R extension demo

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Ahdekker Anthony Dekker (Author)

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extensions 

Tagged by Anthony Dekker over 5 years ago

r 

Tagged by Anthony Dekker over 5 years ago

r extension 

Tagged by Anthony Dekker over 5 years ago

tutorials 

Tagged by Anthony Dekker over 5 years ago

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Model was written in NetLogo 5.0.3 • Viewed 410 times • Downloaded 41 times • Run 0 times
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WHAT IS IT?

This program implements Conway's "Game of Life" together with a simulation of bacterial chemical-gradient-climbing, in order to demo the R extension for a tutorial at http://scientificgems.wordpress.com/2014/02/11/the-r-extension-for-netlogo-a-tutorial/

HOW TO USE IT

The "average-density" slider sets the initial average fraction of live cells for the "Game of Life."

The "Setup Life" or "Setup Bacteria" buttons initialise one or the other simulation.

The "Run" button runs the selected simulation.

The "Plot Life" button plots the "Game of Life" density over time, using the R extension. An input box allows editing of the default file name.

Comments and Questions

Explanation

This model is associated with a tutorial at http://scientificgems.wordpress.com/2014/02/11/the-r-extension-for-netlogo-a-tutorial/

Posted over 5 years ago

Click to Run Model

extensions [ r ]

globals [
  is-life?   ;; distinguish between the two demos
  
  ;; LIFE
  cell-count ;; total number of cells
  total      ;; total number of live cells
  history    ;; list of totals
  
  ;; BACTERIA
  window     ;; number of steps over which to analyse
]

patches-own [
  ;; LIFE
  alive?     ;; is cell alive?
  counter    ;; used to pass number of live neighbours between Phase 1 and Phase 2

  ;; BACTERIA
  value      ;; simulated chemical concentration
]

turtles-own [
  ;; BACTERIA
  hist       ;; history of concentration values
]

to rplot-graph  ;; R interface -- plot the LIFE history
  if (is-life?) [
    r:put "life.hist" history
    r:put "plotfile" life-plot-filename
  
    r:eval "png (filename = plotfile, width = 1600, height = 800, pointsize=18)"
    r:eval "par (mar=c(5,5,0.8,0.5))"
    r:eval "xs <- 0:(length(life.hist)-1)"
    r:eval "plot (life.hist ~ xs, type=\"l\", lwd=4, col=\"red\", xlab=\"Step\", ylab=\"Density\", ylim=c(0,max(life.hist)), cex.lab=2, cex.axis=1.5)"
    r:eval "dev.off()"
  ]
end 

to-report calculate-slope [ lst ]  ;; R interface -- calculate slope for values in lst
  r:put "valu.hist" lst
  
  r:eval "valu.index <- 1:length(valu.hist)"
  r:eval "valu.lm <- lm(valu.hist ~ valu.index)"
  report r:get "valu.lm$coefficients[2]"
end 

;; code for SETUP button -- Life

to setup-life
  clear-all
  set is-life? true
  set life-plot-filename "C:/NetLogo/Life_plot.png"
  set cell-count (count patches)
  ask patches [
    ifelse (random-float 1 < average-life-density) [birth] [death]
  ]
  reset-ticks
  set history (list (total / cell-count))
end 

to death  ;; this procedure applies to a specific patch
  set alive? false
  set pcolor white
end 

to birth  ;; this procedure applies to a specific patch
  set alive? true
  set pcolor blue
  set total (total + 1)
end 

;; code for SETUP button -- Bacteria

to setup-bacteria
  clear-all
  set is-life? false
  set life-plot-filename "** NOT USED **"
  set window 4
  
  ;; create gradient
  repeat 3 [
    let x random-xcor
    let y random-ycor
    let v (0.1 + random-float 0.5)
    let r (1 + v * world-width / 2)
    ask patches [
      let d ((distancexy x y) / r)
      set value (value + v * exp (- d))
    ]
  ]
  let min-value (min ([value] of patches))
  let max-value (max ([value] of patches))
  ask patches [
    set pcolor (30 + (9.9 * (value - min-value) / (max-value - min-value)))
  ]
    
  ;; create some bacteria
  crt 20 [
    setxy random-xcor random-ycor
    set color red
    set size 6
    set hist (list value)
  ]

  reset-ticks
end 

to go  ;; single simulation step for both demos
  if-else (is-life?) [
    
    ;; LIFE
    
    ;; First phase
    ask patches [ set counter (count neighbors with [alive?]) ]
    
    ;; Second phase
    set total 0
    ask patches [
      ifelse (counter = 3 or (counter = 2 and alive?))
      [ birth ]
      [ death ]
    ]
    
    set history (lput (total / cell-count) history)  ;; Record current density
    tick
  
  ] [
    
    ;; BACTERIA
    
    ask turtles [
      fd 1
      set hist (lput value hist)
      if (length(hist) > window) [ set hist (bf hist) ]
      
      if (length(hist) = window) [
        if (calculate-slope hist <= 0) [
          set heading (random-float 360)
          set hist (list value)
        ]
      ]
    ]
    
    tick
  ]
end 

There is only one version of this model, created over 5 years ago by Anthony Dekker.

Attached files

File Type Description Last updated
BacteriaDemoRview.png png Screenshot of "bacteria" mode over 5 years ago, by Anthony Dekker Download
R extension demo.png preview Preview for 'R extension demo' over 5 years ago, by Anthony Dekker Download

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