Eelgrass Model v2.10

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;;;;;;;; VARIABLE DECLARATIONS ;;;;;;;
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extensions [array]
globals [
  x y                               ; x and y coordinates, in meters
  month                             ; integer representing the month (from 0-12)
  month-name                        ; array of month names, from JAN-DEC
  temperature                       ; average water temperature, in C
  initial-extent-eelgrass           ; count of how many seedlings we planted
  max-extent-eelgrass               ; the maximum extent of the meadow (largest veg-mass amount)
  seed-germination                  ; the probability of seed germination and survival (decimal)
  simulation-started                ; alerts the free draw mode that the simulation is actively running
]
breed [eelgrasses eelgrass]         ; each eelgrass turtle is a clump of eelgrass representing many shoots
breed [green-turtles green-turtle]  ; each green-turtle turtle is a literal sea turtle
eelgrasses-own [
  veg-mass                          ; the biomass of eelgrass shoots, in gC/m2
  rhizome-mass                      ; the biomass of eelgrass root & rhizomes, in gC/m2
  epiphyte                          ; the biomass of epiphyte growth, in gC/m2
  age                               ; the birth month (planting month) of the eelgrass seedling (tick)
  seeds                             ; the maximum biomass of the eelgrass clump (used for computing seeds)
]
green-turtles-own [energy]          ; energy represents the turtles' stomach and fat stores
turtles-own []
patches-own [
  depth                             ; mean water depth, neglecting tides [Wetzel (1986) found no tidal impact]
]



;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;; MODEL SETUP ;;;;;;;;;;;;
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to setup
  clear-all                         ; reset everything to NetLogo default
  reset-ticks                       ; reset ticks to 0
  set simulation-started false      ; alerts free draw mode that we're in setup mode

  ;; Set up the calendar and initial water temperature
  set month 10       ;Calendar month in ordinal numbers: 10=October.
  set temperature 16.25 - 13.75 * (cos(360 * (month + .5) / 12 - 25)) ; from Buzzelli et al (1999)
  set temperature temperature + Global-Warming ;for experiment
  set month-name array:from-list [ "JAN" "FEB" "MAR" "APR" "MAY" "JUN" "JUL" "AUG" "SEP" "OCT" "NOV" "DEC" ]
  Display-month-year                ; Display the month and year so we can see it on the setup screen

  ;; Set the contour of the seafloor (water depth)
  ask patches [
    setup-depth
  ]

  ;; All new turtles will be eelgrass shape unless otherwise specified
  set-default-shape eelgrasses "eelgrass"

  ;; Plant the initial crop of eelgrass in the pattern specified by the pick-list
  plant-initial-eelgrass-pattern

  ;Remember how much eelgrass we planted so that we can tell the % increase in growth
  set initial-extent-eelgrass count eelgrasses        ; # of initial seedlings
  set max-extent-eelgrass initial-extent-eelgrass     ; the initial max = initial seedlings
end 



;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;; MODEL GO ;;;;;;;;;;;;;;
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to go
  ;This model represents the passage of time for a small section of the Chesapeake Bay.
  ;Each tick represents one month in time.  The water temperature changes per month.
  set month month + 1
  if month > 12 [set month 1]
  ;set the water temperature depending on which month it is
  set temperature 16.25 - 13.75 * (cos(360 * (month + .5) / 12 - 25)) ; from Buzzelli et al (1999)
  Display-Month-Year

  ;Alert free draw mode that the simulation has started so that it will stop resetting ticks to 0
  set simulation-started true

  ;Don't start the model if the user didn't plant any eelgrass
  if ticks = 0 and count eelgrasses = 0 [
    user-message ["You must plant some eelgrass, either by using a preset pattern, or by using free plant mode and manually picking a pattern."]
    stop
  ]

  ;; Model the migration of green turtles
  ;; A user-specified number of green turtles will migrate into this area every spring
  if month = 5 [
    ;Green Turtles migrate into the bay in late spring (May)
    set-default-shape green-turtles "turtle"
    create-green-turtles migrating-green-turtles  ;; create the turtles, then initialize their variables
    [
      set color black
      set size 1.5               ;; easier to see, though a bit exaggerated in size
      set energy 4               ;; Assume each turtle has some fat and has eaten a recent meal
      move-to one-of eelgrasses  ;; Seek out the nearest eelgrass to eat
    ]
  ]
  ;; Green turtles migrate out of the bay in mid-Sept (deleted from the model in Oct)
  if month = 10 [
    ask green-turtles [die]   ; All green turtles either leave or die
  ]

  ;; Model the growth of eelgrass
  ;; Use Jarvis et al (2014), Buzzelli et al (1999) and Wetzel & Neckles (1986) model equations,
  ;; adapted for agent-based modeling.
  ask eelgrasses [
    grow-eelgrass                ; metabolic growth demon
    rhizome-eelgrass             ; rhizone reproduction demon
  ]


  ;; Model the behavior of green turtles based on a simple grazing model
  ;; Turtles will seek out the closest eelgrass and eat it
  repeat 30 [                    ; repeat each day for each month (30 times per tick)
    ask green-turtles [
      move                       ; movement demon (move to eelgrass)
      set energy energy - 1      ; metabolism requires energy (digestion & fat stores)
      eat-eelgrass               ; grazing demon
      death                      ; mortality demon
    ]
  ]

  ;If this was the new seasonal high for eelgrass growth, remember it
  let present-extent-eelgrass sum [veg-mass] of eelgrasses
  if present-extent-eelgrass > max-extent-eelgrass [
    set max-extent-eelgrass present-extent-eelgrass
  ]

  ;Release seeds in late summer; model as released in Oct so that
  ;the seeds will germinate in Nov.
  if month = 10 [
    ; Equation from Jarvis et al(2014) adapted assuming 3cm seed burial and 1.25% SOC (.
    ; Seed-germination represents the percent chance of seed germinating and surviving
    ; Seed-survival is a user-entered base probability of seed survival
    set seed-germination seed-survival * 0.4 / (1 + e ^ ( -0.1432 + (1.1261 * 0.03) - (1.3964 * .0125)) )
    ask eelgrasses [
      seed-eelgrass              ; seed reproduction demon
    ]
  ]

  tick
  if ticks = Months-of-experiment [stop] ;stop after a user-input number of months, usually 60-72 months

  ;stop if all the eelgrasses are dead or eaten
  if count eelgrasses = 0 [
    user-message ("All the eelgrass has died or been eaten.  Very sad.  Fortunately, this was just a computer simulation!")
    stop
  ]
end 



;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;; EELGRASS GROWTH ;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

to grow-eelgrass
  ;; This subroutine models the growth of a particular groups of shoots of eelgrass represented by each turtle
  ;; This growth is based upon models by Verhagen et al and Jarvis et al (2014)
  ;; and varies by month, depth (vs plant height), water temperature, and water turbidity
  ;;
  ;; The maximum size of a shoot in this model is 1m, and is tracked by the turtle size property.
  ;; For simplification purposes, biomass is modeled as proportionate to size.

  ;Jarvis et al (2014) equations for Z. Marina (based on Buzzelli):
  ;vegatative biomass: Czms=Czms(t-dt)+(Pzms+Tczmss-Mzms-Rzms-Td)dt
  ;rhizome biomass: Czmr=Czmr(t-dt)+(Td+Tczmsr-Mzmr-Rzmr)dt
  ;Td = translocation down from shoots to roots = Tzms
  ;  Tzms = 0.3 (unitless)
  ;Pzms = Z. marina shoot production = unknown
  ;Tczmss = transfer of seedling biomass to vegetative shoot biomass
  ;Tczmsr = transfer of seedling biomass to rhizome biomass
  ;Mzms = shoot mortality = MRzms = 0.007/day
  ;Mzmr = rhizome mortality = MRzmr = 0.000085/day (jan-jun) or 0.0095/day (jul-dec)
  ;Rzms = shoot respiration
  ;Rzmr = root and rhizome respiration, Arrhenius relationship at optimal 20C
  ;  RRzmr = root respiration at 20C = 0.0005/day
  ;  THETAzmr = root and rhizome Arrhenius constant = 1.25 (unitless)
  ;Td = translocation down, shoot-to-rhizome transfer = Tzms
  ;Tzms = Z. marine shoot-to-root transfer = 0.3 (unitless)
  ;Note: Jarvis calculated mortality as a fraction in the biomass model, but we will calculate it
  ;probabilistically and separately.

  ;Buzzelli et al (1999) equations for Z. Marina (based on Wetzel):
  ;Czs(t) = shoot carbon
  ;       = Czs(t-dt) + (Pzs - Rzs - Mzs - Tzc)dt
  ;Czr(t) = rhizome carbon
  ;       = Czr(t-dt) + (Tzc - Rzrr - Mzrr)dt
  ;Tzc = translocation, shoot to rhizome
  ;Pmzm = maximum photosynthesic rate
  ;     = (0.0025*T + 0.0049) * (1 - (Tw-25)/10) per day
  ;  Tw = water temperature, approximated seasonally using Wetzel's sinusoidal model (1986)
  ;Rzs = shoot respiration
  ;    = PRzs*(0.00317*(Tw+0.105)+e(0.135*Tw-10.1)) per day
  ;Rzrr= root and rhizome respiration, Arrhenius relationship at optimal 20C
  ;    = Rkzr & THETAzr ^ (Tw-Topt)
  ;    = 0.0005 * 1.25 ^ (Tw - 20)
  ;  Rkzr = root respiration at 20C = 0.0005/day
  ;  THETAzmr = root and rhizome Arrhenius constant = 1.25 (unitless)
  ;FBzsc = feedback relationship between maximum and limiting shoot biomass levels
  ;      = (Czs - Climzs) / (Cmaxzs - Climzs)
  ;      = (Czs - 100) / 100
  ;Czs   = shoot biomass
  ;Climzs = 100
  ;Cmaxzs = 200
  ;Does Td = 0.3*FBzsc ?? Buzzelli describes this but doesn't explicitely show it
  ;Cepi = Epiphyte biomass
  ;     = Depi(t-dt) + (Pepi - Repi - Mepi - Gepi)dt
  ;Pij = Photosynthesis rate coefficient
  ;    = Pmax(t)*[PARvp / (Ik' + PARvp)]
  ;Gepi= grazing
  ;Pmepi=epiphyte photosynthesis
  ;     =0.0091 * Tw * [1.0 - (Tw-25)/20)]
  ;PARzm=photosynthetically active radiation reaching the eelgrass
  ;     =PARh * (1 - (.75 * sqrt(Cepi/Czs/2.9) ) )
  ;PARh = depth corrected for habitat
  ;     = PAR0 * e^(-kd*hhab)
  ;   kd= light extinction coefficient, function of chlorophyll, POC and DOC
  ;     = 0.04
  ; hhab= habitat depth (m)

  ;Wetzel & Neckles (1986) equations for Z. Marina (based on Wiegart):
  ;Fij = Carbon transfer from CO2 into eelgrass leaves, general form
  ;    = Pij*Xj*[1-FBij)(1-(GBjj*Cjj))]
  ; Xj = Leaf biomass
  ; Cij= metabolic correction rate
  ;    = 1.0 - (Rj / Pij)
  ;Pmax= linear statistically fitted function represented light-saturated rate at tempereature (t)
  ;PARvp = photosynthetically active radiation, or intensity of light reaching the leaves
  ;Ik' = half-saturation PAR intensity, based upon assumption that fresh new leaves were epiphyte-free
  ;FBij=non-linear feedback function of CO2 concentration
  ;    =1 - [(Xi - Gij) / (Aij - Gij)]
  ; Xi =CO2 concentration
  ; Aij=CO2 concentration below which carbon became limiting
  ; Gij=CO2 concentration at which photosynthesis by eelgrass became zero
  ;FBjj=non-linear feedback function of metabolic limitations (crowding, nutrients, etc.)
  ;NOTE: Wetzel assumed Td was 17% of net leaf organic matter production, reduced
  ;when either above or below-ground compartments became limiting.
  ;Wetzel found epiphye:eelgrass biomass ratio was 0.04 during early spring and 1.5 during the late-summer decline
  ;PAR reaching the plant was reduced 22% due to epiphytes and another 10% due to epiphyte-limited CO2 diffusion.
  ;Maximum density was set at 150gC/m2 in the density feedback as this is the densest observed in the Chesapeake

  ;; Programming note: these calibration levels worked well during model validation.
  ;Td-Calibration = 4.1
  ;Rzms-Calibration = 1.0
  ;Rzmr-Calibration = 3.3
  ;mortality-calibration = 0.1
  ;max-clumps-per-patch = 10
  ;Rhizome-shoot-distance = .50

  ;;Eelgrass metabolic equations
  let PARzm  e ^ (-0.4 * ([depth] of patch-here)) * (1 - .32) ;represents light decrease from epiphytes and depth, from Wetzel 1986.
  let Pzms PARzm * (0.0025 * (temperature - 10 ) + 0.0049) * (1 - (temperature - 35) / 10)   ;adapted from Buzzelli et al (1999)
  if Pzms < 0 [set Pzms 0]
  let Tczmss  0 ;transfer of seedling biomass to vegetative shoot biomass
  let Rzms  Pzms * veg-mass * Rzms-calibration * (0.00317 * (temperature + 0.105) + e ^ (0.135 * temperature - 10.1)) ;from Buzzelli et al (1999)  *Pzms??
  ;if temperature <= 14 [set Rzms 0] ;Jarvis et al 2014: reduce respiration to 0 below 14C.
  let Rzmr  0.0005 * rhizome-mass * Rzmr-calibration * (1.25 ^ (temperature - 20) + 2)  ;adapted from Buzzelli et al (1999)
  let MRzms  0.0095   ; (jul-dec)
  if month < 7 [set MRzms  0.000085] ; (jan-jun)
  set MRzms MRzms * mortality-calibration

  let Tflower 0                                                               ;Initially assume no flower/seed production
  if month >= 6 and temperature < 21 and age > 12 [set Tflower veg-mass * .1] ;Calculate flower / seed production for flowering plants

  ;Td = translocate down biomass from shoots to rhizome
  let Td .3 * Td-calibration * (veg-mass) / 100 ;adapted from Jarvis et al (2014) and Buzzelli et al (1999)
  if Td < 0 [set Td 0] ;no translocation up, just translocation down
  if veg-mass > 0 or month < 7  [ ;Inhibit regrowth of died-off shoots in late summer/fall
    set veg-mass veg-mass + 30 * (Pzms - Rzms - Tflower) ; adapted Jarvis et al (2014) equation
  ]
  if veg-mass < 0 [set veg-mass 0] ; cannot have negative vegetative mass
  ifelse (veg-mass > (30 * Td))    ; if there is shoot biomass to translocate into the rhizome
    [ set veg-mass veg-mass - 30 * Td]    ;translocate shoot biomass into the rhizome if that biomass exists
    [ set Td veg-mass / 30                ;translocate all remaining shoot biomass to translocate
      set veg-mass 0]
  set rhizome-mass rhizome-mass + 30 * (Td - Rzmr) ;  Jarvis et al (2014) equation

  ;let calibration-constant .1 ;converts biomass equations to model clumps - not yet fully implemented

  ;Check for random mortality based on Jarvis et al values
  if random-float 1 < MRzms * 30 [die]


  ;Estimate the amount of seeds as proportionate to the maximum vegetative mass of the eelgrass.
  if veg-mass > seeds and (ticks - age) > 12 [set seeds veg-mass]

  ;Render the visual model based on shoot biomass, but not smaller than size 0.5.
  set color green - 2
  ifelse veg-mass > 1.5
    [set size veg-mass / 3]
    [set size .5]
end 



;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;; EELGRASS RHIZOME GROWTH ;;;;;;;
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to rhizome-eelgrass
  ; Simulates new rhizome reproduction sprouting at a random point near the parent shoot
  ; A new sprout is hatched if the plant is mature enough and the immediate area is not already overcrowded
  if ((veg-mass > .8) or (veg-mass > .8 * [depth] of patch-here)) and count eelgrasses-here <= Max-clumps-per-patch  [
    hatch-eelgrasses 1 [                                       ; create a new clone of this clump
      set veg-mass 0                                           ; Starts off with no shoots (yet)
      set epiphyte 0                                           ; No epiphtye without shoots to grow on
      set rhizome-mass .01                                     ; Model a small piece of rhizome as a new plant
      set heading random 360                                   ; Sets the random direction the new clump will be
      forward (random-float (Rhizome-shoot-distance) + Rhizome-shoot-distance / 2) ;sets the random distance the new clump will be
      set size .1                                              ; Render as a very small dot
      set heading 0                                            ; Reset heading to 0 so that the eelgrass turtle looks like grass when it renders
    ]
    if rhizome-mass > 0.01 [set rhizome-mass rhizome-mass - 0.01] ;This rhizome mass just transferred to the new clump.
  ]
end 



;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;; EELGRASS SEED PROPAGATION ;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

to seed-eelgrass
  ;; algorithm model for ellgrass sexual reproduction through seeds
  ; Flowers and seeds grow between may/june and sept.  (http://seagrant.mit.edu/eelgrass/eelgrassscience/biology.html)
  ; germination is initiated below 20C, typically in November.
  ; Floating flowering shoots spread seeds throughout the bay.
  ; Eelgrass in the Chesapeake doesn't flower the first year (Jarvis et al, 2014).
  ; 10% of shoot density flowers when it's <21C in June.
  ; .33 seed predation rate

  ;The seeds variable stored information about vegetative mass of flower-producing shoots
  ;if seeds > 0, then this shoot flowered.
  if seeds > 0 [
    set seeds seeds / 3 ;reduce # of seeds due to predation (Jarvis et al, 2014)

    ;Estimate the probability of seed germination based on # of seeds in the clump
    ;The individual germination rate is very low but is multiplied by the # of seeds
    ;in each clump.
    if random-float (1) > (1 - seed-germination ^ seeds) [
      ifelse random (100) < 5
        ;Assume 5% of seeds are distributed purely randomly
        [ set x random (max-pxcor * 2 ) + min-pxcor
          set y random (max-pycor * 2 ) + min-pycor
          ;If this seed did not land in an overpopulated area, create a new eelgrass clump
          if count eelgrasses-at x y <= Max-clumps-per-patch  and x <= max-pxcor [
            hatch-eelgrasses 1 [
              set veg-mass 0
              set epiphyte 0
              set rhizome-mass .01
              set xcor x
              set ycor y
              set size .1
              set heading 0
            ]
          ]
        ]
        ;Assume prevailing rising tides normally carry seeds a logarithmic distance to the left
        [ let seed-angle 90 + random-float (10) - 5     ;Assume seeds are carried by the rising tide in the direction seed-angle
          let seed-distance e ^ random-float (5)        ;Seeds drop to the bottom after a random distance, seed-distance
          set x xcor + seed-distance * cos (seed-angle) ;Convert polar coordinate to (x,y)
          set y ycor + seed-distance * sin (seed-angle) ;Convert polar coordinate to (x,y)

          ;If this seed did not land in an overpopulated area or outside of the model area, create a new eelgrass clump
          if count eelgrasses-at x y <= Max-clumps-per-patch  and x <= max-pxcor [
            hatch-eelgrasses 1 [
              set veg-mass 0
              set epiphyte 0
              set rhizome-mass .01
              set heading seed-angle
              forward seed-distance
              set size .1
              set heading 0
            ]
          ]
        ]
    ]
  ]
end 



;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;; PLANT EELGRASS ;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

to plant-eelgrass
  create-eelgrasses 1 ;plant an eelgrass clump
  [
    set color yellow       ;; Color it yellow for visualization so that it's easy to see
    set shape "eelgrass"   ;; Make it eelgrass-shaped
    set veg-mass 0         ;; Starts off with no grass
    set rhizome-mass .01   ;; Starts off with a small amount of seedling/rhizome mass
    set size 1.5           ;; Exaggerate the size for visualization so that it's easy to see
    setxy x y              ;; Place the eelgrass at the coordinates x,y (global variables set before calling this subroutine)
    set heading 0          ;; Orient the eelgrass for display purposes so that it looks more realistic
    set age ticks          ;; Remember what month this eelgrass was planted
  ]
end 

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;; EELGRASS MISC ;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

to graze-eelgrass
  ;; algorithm representing grazing by waterfowl and other consumers.  This is not yet fully implemented.
  ; little grazing activity in the Chesapeake from NOV-MAR when water temps are <10C. (Wetzel, 1986)
  ; grazing populations decline mid-summer as predatory fish increase. (Wetzel, 1986)
  ; Green Turtle grazing handled via the eat-eelgrass subroutine
end 

to stress-eelgrass
  ;;algorithm representing environmental stress on eelgrass from water quality, waves, etc.
  ; at temps above 20C respiration increases at a greater rate than photosynthesis.  mortality above 25C.
  ; epophytic growth blocks sunlight
end 


;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;; SEA TURTLE BEHAVIOR ;;;;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

to move  ;; turtle procedure
  if count eelgrasses > 0 [                           ; If there are eelgrasses
    face min-one-of eelgrasses [distance myself]      ; turn towards the closes eelgrass
    fd 1                         ; swim 1 meter
  ]
end 

to eat-eelgrass  ;; herbivious animal procedure
  ;In this procedure, the animal eats a piece of eelgrass in its patch.
  let meal one-of eelgrasses-here                   ; Look for random nearby eelgrass
  if meal != nobody [                               ; If there is some eelgrass here,
    ask meal [                                      ; eat some eelgrass.
      set veg-mass veg-mass - turtles-eat           ; Reduce the eelgrass by what the turtle just ate.
      if veg-mass <= 0 [ die ]                      ; The eelgrass clump dies if the turtle ate all of it.
    ]
    set energy energy + 2                           ; Put that eelgrass in the turtle's belly.
    if energy > 20 [set energy 20]                  ; Don't exceed 20 energy (stomach + fat).
  ]
end 

to death  ;; turtle procedure
  ;; when energy dips below zero, die
  if energy < 0 [ die ]
end 



;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;; SETUP ROUTINES ;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

to setup-depth
  ;Create a slope to the bay floor.  Per Wetzel (1986), tidal variations do not influence
  ;estimated modeling coefficients in the Chesapeake, so depth is estimated as static.
  set depth (0 - pycor) / max-pycor * 0.75 + 1.25  ;Set depth at .5m (top of window) slowing linearally to 2.0m (bottom of window)
  set pcolor scale-color cyan depth 2.5 -1         ;Display deeper depths as a darker shade of cyan
end 

to Display-month-year
  ;; Display the month, year, and temperature (C) in the upper-right corner
  ask patch (max-pxcor - 1) (max-pycor - 3) [
    set plabel array:item month-name (month - 1)
    set plabel word word word word word plabel " " (floor ((ticks - 2) / 12) + Planting-Year + 1) ", " round temperature "C"
  ]
end 

to plant-initial-eelgrass-pattern
  ;; Eelgrass is planted in the pattern specified by the picklist

  ;; Plant a single clump in the center of the model
  if eelgrass-pattern = "Single clump" [
    set x 0
    set y 0
    plant-eelgrass
  ]

  ;; Plant a spaced 100m square with clumps every 5m
  if eelgrass-pattern = "100m Dotted Square"  or eelgrass-pattern = "100m Dotted Inscribed Square" [
    set x -50
    set y -50
    repeat 21 [
      plant-eelgrass
      set y y + 5
    ]
    set x 50
    set y -50
    repeat 21 [
      plant-eelgrass
      set y y + 5
    ]
    set x -45
    set y -50
    repeat 19 [
      plant-eelgrass
      set x x + 5
    ]
    set x -45
    set y 50
    repeat 19 [
      plant-eelgrass
      set x x + 5
    ]
  ]

  ;; Plant a spaced 100m line with clumps every 5m
  if eelgrass-pattern = "100m Dotted Line" [
    set x 0
    set y -50
    repeat 21 [
      plant-eelgrass
      set y y + 5
    ]
  ]


  ;; Plant a 100m square with clumps every 1m
  if eelgrass-pattern = "100m Square" or eelgrass-pattern = "100m Inscribed Square" [
    set x -50
    set y -50
    repeat 101 [
      plant-eelgrass
      set y y + 1
    ]
    set x 50
    set y -50
    repeat 101 [
      plant-eelgrass
      set y y + 1
    ]
    set x -49
    set y -50
    repeat 99 [
      plant-eelgrass
      set x x + 1
    ]
    set x -49
    set y 50
    repeat 99 [
      plant-eelgrass
      set x x + 1
    ]
  ]

  ;; Plant a 50m circle with clumps every 1m
  if eelgrass-pattern = "50m Circle" or eelgrass-pattern = "100m Inscribed Square" [
    let theta 0
    repeat 157 [                ; A 50m circle has a circumference of 157 and requires 157 clumps
      set x 25 * sin (theta)    ; Convert polar coordinates to cartesian for planting
      set y 25 * cos (theta)    ; Convert polar coordinates to cartesian for planting
      plant-eelgrass
      set theta theta + 2.293   ; At 25m radius, 2.293 degrees is a 1m arclength.
    ]
  ]

  ;; Plant a 50m circle with clumps every 5m
  if eelgrass-pattern = "50m Dotted Circle" or eelgrass-pattern = "100m Dotted Inscribed Square" [
    let theta 0
    repeat 31 [                ; A 50m circle has a circumference of 157 and requires 31 clumps 5.064, apart
      set x 25 * sin (theta)    ; Convert polar coordinates to cartesian for planting
      set y 25 * cos (theta)    ; Convert polar coordinates to cartesian for planting
      plant-eelgrass
      set theta theta + 11.612   ; At 25m radius, 2.293 degrees is a 1m arclength.
    ]
  ]

  ;; Plant a 50m grid with clumps 7m apart  (actually 49m, not 50m)
  if eelgrass-pattern = "50m Checkerboard" [
    set x -24.5
    repeat 7 [
      set y -24.5
      repeat 7 [
        plant-eelgrass
        set y y + 7
      ]
      set x x + 7
    ]
  ]
end 

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;; FREE PLANT MODE ;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

to free-plant
  ;If the user clicks while in free plant mode, plant a clump where the user clicked
  if mouse-down? [
    set x mouse-xcor
    set y mouse-ycor
    plant-eelgrass
  ]
  ;We tick to render the new seedling so the user can see it, but only if the model hasn't already been started
  if not simulation-started [
    ;Remember how much eelgrass we planted so that we can tell the % increase in growth
    set initial-extent-eelgrass count eelgrasses        ; # of initial seedlings
    set max-extent-eelgrass initial-extent-eelgrass     ; the initial max = initial seedlings

    tick                                                ; refresh the display so the user can see the new seedling
    reset-ticks                                         ; set ticks back to 0
    clear-plot                                          ; clears the output plot
  ]
end