Bio 14 Lab 2 model 1

;; this is the most up-to-date version



globals [
  regions ; a list of regions definitions, where each region is a list of its min pxcor and max pxcor
]

breed [ blue-strains blue-strain ]

breed [ red-strains red-strain ]

;;red-strains-own [red-resistance-cost]
;;blue-strains-own [blue-resistance-cost] ; removing cost of resistance as a paramter for now

turtles-own [ resistant? energy mutation-rate cost-of-repair benefit? benefit-gain] ;; some variables that apply to both strains, ;resistance-cost removed

patches-own [
  region ; the region that the patch is in, patches outside all regions have region = 0
  antibiotic ;
]

to setup ; this procedure sets up the "world" into 2 different regions. It contains a few subprocedures described next
  clear-all
  setup-regions 2
  color-regions
  ; Finally, distribute the turtles in the different regions
  setup-turtles
  if (resistance + lethal + metabolic-benefit) > 100.00 [user-message ("Mutation rates should not sum to more than 100%")] ; this message appears to warn users about mutation rate settings
  reset-ticks
end 

to color-regions ;this subprocedure colors the regions
  ; The patches with region = 0 act as dividers and are
  ; not part of any region. All other patches get colored
  ; according to the region they're in.
  ask patches with [ region != 0 ] [
    set pcolor 1 ;; what color is this - started at  times 10
    set plabel-color pcolor + 0
    ;set plabel region
    check-antibiotic
  ]
end 

to setup-turtles ; this subprocedure creates the strains

  foreach n-values length regions [ [?1] -> ?1 + 1 ] [ [?1] ->
    let region-patches patches with [ region = ?1 ]
    create-blue-strains initial-blue-strain-population [
      move-to one-of region-patches
      if (count other turtles-here > 1) [move-to one-of region-patches]
      set shape "circle"
      set size 0.15
      set color blue
      set resistant? false ;; they all start not resistant
      ;;if ( show-resistance? ) [ show-resistance ]
      set energy random blue-life-span ;;they all start out with some amt of energy - a random value between 0 and blue-life-span
      set mutation-rate blue-mutation-rate
      set benefit? false ; they all start without beneficial mutations
    ]
    create-red-strains initial-red-strain-population [
      move-to one-of region-patches
      set shape "circle"
      set size 0.15
      set color red
      set resistant? false ;; they all start not resistant
      ;;if ( show-resistance? ) [ show-resistance ]
      set energy random red-life-span ;;they all start out with some amt of energy
      set mutation-rate red-mutation-rate
      set benefit? false
    ]
  ]
end 

to go
  every 0.1 [ ; can be manipulated to make things happen faster
    ask turtles [ ; below are the things turtles do every half tick
      move ; see details under this procedure
      metabolize ; see details under this procedure
      mutate ; see details under this procedure
      if ( count other turtles-here > 20) [ die ] ;; this is where carrying capacity is specified at the moment
      if ( [antibiotic] of patch-here = true and not resistant? ) [ die ] ;; womp womp...notice antibiotic is 100% lethal
      if (energy <= 0) [die] ;; so tired...
      reproduce ;; see details under this procedure
    ;;if ( show-resistance? ) [ show-resistance ]
    ;if ( show-benefit?) [show-benefit] ;; obviously
    ;set-resistance-values
    ;]

   ; ifelse (resistant?)
  ; [
 ; if cost-of-resistance = "high" [set resistance-cost 5]
 ; if cost-of-resistance = "low" [set resistance-cost 2]
 ; if cost-of-resistance = "none" [set resistance-cost 0]
 ; ]
 ;  [set resistance-cost 0]
show-resistance
  ]
    check-antibiotic ; this checks the status of the antibiotic so that it can be changed mid run
    check-mutation-rates ; this checks to see if the mutation rate has been changed mid-run
  if ( count turtles = 0 ) [ stop ] ; the simulation stops if all the turtles die
  update-plots
  display
    ;if vid:recorder-status = "recording" [ vid:record-interface ]
  tick
  ]
end 

to move ; turtle procedure

  ; First, save the region that the turtle is currently in:
  let current-region region
  ; Then, after saving the region, we can move the turtle:
  right random 30
  left random 30
  forward 0.25
  ; Finally, after moving, make sure the turtle
  ; stays in the region it was in before:
  keep-in-region current-region
end 

to check-mutation-rates
  ask red-strains [if red-mutation-rate != mutation-rate [user-message ("You cannot change the mutation rate in the middle of a run. Restart the model!")]]
  ask blue-strains [if blue-mutation-rate != mutation-rate [user-message ("You cannot change the mutation rate in the middle of a run. Restart the model!")]]
end 

to show-resistance ;; turtle procedure that colors bacteria to show resistance
 ifelse resistant?
 [ifelse (breed = red-strains) [ set color red + 3] [set color blue + 3]] ; if resistant set to lighter colors
 [ifelse (breed = red-strains) [ set color red ] [set color blue]] ; otherwise keep original colors
end 

to show-benefit ;; turtle procedure that colors bacteria to show resistance
 ifelse benefit?
 [ifelse (breed = red-strains) [ set color yellow] [set color green]] ; if resistant set to lighter colors
 [ifelse (breed = red-strains) [ set color red ] [set color blue]] ; otherwise keep original colors
end 

to mutate ;; turtle procedure

  if random-float 100 < mutation-rate [ ;; random float chooses a number between 0-100. If that number is less than mutation-rate (set by a slider on the interface) then...

    if random-float 100 < resistance ;; roll the resistant dice (this used to be ifelse for some reason)
    [ ;; this is the if part
      if ( not resistant? ) [ ;; toggle the resistance
      set resistant? true ] ;; YOUR POISON IS FUTILE!!
      ;[set resistant? false]
        ;[ if random-float 100 < 20 [set resistant? false ]
         ;] ;; back mutations set to 20%
    ]

     ;this is the else part
      if random-float 100 < lethal [ ;; roll the lethal dice...switch the greater than to less than
        die ;; end of the line :(
      ]


    ifelse benefit? [set benefit-gain random 2] [set benefit-gain 0] ; make this a random value - this specifies the value of benefit from beneficial mutation
    if random-float 100 > ( 100 - metabolic-benefit)
    [if ( not benefit?)
      [set benefit? true]
    ]


  ]
end 

to metabolize ;; turtle procedure that sucks your life away
  let total-cost ( cost-of-repair  + 1) ;; metabolic cost is sum of all costs, + resistance-cost removed
  set energy (energy - total-cost + benefit-gain)
end 

to reproduce ;; turtle procedure
  ;; i guess we'll make all the bacteria reproduce all the time.
  set energy energy / 2 ;; takes money to make money - but what is the point of this? sets effective lifespan to half so changed it to same energy as parents
  hatch 1 [ ;; they're cloning, so inherits any mutation including resistance (or not) and they are the same strain as parent
    rt random 360
    let current-region region
    fd random-float .5 ;; move a bit
    keep-in-region current-region
    ifelse breed = red-strains [set energy red-life-span] [set energy blue-life-span] ;; so lively
  ]
end 

to check-antibiotic
  ifelse antibiotic? [
    ask patches with [pxcor >= 0] [set pcolor grey set antibiotic true]
    ask patches with [pxcor < 0] [set antibiotic false]
  ]
  [
  ask patches with [pxcor >= 0] [set pcolor 22 set antibiotic false]
    ask patches with [pxcor < 0] [set antibiotic false]
  ]
end 

;;to plate-on-agar
 ;; let blue-plated-cells round concentration / 100 * count blue-strains
 ;;set blue-plated-cells count blue-strains - blue-plated-cells
 ;; ask n-of blue-plated-cells blue-strains [
;;    die]
;;  let red-plated-cells round concentration / 100 * count red-strains
;; set red-plated-cells count red-strains - red-plated-cells
;;  ask n-of red-plated-cells red-strains [
;;    die]
;;end

;;to plate-on-antibiotic
 ;; let blue-plated-cells round concentration / 100 * count blue-strains
;; set blue-plated-cells count blue-strains - blue-plated-cells
;;  ask n-of blue-plated-cells blue-strains [
;;    die
;;  ]
;;  ask blue-strains [
;;    if not resistant? [die]]
;;  let red-plated-cells round concentration / 100 * count red-strains
;; set red-plated-cells count red-strains - red-plated-cells
;;  ask n-of red-plated-cells red-strains [
;;    die]
;;  ask red-strains [
;;    if not resistant? [die]]
;;end

to setup-regions [ n ]
  ; First, draw some dividers at the intervals reported by `region-divisions`:
  foreach region-divisions n draw-region-division
  ; Store our region definitions globally for faster access:
  set regions region-definitions n
  ; Set the `region` variable for all patches included in regions:
  (foreach regions (n-values n [ [?1] -> ?1 + 1 ]) [ [?1 ?2] ->
    ; We're looping through region definitions (?1) and region numbers (?2)
    ask patches with [ pxcor >= first ?1 and pxcor <= last ?1 ] [ set region ?2 ]
  ])
end 

to-report region-definitions [ n ]
  ; The region definitions are built from the region divisions:
  let divisions region-divisions n
  ; Each region definition lists the min-pxcor and max-pxcor of the region.
  ; To get those, we use `map` on two "shifted" copies of the division list,
  ; which allow us to scan through all pairs of dividers
  ; and built our list of definitions from those pairs:
  report (map [ [?1 ?2] -> list (?1 + 1) (?2 - 1) ] (but-last divisions) (but-first divisions))
end 

to-report region-divisions [ n ]
  ; This procedure reports a list of pxcor that should be outside every region.
  ; Patches with these pxcor will act as "dividers" between regions.
  report n-values (n + 1) [ [?1] ->
    [ pxcor ] of patch (min-pxcor + (?1 * ((max-pxcor - min-pxcor) / n))) 0
  ]
end 

to draw-region-division [ x ]
  ; This procedure makes the division patches grey
  ; and draw a vertical line in the middle. This is
  ; arbitrary and could be modified to your liking.
  ask patches with [ pxcor = x ] [
    set pcolor grey + 1.5
  ]
  create-turtles 1 [
    ; use a temporary turtle to draw a line in the middle of our division
    setxy x max-pycor + 0.5
    set heading 0
    set color grey - 3
    pen-down
    forward world-height
    set xcor xcor + 1 / patch-size
    right 180
    set color grey + 3
    forward world-height
    die ; our turtle has done its job and is no longer needed
  ]
end 

to keep-in-region [ which-region ] ; turtle procedure

  ; This is the procedure that make sure that turtles don't leave the region they're
  ; supposed to be in. It is your responsability to call this whenever a turtle moves.
  if region != which-region [
    ; Get our region boundaries from the global region list:
    let region-min-pxcor first item (which-region - 1) regions
    let region-max-pxcor last item (which-region - 1) regions
    ; The total width is (min - max) + 1 because `pxcor`s are in the middle of patches:
    let region-width (region-max-pxcor - region-min-pxcor) + 1
    ifelse xcor < region-min-pxcor [ ; if we crossed to the left,
      set xcor xcor + region-width   ; jump to the right boundary
    ] [
      if xcor > region-max-pxcor [   ; if we crossed to the right,
        set xcor xcor - region-width ; jump to the left boundary
      ]
    ]
  ]
end 


; Public Domain:
; To the extent possible under law, Uri Wilensky has waived all
; copyright and related or neighboring rights to this model.