Sleepy IBM_v.6.1.1_two strategies_shadedens.nlogo

;**********************************************************************************************************************
;********************************************                          ************************************************
;********************************************  Soft foraging submodel  ************************************************
;********************************************                          ************************************************
;**********************************************************************************************************************

;*********************************************************
;*******    Space and time specifics of model    *********
;*********************************************************

; Spatial scale: 1500 * 1500 m
; 1 patch = 2 m
; 1 tick = 2 min
; 1 day = 720 ticks
; 1 tick = 2 bites possible for small food; 4 bites possible for large food

;*********************************************************
;*********************   Interface    ********************
;*********************************************************

; Energy cost of individual
; =========================
; Movement-cost:    Cost (J) of moving one patch (2 m). Calculated from DEB model.
; Maintenance-cost: Cost (J) of paying maintenance. Calculated from DEB model.

; Energy gain of individual
; =================
; Low-food gain:  Energy gain (J) from small food items (Brown 1991).
; kap_X:          Converison efficiency of assimilated energy from food (J) (Kooijman 2010).

; Food patch growth
; =================
; Food-growth:        Growth of plant material (J) per tick (Norman et al. 2008).
; Large-food-initial: Initial energy level (J) of large food items at setup. Parameterised from literature.
; Small-food-initial: Initial energy level (J) of small food items at setup. Parameterised from literature.

; Individual attributes
; ===================
; Maximum-reserve: Maximum reserve level (J). Appears in 'to setup' and 'to make decision'.
; Minimum-reserve: Define the critical starvation period. Individuals can survive without food for two hours in this state (reasonable estimate). The threshold of reserve that induces the increasing visual scope of the individual. Vision increases by 2 patches every tick to the maximum vision range (10 patches (20 m)).

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

; extensions [r]  ; Extension for calling R commands from NetLogo

globals
[
  in-shade?          ; Reports TRUE if turtle is in shade
  in-food?           ; Reports TRUE if turtle is in a food patch
  min-energy         ; Minimum food unit level for individual to lose interest and move away from patch. This eliminates the incentive for individuals to return immediately to the previously visited food patch after vacating it.
  reserve-level      ; Reserve level of individual.
  min-vision         ; Minimum (normal) vision range of individuals (Auburn et al. 2009).
  max-vision         ; Maximum vision range of individuals activated by starvation mode. See 'to starving' procedure (Auburn et al. 2009)
  ctmincount         ; Counter for time spent under min_T_b_
  feedcount          ; Counter for time spent in feeding state.
  restcount          ; Counter for the time spent resting in shade
  searchcount        ; Counter for time spent searching for food.
  starvecount        ; Counter for time spent in starvation state.
  shadecount         ; Counter for time spent searching for shade following a feeding bout.
  transcount         ; Counter for frequency of transitions between any of the three activity states--searching, feeding, resting.
  zenith             ; Zenith angle of sun (update-sun procedure).
  tempX
  tempY
  tempXY
  gutfull            ; Reports gut level of DEB model
  movelist           ; List of cumulative movement costs
  fh_                ; String for working dir to export results
  ;Shade-density      ; Choose between randomly distributed or randomly clumped shade patches in landscape
  ]

turtles-own
[
  activity-state     ; Individual is either under a Searching, Feeding, or Resting state for each tick. The transition between the various activity states defines the global behavioural repetoire.
  energy-gain        ; Converted energy gained from food
;  high-energy-gain   ; Converted energy gained from large food items
;  search-energy      ; Minimum reserve that satisficing individual reaches to stop resting and start searching. Defined in Setup as fraction of total reserve. This is the crux of the satisficing strategy--rest only until food is needed.
  ;T_b_init_         ; Initial body temperature (T_b_init) of individual (Celcius)
  T_b_               ; Body temperature (T_b) of individual (Celcius)
  T_b_basking_       ; Basking body temperature of individual (Celcius)
  T_opt_range        ; Foraging body temperature range of individual (Celcius)
  T_opt              ; Median foraging body temperature of individual (Celcius)
  T_opt_lower_        ; Lower foraging body temperature of individual (Celcius)
  T_opt_upper_        ; Upper foraging body temperature of individual (Celcius)
  min-T_b_           ; Lower critical body temperature (min-T_b) of individual (Celcius)
  max-T_b_           ; Upper critical body temperature (max-T_b) of individual (Celcius)
  vision-range       ; Vision (no. of patches) range of individual.
  ;strategy_         ; *> Interface <* Defines the foraging strategy of individual. This is set in the Interface and is thus masked in the code.
  has-been-starving? ; Results reporter only variable for reporting stavation time only if individual has starved
  has-been-feeding?  ; Results reporter only variable for reporting feeding time only if individual has been feeding
  X                  ; List of x coords for homerange
  Y                  ; List of y coords for homerange
  gutthresh_         ; Threshold for gutlevel to motivate turtle to move
  V_pres_            ; DEB structural volume
  wetgonad_          ; DEB wet mass reproductive organ volume
  wetstorage_        ; DEB wet mass storage
  wetfood_
  hungerstate
  thermalstate
  matestate
  fearstate
  ]

patches-own
[
  patch-type    ; Defines type of patches in environment as either Food or Shade.
  food-level    ; *> Interface <* Defines the initial and updated level of energy (J) in food patches. Food level increases (plant growth; see 'Food patch growth' in Interface) and decreases (feeding by individual) with each tick.
  shade-level   ; *> Interface <* Defines the initial and updated level of shade in shade patches. Shade levels remain constant throughout simulation.
  ]

breed
[suns sun]
breed
[homeranges homerange]

;********************************************************************************************************************
;***********************************************      SETUP      ****************************************************
;********************************************************************************************************************

;;; testing file import of sleepy lidar
;to startup
;  ;; read the elevations from an external file
;  ;; note that the file is formatted as a list
;  ;; so we only have to read once into a local variable.
;  file-open "/Users/matthewmalishev/Documents/Postgrad study/Melbourne Uni/Data/Sleepies/waddleometer_shade/"
;  let patch-elevations file-read
;  file-close
;  set color-max max patch-elevations  ;; put a little padding on the upper bound so we don't get too much
;                                           ;; white and higher elevations have a little more variation.
;  let min-elevation min patch-elevations
;  ;; adjust the color-min a little so patches don't end up black
;  set color-min min-elevation - ((color-max - min-elevation) / 10)
;  ;; transfer the date from the file into the sorted patches
;  ( foreach sort patches patch-elevations
;    [ ask ?1 [ set elevation ?2 ] ] )
;  ;setup
;end


to setup
  ca
  if Food-patches + Shade-patches > count patches
  [ user-message (word "Lower the sum of shade and food patches to < " count patches ".")
    stop ]
  random-seed 1                          ; Outcomment to generate seed for spatial configuration of all patches in the landscape (food and shade). For reproducibility. NB: turtle movement is still stochastic. See below random-seed primitive for complete function.
  set min-energy Small-food-initial
  set min-vision 5                         ; 10m (Auburn et al. 2009)
  set max-vision 10                        ; 20m (Auburn et al. 2009)

  ask patches
  [set patch-type "Sun"
    set pcolor (random 1 + blue)]

  let NumFoodPatches Food-patches / 10
  ask n-of NumFoodPatches patches [
    ask n-of 10 patches in-radius 4 [ ; Sets 10 random food patches within a 5-patch radius of Food-patches
    let food-amount random 100
    ifelse food-amount < 50
    [set food-level (Small-food-initial) + random-float 1 * 10 ^ -5] ; Makes only one food patch attractive to turtle
    [set food-level (Large-food-initial) + random-float 1 * 10 ^ -5]
      set pcolor PatchColor
      set patch-type "Food"
      ]
  ]

ifelse Shade-density = "Random"[ ; chooser for setting Random or Clumped shade patches (similar to food patch arrangement)
  let NumShadePatches Shade-patches
  ask n-of NumShadePatches patches [
    let shade-amount random 100
    ifelse shade-amount < 50
    [set shade-level (Low-shade + random-float 1 * 10 ^ -5) ; Makes only one shade patch attractive to turtle
      set pcolor black + 2]
    [set shade-level (High-shade + random-float 1 * 10 ^ -5)
      set pcolor black]
      set patch-type "Shade"
      ]
]
[
    let NumShadePatches Shade-patches / 10
    ask n-of NumShadePatches patches [
    ask n-of 10 patches in-radius 4 [ ; Sets 10 random food patches within a 5-patch radius of Food-patches
    let shade-amount random 100
    ifelse shade-amount < 50
    [set shade-level (Low-shade + random-float 1 * 10 ^ -5) ; Makes only one shade patch attractive to turtle
      set pcolor black + 2]
    [set shade-level (High-shade + random-float 1 * 10 ^ -5)
      set pcolor black]
      set patch-type "Shade"
      ]
]
]; close else shade loop


ask patch 0 0 [set patch-type "Shade"
  set pcolor black]

set movelist (list 0)
;  ask one-of patches with [patch-type = "Shade"]
;  [sprout 1]
crt 1

 random-seed new-seed                    ; Outcomment to generate seed for spatial configuration of all patches in the landscape (food and shade).

  ask turtle 0
  [
    setxy 0 0 ;random-xcor random-ycor
    set reserve-level Maximum-reserve
    set T_b_basking_ 14
    set T_opt_range (list 26 27 28 29 30 31 32 33 34 35 )        ; From Pamula thesis
    set T_opt_upper last T_opt_range
    set T_opt_lower first T_opt_range
    set T_opt median T_opt_range
    set min-T_b_ min-T_b
    set max-T_b_ max-T_b
    set V_pres_ V_pres
    set wetgonad_ wetgonad
    set wetstorage_ wetstorage
    set wetfood_ wetfood
    set activity-state "S"
    ;set strategy_ Strategy
    set vision-range min-vision
    if [patch-type] of patch-here = "Shade"
    [set in-shade? TRUE]
     if [patch-type] of patch-here = "Food"
    [set in-food? TRUE]
    set shape "lizard"
    set size 2
    set color red
    pen-down
    set X (list xcor)
    set Y (list ycor)
    ]
setup-spatial-plot
set fh_ fh
;create-sun
reset-ticks
;r:clear                                  ; extensions [r] command. Outcomment if calling R from Netlogo.
end

;********************************************************************************************************************
;***********************************************      GO        *****************************************************
;********************************************************************************************************************

to go
  tick
  if not any? turtles
  [
    get-homerange
    print "All turtles dead. Check output of model results."
    repeat 5 [beep wait 0.5]
    stop
    save-world
    ]
  if (ticks * 2 / 60 / 24) = No.-of-days
  [
    ask turtle 0
    [report-results]
    save-plots
    stop
    save-world
    ]
  ifelse show-plots?
  []
  [clear-all-plots]
  ask turtle 0
  [
    report-patch-type
 ;   set reserve-level reserve-level - Maintenance-cost
    ask turtles with [reserve-level > Minimum-reserve]
    [set vision-range min-vision]
    update-T_b
    ;if (activity-state = "R" and [patch-type] of patch-here != "Shade")
;    [shade-search]
    make-decision
    update-wetmass
;    if activity-state = "R" and [patch-type] of patch-here = "Shade"
;    [rest]
    set X lput xcor X ; populate X list with turtle's X coords to generate home range
    set Y lput ycor Y ; populate Y list with turtle's Y coords to generate home range
  ]
  if any? turtles with [reserve-level <= 0]
  [ask turtle 0 [report-results]
    stop
    ]
  ask patches with [patch-type = "Food"]
    [update-food-levels]
  ;update-sun
end

;*****************************************************************************************************************************
;*************************************************    TO UPDATE T_b     ******************************************************
;*****************************************************************************************************************************

to update-T_b
  ask turtles with [T_b >= max-T_b]
    [stop]
  if T_b <= min-T_b
    [set ctmincount ctmincount + 1]
    if (ctmincount * 2 / 60) = ctminthresh
    [stop]
end

;*****************************************************************************************************************************
;*************************************************    TO MAKE DECISION      **************************************************
;*****************************************************************************************************************************

to make-decision

;-------------------------------------------------------------------------------------
;-------------------------------------Optimising-------------------------------------
;-------------------------------------------------------------------------------------
  ifelse (strategy = "Optimising")
  [; start optimising loop
    ifelse (T_b > T_opt_upper) or (T_b < T_opt_lower)
  [
    ask turtle 0
    [;set label "Resting"
      set activity-state "R"
;      ifelse gutfull >= gutthresh and T_b < T_opt_upper and T_b > T_opt_lower
;      [;set label "Full gut"
;        stop ]
;      [
        if [patch-type] of patch-here != "Shade"
      [shade-search]
;     ] ;close else loop for ifelse gutthresh and T_b conditional above
      if ([patch-type] of patch-here = "Shade") and (T_b < T_b_basking_)
      [set in-shade? TRUE
       set in-food? FALSE
         set restcount restcount + 1; *** Outcomment to exclude time spent searching for shade in restcount ***
         ]
      ]
    if (activity-state = "R") and (T_b >= T_b_basking_) and (T_b < T_opt_upper) ; Basking behaviour
    [set in-shade? FALSE
      set in-food? FALSE
 ;      set transcount transcount + 1 ; Outcomment to include basking behaviour as activity state
 ;      plotxy xcor ycor
    ]
; set restcount restcount + 1 ; *** uncomment to include time spent searching for shade in restcount ***
    ]
     [; else optimising loop
        if (activity-state = "R")
    [
;        set restcount restcount + 1 ; *** uncomment to include time spent searching for shade in restcount ***
       ; set label "Resting"
      if ((T_b <= T_opt_upper) and (T_b >= T_opt_lower)); and reserve-level < search-energy
      [set transcount transcount + 1
        plotxy xcor ycor
        set activity-state "S"]
     ; [set activity-state "R"]
    ]

                               ; 28-11-14: Only works with maint. or movement costs, otherwise reserve level = Max. reserve and turtle chooses to rest
    if (activity-state = "F"); Use this procedure to eliminate turtle returning to shade patch after every feeding bout and to eliminate min-energy parameter. Using min-energy will cause problems in model with soil moisture profile updating food growth.
    [                          ; Turning empty food patches into Sun patches elimates the need for min-energy.
      ifelse (gutfull < gutthresh) ;and ([patch-type] of patch-here = "Food") ; if gut is not full, keep feeding
      [
      ask turtle 0
      [handle-food
        ;set label "Feeding"
        set has-been-feeding? TRUE]
      if [patch-type] of patch-here != "Food" ; if patch isn't food, search for food
      [set activity-state "S"
        set transcount transcount + 1
        plotxy xcor ycor
        set energy-gain 0]
      if reserve-level >= Maximum-reserve ; turtle will fight between feeding and resting if DEB model not activated i.e. reserve incurs no cost.
      [set transcount transcount + 1
        plotxy xcor ycor
;        ifelse (strategy = "Optimising")
;        [set activity-state "S"]
        set activity-state "R"
        stop]
      ]
      [;set label "Gut is full" ; otherwise, turtle moves during active hours of the day
        socialise
        set searchcount searchcount + 1
        set in-food? FALSE
        plotxy xcor ycor
        ]
    ]

    if (activity-state = "S")
    [
      ask turtle 0
      [search
       ; set label "Searching for food"
       ]
      set searchcount searchcount + 1
      set in-food? FALSE
      if ([patch-type] of patch-here = "Food") and (gutfull < gutthresh) ;and ([food-level] of patch-here > min-energy)
      [set transcount transcount + 1
        plotxy xcor ycor
        set activity-state "F"]
      ]
  ]
  ]; end optimising loop



;-------------------------------------------------------------------------------------
;-------------------------------------Satisficing-------------------------------------
;-------------------------------------------------------------------------------------

  [; else satisfice, i.e. move only when gutfull is below the gut threshold
  ifelse (T_b > T_opt_upper) or (T_b < T_opt_lower) or (gutfull >= gutthresh); 'gutfull' is DEB.R input
  [
    ask turtle 0
    [;set label "Resting"
      set activity-state "R"
      ifelse gutfull >= gutthresh and T_b < T_opt_upper and T_b > T_opt_lower
      [;set label "Full gut"
        stop ]
      [if [patch-type] of patch-here != "Shade"
      [shade-search]]
      if ([patch-type] of patch-here = "Shade") and (T_b < T_b_basking_)
      [set in-shade? TRUE
       set in-food? FALSE
        set restcount restcount + 1] ; *** uncomment to exclude time spent searching for shade in restcount ***
      ]
    if (activity-state = "R") and (T_b >= T_b_basking_) and (T_b < T_opt_upper) ; Basking behaviour
    [set in-shade? FALSE
      set in-food? FALSE
 ;      set transcount transcount + 1 ; Outcomment to include basking behaviour as activity state
 ;      plotxy xcor ycor
    ]
; set restcount restcount + 1 ; *** uncomment to include time spent searching for shade in restcount ***
    ]

  [
        if (activity-state = "R")
    [
;        set restcount restcount + 1 ; *** uncomment to include time spent searching for shade in restcount ***
       ; set label "Resting"
      if ((T_b <= T_opt_upper) and (T_b >= T_opt_lower)); and reserve-level < search-energy
      [set transcount transcount + 1
        plotxy xcor ycor
        set activity-state "S"]
     ; [set activity-state "R"]
    ]

                               ; 28-11-14: Only works with maint. or movement costs, otherwise reserve level = Max. reserve and turtle chooses to rest
    if (activity-state = "F"); Use this procedure to eliminate turtle returning to shade patch after every feeding bout and to eliminate min-energy parameter. Using min-energy will cause problems in model with soil moisture profile updating food growth.
    [                          ; Turning empty food patches into Sun patches elimates the need for min-energy.
      ifelse (gutfull < gutthresh) ;and ([patch-type] of patch-here = "Food") ; if gut is not full, keep feeding, else stop.
      [
      ask turtle 0
      [handle-food
        ;set label "Feeding"
        set has-been-feeding? TRUE]
      if [patch-type] of patch-here != "Food"
      [set activity-state "S"
        set transcount transcount + 1
        plotxy xcor ycor
        set energy-gain 0]
      if reserve-level >= Maximum-reserve ; Turtle will fight between feeding and resting if DEB model not activated i.e. reserve incurs no cost.
      [set transcount transcount + 1
        plotxy xcor ycor
;        ifelse (strategy = "Optimising")
;        [set activity-state "S"]
        set activity-state "R"
;        set restcount restcount + 1 ; part of regular restcount because satisficing animals rest in open sun
        stop]
      ]
      [;set label "Gut is full"
        stop]
    ]

    if (activity-state = "S")
    [
      ask turtle 0
      [search
       ; set label "Searching for food"
       ]
      set searchcount searchcount + 1
      set in-food? FALSE
      if ([patch-type] of patch-here = "Food")  ;and ([food-level] of patch-here > min-energy)
      [set transcount transcount + 1
        plotxy xcor ycor
        set activity-state "F"]
      ]
    ]
  ]; end satisficing loop

end

;**********************************************************************************************************************
;***********************************************     TO SEARCH      ***************************************************
;**********************************************************************************************************************

to search
  set reserve-level reserve-level - Movement-cost ; add miniscule movement cost to avoid turtle exiting green food patches for one time step when feeding
  set movelist lput Movement-cost movelist
  bounce
  let local-food-patches patches with [(distance myself < [vision-range] of turtle 0) and (patch-type = "Food")]
  ifelse any? local-food-patches
  [let my-food-patch local-food-patches with-min [distance myself] ;with-max [food-level]
  face one-of my-food-patch]
  [lt random 180 - 90 ]
  fd 1
  if [patch-type] of patch-here = "Food"
  [set activity-state "F"]
end

;**************************************************************************************************************************
;**********************************************    TO BOUNCE     **********************************************************
;**************************************************************************************************************************

to bounce
                  ;; Turtles turn a random angle ~180 when encountering a wall
  ask turtle 0
 [ if abs pxcor = abs max-pxcor or
      abs pycor = abs max-pycor
    [lt random-float 180 ]
 ]
end

;**************************************************************************************************************************
;**********************************************    TO HANDLE FOOD      ****************************************************
;**************************************************************************************************************************

to handle-food
  set energy-gain Low-food-gain
  set in-food? TRUE
  set in-shade? FALSE
  set feedcount feedcount + 1
  set-current-plot "Spatial coordinates of transition between activity states"
  set-current-plot-pen "Feeding"
  ifelse [pcolor] of patch-here = 45
  [set-plot-pen-color 45]
  [set-plot-pen-color 55]
  plotxy xcor ycor
end

;**************************************************************************************************************************
;********************************************     TO SHADE SEARCH       ***************************************************
;**************************************************************************************************************************

to shade-search
;  set activity-state "S"
  set reserve-level reserve-level - Movement-cost ; add miniscule movement cost to avoid turtle exiting green food patches for one time step when feeding
  set movelist lput Movement-cost movelist
  let local-shade-patches patches with [(distance myself < [vision-range] of turtle 0) and (patch-type = "Shade")]
  ifelse any? local-shade-patches
  [let my-shade-patch local-shade-patches with-min [distance myself] with-max [shade-level]
    face one-of my-shade-patch
    set shadecount shadecount + 1]
  [lt random 180 - 90]
  fd 1
 ; set label "Searching for shade"
;  if [patch-type] of patch-here = "Shade"
;  [set activity-state "R"]
end

;**************************************************************************************************************************
;*********************************************       TO REST      *********************************************************
;**************************************************************************************************************************

to rest
  ifelse strategy = "Optimising"
  [set activity-state "S"]
  [set activity-state "R"]
end

;**************************************************************************************************************************
;*********************************************       TO STARVE       ******************************************************
;**************************************************************************************************************************

to starving
 set vision-range vision-range + (max-vision / 6)
 ask turtle 0
 [set label "Starving"
 print "I'm starving"
 set has-been-starving? TRUE]
end

;**************************************************************************************************************************
;*********************************************       TO SOCIALISE       ***************************************************
;**************************************************************************************************************************

to socialise
  set reserve-level reserve-level - Movement-cost ; add miniscule movement cost to avoid turtle exiting green food patches for one time step when feeding
  set movelist lput Movement-cost movelist
  bounce
  lt random 180 - 90
  fd 1
  if gutfull < gutthresh
  [set activity-state "S"]
end

;*********************************************************************************************************************************
;***********************************************     TO UPDATE FOOD LEVELS     ***************************************************
;*********************************************************************************************************************************

to update-food-levels
  let food-deplete food-level - Low-food-gain
  if (count turtles-here with [activity-state = "F"] > 0) and (gutfull < gutthresh)
; [ifelse food-level < Large-food-initial
  [set food-level food-deplete ; yellow food
    set in-food? TRUE
    print "In food"]
;  [set food-level food-level - (Low-food-gain * 2)] ; green food
;  ]
;[set food-level food-level + Food-growth]      ; growing food
  if food-level < Small-food-initial
    [set patch-type "Sun"]
set pcolor PatchColor
end


;*********************************************************************************************************************************
;***********************************************     TO UPDATE WETMASS     *******************************************************
;*********************************************************************************************************************************

to update-wetmass
;  set V_pres_ V_Pres
;  plotxy xcor ycor
;  set wetstorage_ wetstorage
;  plotxy xcor ycor
;  set wetfood_ wetfood
;  plotxy xcor ycor
;  set wetgonad_ wetgonad
;  plotxy xcor ycor
end

;*********************************************************************************************************************************
;***********************************************    TO REPORT PATCH COLOUR     ***************************************************
;*********************************************************************************************************************************

to-report PatchColor
  let PatColor 0
  ifelse food-level >= Large-food-initial
  [set PatColor green]
  [ifelse food-level >= Small-food-initial
    [set PatColor yellow]
    [set PatColor brown]
  ]
  report PatColor
end

;*********************************************************************************************************************************
;***********************************************    TO REPORT PATCH-TYPE     *****************************************************
;*********************************************************************************************************************************

to report-patch-type
ifelse [patch-type] of patch-here = "Food"
    [set in-food? TRUE]
    [
      ifelse [patch-type] of patch-here = "Shade"
      [set in-shade? TRUE]
      [set in-shade? FALSE
        set in-food? FALSE]
    ]
end

;*********************************************************************************************************************************
;***********************************************     TO REPORT RESULTS     *******************************************************
;*********************************************************************************************************************************

to report-results
    output-print (word "Number of real days:,, " precision (ticks * 2 / 60 / 24) 5)
    output-print ""
    output-print (word "Time spent searching for food (mins/days):, " (searchcount * 2) " , " precision (searchcount * 2 / 60 / 24) 3 "")
    output-print ""
    output-print (word "Time spent feeding (mins/days):, " (feedcount * 2) " , " precision (feedcount * 2 / 60 / 24) 3 "")
    output-print ""
    output-print (word "Time spent searching for shade  (mins/days):, " (shadecount * 2) " , " precision (shadecount * 2 / 60 / 24) 3 "")
    output-print ""
    output-print (word "Time spent resting in shade (mins/days):, " (restcount * 2) " , " precision (restcount * 2 / 60 / 24) 3 "")
    output-print ""
    output-print (word "Time spent in critical starvation (mins/days):, " (starvecount * 2) " , " precision (starvecount * 2 / 60 / 24) 3 "")
    output-print ""
    output-print (word "Number of transitions between activity states:, " transcount)
    output-print ""
    ifelse has-been-feeding? = TRUE
    [output-print (word "Proportion of feeding to searching:, " precision (feedcount / searchcount) 3)]
    [output-print (word "Proportion of feeding to searching:, " 0)]
    output-print ""
    ifelse has-been-starving? = TRUE
    [output-print (word "Proportion of feeding to starving:, " precision (feedcount / starvecount) 3)]
    [output-print (word "Proportion of feeding to starving:, " 0)]
    output-print ""
    output-print (word "Patches with pcolor = brown (eaten): " patches with [pcolor = 35])
    stop;die

end

;*********************************************************************************************************************************
;***********************************************     TO SAVE WORLD     ***********************************************************
;*********************************************************************************************************************************

to save-world                          ; This procedure saves the model world. The file output procedure then outputs the saved model world as a .txt file to the Desktop.
  let world user-new-file
  if ( world != false )
  [
    file-write world
    ask patches
    [
      file-write pxcor
      file-write pycor
       if patch-type = "Food"
       [file-write pxcor and pycor and (patch-type = "Food") and food-level]
       if patch-type = "Shade"
       [file-write pxcor and pycor and (patch-type = "Shade") and shade-level]
    ]
    file-close
  ]
end

to save-plots

;export-plot "Spatial coordinates of transition between activity states" "/Users/matthewmalishev/Documents/Manuscripts/Malishev and Kearney/Figures/Simulations/spatialplottest.csv"
end

;*********************************************************************************************************************************
;***********************************************         SPATIAL PLOT         ****************************************************
;*********************************************************************************************************************************

to setup-spatial-plot
  set-current-plot "Spatial coordinates of transition between activity states"
  set-plot-x-range min-pxcor max-pxcor
  set-plot-y-range min-pycor max-pycor
  clear-plot
end


;*********************************************************************************************************************************
;***********************************************         GET HOMERANGE         ***************************************************
;*********************************************************************************************************************************

to get-homerange
;r:eval "library(adehabitatHR)" ; load the r packages
;r:eval "library(sp)"
;
;r:eval "turtles<-data.frame()" ; make an empty data frame
;
;ask turtle 0
;[
;  (r:putdataframe "turtle" "X" X "Y" Y) ; put the X and Y coords into a dataframe
;  r:eval (word "turtle<-data.frame(turtle,ID = '"ID"')")
;  r:eval "turtles<-rbind(turtles,turtle)"
;  ]
;
;r:eval "spdf<-SpatialPointsDataFrame(turtles[1:2], turtles[3])" ; creates a spatial points data frame (adehabitatHR package)
;r:eval "homerange<-mcp(spdf)"

draw-homerange
save-homerange
;plot-area

end

;*********************************************************************************************************************************
;***********************************************         DRAW HOMERANGE         **************************************************
;*********************************************************************************************************************************

to draw-homerange
  clear-drawing
  if any? turtles [
    ask turtle 0
  [
   pu
   ; calculate homerange points
;   r:eval (word "temp <- slot(homerange,'polygons')[[which(slot(homerange,'data')$id == '"ID"')]]@Polygons[[1]]@coords")
;   set tempX tempX
;   set tempY tempX
;   set tempXY tempXY

   ; hatch a turtle to draw the homerange boundary points
   hatch-homeranges 1
   [
     hide-turtle
 ;    set ID [ID] of myself
     set color red
     ]

   ; draw the homerange
   foreach tempXY
   [
     ask homeranges
     [
       move-to patch (item 0 ?) (item 1 ?)
       pd
       ]
     ]

   ; close the homerange polygon
   ask homeranges
   [
     let lastpoint first tempXY
     move-to patch (item 0 lastpoint) (item 1 lastpoint)
     ]
  ]
  ]
end

;*********************************************************************************************************************************
;***********************************************         SAVE HOMERANGE         **************************************************
;*********************************************************************************************************************************

to save-homerange

  ; save the homerange polygon into a pdf
;  r:eval (word "pdf('" Homerange-poly_dir ".pdf')" )
;  r:eval (word "plot(homerange, xlim=c(" min-pxcor "," max-pxcor "), ylim=c(" min-pycor "," max-pycor "))")
;  r:eval "plot(spdf,col=as.data.frame(spdf)[,1],add=T)"
;  r:eval "dev.off()"
;
;  ; save a plot of the homerange area level into a pdf
;  r:eval (word "pdf('"Homerange-plot_dir".pdf')")
;  r:eval "plot(mcp.area(spdf,unout='m2'))"
; ; r:eval (word "plot(mcp.area(spdf,unout='m2'), main=Homerange polygon for "No.-of-days" days with "Shade-patches" shade and "Food-patches" food patches)")
;  r:eval "dev.off()"

end


;*********************************************************************************************************************************
;***********************************************         CREATE AND UPDATE SUN         *******************************************
;*********************************************************************************************************************************

to create-sun
  create-suns 1
  [
    set shape "orbit 1" ;"clock"
    set size 5
    set color yellow
    setxy (max-pxcor - 3) (max-pycor - 3)
    set heading 270
    set label (word 0 "  " "days")
    set heading zenith
    set label zenith
    ]
end

to update-sun
  ask suns
  [set heading heading + 0.5
    set label (word precision (ticks * 2 / 60 / 24) 1 "  " "days")
    ifelse (heading > 270) or (heading < 90)
    [set shape "orbit 1"
      set color yellow]
    [set shape "moon zenith"
      set size 5
      set color [pcolor] of patch-here]
    set heading zenith
    set label ticks
  ]
end

;*********************************************************************************************************************************
;*******************************************           REFERENCES         ********************************************************
;*********************************************************************************************************************************

; Auburn, Z. M., Bull, C. M. and Kerr G. D. (2009) The visual perceptual range of a lizard, Tiliqua rugosa, J. Ethol. 27:75-81.
; Brown, G. W. (1991) Ecological feeding analysis of south-eastern Australian Scincids  (Reptilia--Lacertilia), Aust. J. Zool. 39:9-29.
; Kooijman, S. A. L. M. (2010) Dynamic Energy Budget theory for metabolic organisation. Cambridge University Press.
; Norman, H. C., Mayberry, D. E., McKenna, D. J., Pearce, K. L. & Revell D. K. (2008) Old man saltbush in agriculture: feeding value for livestock production systems, 2nd International Salinity Forum: Salinity, water and society--global issues, local action.
; Pamula Y (1997) Ecological and physiological aspects of reproduction in the viviparous skink Tiliqua rugosa, Ph.D. thesis, Flinders University.
@#$#@#$#@
GRAPHICS-WINDOW
386
10
1155
800
375
375
1.011
1
10
1
1
1
0
0
0
1
-375
375
-375
375
1
1
1
ticks
30.0

BUTTON
7
502
70
535
NIL
setup
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

BUTTON
136
502
217
535
go once
go
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

BUTTON
72
502
135
535
NIL
go
T
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

MONITOR
804
856
939
901
Time spent feeding
feedcount
17
1
11

PLOT
1165
762
1645
1011
Total wetmass plot
Time
Total wetmass
0.0
10.0
0.0
10.0
true
true
"" "let total 0\n\nset-current-plot-pen \"V_pres\"\nplot-pen-up plotxy ticks total\nset total V_pres + total \nplot-pen-down plotxy ticks total\n\nset-current-plot-pen \"wetstorage\"\nplot-pen-up plotxy ticks total\nset total wetstorage + total \nplot-pen-down plotxy ticks total\n\n\nset-current-plot-pen \"wetfood\"\nplot-pen-up plotxy ticks total\nset total wetfood + total\nplot-pen-down plotxy ticks total\n\nset-current-plot-pen \"wetgonad\"\nplot-pen-up plotxy ticks total\nset total wetgonad + total\nplot-pen-down plotxy ticks total"
PENS
"V_pres" 1.0 0 -955883 true "" ""
"wetstorage" 1.0 0 -6459832 true "" ""
"wetfood" 1.0 0 -13840069 true "" ""
"wetgonad" 1.0 0 -5825686 true "" ""

OUTPUT
424
960
868
1267
13

INPUTBOX
6
572
111
632
Movement-cost
1.0E-9
1
0
Number

INPUTBOX
118
571
223
631
Maintenance-cost
43.612
1
0
Number

INPUTBOX
10
758
91
818
Food-growth
30
1
0
Number

TEXTBOX
8
546
158
564
Energy cost of individual
12
0.0
0

TEXTBOX
11
737
122
755
Food patch growth
12
0.0
0

INPUTBOX
9
666
100
726
Low-food-gain
3000
1
0
Number

TEXTBOX
8
642
158
660
Energy gain of individual
12
0.0
0

INPUTBOX
173
852
273
912
Minimum-reserve
100
1
0
Number

TEXTBOX
12
829
130
847
Individual attributes
12
0.0
1

INPUTBOX
97
758
201
818
Large-food-initial
6000
1
0
Number

INPUTBOX
207
759
311
819
Small-food-initial
3000
1
0
Number

PLOT
1165
10
1642
254
Reserve level and starvation reserve over time
Time
Reserve (J/cm^3)
0.0
10.0
0.0
10.0
true
true
"" ";let t reserve-plot-range \n;if ticks > t                               \n;[set-plot-x-range (ticks - t) ticks]"
PENS
"Reserve level" 1.0 0 -16777216 true "" "if any? turtles\n[plot [reserve-level] of turtle 0]"
"Starvation reserve" 1.0 0 -5298144 true ";plot Minimum-reserve\nauto-plot-off\nplotxy 0 Minimum-reserve \nplotxy 100000000 0\nauto-plot-on" ""

TEXTBOX
7
137
157
155
Individual characteristics\n
12
0.0
0

TEXTBOX
7
12
215
134
*********************************\n**********  Instructions **********\n*********************************\n\n1. Set the foraging strategy of the \n    individual using the chooser. \n    Read the notes within the Info \n    tab to learn about the strategies.
12
125.0
1

TEXTBOX
8
463
239
492
4. 'Setup' generates the landscape. \n    'Go' runs the model. \n\n
12
125.0
1

INPUTBOX
6
257
98
317
Shade-patches
100000
1
0
Number

INPUTBOX
100
257
190
317
Food-patches
100000
1
0
Number

TEXTBOX
7
212
303
242
2. Define the number of food and shade patches \n    in the landscape, and the simulation length.
12
125.0
1

TEXTBOX
425
932
790
962
Output of model results.
12
0.0
1

INPUTBOX
12
852
167
912
Maximum-reserve
7222.30069902594
1
0
Number

PLOT
1165
517
1644
754
Global time budget
Time
Frequency of activity states
0.0
10.0
0.0
10.0
true
true
"" "let total 0\n\nset-current-plot-pen \"Starving\"\nplot-pen-up plotxy ticks total\nset total starvecount + total \nplot-pen-down plotxy ticks total\n\nset-current-plot-pen \"Resting\"\nplot-pen-up plotxy ticks total\nset total restcount + total \nplot-pen-down plotxy ticks total\n\n\nset-current-plot-pen \"Transcount\"\nplot-pen-up plotxy ticks total\nset total transcount + total\nplot-pen-down plotxy ticks total\n\nset-current-plot-pen \"Searching\"\nplot-pen-up plotxy ticks total\nset total searchcount + total\nplot-pen-down plotxy ticks total\n\nset-current-plot-pen \"Feeding\"\nplot-pen-up plotxy ticks total\nset total feedcount + total\nplot-pen-down plotxy ticks total\n\n;let t2 time-budget-range\n;if ticks > t2         \n;[set-plot-x-range (ticks - t2) ticks]"
PENS
"Feeding" 1.0 1 -10899396 true "" ""
"Searching" 1.0 1 -13345367 true "" ""
"Transcount" 1.0 1 -7500403 true "" ""
"Resting" 1.0 1 -16777216 true "" ""
"Starving" 1.0 1 -2674135 true "" ""

PLOT
1647
11
2104
254
Spatial coordinates of transition between activity states
Xcor
Ycor
-25.0
25.0
-25.0
25.0
true
false
"set-plot-pen-mode 2\n;set-plot-pen-interval 5" ""
PENS
"pen-0" 1.0 0 -7500403 true "" ""
"Feeding" 1.0 2 -10899396 true "" ";ask turtle 0 [\n;if ([patch-type] of patch-here = \"Food\") and (activity-state = \"F\")\n;[plotxy xcor ycor]\n;]\n\n; current working version 30-4-15 \n;ask turtle 0 [\n;if activity-state = \"F\"\n;[plotxy xcor ycor]\n;]\n\n;ask turtles with [activity-state = \"F\"] [\n;if [patch-type] of patch-here = \"Food\"\n;[plotxy xcor ycor]\n;]"
"Searching" 1.0 0 -13345367 true "" ";ask turtle 0 [if (activity-state = \"S\") or (activity-state = \"F\") or (activity-state = \"R\")\n;[plotxy xcor ycor]\n;]\n\nask turtle 0 [plotxy xcor ycor]"
"Resting" 1.0 2 -16777216 true "" "ask turtle 0 [\nif [patch-type] of patch-here = \"Shade\" \n[plotxy xcor ycor]\n]"

MONITOR
458
855
592
900
Number of transitions
transcount
17
1
11

SWITCH
200
173
318
206
show-plots?
show-plots?
0
1
-1000

MONITOR
615
806
798
851
Time spent searching for food
searchcount
17
1
11

MONITOR
614
857
798
902
Time spent searching for shade
shadecount
17
1
11

INPUTBOX
12
948
88
1008
Low-shade
10
1
0
Number

INPUTBOX
94
948
173
1008
High-shade
90
1
0
Number

TEXTBOX
13
924
95
942
Shade levels
12
0.0
1

INPUTBOX
194
257
273
317
No.-of-days
1
1
0
Number

PLOT
1166
262
1641
507
Body temperature (T_b)
Time
Body temperature
0.0
10.0
0.0
10.0
true
false
"" ""
PENS
"default" 1.0 0 -16777216 true "set-plot-y-range 0 max-T_b + 5" "if any? turtles\n[plot [T_b] of turtle 0]"
"T_opt_lower" 1.0 0 -2674135 true "auto-plot-off\nplotxy 0 [T_opt_lower] of turtle 0\nplotxy 1000000000 [T_opt_lower] of turtle 0\nauto-plot-on" ""
"T_opt_upper" 1.0 0 -2674135 true "auto-plot-off\nplotxy 0 [T_opt_upper] of turtle 0\nplotxy 1000000000 [T_opt_upper] of turtle 0\nauto-plot-on" ""

INPUTBOX
79
389
157
449
T_opt_lower
26
1
0
Number

INPUTBOX
9
389
74
449
T_b
19.05
1
0
Number

INPUTBOX
160
389
239
449
T_opt_upper
35
1
0
Number

TEXTBOX
10
365
230
395
Body temperature (T_b) of individual
12
0.0
1

TEXTBOX
9
328
284
358
3. Define body temperature (T_b), plus lower \n    and upper critical thermal temperatures.
12
125.0
1

MONITOR
1647
262
1697
307
T_b
[T_b] of turtle 0
1
1
11

MONITOR
459
802
540
847
Activity state
[activity-state] of turtle 0
1
1
11

MONITOR
1648
311
1714
356
in-shade?
in-shade?
1
1
11

MONITOR
615
906
749
951
Time spent resting
restcount
17
1
11

MONITOR
1649
361
1728
406
Zenith angle
zenith
1
1
11

MONITOR
388
806
454
851
NIL
in-food?
17
1
11

MONITOR
804
904
887
949
eaten patches
count patches with [pcolor = 35]
17
1
11

MONITOR
1527
65
1638
110
Diff in reserve level
Maximum-reserve - [reserve-level] of turtle 0
3
1
11

PLOT
1730
259
2103
513
Difference in reserve level over time
NIL
NIL
0.0
5040.0
-10.0
10.0
true
false
"" ""
PENS
"default" 1.0 0 -16777216 true "plot Maximum-reserve - [reserve-level] of turtle 0" "plot Maximum-reserve - [reserve-level] of turtle 0"
"pen-1" 1.0 0 -7500403 true "auto-plot-off\nplotxy 0 0\nplotxy 1000000000 0\nauto-plot-on" ""

INPUTBOX
13
1042
125
1102
ctminthresh
120000
1
0
Number

TEXTBOX
13
1020
204
1048
Consecutive hours below min-T_b
11
0.0
1

MONITOR
804
806
960
851
Time spent under min-T_b
[ctmincount] of turtle 0
0
1
11

MONITOR
1529
117
1618
162
Energy gain
[energy-gain] of turtle 0
0
1
11

INPUTBOX
106
666
176
726
Gutthresh
0.75
1
0
Number

MONITOR
1529
165
1635
210
Gutfull
[gutfull] of turtle 0
3
1
11

INPUTBOX
1651
765
1737
825
V_pres
45.92071
1
0
Number

INPUTBOX
1652
828
1737
888
wetstorage
45.16531
1
0
Number

INPUTBOX
1653
957
1736
1017
wetgonad
0
1
0
Number

INPUTBOX
1652
893
1737
953
wetfood
2.1789
1
0
Number

PLOT
1656
516
2017
762
Gutfull
Time
Gut level
0.0
10.0
0.0
1.0
true
true
"" ""
PENS
"gutfull" 1.0 0 -16777216 true "" "plot [gutfull] of turtle 0"

INPUTBOX
244
389
309
449
Min-T_b
3.7
1
0
Number

INPUTBOX
314
389
379
449
Max-T_b
51
1
0
Number

MONITOR
1061
804
1151
849
NIL
searchcount
17
1
11

CHOOSER
6
160
98
205
Strategy
Strategy
"Optimising" "Satisficing"
0

PLOT
1741
768
2107
1018
Movement costs
Time
Movement cost (J/cm^3)
0.0
10.0
0.0
10.0
true
false
"" ""
PENS
"Movement cost" 1.0 0 -11221820 true "" ";plot [Movement-cost] of turtle 0\nplot precision sum movelist 10"

MONITOR
974
975
1124
1020
NIL
movelist
2
1
11

INPUTBOX
1165
1034
1692
1094
fh
/Users/malishev/Documents/Melbourne Uni/Programs/Sleepy IBM/Results/
1
0
String

CHOOSER
103
161
196
206
Shade-density
Shade-density
"Random" "Clumped"
1

MONITOR
388
856
454
901
NIL
in-shade?
17
1
11

MONITOR
2109
59
2256
104
NIL
Reserve-level
17
1
11

MONITOR
2108
10
2257
55
NIL
Maximum-reserve
17
1
11

MONITOR
2111
108
2334
153
NIL
Maximum-reserve - Reserve-level
17
1
11

@#$#@#$#@
> ##Version 6.1.1 (3-1-17)

> 6.1.1_two strategies_shadedens (5-6-17)
> Added further 'in-food?=FALSE' reporters to searching and resting activity states
> Added in-food? TRUE to handle-food procedure
> Removed extra restcount when Reserve-level = Maximum-reserve

> 6.1.1_two strategies_shadedens (1-5-17)
> Removed restcount counter when turtle is searching for shade.
> Added restcount to basking behaviour

> 6.1.1  (6-1-17)
> Set patch 0 0 as Shade

> 6.1.1_two strategies_shadedens (3-1-17)
> Added random and clumped shade patch distribution
> Matched food and shade patch output with input so initial food/shade patch load is divided by 10

> 6.1.1 (26-10-16)
> Added 'fh' variable to set file handle for exporting plots to local hard drive

>> In progress due to "NLCommand("set strategy", NL_strategy)" error in R ('RNL_new trans model_with DEB_1.6.1_olve_movement cost.R')

> 6.1.1 (25-10-16)
> Added movement cost plot and 'movelist' list to calculate cumulative sum of movement costs.

> 6.1.1 (24-10-16)
> Added movement cost to Socialise state (Optimising strategy). Movement cost now added to all movement phases (Searching, Socialising, Shade searching).

> 6.1.1 (19-10-16)
> Added miniscule movement cost (Movement-cost) to avoid turtle exiting green food patches for one time step when feeding.

> 6.1.1. (29-6-16)

> Added movement cost variable to 'to search' and 'to shade-search' procedures (set reserve-level reserve-level - Movement-cost).

> 6.1.1. (16-6-16)

> Changed all instances of Min-T_b and Max-T_b to T_opt_lower and T_opt_upper

> Two movement strategies: 1) move only when hungry or 2) move during all active hours, then feed when hungry. Gut threshold remains at <75% for both strategies.
>> Added 'socialise' procedure to make turtle move when in activity range and when gutfull > gutthresh, i.e. not hungry. Turtle searches for food if gutfull < gutthresh, i.e. hungry

>> Added (gutfull < gutthresh statement) to update-food-levels procedure so turtle doesn't deplete food when passing over patch

>> Added (gutfull < gutthresh) to activity-state = "S" procedure under Optimising strategy

> ##Version 6.1 (30-5-16)

> 6.1 (8-4-16)
> Updated spatial plot area to 750 x 750 patches (1500 x 1500 m)

> 6.1 (2-2-16)
> Converted report-results output to .csv. friendly file

> 6.1 (14-1-16)
> Added gutfull threshold to make turtle feed until gutfull reaches gutthresh level (0.75 or 1), then rest in open sun.

> Added gutfull variable and gutthresh parameter to update turtle gut levels from DEB.R and RNL model

> ##Version 6 (11-5-15)

> Added ctmincounter to tally time spent with Tb under min_T_b_ (critical thermal minimum)

> Fixed spatial plot update commands to correctly plot feeding and resting xy cords--used set-current-plot-pen function in 'to handle-food' procedure, separating food by plot pen color

> Turtle no longer dies--fixes homerange call command and NLGetAgentSet error in RNL model

> Added bounce procedure to make turtle turn a random ~180 degree angle when encountering x and y edges of landscape. This means world margins do not wrap.

> ##Version 5_DEB_no reserve (28-11-14)

> RNL_new trans model_with DEB_1.1.R updates reserve-level, T_b, food intake.

>> Reserve-level and Minimum-reserve should be commented out once gut model in RNL_new trans model_with DEB_1.1.R works.

> Food patches have random floats values to make turtle move to only one food patch

> Includes small and large food patches. Large food incurs twice the handling time (2 ticks).

>> Small food = 3000 J
>> Large food = 6000 J
>> Feeding rate = 3000 J (Low-food-gain) / tick
>> Energy gain = Small food * kap_X (0.8)
>> No min-energy because no food growth. Else, energy of food patch to limit incentive for turtle to revisit food immediately upon leaving food patch (Min-energy) = Small-food-initial

> No food growth

>> Food will grow with water bucket model to update soil moisture profile

> Movement and maintenance cost reduced by ten-fold

>> Maintenance cost should be commented out once DEB model works

> ##Version 5 (2-5-14)

> Basking temperature (T_b_basking) of turtle. When T_b is equal to or greater than T_b_basking and less than T_b_lower, turtle will be in shade but report "in-shade? false" (basking). When greater than T_b_upper, turtle will rest in shade but report "in shade? true.

> Shade level (10 or 90) of shade patches have random float values attached so turtle can choose max-one-of shade patches when confronted with a choice between two shade patches.

> ###Ongoing issues

> Under transient model input, turtle ignores feeding cue if hasn't found shade since start of simulation. Hence, misses feeding period for the day regardless of whether near food. To overcome this: 1) Could always start turtle on shade patch; 2) change make-decision strategy so turtle abandons resting state when within T_opt_range.

> Update reference list with Pamula thesis

#Overview
##Purpose

This soft version of the foraging sub-model focuses on an individual encountering food and shade patches in space and time under one of two contrasting foraging strategies, optimising or satisficing. The individual switches between three different activity states of searching for food, handling food, and resting. This activity generates a global time budget. Foraging performance is measured by the time spent in each state. Thus, we conceive a state-space model. Individuals aim to minimise starvation time. Therefore, the foraging strategy that returns a higher proportion of time spent feeding in the state-space representation is the dominant strategy.

###Questions

What foraging strategy returns a more efficient series of feeding bouts and			 limits starvation over time?

How does time in each activity state influence how the individual is distributed		 in space under the two strategies?

Which strategy performs better on a short hourly compared to a long daily time			 horizon?

###Hypotheses

Satisficing individuals switch less frequently between behavioural states on smaller spatial scales with lower food density.

Satisficing individuals under their risk avoiding strategy experience less starvation periods on long time scales.


## Entities, state variables, and scales

Global state variables of the model:
> Minimum energy of food patches

> Searching state time counter (numeric) [t]

> Feeding state time counter (numeric) [t]

> Resting state time counter (numeric) [t]

> Starvation time counter (numeric; defined by time with maximum vision) [t]

> Transition between activity states time counter (numeric) [t]

There are two entities implemented in the model: the individual and patches.

The individual represent a lizard species (Tiliqua rugosa) and owns the following state-variables:
> Reserve level (numeric value) [J]

> Activity state (factorial; Searching, Feeding, and Resting) []

> Foraging strategy (factorial; Optimising or Satisficing) []

> Search-threshold, below which an individual following the satisficing strategy 			switches from the resting state to the searching state (numeric value) [J]

> Vision radius (numeric; range limited) [m]

Patches are 2*2m in the model space and own the following state variables:
> Patch type (factorial; food patch, shade patch, and bare ground) []

> Energy level (numeric value) [J]


## Process overview and scheduling
Time is scheduled as discrete steps of two minutes.

The model consists of the following sub-modules:

--	Update reserves
--	Decision-making process
--	Searching for food
--	Handling food
--	Searching for shade
--	Resting state
--	Update of habitat variables

At the beginning of each two-minute time step, individuals incur a maintenance cost of 30 J and check their current reserve; if below a critical reserve threshold, the individual will die. Otherwise, the individual makes a decision on the next activity via the decision-making process, which depends on the chosen foraging strategy, current reserve, and current activity state.

The following pseudo code highlights this procedure:

> 	ask individuals
	[
	subtract maintenance cost
	check reserves
		if below a minimum threshold [ die ]
		otherwise [ execute foraging strategy ]
	]

Feeding

If the animal is currently feeding, it continues feeding until reaching a maximum threshold or until the exploitation of the food resource. Both scenarios shift the individual out of a feeding state into a resting state where the individual searches for shade.

Searching

When searching, individuals randomly search for food patches. Food intake and thus reserve level increase stepwise.

Resting

If the individual is currently in the resting state and has reserve above its search-threshold, it stays in this state, otherwise switches to the searching state.

Starvation

Starvation in this model is defined by time not in a feeding state. Starvation periods form a proportion of the global time budget. Only with critical reserves do individuals modify their search strategy to move to the closest available food patch.

Vision

Individual possesses a vision radius, receptive to the nearest food patch and sensitive to reserve. Vision has a minimum radius of spatial units, which increases linearly with depleting reserve of the individual until reaching a maximum level, both defined by state variables. Time spent in the maximum vision range defines the starvation period.

If food patches are absent from the vision range, the individual each time step moves randomly one patch further if under a searching state. If one food patch is in the vision range, the individual aborts a random search strategy and moves to the nearest available food patch.

Patches

Food patches grow by increasing their energy stepwise. Patches check their state variables at each time step to verify their occupancy by an individual in a feeding state, thus reducing its energy-level stepwise until reaching a minimum energy level defined by a global state variable (under feeding state).

Time counter

Transition between activity states increases the activity state counter by 1 tick. Time spent in all states is tallied in 1 tick increments.


### Process

Searching

Individuals move around the environment and lose 217 J per time step in addition to the maintenance cost. Encounter rate with food patches increases energy. Individuals gain 200 and 500 J per small (yellow) and large (green) food patch, respectively.


The following pseudo-code defines the searching procedure:

> 	to execute foraging strategy
		ask individuals
		[
		move randomly
			if food found within vision range
			[move-to food patch]
		]

Handling

Handling time of small and large food patches is two and four ticks, respectively. Conversion of food to usable energy incurs a cost (conversion efficiency of 0.8).

Decision making

Individuals follow one of two foraging strategies.

Satisficing
Individuals follow a demand energy system where food intake is guided toward meeting energy demands and costs only. Individuals satisfy their energy needs by consuming what is currently needed for maintenance and growth. Long patch residence time means an individual requires more time to satisfy energy needs.

Optimising
Individuals follow a supply energy system where food intake decisions are energy maximising depending on total available energy in the environment. Individuals follow rules for leaving food patches based on the Marginal Value Theorem and feed in a patch until the energy intake is lower than the average energy intake of all available patches in the environment. The patch residence time can equal that of satisficing when food patch density is low.

Under both strategies, when reserve falls to a critical value of 5000 J, individuals are at risk of fatal starvation.

Under satisficing, the individual's vision range widens to encompass a greater number of potential food patches. Individuals then abandon random searching and target and move to the closest available food patch.


### Initialisation

At the beginning of the simulation, a fixed number of patches are identified randomly as food patches and attributed small or large food values. Shade patches are also randomly identified. The individual is placed randomly in the landscape with 200,000 J of reserve. Foraging strategy is permanent once model begins. The start activity is set to 'Searching'.


## EXTENDING THE MODEL

See 'Overview, Design concepts, and Details (ODD) protocol for Tiliqua rugosa foraging model' for full model.

## NETLOGO FEATURES

N/A

## RELATED MODELS
For full model see Overview, Design concepts, and Details (ODD) protocol for Tiliqua rugosa foraging model.

## CREDITS AND REFERENCES

Copyright Matt Malishev 2014

Auburn, Z. M. & Bull, C. M (2009) The visual perceptual range of a lizard, Tiliqua rugosa, J. Ethol. 27:75-81
Brown, G. W. (1991) Ecological feeding analysis of south-eastern Australian Scincids  (Reptilia--Lacertilia), Aust. J. Zool. 39:9-29.
Kooijman, S. A. L. M. (2010) Dynamic Energy Budget theory for metabolic organisation. Cambridge University Press.
Norman, H. C., Mayberry, D. E., McKenna, D. J., Pearce, K. L. & Revell D. K. (2008) Old man saltbush in agriculture: feeding value for livestock production systems, 2nd International Salinity Forum: Salinity, water and society--global issues, local action.
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