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globals [ sp_param colorlist Tjan Tjuly]
breed [trees tree]
breed [speciesnames speciesname]
patches-own [ steepness soiltype moisture elevation trees-on-plot temperature light_available_at_floor]
trees-own [ age species species_index diameter height diametermax diameter-growth heightmax G B2 B3 agemax
canopy leaf_index light_type light_available light_relative_growth growth_modifier status
DEGD DEGDmax DEGDmin TDEGD TF ba max_saplings_per_year]
speciesnames-own [ speciesindex colorindex species0 diametermax0 heightmax0 G0 B20 B30 agemax0 leaf_index0 light_type0 growth_modifier0 DEGD0 DEGDmax0 DEGDmin0 TDEGD0 max_saplings_per_year0 ]
;; ba is basal area in square meters, diameter is in cm
;; status used in 1990 & 2000: 1=new 2=growing 3=standing dead 4=fallen 5=cut
to setup
;; (for this model to work with NetLogo's new plotting features,
;; __clear-all-and-reset-ticks should be replaced with clear-all at
;; the beginning of your setup procedure and reset-ticks at the end
;; of the procedure.)
__clear-all-and-reset-ticks
load-species-data
set-default-shape trees "tree"
initialize_1980
ask patches [
set pcolor brown + 1 + random-float 1 ]
do-histogram
end
to clearcut
ask trees with [ycor < 5 and ycor > 2]
[ die ]
end
;; This procedure loads in the parameters for tree species 1 in the order speciesnumber agemax diametermax heightmax B2 B3 G leaf_index light_type
to load-species-data
ifelse ( file-exists? "SpeciesParameterData.txt" ) [ ;; We check to make sure the file exists first
set sp_param [] ;; We will save the data into a matrix, initialized to be empty.
set colorlist [ 54 45 13 15 17 73 6 66 96 ]
file-open "SpeciesParameterData.txt" ;; This opens the file, so we can read it.
let spnum 0
while [ not file-at-end? ] [ ;; Reads data for each species in file.
set sp_param sentence sp_param (list (list file-read file-read file-read file-read file-read file-read file-read file-read file-read file-read file-read file-read file-read))
;; Each iteration we append the next 13-tuple to the current matrix (as a new row); indexing starts at 0
create-speciesnames 1 [
set speciesindex spnum
set species0 item 0 item spnum sp_param
set agemax0 item 1 item spnum sp_param
set diametermax0 item 2 item spnum sp_param
set heightmax0 item 3 item spnum sp_param
set B20 item 4 item spnum sp_param
set B30 item 5 item spnum sp_param
set G0 item 6 item spnum sp_param
set leaf_index0 item 7 item spnum sp_param
set light_type0 item 8 item spnum sp_param
set DEGDmin0 item 9 item spnum sp_param
set DEGDmax0 item 10 item spnum sp_param
set growth_modifier0 item 11 item spnum sp_param
set max_saplings_per_year0 item 12 item spnum sp_param
set colorindex item spnum colorlist
hide-turtle
]
set spnum spnum + 1 ]
file-close ;; Done reading in patch information. Close the file.
]
[ user-message "There is no SpeciesParameterData.txt file in current directory!" ];; reports error if no such file
end
to initialize_1980
ifelse ( file-exists? "Plot206diameters.txt" ) [ ;; We check to make sure the file exists first
file-open "Plot206diameters.txt" ;; This opens the file, so we can read it.
while [ not file-at-end? ] [ ;; Reads diameter of each tree in file.
create-trees 1 [
let spnum file-read
set species_index spnum
set species item 0 item spnum sp_param
set diameter file-read;;cm
set color item spnum colorlist
set diametermax item 2 item spnum sp_param
set size diameter / diametermax / 1 ;;scale by diameter to indicate relative size
setxy (random-float 4 - 0.5) (random-float 2 - 0.5) ;; random position within world
set ba pi * (diameter / 200) ^ 2 ;; in square meters
set agemax item 1 item spnum sp_param
set age agemax * diameter / diametermax ;; rough estimate of age in years using agemax*diameter/diametermax
set heightmax item 3 item spnum sp_param
set B2 item 4 item spnum sp_param
set B3 item 5 item spnum sp_param
set G item 6 item spnum sp_param
set height 137 + (B2 * diameter) - (B3 * diameter ^ 2)
set leaf_index item 7 item spnum sp_param
set light_type item 8 item spnum sp_param
set DEGDmin item 9 item spnum sp_param
set DEGDmax item 10 item spnum sp_param
set status 2
set growth_modifier item 11 item spnum sp_param
set max_saplings_per_year item 12 item spnum sp_param
] ]
file-close ;; Done reading in patch information. Close the file.
]
[ user-message "There is no Plot206diameters.txt file in current directory!" ];; reports error if no such file
ifelse ( file-exists? "Plot346diameters.txt" ) [ ;; We check to make sure the file exists first
file-open "Plot346diameters.txt" ;; This opens the file, so we can read it.
while [ not file-at-end? ] [ ;; Reads diameter of each tree in file.
create-trees 1 [
let spnum file-read
set species_index spnum
set species item 0 item spnum sp_param
set diameter file-read;;cm
set color item spnum colorlist
set diametermax item 2 item spnum sp_param
set size diameter / diametermax / 1 ;;scale by diameter to indicate relative size
setxy (random-float 4 - 0.5) (random-float 2 + 1.5) ;; random position within world
set ba pi * (diameter / 200) ^ 2 ;; in square meters
set agemax item 1 item spnum sp_param
set age agemax * diameter / diametermax ;; rough estimate of age in years using agemax*diameter/diametermax
set heightmax item 3 item spnum sp_param
set B2 item 4 item spnum sp_param
set B3 item 5 item spnum sp_param
set G item 6 item spnum sp_param
set height 137 + (B2 * diameter) - (B3 * diameter ^ 2)
set leaf_index item 7 item spnum sp_param
set light_type item 8 item spnum sp_param
set DEGDmin item 9 item spnum sp_param
set DEGDmax item 10 item spnum sp_param
set status 2
set growth_modifier item 11 item spnum sp_param
set max_saplings_per_year item 12 item spnum sp_param
] ]
file-close ;; Done reading in patch information. Close the file.
]
[ user-message "There is no Plot346diameters.txt file in current directory!" ];; reports error if no such file
ifelse ( file-exists? "Plot401diameters.txt" ) [ ;; We check to make sure the file exists first
file-open "Plot401diameters.txt" ;; This opens the file, so we can read it.
while [ not file-at-end? ] [ ;; Reads diameter of each tree in file.
create-trees 1 [
let spnum file-read
set species_index spnum
set species item 0 item spnum sp_param
set diameter file-read;;cm
set color item spnum colorlist
set diametermax item 2 item spnum sp_param
set size diameter / diametermax / 1 ;;scale by diameter to indicate relative size
setxy (random-float 4 - 0.5) (random-float 2 + 3.5) ;; random position within world
set ba pi * (diameter / 200) ^ 2 ;; in square meters
set agemax item 1 item spnum sp_param
set age agemax * diameter / diametermax ;; rough estimate of age in years using agemax*diameter/diametermax
set heightmax item 3 item spnum sp_param
set B2 item 4 item spnum sp_param
set B3 item 5 item spnum sp_param
set G item 6 item spnum sp_param
set height 137 + (B2 * diameter) - (B3 * diameter ^ 2)
set leaf_index item 7 item spnum sp_param
set light_type item 8 item spnum sp_param
set DEGDmin item 9 item spnum sp_param
set DEGDmax item 10 item spnum sp_param
set status 2
set growth_modifier item 11 item spnum sp_param
set max_saplings_per_year item 12 item spnum sp_param
] ]
file-close ;; Done reading in patch information. Close the file.
]
[ user-message "There is no Plot401diameters.txt file in current directory!" ];; reports error if no such file
ifelse ( file-exists? "Plot540diameters.txt" ) [ ;; We check to make sure the file exists first
file-open "Plot540diameters.txt" ;; This opens the file, so we can read it.
while [ not file-at-end? ] [ ;; Reads diameter of each tree in file.
create-trees 1 [
let spnum file-read
set species_index spnum
set species item 0 item spnum sp_param
set diameter file-read;;cm
set color item spnum colorlist
set diametermax item 2 item spnum sp_param
set size diameter / diametermax / 1 ;;scale by diameter to indicate relative size
setxy (random-float 4 - 0.5) (random-float 2 + 5.5) ;; random position within world
set ba pi * (diameter / 200) ^ 2 ;; in square meters
set agemax item 1 item spnum sp_param
set age agemax * diameter / diametermax ;; rough estimate of age in years using agemax*diameter/diametermax
set heightmax item 3 item spnum sp_param
set B2 item 4 item spnum sp_param
set B3 item 5 item spnum sp_param
set G item 6 item spnum sp_param
set height 137 + (B2 * diameter) - (B3 * diameter ^ 2)
set leaf_index item 7 item spnum sp_param
set light_type item 8 item spnum sp_param
set DEGDmin item 9 item spnum sp_param
set DEGDmax item 10 item spnum sp_param
set status 2
set growth_modifier item 11 item spnum sp_param
set max_saplings_per_year item 12 item spnum sp_param
] ]
file-close ;; Done reading in patch information. Close the file.
]
[ user-message "There is no Plot540diameters.txt file in current directory!" ];; reports error if no such file
end
to go
;ifelse stop_after_20 [
; if ticks = 20
; [ do-histogram
; stop ]]
; [do-histogram]
set Tjan 24 + Temp_change
set Tjuly 70 + Temp_change
mortality
calculate_light
grow ;; trees
regenerate
do-plots
do-histogram
;ask trees with [status = 2] [ set label round diameter ]
tick
end
to mortality
ask trees with [status = 2] [
let prob_die (2.987 * (age / agemax) ^ 6 - 8.960 * (age / agemax) ^ 5 + 10.907 * (age / agemax) ^ 4 - 6.880 * (age / agemax) ^ 3 + 2.447 * (age / agemax) ^ 2 - 0.500 * (age / agemax) + 0.05)
if random-float 1 < prob_die
[;set status 3
;set color brown
die
] ]
end
to grow
ask trees with [status = 2]
[
set diameter-growth (G * diameter * ((1 - (diameter * (137 + (B2 * diameter) - (B3 * diameter ^ 2))) / (diametermax * heightmax)) * (light_relative_growth * TF * growth_modifier)) / (274 + (3 * B2 * diameter) - (4 * B3 * diameter ^ 2)))
set diameter diameter + diameter-growth
set height 137 + (B2 * diameter) - (B3 * diameter ^ 2)
set age age + 1
set ba pi * (diameter / 200) ^ 2
set size diameter / diametermax / 1 ;;scale by diameter to indicate relative size
]
end
to calculate_light ;; need to include environmental fudge factor
ask trees with [status = 2]
[ let currh height
; ifelse patch-based-light [
set canopy trees-here with [height > currh and status = 2]
set light_available Exp (-1 * sum [leaf_index * (diameter ^ 2) * 0.0000756] of canopy);]
;[ set canopy other trees in-radius .5 with [height > currh and status < 4] ;;change trees affecting light to be within a certain radius of the tree, rather than the tree's patch
; ifelse any? canopy
; [ let currx xcor
; let curry ycor
; set light_available Exp (-1 * sum [leaf_index * (diameter ^ 2) * 0.0000756] of canopy / (1 + sum [sqrt((currx - xcor) ^ 2 + (curry - ycor) ^ 2)] of canopy )) ] ;;weights how much trees affect the light of other trees by their distance
; [ set light_available 1 ]
;]
if light_type = 1
[set light_relative_growth 1.218 * (1 - Exp (-1.136 * light_available - .097 )) ]
if light_type = 2
[set light_relative_growth 0.9875 * (1 - Exp (-4.62 * light_available - .0637 )) ]
if light_type = 3
[set light_relative_growth 1.045 * (1 - Exp (-5.3592 * light_available - .0637 )) ]
if light_relative_growth < 0
[set light_relative_growth 0]
set DEGD ((365 / (2 * 3.14)) * (Tjuly - Tjan)) - ((365 / 3.14) * (40 - ((Tjuly + Tjan) / 2 ))) + (365 / 3.14) * (((40 - ((Tjuly - Tjan) / 2)) ^ 2) / (Tjuly - Tjan) )
set TDEGD (4 * (DEGD - DEGDmin) * (DEGDmax - DEGD)) / ((DEGDmax - DEGDmin) ^ 2)
ifelse TDEGD > 0
[set TF TDEGD]
[set TF 0]
]
end
to regenerate
ask patches [
set light_available_at_floor Exp (-1 * sum [leaf_index * (diameter ^ 2) * 0.0000756] of trees-here with [status = 2])
let xx pxcor
let yy pycor
ifelse light_available_at_floor > 0.5 [
let light_relative_gr 1.218 * (1 - Exp (-1.136 * light_available_at_floor - .097 )) ; environmental factor ?
ask speciesnames with [ light_type0 = 1 ] [
let spnum speciesindex
hatch-trees round random-float ( light_relative_gr * max_saplings_per_year0)
[ set species_index spnum
set species item 0 item spnum sp_param
set diameter random-float 10 + 10;;cm
set color item spnum colorlist;51 + species_index
set diametermax item 2 item spnum sp_param
set size diameter / diametermax / 1 ;;scale by diameter to indicate relative size
setxy (xx - 0.5 + random-float 1) (yy - 0.5 + random-float 1)
set ba pi * (diameter / 200) ^ 2 ;; in square meters
set agemax item 1 item spnum sp_param
set age agemax * diameter / diametermax
set heightmax item 3 item spnum sp_param
set B2 item 4 item spnum sp_param
set B3 item 5 item spnum sp_param
set G item 6 item spnum sp_param
set height 137 + (B2 * diameter) - (B3 * diameter ^ 2)
set leaf_index item 7 item spnum sp_param
set light_type item 8 item spnum sp_param
set DEGDmin item 9 item spnum sp_param
set DEGDmax item 10 item spnum sp_param
set status 2
set growth_modifier item 11 item spnum sp_param
set max_saplings_per_year item 12 item spnum sp_param
show-turtle
]]] [
ifelse light_available_at_floor > 0.12 [
let light_relative_gr 0.9875 * (1 - Exp (-4.62 * light_available_at_floor - .0637 ))
ask speciesnames with [ light_type0 = 2 ] [
let spnum speciesindex
hatch-trees round random-float ( light_relative_gr * max_saplings_per_year0)
[ set species_index spnum
set species item 0 item spnum sp_param
set diameter random-float 10 + 10;;cm
set color item spnum colorlist;51 + species_index
set diametermax item 2 item spnum sp_param
set size diameter / diametermax / 1 ;;scale by diameter to indicate relative size
setxy (xx - 0.5 + random-float 1) (yy - 0.5 + random-float 1)
set ba pi * (diameter / 200) ^ 2 ;; in square meters
set agemax item 1 item spnum sp_param
set age agemax * diameter / diametermax
set heightmax item 3 item spnum sp_param
set B2 item 4 item spnum sp_param
set B3 item 5 item spnum sp_param
set G item 6 item spnum sp_param
set height 137 + (B2 * diameter) - (B3 * diameter ^ 2)
set leaf_index item 7 item spnum sp_param
set light_type item 8 item spnum sp_param
set DEGDmin item 9 item spnum sp_param
set DEGDmax item 10 item spnum sp_param
set status 2
set growth_modifier item 11 item spnum sp_param
set max_saplings_per_year item 12 item spnum sp_param
show-turtle
]] ] [
let light_relative_gr 1.045 * (1 - Exp (-5.3592 * light_available_at_floor - .0637 ))
ask speciesnames with [ light_type0 = 3 ] [
let spnum speciesindex
hatch-trees round random-float ( light_relative_gr * max_saplings_per_year0)
[ set species_index spnum
set species item 0 item spnum sp_param
set diameter random-float 10 + 10;;cm
set color item spnum colorlist;51 + species_index
set diametermax item 2 item spnum sp_param
set size diameter / diametermax / 1 ;;scale by diameter to indicate relative size
setxy (xx - 0.5 + random-float 1) (yy - 0.5 + random-float 1)
set ba pi * (diameter / 200) ^ 2 ;; in square meters
set agemax item 1 item spnum sp_param
set age agemax * diameter / diametermax
set heightmax item 3 item spnum sp_param
set B2 item 4 item spnum sp_param
set B3 item 5 item spnum sp_param
set G item 6 item spnum sp_param
set height 137 + (B2 * diameter) - (B3 * diameter ^ 2)
set leaf_index item 7 item spnum sp_param
set light_type item 8 item spnum sp_param
set DEGDmin item 9 item spnum sp_param
set DEGDmax item 10 item spnum sp_param
set status 2
set growth_modifier item 11 item spnum sp_param
set max_saplings_per_year item 12 item spnum sp_param
show-turtle
]]]
] ]
end
to do-plots
set-current-plot "Number of growing trees per 100 sq m"
set-plot-x-range 0 100
set-plot-y-range 0 10
set-current-plot-pen "WhitePine"
plot count trees with [species = 1 and status = 2] / count patches ;* 8
set-current-plot-pen "Hemlock"
plot count trees with [species = 6 and status = 2] / count patches ;* 8
set-current-plot-pen "RedPine"
plot count trees with [species = 11 and status = 2] / count patches ;* 8
set-current-plot-pen "RedMaple"
plot count trees with [species = 21 and status = 2] / count patches ;* 8
set-current-plot-pen "RedOak"
plot count trees with [species = 30 and status = 2] / count patches ;* 8
set-current-plot-pen "BlackOak"
plot count trees with [species = 31 and status = 2] / count patches ;* 8
set-current-plot-pen "WhiteOak"
plot count trees with [species = 40 and status = 2] / count patches ;* 8
set-current-plot-pen "BlackBirch"
plot count trees with [species = 51 and status = 2] / count patches ;* 8
set-current-plot-pen "WhiteAsh"
plot count trees with [species = 55 and status = 2] / count patches ;* 8
; set-current-plot "Basal area of trees per 100 sq m"
; set-plot-x-range 0 100
; set-plot-y-range 0 1.5
; set-current-plot-pen "WhitePine"
; plot sum [ ba ] of trees with [species = 1 and status = 2] / count patches ;* 8 ;; report basal area in square meters
; set-current-plot-pen "Hemlock"
; plot sum [ ba ] of trees with [species = 6 and status = 2] / count patches ;* 8
; set-current-plot-pen "RedPine"
; plot sum [ ba ] of trees with [species = 11 and status = 2] / count patches ;* 8
; set-current-plot-pen "RedMaple"
; plot sum [ ba ] of trees with [species = 21 and status = 2] / count patches ;* 8
; set-current-plot-pen "RedOak"
; plot sum [ ba ] of trees with [species = 30 and status = 2] / count patches ;* 8
; set-current-plot-pen "BlackOak"
; plot sum [ ba ] of trees with [species = 31 and status = 2] / count patches ;* 8
; set-current-plot-pen "WhiteOak"
; plot sum [ ba ] of trees with [species = 40 and status = 2] / count patches ;* 8
; set-current-plot-pen "BlackBirch"
; plot sum [ ba ] of trees with [species = 51 and status = 2] / count patches ;* 8
; set-current-plot-pen "WhiteAsh"
; plot sum [ ba ] of trees with [species = 55 and status = 2] / count patches ;* 8
end
to do-histogram
set-current-plot "Histogram of white pine diameters"
set-plot-x-range 0 100
set-plot-y-range 0 1
set-current-plot-pen "Species1"
;set-histogram-num-bars 10
histogram [diameter] of trees with [species = 1 and status = 2]
set-current-plot "Histogram of red maple diameters"
set-plot-x-range 0 100
set-plot-y-range 0 1
set-current-plot-pen "Species21"
;set-histogram-num-bars 10
histogram [diameter] of trees with [species = 21 and status = 2]
; set-current-plot "Histogram of black birch diameters"
; set-plot-x-range 0 100
; set-plot-y-range 0 1
; set-current-plot-pen "BlackBirch"
; ;set-histogram-num-bars 10
; histogram [diameter] of trees with [species = 30 and status = 2 ]
; set-current-plot "Histogram of population of each species"
; set-plot-x-range 0 9
; set-plot-y-range 0 5
; set-current-plot-pen "default"
; set-plot-pen-mode 1
; set-plot-pen-interval 1
; histogram [species_index] of trees with [status = 2]
end