---pestilence.nlogo

NETLOGO

              fd 25]
           if Left_Quadrant = "Low Outside"
             [set heading -90
              fd 75
              set heading 180
              fd 25]
           if Left_Quadrant = "Low Center"
             [set heading -90
              fd 25
              set heading 180
              fd 25]
           if Left_Quadrant = "Bottom Outside"
             [set heading -90
              fd 75
              set heading 180
              fd 75]
           if Left_Quadrant = "Bottom Center"
             [set heading -90
              fd 25
              set heading 180
              fd 75]
           set heading (random 360)
           repeat (random (100 - Density_Left)) 
             [check-approp
              fd 1]]
          [if Right_Quadrant = "Top Outside"
             [set heading 90
              fd 75
              set heading 0
              fd 75]
           if Right_Quadrant = "Top Center"
             [set heading 90
              fd 25
              set heading 0
              fd 75]
           if Right_Quadrant = "High Outside"
             [set heading 90
              fd 75
              set heading 0
              fd 25]
           if Right_Quadrant = "High Center"
             [set heading 90
              fd 25
              set heading 0
              fd 25]
           if Right_Quadrant = "Low Outside"
             [set heading 90
              fd 75
              set heading 180
              fd 25]
           if Right_Quadrant = "Low Center"
             [set heading 90
              fd 25
              set heading 180
              fd 25]
           if Right_Quadrant = "Bottom Outside"
             [set heading 90
              fd 75
              set heading 180
              fd 75]
           if Right_Quadrant = "Bottom Center"
             [set heading 90
              fd 25
              set heading 180
              fd 75]
           set heading (random 360)
           repeat (random (100 - Density_Right)) 
             [check-approp
              fd 1]]
    ]
    set isset 1
end

;;--------------------------------------------------------------------------------------------------------

to infect
  set radius Infection_Radius
  check-radius
  if shade-of? blue color and (Contact_Infection > (random 100)) and 
     any? turtles in-radius-no-wrap radius with [shade-of? red color] and 
     not(size <= 5 + .001 + (.001 * Recover_Immune_Time) and size > 5)
     [ifelse color < 106
         [if (color - blue) < (.001 * Susceptible_Below) or (color - blue) > (.001 * Susceptible_Above)
           [set weak true]]
         [if (color - blue) < 3 + (.001 * Susceptible_Below) or (color - blue) > 3 + (.001 * Susceptible_Above)
           [set weak true]]
      set color red + (color - blue)  ;; add current age
      set size 5
      if random 100 < Deadly_Mutations
       [set color (color + .010)]
      if random 100 < Percent_Recovery
       [set color blue + (color - red)
        set size size + .001
        set weak false]
      ]
end

;;--------------------------------------------------------------------------------------------------------

to check-radius
loop[
      ifelse any? patches in-radius-no-wrap radius with [pcolor = black]
        [set radius radius - 1]
        [stop]
    ]
end

;;--------------------------------------------------------------------------------------------------------

to reproduce
locals[
       mat-blue-trav
       mat-blue-meand
       nei-mat-blue-trav
       nei-mat-blue-meand
       mat-red-trav
       mat-red-meand
       nei-mat-red-trav
       nei-mat-red-meand
       myWho ;; any? turtles in-radius-no-wrap includes calling turtle
      ]
  if radius > 5
    [set radius 5]
  set myWho who
  if ((random 100) < 25) and  ;; 50% chance of running into opposite sex also, no reproduction 2x a time interval
       count turtles in-radius-no-wrap radius < Carrying_Capacity and 
       count turtles in-radius-no-wrap radius > 1
    [  set mat-blue-trav (shade-of? blue color and color >= blue + (.001 * Procreation_Age) and shape = "default")
       set mat-blue-meand (shade-of? blue color and color >= blue + (.001 * Procreation_Age) and shape = "circle") 
       set nei-mat-blue-trav any? turtles in-radius-no-wrap radius with
         [not (who = myWho) and shade-of? blue color and color >= blue + (.001 * Procreation_Age) and shape = "default"]
       set nei-mat-blue-meand any? turtles in-radius-no-wrap radius with
         [not (who = myWho) and shade-of? blue color and color >= blue + (.001 * Procreation_Age) and shape = "circle"]
       set mat-red-trav (shade-of? red color and color >= (red + (.001 * Procreation_Age)) and shape = "default") 
       set mat-red-meand (shade-of? red color and color >= (red + (.001 * Procreation_Age)) and shape = "circle") 
       set nei-mat-red-trav any? turtles in-radius-no-wrap radius with
         [not (who = myWho) and shade-of? red color and color >= red + (.001 * Procreation_Age) and shape = "default"]
       set nei-mat-red-meand any? turtles in-radius-no-wrap radius with
         [not (who = myWho) and shade-of? red color and color >= red + (.001 * Procreation_Age) and shape = "circle"]
       ifelse mat-blue-meand and nei-mat-blue-meand and (random 1000) < (Healthy_Meanderer_Fertility * Healthy_Meanderer_Fertility)
           [hatch Healthy_Birth_Number
             [set color blue
              set weak false 
              set size 5]]
       [ifelse mat-blue-trav and nei-mat-blue-trav and (random 1000) < (Healthy_Traveler_Fertility * Healthy_Traveler_Fertility)
           [hatch Healthy_Birth_Number  ;; repetitive but nested ifelse the only way to do case
             [set color blue
              set weak false 
              set size 5]]
       [ifelse ((mat-blue-meand and nei-mat-red-meand) or (nei-mat-blue-meand and mat-red-meand)) and (random 1000) < (Healthy_Meanderer_Fertility * Infected_Meanderer_Fertility)
         [ifelse (random 100) < 50
            [hatch Healthy_Birth_Number
              [set color blue
               set weak false 
               set size 5]]
            [hatch Infected_Birth_Number
              [set color red
              set weak true
              set size 5
              if random 100 < Percent_Recovery
                [set color blue + (color - red)
                 set size size + .001
                 set weak false]
              if random 100 < Deadly_Mutations
                 [set color (color + .010)]]]]
       [ifelse ((mat-blue-trav and nei-mat-red-trav) or (nei-mat-blue-trav and mat-red-trav)) and (random 1000) < (Healthy_Traveler_Fertility * Infected_Traveler_Fertility)
         [ifelse (random 100) < 50
            [hatch Healthy_Birth_Number
              [set color blue
               set weak false 
               set size 5]]
            [hatch Infected_Birth_Number
              [set color red
              set weak true
              set size 5
              if random 100 < Percent_Recovery
                [set color blue + (color - red)
                 set size size + .001
                 set weak false]
              if random 100 < Deadly_Mutations
                 [set color (color + .010)]]]]
       [ifelse mat-red-meand and nei-mat-red-meand and (random 1000) < (Infected_Meanderer_Fertility * Infected_Meanderer_Fertility)
         [hatch Infected_Birth_Number
           [set color red
           set weak true
           set size 5
           if random 100 < Percent_Recovery
                [set color blue + (color - red)
                 set size size + .001
                 set weak false]
            if random 100 < Deadly_Mutations
             [set color (color + .010)]]]
       [if mat-red-trav and nei-mat-red-trav and (random 1000) < (Infected_Traveler_Fertility * Infected_Traveler_Fertility)
         [hatch Infected_Birth_Number
           [set color red
           set weak true
           set size 5
           if random 100 < Percent_Recovery
                [set color blue + (color - red)
                 set size size + .001
                 set weak false]
            if random 100 < Deadly_Mutations
             [set color (color + .010)]]]]]]]]
            
    ]
end

;;--------------------------------------------------------------------------------------------------------

to move
  ifelse shape = "default"
    [repeat Traveler_Moves ;; how many steps per move
      [check-approp
       fd 1]]
    [repeat Meanderer_Moves
      [check-approp 
       fd 1]]
end
          
;;--------------------------------------------------------------------------------------------------------

to age
  set color (color + .001)
  if (color >= (blue + (.001 * Procreation_Age)) and color < 106) or 
     (color >= (red + (.001 * Procreation_Age))  and color < 16)
     [set color color + 3]
  ifelse shade-of? blue color 
    [if size > 5 [set size (size + .001)]
     ifelse color < 106
         [if color >= (blue + (.001 * Healthy_Lifespan))
           [set dead dead + 1
            die]]
         [if color >= ((blue + 3) + (.001 * Healthy_Lifespan))
           [set dead dead + 1
            die]]]
     [set size (size + .001)
     ifelse color < 16 
       [if color >= (red + (.001 * Healthy_Lifespan))
         [set dead dead + 1
         die]]
       [if color >= ((red + 3) + (.001 * Healthy_Lifespan)) 
         [set dead dead + 1
          die]]
     ifelse weak
       [if size >=  (5 + (.001 * Susceptible_Infection_Lifespan))
         [set dead dead + 1
          die]]
       [if size >=  (5 + (.001 * Infection_Lifespan))
         [set dead dead + 1
          die]]
    ]
end

;;--------------------------------------------------------------------------------------------------------

to do-plots
  set-current-plot "Healthy/ Infected"
  set-current-plot-pen "Healthy"
  plot count turtles with [shade-of? blue color]
  set-current-plot-pen "Infected"
  plot count turtles with [shade-of? red color]
  ;;----------------------------------------------
  set-current-plot "Travelers (Arrows)"
  set-current-plot-pen "Healthy Adult"
  plot count turtles with [color > 106 and shape = "default"]
  set-current-plot-pen "Healthy Young"
  plot count turtles with [shade-of? blue color and color < 106 and shape = "default"]
  set-current-plot-pen "Infected Adult"
  plot count turtles with [shade-of? red color and color > 16 and shape = "default"]
  set-current-plot-pen "Infected Young"
  plot count turtles with [shade-of? red color and color < 16 and shape = "default"]
  ;;----------------------------------------------
  set-current-plot "Meanderers (Circles)"
  set-current-plot-pen "Healthy Adult"
  plot count turtles with [color > 106 and shape = "circle"]
  set-current-plot-pen "Healthy Young"
  plot count turtles with [shade-of? blue color and color < 106 and shape = "circle"]
  set-current-plot-pen "Infected Adult"
  plot count turtles with [shade-of? red color and color > 16 and shape = "circle"]
  set-current-plot-pen "Infected Young"
  plot count turtles with [shade-of? red color and color < 16 and shape = "circle"]
end

;;--------------------------------------------------------------------------------------------------------

to setup-file
locals[line]
  ifelse file-exists? "C:/WINDOWS/Desktop/Pestilence/Pestilence Data.csv"
    [set file "C:/WINDOWS/Desktop/Pestilence/Pestilence Data.csv"] ;;Because file locations will vary from system to system, you may want to change this to aviod continuous file selection.
    [ifelse file-exists? "C:/Documents and Settings/All Users/Desktop/Pestilence/Pestilence Data.csv"
      [set file "C:/Documents and Settings/All Users/Desktop/Pestilence/Pestilence Data.csv"]
      [set file user-choose-file]
    ] 
  file-open file
  set line file-read-line ;; You need to close the Excel SS if you get an error here.
  file-close
  if line = "first"
    [file-delete file]
  file-open file	
  if line = "first"
    [file-print "This file MUST be closed while running the pestilence model. Do NOT save when prompted."
     file-print "To format: 1) Open 'Template' Excel document(Enable Macros) 2) View this window 3)Press Alt + F8 4) Select Template.xls!Macro1 and Run" 
    ]
  if line = "first"
    [user-message "File output will be found on the Desktop in the Pestilence folder (The image with a,). This Excel file must be closed while running the Pestilence model. Do NOT save when prompted."]
  file-print "___P_____,____E____,____S____,____T___,____I__,____L____,____E____,____N__,____C___,_____E___,_________,_________"
  file-close
end

;;--------------------------------------------------------------------------------------------------------

to disp-header
  file-type "Initial Conditions"
  file-type ",Density Left: "                file-type Density_Left 
  file-type ",Density Right: "               file-type Density_Right
  file-type ",Travelers Left: "              file-type Travelers_Left
  file-type ",Travelers Right: "             file-type Travelers_Right
  file-type ",Meanderers Left: "             file-type Meanderers_Left
  file-type ",Meanderers Right: "            file-type Meanderers_Right
  file-type ",% Infected Left: "             file-type %_Infected_Left
  file-type ",% Infected Right: "            file-type %_Infected_Right
  file-type ",Background: "                  file-type Background
  file-type ",Left Quadrant: "               file-type Left_Quadrant
  file-type ",Right Quadrant: "              file-print Right_Quadrant
  
  file-type "Susceptible Infection Lifespan: " file-type Susceptible_Infection_Lifespan
  file-type ",Susceptible Below: "              file-type Susceptible_Below  
  file-type ",Susceptible Above: "              file-type Susceptible_Above 
  file-type ",Percent Recovery: "               file-type Percent_Recovery
  file-type ",Recover Immune Time: "            file-type Recover_Immune_Time
  file-type ",Infection Lifespan: "             file-type Infection_Lifespan 
  file-type ",Deadly Mutations: "               file-type Deadly_Mutations 
  file-type ",Healthy Traveler Fertility: "     file-type Healthy_Traveler_Fertility
  file-type ",Healthy Meanderer Fertility: "    file-type Healthy_Meanderer_Fertility
  file-type ",Infected Traveler Fertility: "    file-type Infected_Traveler_Fertility
  file-type ",Infected Meanderer Fertility: "   file-type Infected_Meanderer_Fertility 
  file-type ",Procreation Age: "                file-print Procreation_Age
  
  file-type "Healthy Birth Number: "        file-type Healthy_Birth_Number
  file-type ",Infected Birth Number: "        file-type Infected_Birth_Number
  file-type ",Healthy Lifespan: "             file-type Healthy_Lifespan 
  file-type ",Meanderer Moves: "              file-type Meanderer_Moves
  file-type ",Traveler Moves: "               file-type Traveler_Moves
  file-type ",Carrying Capacity: "           file-type Carrying_Capacity 
  file-type ",Contact Infection: "           file-type Contact_Infection
  file-type ",Infection Radius: "             file-type Infection_Radius 
 
  file-print ""
  file-type "Time,Total,% Healthy,% Infected,Healthy Adult Travelers,Healthy Young Travelers,"
  file-type "Infected Adult Travelers,Infected Young Travelers,Healthy Adult Meanderers,"
  file-type "Healthy Young Meanderers,Infected Adult Meanderers,"
  file-print "Infected Young Meanderers"
end  

;;--------------------------------------------------------------------------------------------------------

to update-file
  file-type time file-type ","
  file-type count turtles file-type ","
  ifelse count turtles > 0
    [file-type precision ((count turtles with [shade-of? blue color] / count turtles) * 100) 3 file-type ","
     file-type precision ((count turtles with [shade-of? red color] / count turtles) * 100) 3 file-type ","
    ]
    [file-type 0 file-type "," file-type 0 file-type ","]
  file-type count turtles with [color > 106 and shape = "default"] file-type ","
  file-type count turtles with [shade-of? blue color and color < 106 and shape = "default"] file-type ","
  file-type count turtles with [shade-of? red color and color > 16 and shape = "default"] file-type ","
  file-type count turtles with [shade-of? red color and color < 16 and shape = "default"] file-type ","
  file-type count turtles with [color > 106 and shape = "circle"] file-type ","
  file-type count turtles with [shade-of? blue color and color < 106 and shape = "circle"] file-type ","
  file-type count turtles with [shade-of? red color and color > 16 and shape = "circle"] file-type ","
  file-type count turtles with [shade-of? red color and color < 16 and shape = "circle"] file-print ""
end
@#$#@#$#@
GRAPHICS-WINDOW
432
10
912
511
100
100
2.34
1
5
1
1
1
0

CC-WINDOW
5
645
1026
740
Command Center

BUTTON
366
47
434
84
NIL
Go
NIL
1
T
OBSERVER
T
NIL

BUTTON
366
10
434
47
NIL
Setup
NIL
1
T
OBSERVER
T
NIL

SLIDER
0
412
212
445
Healthy_Lifespan
Healthy_Lifespan
0
100
80
1
1
NIL

SLIDER
0
181
212
214
Infection_Lifespan
Infection_Lifespan
0
50
20
1
1
NIL

SLIDER
212
313
367
346
Procreation_Age
Procreation_Age
0
30
16
1
1
NIL

SLIDER
0
445
212
478
Contact_Infection
Contact_Infection
0
100
83
1