;; Diversity 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]

;; one patch equals a plot of 1 ha
;; at each plot the number of trees will be counted
;; trees are individuals/turtles

breed [beeches beech]
breed [birches birch]
breed [hornbeams hornbeam]
breed [oaks oak]
breed [maples maple]
breed [ashs ash]
breed [poplars poplar]

patches-own
[
  beechcount
  birchcount
  hornbeamcount
  oakcount
  maplecount
  ashcount
  poplarcount
  speccount
  shannon
  simpson
  pielou
]


to setup
  clear-all

  ;; reset the R-workspace
  r:clear

  ;; create the forest
  set-default-shape turtles "tree"
  create-beeches random 100
  [
    set xcor random-xcor
    set ycor random-ycor
  ]
  create-birches random 100
  [
    set xcor random-xcor
    set ycor random-ycor
  ]
  create-hornbeams random 100
  [
    set xcor random-xcor
    set ycor random-ycor
  ]
  create-oaks random 100
  [
    set xcor random-xcor
    set ycor random-ycor
  ]
  create-maples random 100
  [
    set xcor random-xcor
    set ycor random-ycor
  ]
  create-ashs random 100
  [
    set xcor random-xcor
    set ycor random-ycor
  ]
  create-poplars random 100
  [
    set xcor random-xcor
    set ycor random-ycor
  ]

  let insp one-of patches with [count beeches-here > 0]
  inspect insp
end


to calc-diversity
  ;; calculate the number of individuals of each species for each patch
  ask patches
  [
    set beechcount count beeches-here
    set birchcount count birches-here
    set hornbeamcount count hornbeams-here
    set oakcount count oaks-here
    set maplecount count maples-here
    set ashcount count ashs-here
    set poplarcount count poplars-here
  ]

  ;; assign a new data.frame with patch-variables (the patches will be asigned in lines from upper left to lower right)
  (r:putagentdf "dfpatches" patches "pxcor" "pycor" "beechcount" "birchcount" "hornbeamcount" "oakcount" "maplecount" "ashcount" "poplarcount")

  ;; create a data.frame without the coordinates
  r:eval "df <- dfpatches[,3:7]"

  ;; load R-library vegan (must be installed!)
  r:eval "library(vegan)"

  ;; calculate diversity
  r:eval "spec <- specnumber(df)"
  r:eval "shan <- diversity(df, 'shannon')"
  ;; Pielou's evenness (J), if spec = 0, value of pielou will be NaN:
  r:eval "pielou <- shan/log(spec)"
  r:eval "simp <- diversity(df, 'simpson')"


  ;; the following section is a little bit complicated
  ;; it's done to save the calculated diversity values in the corresponding patch-variables
  ;; to get just the diversity values as a list, call: print r:get "shan"


  ;; create lists with the coordinates
  let xlist r:get "dfpatches$pxcor"
  let ylist r:get "dfpatches$pycor"
  let xylist (map [ [?1 ?2] -> list ?1 ?2 ] xlist ylist)

  ;; save the diversity value into the corresponding patch-variables
  let counter 1
  foreach xylist
  [ [?1] ->
    ask patch (item 0 ?1) (item 1 ?1)
    [
      set speccount (r:get (word "spec[" counter "]"))
      set shannon (r:get (word "shan[" counter "]"))
      set simpson (r:get (word "simp[" counter "]"))
      set pielou (r:get (word "pielou[" counter "]"))
    ]
    set counter counter + 1
  ]

end
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## WHAT IS IT?

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