Report array of values from first tick NetLogo

Question

I'm writing some code to vaccinate individuals in a population where flu is circulating. The code has two kinds of vaccines named HOV and HEV. HOV gives an identical vaccine strain to the proportion of the population I want to target. HEV gives different vaccine strains (determined randomly) to this proportion.

I wanted a line of code that reports each turtle's immune status in the first tick of each simulation. Immune status is represented by an integer in this model, so different turtles will have different immune labels depending on whether or not they were vaccinated. I'm hoping to end up with a column containing the array of immune labels of all turtles in the first tick for each run in the final BehaviourSpace .csv output.

My code is below:

extensions [csv]
globals [strain_list_list epidemic-threshold cumulative-infections proportion-of-infection currently-infected peak-prevalence vax-strain]
turtles-own [infection-period infection-number tflu-strain immune-label ant-distance cross-immunity]
patches-own [fomite-age pflu-strain]

to setup
  clear-all
  setup-turtles
  reset-ticks
end

to setup-turtles
  create-turtles 100
  ask turtles [setxy random-xcor random-ycor]
  ask turtles [set color white set infection-number 0 set immune-label -999999999999 set tflu-strain -999999999999]
  ask one-of turtles [set color red set infection-period 0 set infection-number 1 set immune-label 0 set tflu-strain 0]
  if vaccine = "HOV" [
    ifelse (one-of [1 2] = 1) [
      set vax-strain (random ((2 * drift-size) + 1))]
    [set vax-strain (-1 * random ((2 * drift-size) + 1))]
  ask n-of prop-vax turtles with [color = white] [set color blue set immune-label vax-strain]
  ]
  if vaccine = "HEV" [
    let vax-turtles (list turtles with [color = blue])
    ask n-of prop-vax turtles with [color = white] [set color blue] 
    foreach [vax-turtles] [
      ifelse (one-of [1 2] = 1) [
      set vax-strain (random ((2 * drift-size) + 1))]
    [set vax-strain (-1 * random ((2 * drift-size) + 1))]
      ]
    ]
  set epidemic-threshold "no"
  set cumulative-infections 0
  set peak-prevalence 0
end

to go
  if ticks = flu-season-length [stop]
  move-infecteds
  move-uninfecteds
  transmit
  mutate
  update-immunity
  track-infecteds
  set cumulative-infections (count turtles with [infection-period = 1] + cumulative-infections)
  set proportion-of-infection (100 - (count turtles with [immune-label = -999999999999]))
  set currently-infected (count turtles with [infection-period = 1])
  tick
end

to move-infecteds ;; infected turtles move slower than uninfected ones and always transmit infection to patches before they leave them
  ask turtles with [color = red] [
  if pcolor = black [
      set pcolor red
    set fomite-age 0
    set pflu-strain tflu-strain]
  right random 360
  forward 3
]
end

to transmit ;; uninfected turtles are infected by fomites (red patches) with some probability. immune-labelling currently first infection
  ask turtles with [color = white or color = blue and pcolor = red] [
    if immune-label != pflu-strain [
      set ant-distance (abs (immune-label - pflu-strain))
      set cross-immunity (natural-immunity * (1 - (ant-distance / antigenic-distance-limit)))
    if cross-immunity < 0 [set cross-immunity 0]
    if random 100 < (((100 - cross-immunity) / 100) * probability-of-infection)
      [set color red set infection-period 0 set infection-number infection-number + 1 set tflu-strain pflu-strain]
        ] 
  if immune-label = pflu-strain [ 
    if random 100 < (((100 - natural-immunity) / 100) * probability-of-infection)
      [set color red set infection-period 0 set infection-number infection-number + 1 set tflu-strain pflu-strain]
    ] 
]
end

to mutate ;; some probability of mutation (change in strain label) when an individual receives infection from a patch
  ifelse in-host [
    ask turtles with [color = red] [
     if random 100 < probability-of-mutation [
      ifelse (one-of [1 2] = 1) [
      set tflu-strain (tflu-strain + (random (drift-size + 1)))]
      [set tflu-strain (tflu-strain - (random (drift-size + 1)))]
     ]
    ]
   ]
  [ask turtles with [color = red and infection-period = 0] [
     if random 100 < probability-of-mutation [
      ifelse (one-of [1 2] = 1) [
      set tflu-strain (tflu-strain + (random (drift-size + 1)))]
      [set tflu-strain (tflu-strain - (random (drift-size + 1)))]
      ]
     ]
    ]
end

to update-immunity
  ask turtles with [color = red and infection-period = 0] [
    ifelse immune-labelling = "first-infection" [
  if immune-label = -999999999999 [
        set immune-label tflu-strain]]
  [set immune-label tflu-strain]
]
end

 to track-infecteds ;; turtles with given infection period should become uninfected
  ask turtles with [color = red] [
    set infection-period infection-period + 1
  if infection-period = age-infection-max [
    set color white set infection-period 0 set tflu-strain -999999999999
    ]
  ]
  ask patches with [pcolor = red] [
  set fomite-age fomite-age + 1
  if fomite-age > max-fomite-persistence [
  set pcolor black
    ]
  ]
end

Any advice would be greatly appreciated! Thanks!

Report array of values from first tick NetLogo

Answers (1)

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