling-efectivity > 0.6
      [ set partner potential-partner
        if relacion = true [create-link-with partner]
        set coupled? true
        ask partner [ set coupled? true ]
        ask partner [ set partner myself ]
        move-to patch-here ;; move to center of patch
        ask potential-partner [move-to patch-here] ;; partner moves to center of patch
        set pcolor gray - 3
        ask (patch-at -1 0) [ set pcolor gray - 3 ] ] ]
    if turtles-here = nobody [set pcolor black]
end 

;; If two peoples are together for longer than either person's commitment variable
;; allows, the couple breaks up.

to uncouple  ;; turtle procedure
  ask women [if coupled? = true
    [ if (couple-length > commitment) or
         ([couple-length] of partner) > ([commitment] of partner) or promiscuity > 0.7
        [ set coupled? false
          set couple-length 0
          ask partner [ set couple-length 0 ]
          set pcolor black
          ask (patch-at -1 0) [ set pcolor black ]
          ask partner [ set partner nobody ]
          ask partner [ set coupled? false ]
          set partner nobody ] ]]
end 

;; Infection can occur if either person is infected, but the infection is unknown.
;; This model assumes that people with known infections will continue to couple,
;; but will automatically practice safe sex, regardless of their condom-use tendency.
;; Note also that for condom use to occur, both people must want to use one.  If
;; either person chooses not to use a condom, infection is possible.  Changing the
;; primitive to AND in the third line will make it such that if either person
;; wants to use a condom, infection will not occur.

to infect  ;; turtle procedure
  if coupled? = true and infected? = true and  known? = false and vaccinated? = false
        [ if random-float 100 < infection-chance
            [ ask partner [ set infected? true ] ] ] ;]

   if vaccine-type = "vac1"[
   if coupled? = true and infected? = true and  known? = false and [vaccinated?] of partner = true and [vaccine-lenght] of partner < 2 and virus-type > 2
        [ if random-float 100 < infection-chance
            [ ask partner [ set infected? true ] ] ] ]

   if vaccine-type = "vac2"[
   if coupled? = true and infected? = true and  known? = false and [vaccinated?] of partner = true and [vaccine-lenght] of partner < 2 and virus-type = 3
         [ if random-float 100 < infection-chance
            [ ask partner  [set infected? true ] ] ] ];]
end 


;; People have a tendency to check out their health status based on a slider value.
;; This tendency is checked against a random number in this procedure. However, after being infected for
;; some amount of time called SYMPTOMS-SHOW, there is a 5% chance that the person will
;; become ill and go to a doctor and be tested even without the tendency to check.

to test  ;; turtle procedure
  if random-float 52 < test-frequency
    [ if infected? = true
        [ set known? true ] ]
  if infection-length > symptoms-show
    [ if random-float 100 < 5
        [ set known? true ] ]
end 

;;;
;;; MONITOR PROCEDURES
;;;

to-report %infected
  ifelse any? turtles
    [ report (count turtles with [infected? = true] / count turtles) * 100 ]
    [ report 0 ]
end 

to-report %vaccinated
  ifelse any? women
    [ report (count women with [vaccinated? = true] / count women) * 100 ]
    [ report 0 ]
end 

to-report global-clustering-coefficient
  let closed-triplets sum [ nw:clustering-coefficient * count my-links * (count my-links - 1) ] of turtles
  let triplets sum [ count my-links * (count my-links - 1) ] of turtles
  report closed-triplets / triplets
end