globals
[
  grid-x-inc               ;; the amount of patches in between two roads in the x direction
  grid-y-inc               ;; the amount of patches in between two roads in the y direction
 
  ;; patch agentsets
  roads         ;; agentset containing the patches that are roads
]

patches-own [
  invasive?       ;; indicates if the patch is occupied by invasive species
  disturbed?       ;;indicates if patch is disturbed
  invaded-neighbors  ;; counts how many neighboring patches have invasive species
  disturbed-neighbors  ;; counts how many neighboring patches are disturbed

]


;; Initialize the global variables to appropriate values
to setup-globals
 set grid-x-inc world-width / grid-size-x
  set grid-y-inc world-height / grid-size-y

end


to setup
  clear-all
  setup-globals
  ;; First we ask the patches to draw themselves and set up a few variables

if have-roads = true [setup-roads]



  ask patches
    [ if pcolor != white 
    [ ifelse random-float 1000.0 < initial-density
        [ invade-patch ]
        [ reclaim-patch ] ] ]

plot-patches

end


to invade-patch
 set disturbed? false
  set invasive? true
  set pcolor red
end


to reclaim-patch
  set disturbed? false
  set invasive? false
  set pcolor green
end


to go
  ask patches
    [ set invaded-neighbors count neighbors with [invasive?] set disturbed-neighbors count neighbors with [disturbed?]
     ]
  ;; Starting a new "ask patches" here ensures that all the patches
  ;; finish executing the first ask before any of them start executing
  ;; the second ask.  This keeps all the patches in synch with each other,
  ;; so the births and deaths at each generation all happen in lockstep.
  ask patches
    [ ifelse invaded-neighbors > 0 and invaded-neighbors + disturbed-neighbors >= invade-threshold and pcolor != white
        [ invade-patch ]
        [ if invaded-neighbors + disturbed-neighbors < reclaim-threshold and pcolor != white
            [ reclaim-patch ] ] ]
  tick
  plot-patches
end

to add-invasive
  while [mouse-down?]
    [ ask patch mouse-xcor mouse-ycor
        [ invade-patch ]
      display ]
end

to remove-invasive
  while [mouse-down?]
    [ ask patch mouse-xcor mouse-ycor
        [ reclaim-patch ]
      display ]
end



;; Make the patches have appropriate colors, set up the roads and intersections agentsets,
;; and initialize the traffic lights to one setting
to setup-roads

  ;; initialize the global variables that hold patch agentsets
  set roads patches with
    [(floor((pxcor + max-pxcor - floor(grid-x-inc - 1)) mod grid-x-inc) = 0) or
    (floor((pycor + max-pycor) mod grid-y-inc) = 0)]

  ask roads [ set pcolor white set disturbed? true set invasive? false]

end


to plot-patches ;; this creates creates the bar graph 
    set-current-plot "Invasive and Native Patches"
    clear-plot
    set-current-plot-pen "native"
    plotxy 1 count patches with [pcolor = green] 
    plot-pen-down
    set-current-plot-pen "invasive"
    plotxy 2 count patches with [pcolor = red] 
    plot-pen-down
end

; This model was created as part of the 2008 BioQUEST Curriculum Consortium
; Summer Workshop.  
;
; Copyright 2008 by Steven Brewer.  All rights reserved.
; This model was inspired by many of the sample Netlogo models and parts 
; were based on functions from the "Life" and "Traffic Grid" models.  (Wilensky, U. (2001).  
; NetLogo Enzyme Kinetics model. http://ccl.northwestern.edu/netlogo/models/EnzymeKinetics. 
; Center for Connected Learning and Computer-Based Modeling, Northwestern University, 
; Evanston, IL.) 
;
; Permission to use, modify or redistribute this model is hereby granted,
; provided that both of the following requirements are followed:
; a) this copyright notice is included.
; b) this model will not be redistributed for profit without permission
;    from the authors.
; Contact the authors for appropriate licenses for redistribution for
; profit.
;
; To refer to this model in academic publications, please use:
; Brewer, S.D. (2008).  Invasive Plants and Disturbance.  http://bcrc.bio.umass.edu/netlogo/models/InvasivePlants
; Biology Computer Resource Center
;
; In other publications, please use:
; Copyright 2008 by Steven Brewer.  All rights reserved.  See
; http://bcrc.bio.umass.edu/netlogo/models/InvasivePlants
; for terms of use.


@#$#@#$#@
GRAPHICS-WINDOW
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PLOT
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Invasive and Native Patches
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PENS
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"invasive" 1.0 1 -2674135 true

@#$#@#$#@
WHAT IS IT?
-----------
Invasive species are non-native species that move into and disrupt native communities.  Some, like Garlic Mustard, can produce a monoculture that crowds out other species.  This simulation, based on a cell automata model, shows the role that disturbed areas can play in the distribution of an invasive plant.

HOW IT WORKS
------------
Each patch looks at surrounding patches.  If a patch is adjacent to enough invaded and/or disturbed patches, it will be invaded also.  If it has few or no invaded or disturbed neighboring patches, it will be reclaimed by the native flora.  The thresholds for these values are set with sliders.  Roads represent disturbed areas which make it easier for an invasive species to gain a foothold.


HOW TO USE IT
-------------
First explore increasing the initial density of the invasive plant.  Then add a network of roads and explore the effects of density.


THINGS TO NOTICE
----------------
This section could give some ideas of things for the user to notice while running the model.


THINGS TO TRY
-------------
Try increasing and decreasing the threshold values.  The model is extremely sensitive to changes in these values.  


EXTENDING THE MODEL
-------------------
Currently, the only mechanism for plants to spread is by being adjacent.  This prevents the invasive species from spreading across roads, for example.  In fact, most invasive species have extremely small seeds which are easily blown across roads.  Add a mechanism for patches to expand to non-adjacent patches.


RELATED MODELS
--------------
This model uses the same logic as the "Life" and "Traffic Grid" models in the Netlogo library.  


CREDITS AND REFERENCES
----------------------
This model was created as part of the 2008 BioQUEST Curriculum Consortium Summer Workshop.  

Copyright 2008 by Steven Brewer.  All rights reserved.
This model was inspired by many of the sample Netlogo models and parts 
were based on functions from the "Life" and "Traffic Grid" models.  (Wilensky, U. (2001).  NetLogo Enzyme Kinetics model. http://ccl.northwestern.edu/netlogo/models/EnzymeKinetics. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.) 

Permission to use, modify or redistribute this model is hereby granted, provided that both of the following requirements are followed:
a) this copyright notice is included.
b) this model will not be redistributed for profit without permission
   from the authors.
Contact the authors for appropriate licenses for redistribution for profit.

To refer to this model in academic publications, please use:
Brewer, S.D. (2008).  Invasive Plants and Disturbance. http://bcrc.bio.umass.edu/netlogo/models/InvasivePlants Biology Computer Resource Center

In other publications, please use:
Copyright 2008 by Steven Brewer.  All rights reserved.  See http://bcrc.bio.umass.edu/netlogo/models/InvasivePlants for terms of use.

@#$#@#$#@
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NetLogo 4.0.2
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