AnimDens NetLogo

AnimDens NetLogo preview image

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Elphinstone_se_040 Miguel Pais (Author)

Tags

bias estimation 

Tagged by Miguel Pais almost 4 years ago

biology 

Tagged by Miguel Pais almost 4 years ago

ecology 

Tagged by Miguel Pais almost 4 years ago

ecosystem 

Tagged by Miguel Pais almost 4 years ago

fish 

Tagged by Miguel Pais almost 4 years ago

sampling 

Tagged by Miguel Pais almost 4 years ago

underwater visual census 

Tagged by Miguel Pais almost 4 years ago

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Click to Run Model

;AnimDens Model

;Original model implemented in R by Christine Ward-Paige et al.

;Adapted and implemented in NetLogo by Miguel Pessanha Pais


;FOR MORE INFORMATION, LOOK IN THE INFO TAB



;Global variables not represented in the main screen


globals[
  actual.area
  trans.viewangle
  stat.viewangle
  rov.viewangle
  transect.mean.speed
  roving.mean.speed
  transect.area
  stationary.area
]

;Agent types


breed [animals animal]

breed [transsurveyors transsurveyor] ;belt transect surveyor


breed [statsurveyors statsurveyor] ;stationary point count surveyor


breed [rovsurveyors rovsurveyor] ;roving surveyor     ; roving surveyors can't calculate densities accurately, yet they can estimate speceis richness and frequency of occurence.


;Agent variables


animals-own [
  speed
  species
]

transsurveyors-own [
  counted.animals
  speed
  memory
  t.bias
]


statsurveyors-own [
  counted.animals
  memory
  s.bias
]

rovsurveyors-own [
  counted.animals
  speed
  memory
]

;Setup and go procedures


to setup
  ca
  stop-inspecting-dead-agents                           ; clears surveyor detail windows from previous simulation runs

  resize-world 0 (area.width - 1) 0 (area.length - 1)
  set-patch-size (100 / area.length) * 10
  ask patches with [pycor mod 2 = 0 and pxcor mod 2 = 0] [set pcolor environment.color]   ; create background grid

  ask patches with [pycor mod 2 = 1 and pxcor mod 2 = 1] [set pcolor environment.color]
  ask patches with [pcolor = black] [set pcolor environment.color + 1]
  set actual.area world-height * world-width
  set trans.viewangle 180
  set stat.viewangle 160
  set rov.viewangle 160
  set transect.mean.speed (transect.speed / 60)  ; these 4 lines just convert interface speeds (in m/min) to m/s

  set roving.mean.speed (roving.speed / 60)

  ; on the original model, the final part of the sampled area of the transect is assumed to be a rectangle (transect.width x visibility.length)


  set transect.area transect.width * (transect.mean.speed * survey.time) + transect.width * visibility.length
  set stationary.area pi * stationary.radius ^ 2

; if animal density is set to some number, then use that to calculate the number of animals to deploy. Otherwise, just use the numb.animals.


  ifelse animal.density != 0 [set numb.animals ceiling actual.area * animal.density] [set animal.density numb.animals / actual.area]

  create-animals numb.animals [
   setxy random-xcor random-ycor
   set color animal.color
   set shape animal.shape
   set size 1
   set species "Sp1"                                          ; There is only one species, but this is what surveyors register and count

   set speed animal.mean.speed
  ]

if transect? [                                         ;transect surveyor setup

  create-transsurveyors 1 [
 set heading 0
 set shape surveyor.shape
 set color blue
 set size 2
 setxy (world-width / 2) (world-height / 2)
 if show.paths? [pen-down]                                                           ;this shows the path of the surveyor

 set speed transect.mean.speed
 set counted.animals [] ; sets counted.animals as an empty list

]
]

if stationary? [                                      ;stationary setup

  create-statsurveyors 1 [
 set heading 0
 set shape surveyor.shape
 set color red
 set size 2
 setxy (world-width / 2) (world-height / 2)
 set counted.animals [] ; sets counted.animals as an empty list

]
]

if roving? [                                          ;roving setup

  create-rovsurveyors 1 [
 set heading 0
 set shape surveyor.shape
 set color green
 set size 2
 setxy (world-width / 2) (world-height / 2)
 if show.paths? [pen-down]                                                           ;this shows the path of the surveyor

 set speed roving.mean.speed
 set counted.animals [] ; sets counted.animals as an empty list

]
]
 ask transsurveyors [                                           ; empty the memory of all surveyors

      set memory []
      ]
 ask statsurveyors [
      set memory []
      ]
 ask rovsurveyors [
      set memory []
    ]
reset-ticks
if show.surveyor.detail.windows? [
  if any? transsurveyors [inspect one-of transsurveyors]         ;here I had to use "if any?" because inspect will return an error if it finds nobody

  if any? statsurveyors [inspect one-of statsurveyors]
  if any? rovsurveyors [inspect one-of rovsurveyors]
]
end  ;of setup procedure


to go
  tick                                      ; time starts at 1 seconds (not 0)

  if ticks > survey.time [
    do.outputs
    stop]                                   ; end the simulation run when survey.time is reached, but include the last tick (if survey.time is 300, stop running at 301)

  if stationary.radius > visibility.length [
   output-print "ERROR: stationary.radius is set to a value greater than visibility.length"              ; if the stationary radius is higher than visibility, stop and output an error description

   output-print "The surveyor will not commit to sampling an area that it will not be able to see"
   output-print "Stopping simulation"
   stop
  ]
  ask transsurveyors [                                ; move the surveyors

   do.tsurveyor.movement
  ]
  ask statsurveyors [
   do.stsurveyor.movement
  ]
  ask rovsurveyors [
    do.rsurveyor.movement
  ]
  ask animals [                                    ; move the animals

    do.animal.movement
  ]
  ifelse count.time.step = 1 [                    ; if count.time.step is 1, ask surveyors to count animals every second

    ask transsurveyors [
     t.count.animals
   ]
    ask statsurveyors [
     s.count.animals
   ]
    ask rovsurveyors [
     r.count.animals
   ]] [                                          ; if count.time.step is not 1 (meaning it is 2), only ask every 2 seconds

   if ticks mod 2 = 0 [
    ask transsurveyors [
     t.count.animals
   ]
    ask statsurveyors [
     s.count.animals
   ]
    ask rovsurveyors [
     r.count.animals
   ]
     ]
   ]
end   ; of go procedure




;Observer procedures


to do.outputs
  ask transsurveyors [
    let real.count length counted.animals
    let expected.count animal.density * transect.area
    set t.bias (real.count - expected.count) / expected.count
    output-type "Transect surveyor bias was " output-print precision t.bias 2           ; outputs bias with 2 decimal places

  ]

 ask statsurveyors [
    let real.count length counted.animals
    let expected.count animal.density * stationary.area
    set s.bias (real.count - expected.count) / expected.count
    output-type "Stationary surveyor bias was " output-print precision s.bias 2
 ]

 ask rovsurveyors [
    let real.count length counted.animals
    output-type "Roving surveyor swam " output-type survey.time * roving.mean.speed output-type "m and counted " output-type real.count output-print " animals"                     ; the roving surveyor only tells how many animals it counted

 ]
end 

to calculate.bias
ifelse choose.method = "transect" [
ifelse any? transsurveyors [
output-print "The real value using the transect method is"
output-print precision (observed.value / transect.factor.value) 3]
[output-print "You need to re-run the model with this method enabled"
  stop
]
] [
ifelse any? statsurveyors [
output-print "The real value using the stationary method is"
output-print precision (observed.value / stationary.factor.value) 3
] [
output-print "You need to re-run the model with this method enabled"
stop
]]
end 



;animal PROCEDURES



;animal movement


to do.animal.movement
  set heading heading + random-float-between (- animal.dir.angle) animal.dir.angle
  fd speed ; each step is a second, so the speed is basically the distance

end 




;SURVEYOR PROCEDURES



;Transect surveyor procedures


to do.tsurveyor.movement
  fd speed ; each step is a second, so the speed is basically the distance

end 

to t.count.animals
  let myxcor xcor
  let seen.animals animals in-cone visibility.length trans.viewangle
  let eligible.animals seen.animals with [(xcor > myxcor - (transect.width / 2)) and (xcor < myxcor + (transect.width / 2))]  ; this only works for transects heading north, of course

  let surveyor.memory memory
  let new.animals eligible.animals with [not member? who surveyor.memory] ; only animals that were not previously counted are counted

  if any? new.animals [
    let new.records ([species] of new.animals)
    set counted.animals sentence counted.animals new.records
    set memory sentence memory [who] of new.animals
  ]
end 


;Stationary surveyor procedures


to do.stsurveyor.movement
  set heading heading + stationary.turning.angle           ; each second the surveyor rotates "stationary.turning.angle" degrees clockwise

end 

to s.count.animals
  let eligible.animals animals in-cone stationary.radius stat.viewangle
  let surveyor.memory memory
  let new.animals eligible.animals with [not member? who surveyor.memory] ;only animals that were not previously counted are counted

  if any? new.animals [
    let new.records ([species] of new.animals)
    set counted.animals sentence counted.animals new.records
    set memory sentence memory [who] of new.animals
  ]
end 

;Roving surveyor procedures


to do.rsurveyor.movement
  if ticks mod 2 = 0 [set heading heading + random-float-between (- roving.turning.angle) roving.turning.angle]         ;turn every 2 seconds

  fd speed ; each step is a second, so the speed is basically the distance

end 

to r.count.animals
  let eligible.animals animals in-cone visibility.length stat.viewangle
  let surveyor.memory memory
  let new.animals eligible.animals with [not member? who surveyor.memory] ; only animals that were not previously counted are counted

  if any? new.animals [
    let new.records ([species] of new.animals)
    set counted.animals sentence counted.animals new.records
    ; ask new.animals [set color red wait 1 set color gray]   ;for troubleshooting

    set memory sentence memory [who] of new.animals
  ]
end 

;reporters


to-report random-float-between [a b]
  report random-float (b - a + 1) + a
end 

to-report t.bias-result        ; these reporters are outputs for BehaviourSpace experiments

  report [t.bias] of one-of transsurveyors  ; one-of makes it output a single number instead of a list with one value (a list would be [34] instead of 34)

end 

to-report s.bias-result
  report [s.bias] of one-of statsurveyors
end 

to-report stationary.factor.value
  report s.bias-result + 1
end 

to-report transect.factor.value
  report t.bias-result + 1
end 

There are 7 versions of this model.

Uploaded by When Description Download
Miguel Pais about 2 years ago Model version 2.0. Updated to NL6 Download this version
Miguel Pais about 3 years ago World is now 100x100 Download this version
Miguel Pais over 3 years ago World is now 200x200, new diver shape, background grid, interface overhaul. Download this version
Miguel Pais almost 4 years ago Info tab text revised. Added new shape for divers. Download this version
Miguel Pais almost 4 years ago Added contact info. World changed from black to dark blue. Download this version
Miguel Pais almost 4 years ago Just adds the link to the model in the info tab Download this version
Miguel Pais almost 4 years ago Initial upload Download this version

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AnimDens NetLogo.png preview preview about 2 years ago, by Miguel Pais Download

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