DSDEVS-Debugger/debugging_environment/NetLogo/extensions/r/models/homerange-example.nlogo

;; Homerange example of R-extension
;;
;;
;; by Jan C. Thiele
;; University of Goettingen, Germany
;; Department Ecoinformatics, Biometrics and Forest Growth
;; Buesgenweg 4
;; 37077 Goettingen
;; Germany
;;
;; Contact: jthiele@gwdg.de
;;
;; Copyright: 2011, J.C. Thiele

extensions [r]

breed [animals animal]
breed [homeranges homerange]

animals-own
[ Name X Y ]

homeranges-own
[ Name ]

to setup
  clear-all
  r:clear

  ;; create three different animals (rabbit, cat, fox)
  create-animals 3
  [
    if (who = 0)
    [
      set Name "rabbit"
      set color 14
    ]
    if (who = 1)
    [
      set Name "cat"
      set color 44
    ]
    if (who = 2)
    [
      set Name "fox"
      set color 94
    ]
    set xcor random-pxcor
    set ycor random-pycor
    set X (list xcor)
    set Y (list ycor)
    pen-down
  ]

  go
end

to go
  repeat 100
  [
    ;; move the animals randomly
    ask animals
    [
      let nextpatch patch-at-heading-and-distance random 360 random 3
      if (nextpatch != nobody)
      [ move-to nextpatch ]
      set X lput xcor X
      set Y lput ycor Y
    ]
  ]
end


to calc-homerange
  r:eval "library(adehabitat)"

  ;; create an empty data.frame"
  r:eval "turtles <- data.frame()"

  ;; merge the Name, X- and Y-lists of all animals to one big data.frame
  ask animals
  [
    (r:putdataframe "turtle" "X" X "Y" Y)
    r:eval (word "turtle <- data.frame(turtle, Name = '" Name "')")
    r:eval "turtles <- rbind(turtles, turtle)"
  ]

  ;; split the data.frame into coordinates and factor variable
  r:eval "xy <- turtles[,c('X','Y')]"
  r:eval "id <- turtles$Name"
  ;; calculate homerange
  r:eval "homerange <- mcp(xy, id)"


  ifelse (plot-homerange)
  [ plot-into-file ]
  [
    mark-homeranges
    plot-area
  ]
end


to plot-into-file
  ;; plot the homerange polygons (into pdf-file)
  r:eval (word "pdf('" homerange-plot ".pdf')" )
  r:eval (word "plot(homerange, xlim=c(" min-pxcor "," max-pxcor "), ylim=c(" min-pycor "," max-pycor "))")
  r:eval "dev.off()"

  ;; plot the homerange area depending on the homerange level (into pdf-file)
  r:eval (word "pdf('" homerange-level-plot ".pdf')" )
  r:eval "mcp.area(xy, id, unout='m2')"
  r:eval "dev.off()"

end



to mark-homeranges
  clear-drawing

  ask animals
  [
    pen-up
    ;; get the points of the homerange polygon for the current animal
    r:eval (word "temp <- subset(homerange, ID=='"Name"')")
    let tempX r:get "temp$X"
    let tempY r:get "temp$Y"
    let tempXY (map [ [?1 ?2] -> list ?1 ?2 ] tempX tempY)

    ;; create a turtle, which draws the homerange boundary
    hatch-homeranges 1
    [
      hide-turtle
      set Name [Name] of myself
      set color [color] of myself
    ]

    ;; draw the homerange boundary
    foreach tempXY
    [ [?1] ->
      ask homeranges with [Name = [Name] of myself]
      [
        move-to patch (item 0 ?1) (item 1 ?1)
        pen-down
      ]
    ]

    ;; connect the last point of the homerange with the first one, to close the polygon
    ask homeranges with [Name = [Name] of myself]
    [
      let lastpoint first tempXY
      move-to patch (item 0 lastpoint) (item 1 lastpoint)
    ]
  ]
end


to plot-area
  clear-all-plots
  let precstart 20
  let precincre 5
  ;; calculate the size of the homerange depending on homerange level
  r:eval (word "area <- mcp.area(xy, id,  unout='m2', percent = seq(" precstart ",100, by = " precincre "), plotit=FALSE)")

  ;; plot the homerange area of every animal, using temporary plot pen
  ask animals
  [
    let arealist r:get (word "area$" Name)
    set-current-plot "home range area"
    create-temporary-plot-pen Name
    set-plot-pen-color color
    let prec precstart
    foreach arealist
    [ [?1] ->
      plotxy prec ?1
      set prec prec + precincre
    ]
  ]
end
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@#$#@#$#@
## WHAT IS IT?

This section could give a general understanding of what the model is trying to show or explain.

## HOW IT WORKS

This section could explain what rules the agents use to create the overall behavior of the model.

## HOW TO USE IT

This section could explain how to use the model, including a description of each of the items in the interface tab.

## THINGS TO NOTICE

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

## THINGS TO TRY

This section could give some ideas of things for the user to try to do (move sliders, switches, etc.) with the model.

## EXTENDING THE MODEL

This section could give some ideas of things to add or change in the procedures tab to make the model more complicated, detailed, accurate, etc.

## NETLOGO FEATURES

This section could point out any especially interesting or unusual features of NetLogo that the model makes use of, particularly in the Procedures tab.  It might also point out places where workarounds were needed because of missing features.

## RELATED MODELS

This section could give the names of models in the NetLogo Models Library or elsewhere which are of related interest.

## CREDITS AND REFERENCES

This section could contain a reference to the model's URL on the web if it has one, as well as any other necessary credits or references.
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