_new per-capita model

;==================== begin _new per-capita model.nlogo ========================
; _new per-capita model - a template for writing agent-based simulations using
;   reactions and diffusion.  Agents interact via reactions that are
;   implemented via "per-capita-tau-leaping.nls" and move diffusively via
;   "random-walk.nls".
;
; By Rik Blok, 2013 
;
; This is free and unencumbered software released into the public domain.
;
; Anyone is free to copy, modify, publish, use, compile, sell, or
; distribute this software, either in source code form or as a compiled
; binary, for any purpose, commercial or non-commercial, and by any
; means.
;
; Revisions:
;
;   2013-10-08 - don't stop simulation if dt=0.  Instead do small random walk.
;   2013-08-02 - added event counts and error reporters
;   2013-07-01 - initial release by Rik Blok
;-------------------------------------------------------------------------------


__includes
[ "output-wrap.nls"            ; Same as output-print but wraps printed output.
  "per-capita-tau-leaping.nls" ; Approximate Gillespie's SSA.
  "random-walk.nls"            ; Random walk for individuals.
  "sigfigs.nls"                ; Like precision but specifies number of significant figures.
]


globals
[ ; Variable 'dt' not needed here if using System Dynamics Modeler.
  dt  ; Time step.  Automatically set in 'go' by 'per-capita-tau-leap'.
]

to startup
  setup  ; Might as well setup when model loaded.
end 

to setup
  clear-all
  reset-ticks
  output-wrap 27 ; Set output box to wrap at column 27.
  
  ; Create initial population here. For example...
  ; create-turtles 100
  ; [ setxy random-xcor random-ycor
  ; ]
  
  ; Place reactions here. For example, logistic N <--> 2 N could be implemented as...
  ; add-per-capita-event turtles                  ; N -> 2 N @ rate beta
  ;   task [ beta-birth-rate ] 
  ;   task [ hatch 1 ]
  ; add-per-capita-event turtles                  ; N + N -> N @ rate 1
  ;   task [ count other turtles-here ] 
  ;   task [ die ]
end 

to go
  if ticks = 0 ; If just starting, start timing.
  [ reset-timer 
  ]
  set dt per-capita-tau-leap inaccuracy dt
  ; If no events occurred, then dt=0.  
  ; Replace with small dt so a few turtles move to new patches.
  if dt = 0
  [ set dt inaccuracy * random-walk-time-patch diffusion-const
  ]
  random-walk turtles random-walk-jump-size diffusion-const dt
  tick-advance dt
end 

to-report diffusion-const
; Used by 'go' in call to 'diffuse-individual'.
  report 10 ^ log-diffusion
end 

to-report inaccuracy
; Complement of accuracy, depends on err-tolerance.
; Used by 'go' in call to 'per-capita-tau-leap'.
  report 10 ^ ( err-tolerance )
end 


;==================== end _new per-capita model.nlogo ==========================