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.NSB-ABM.tmp.nlogo
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;Main code for the ABM
;Zip file w/ model and data:
;https://drive.google.com/a/alaska.edu/file/d/0B6Qg-B9DYEuKVE5EQldZMjUtRlE/view?usp=sharing
extensions [ gis array matrix table csv profiler]
__includes["nls-modules/insect.nls" "nls-modules/precip.nls" "nls-modules/NDVI.nls" "nls-modules/caribouPop.nls"
"nls-modules/caribou.nls" "nls-modules/moose.nls" "nls-modules/hunters.nls"
"nls-modules/fcm.nls" "nls-modules/patch-list.nls" "nls-modules/utility-functions.nls" "nls-modules/display.nls" "nls-modules/connectivityCorrection.nls" "nls-modules/vegetation-rank.nls"
"nls-modules/migration-grids.nls" "nls-modules/migration-centroids.nls" "nls-modules/caribou-calibration.nls" "nls-modules/kde-sample.nls" ]
breed [moose a-moose]
breed [caribou a-caribou]
breed [cisco a-cisco]
breed [char a-char]
breed [whitefish a-whitefish]
breed [centroids centroid]
breed [grids grid]
breed [deflectors deflector]
breed [mem-markers mem-mark]
breed [hunters hunter]
breed [caribou-harvests caribou-harvest] ;centroids for caribou harvest
directed-link-breed [ cent-links cent-link ]
globals
[
file-output-prepend
npGridId
npGridQual
pGridId
pGridQual
seed
caribouVarCal ;;list containing values of caribou related variables that need to be calibrated.
patches-oil-bounds
patches-roads
patches-pipeline
np-centroid-layer-152
np-centroid-layer-166
np-centroid-layer-180
np-centroid-layer-194
np-centroid-layer-208
np-centroid-layer-222
np-centroid-layer-236
np-centroid-layer-250
p-centroid-layer-152
;GIS DATA
np-centroid-network
p-centroid-network
cent-day-list ;for recording list of days where the centroids need to be reassigned in the simulation
avg-sim-time ;for reporting the average amount of time it takes to simulate each year.
caribou-fcm-perception-weights-list
caribou-fcm-adja-list
caribou-fcm-agentnum-list
caribou-fcm-success-list
patch-roughness-dataset
patch-wetness-dataset
patch-streams-dataset
patch-elevation-dataset
patch-ocean-dataset
patch-whitefish-dataset
patch-caribou-harvest-dataset
;Boundaries for Development
patch-boundary-beartooth
patch-boundary-beecheypoint
patch-boundary-colvilleriver
patch-boundary-dewline
patch-boundary-duckisland
patch-boundary-greatermoosestooth
patch-boundary-kuparukriver
patch-boundary-liberty
patch-boundary-milnepoint
patch-boundary-nikaitchuq
patch-boundary-northstar
patch-boundary-oooguruk
patch-boundary-pikka
patch-boundary-placer
patch-boundary-prudhoebay
patch-boundary-smiluveach
patch-pipes_layer
patch-roads_layer
;globals for the NDVI.nls module.
ndvi-dataset
vegetation-ndvi-list
;ndvi-matrix
ndvi-max
vegetation-CP-list
vegetation-CNP-list
vegetation-PC-list
vegetation-MH-list
vegetation-ML-list
vegetation-OH-list
vegetation-OL-list
vegetation-LS-list
veg-selection-season
ndvi-all-max
season ;set to [0-3] corresponding to current season currently set to summer always
patch-vegetation-dataset
max-roughness
;use boxes;
; mutation-rate
; mutation-amt
; learn-rate
;Globals Precipitation
precipitation-dataset
precipitation-data-list
precipitation-max
precipitation-matrix-number
;;Bounds Data
boundsTestData
current-season
;Reward Online Learning (Q)
a-net-w1
a-net-w2
a-net-wout
adjacency-matrix
;Caribou-Bank
caribou-bank-may22
caribou-bank-jul16
caribou-bank-sep16
caribou-bank-nov16
caribou-bank-jan1
caribou-bank-mar1
;Time Info
year
day
hour
;;FCM
base-fcm-caribou
best-caribou-val
fcm-adja-base
caribou-fcm-perception-weights-base
;PatchList for movement decisions
patch-coord-x
patch-coord-y
patch-list-exists
patch-list-utility
patch-array-iterator
;;WORK AROUND NUMBERS;; These numbers are used to work around limitations with the
; NetLogo language
caribou-var-E-diff
caribou-bio-list
caribou-pop
caribou/agent
r-caribou
;;Caribou Activation Control
;caribou-cent-dist-cutoff
;caribou-util-cutoff
;;magic centroid number - A hack to allow comparison with centriod number
magic-centroid
;;;;; HENRI'S GLOBALS ;;;;;
mosquito-sigma
oestrid-sigma
mosquito-means-list
oestrid-means-list
mosquito-sigma-list
oestrid-sigma-list
mosquito-max-color
oestrid-max-color
mosquito-max-tenth-color
oestrid-max-tenth-color
mosquito-max
oestrid-max
mosquito-max-tenth
oestrid-max-tenth
mosquito-mean
oestrid-mean
time-of-year
;;;; insect modifier
insect-needs-reset
insect-season
hunter-harvest-total
hunter-trip-control
hunter-fcm-list
hunter-streams-restriction
caribou-harvest-selection-list
caribou-harvest-fRanks-list
caribou-harvest-probability-list
]
patches-own
[
patch-id
river-set
river-id
np-network-id
p-network-id
cent-dist
gnpid
gpid
np-grid-id
p-grid-id
grid-util-non-para
grid-util-para
cent-util-list-non-para
cent-util-list-para
npid
pid
cent-util-para
cent-util-non-para
wetness
streams
ocean
roughness
elevation
boundsTest
vegetation-type
ndvi-quality
whitefish? ;for whether or not a patch has been used for broad whitefish harvesting in last 10 yr. (Braund report)
patch-caribou-harvest
;Patches Precipitation.nls
precipitation-amt
prec-paint
;;Utility Values
;caribou
connected? ;boolean for whether or not patches are connected by a stream. Setting to be true for all patches with streams > than 1/2 mean [streams] of patches.
caribou-utility-max
caribou-utility
caribou-utility-para
caribou-utility-non-para
caribou-modifier ;modified based on caribou vists. Add decay?
patch-deflection-oil
patch-deflection-roads
patch-deflection-pipeline
patch-deflection-temp
;moose
moose-utility-max
moose-utility
;all
deflection
vegParRank ;vegetation ranking of patch for pregnant caribou
vegNonParRank ;vegetation ranking of patch for non-pregnant caribou
;;;;; HENRI PATCH VALUES ;;;;;
vegetation-beta
prev-insect-val
mosquito-density
oestrid-density
mosquito-scale
oestrid-scale
gray-scale
;water ;doesn't appear to be used atm, but playing it safe. (Max)
coast
;needed?
;bool-ocean
patch-historic-utility-caribou
]
caribou-harvests-own
[
frequency-rank
]
centroids-own
[
avg-insect
veg-quality
radius
cid
category
]
grids-own
[
grid-id
np-qual-id
p-qual-id
]
deflectors-own
[
;boolean
has-applied
;patch size
area-outer
area-inner
;value -- value should be from (0,1]
deflect-amt
]
turtles-own
[
hidden-label
]
moose-own
[
energy
fd-amt
]
mem-markers-own
[
caribou-id
]
cent-links-own
[
link-weight
]
;wraps to other setup functions
to setup
set file-output-prepend ""
clear-all
set seed -2147483648 + random-num (2147483648 * 2)
random-seed seed
set time-of-year 0
set max-roughness 442.442
set hour 0
set day 152
set year 0
reset-caribou-banks
set cent-day-list [ ]
ask patches
[ set cent-util-list-non-para [ ]
set cent-util-list-para [ ]
set np-grid-id 0
set p-grid-id 0 ]
let counter 1
let xc -64 let yc 64 while [ yc >= -64] [ ask patch xc yc [set patch-id counter] set counter counter + 1 set xc xc + 1 if xc >= 65 [ set yc yc - 1 set xc -64 ] ]
setup-cent-layers
setup-grid-layers
set np-centroid-network np-centroid-layer-152
set p-centroid-network p-centroid-layer-152
centroid-read
grid-read
set season 1
setup-deflectors
set ndvi-all-max 247
reset-timer
set avg-sim-time [ ]
;this must be called to apply first deflector values
go-deflectors
set caribou-bank-may22 [8 4 2 2]
set caribou-bank-jul16 [8 4 2 2]
set caribou-bank-sep16 [8 4 2 2]
set caribou-bank-nov16 [8 4 2 2]
set caribou-bank-jan1 [8 4 2 2]
set caribou-bank-mar1 [8 4 2 2]
set-mosquito-means-list
set-oestrid-means-list
set-mosquito-mean
set-oestrid-mean
set-coastline
setup-precipitation
setup-terrain-layers
setup-caribou-utility ;setup caribou utility code requires a fix, semantics of it don't make sense.
;update-caribou-utility
;update-para-utility
;update-non-para-utility
setup-moose-utility
setup-moose
;setup-centroids
setup-caribou
setup-caribou-q
setup-patch-list
setup-insect
set-precipitation-data-list
go-precipitation
if(is-random?)
[
caribou-random-fcm
]
set caribou-fcm-adja-list [fcm-adja] of caribou
; setup-ndvi
go-veg-ranking
set-streams
ask patches
[ set grid-util-non-para 0
set grid-util-para 0 ]
test-flow
if export-logger-data?
[
setup-logger-data
]
setup-caribou-var-cal
if exportCaribouData? [
setup-caribou-state-data
setup-caribou-fcm-data
]
set hunter-streams-restriction (0.025 * (max [streams] of patches))
set hunter-trip-control 123
if use-hunters? [
setup-caribou-harvests
build-caribou-harvest-lists
build-caribou-harvest-prob-list
initialize-FCM-hunters
setup-hunter-nls
]
setup-caribou-kde-file
setup-hunter-kde-file
reset-ticks
scenario-controller
end
to setup-caribou-harvests
ask patches
[
if (pxcor mod 2 = 0) and (pycor mod 2 = 0)
[
sprout-caribou-harvests 1 [set frequency-rank [patch-caribou-harvest] of patch-here]
]
]
ask caribou-harvests
[
if (frequency-rank = 21)
[
die
]
set color scale-color red frequency-rank 0 20
set size 1
set shape "circle"
]
end
to setup-centroids
let data 0
let arrdata 0
file-open "data/AllCentroids.csv"
let idCounter 0
while [not file-at-end?]
[
set data csv:from-row file-read-line
set arrdata array:from-list data
create-centroids 1
[
set cid idCounter
setxy (array:item arrdata 0) (array:item arrdata 1)
set category (array:item arrdata 2)
set size 0
]
;show idCounter
set idCounter (idCounter + 1)
]
file-close
end
to setup-deflectors
;;create deflectors according to development sites: CD5 and Nuiqsut.
;;create Nuiqsut
;;Using Nuiqsut bounds on Google maps, coordinate center sits in a 3 mi x 3 mi (4828.032 m x 4828.032 m) square
if Nuiqsut? [
create-deflectors 1
[
let patch-x 0.38689265536723383
let patch-y 4.621468926553675
set xcor patch-x
set ycor patch-y
set shape "dot"
set label "NUIQSUT"
set color red
;;set an area over which we consider to be 'developed'. Caribou agents should be able to sense this
;;within 1 km buffer range if following similar setup as the Albert caribou ABM paper.
set area-outer (4828.032 / 2195.35)
set area-inner 0
set deflect-amt 1
set has-applied false
ht
]
]
if CD5? [
create-deflectors 1
[
let patch-x -2.2409039548022633
let patch-y 8.624632768361579
set xcor patch-x
set ycor patch-y
set shape "dot"
set label "CD5"
set color red
;;development bounds of CD5 still need to be selected.
set area-outer (3000 / 2195.35)
set area-inner 0
set deflect-amt 1
set has-applied false
ht
]
]
end
to profile-test
let profileOut "profiler-dat.txt"
profiler:reset
profiler:start
;setup-grid-layers
setup
while [ year != 2 ] [ go ]
profiler:stop
print profiler:report
file-open profileOut
file-print profiler:report
file-close-all
end
to scenario-controller
if scenario != "none" [
;; set variables common to all scenarios
set display-plots? false
set dynamic-display? false
set show-caribou-utility-para? false
set show-caribou-utility-non-para? false
set show-moose-utility? false
set display-centroids? false
set display-grids? false
set Nuiqsut? true
set CD5? true
set BoundsFile "data/development-regions/pipes_layer.asc"
set caribouPopMod? false
set caribou-amt 2500
set caribou-group-amt 50
set caribou-radius 1.5
set caribou-para 0.71
set elevation-limit 221
set use-q false
set Q-rate 0.001
set Q-Gamma 0.999
set debug-fcm? false
set prob-var-recombination .33
set import-caribou-fcm? true
set import-caribou-var? true
set is-random? false
set is-training? true
set randomCaribouVarStart? false
set calibrateCaribouVar? false
set exportCaribouData? true
set mutation-method "fuzzy-logic"
set caribou-recomb-prob 0.2
set caribou-mutate-prob 0.15
set caribou-recombine? true
set caribou-mutate? true
set export-centroids? false
set set-centroid-attraction 0.1
set caribou-max-wetness 0.8
set caribou-max-elevation 700
set caribou-modify-amt 1
set moose-amt 0
set hunter-recomb-prob 0.2
set hunter-mutate-prob 0.15
set hunter-mutate? true
set hunter-recombine? true
;; remove comment later after building hunter fcms up -
set random-hunter-fcm? true
;; set random-hunter-fcm? false
set caribou-harvest-high-constant 0.6
set caribou-harvest-low-constant 0.4
set local-search-radius 3
set hunter-harvest-goal 1
set hunter-centroid-selection 15
set trip-length-max 112
set hunter-vision 2
set hunter-population 35
set use-hunters? true
set export-hunter-data? true
set hunter-training? true
set prey-close-constant .4
set prey-far-constant .6
set trip-long-constant .4
set trip-short-constant .6
set boat-hike-long-constant .4
set boat-hike-short-constant .6
set hunter-density-low-constant .4
set hunter-density-high-constant .6
set deflect-pipeline? false
set deflect-oil? false
set deflect-roads? false
set use-hunters? true
if scenario = "control-w-hunters-lo" [
;; evolve agents for 1000 years.
set use-high-res-ndvi? false
while [ year != 1000 ] [
go
]
scenario-var-reset
;; run scenario and collect results for 100 years.
while [ year != 100 ] [
go
]
] ;; end control with hunters if
if scenario = "control-no-hunters-lo" [
;; make sure variable settings are appropriately set.
set use-hunters? false
set hunter-mutate? false
set hunter-recombine? false
set hunter-training? false
set use-high-res-ndvi? false
;; evolve agents for 1000 years.
while [ year != 1000 ] [
go
]
scenario-var-reset
;; run scenario and collect results for 100 years.
while [ year != 100 ] [
go
]
] ;; end control no hunters if
if scenario = "obd-w-hunters-lo" [
set deflect-pipeline? true
set deflect-oil? true
set deflect-roads? true
set use-high-res-ndvi? false
while [ year != 1000 ] [
go
]
scenario-var-reset
while [ year != 100 ] [
go
]
] ;; end obd w hunters if
if scenario = "obd-no-hunters-lo" [
set deflect-pipeline? true
set deflect-oil? true
set deflect-roads? true
set use-hunters? false
set hunter-mutate? false
set hunter-recombine? false
set hunter-training? false
set use-high-res-ndvi? false
while [ year != 1000 ]
[
go
]
scenario-var-reset
while [ year != 100 ]
[
go
]
] ;; end obd-no-hunters if
if scenario = "veg-later-shift-w-hunters-lo" [
;; add in matrix shift...
set use-high-res-ndvi? false
set-later-shifted-ndvi-data-list
while [ year != 1000 ] [
go
]
scenario-var-reset
while [ year != 100 ] [
go
]
] ;; end veg-shift-w-hunters if
if scenario = "veg-later-shift-no-hunters-lo" [
;; add in matrix shift...
set use-high-res-ndvi? false
set use-hunters? false
set hunter-mutate? false
set hunter-recombine? false
set hunter-training? false
set-later-shifted-ndvi-data-list
while [ year != 1000 ] [
go
]
scenario-var-reset
while [ year != 100 ] [
go
]
] ;; end veg-shift-no-hunters if
if scenario = "veg-early-shift-w-hunters-lo" [
;; add in matrix shift...
set use-high-res-ndvi? false
set-early-shifted-ndvi-data-list
while [ year != 1000 ] [
go
]
scenario-var-reset
while [ year != 100 ] [
go
]
] ;; end veg-shift-w-hunters if
if scenario = "veg-early-shift-no-hunters-lo" [
;; add in matrix shift...
set use-high-res-ndvi? false
set use-hunters? false
set hunter-mutate? false
set hunter-recombine? false
set hunter-training? false
set-early-shifted-ndvi-data-list
while [ year != 1000 ] [
go
]
scenario-var-reset
while [ year != 100 ] [
go
]
] ;; end veg-shift-no-hunters if
if scenario = "caribou-evolution-lo" [
set use-high-res-ndvi? false
set calibrateCaribouVar? true
set randomCaribouVarStart? true
set import-caribou-var? false
set is-random? true
set Nuiqsut? false
set CD5? false
while [ year <= 2500 ] [ go ] ;; user will have to use space bar interrupt in file to stop evolution before end point.
] ;; end caribou-evolution if
if scenario = "hunter-evolution-lo" [
set use-high-res-ndvi? false
set random-hunter-fcm? true
while [ year <= 1 ] [ go ] ;; user will have to use space bar interrupt in file to stop evolution before end point.
] ;; end hunter-evolution if
;;;HIGH RESOLUTION NDVI SCENARIOS
if scenario = "control-w-hunters-hi" [
;; evolve agents for 1000 years.
set use-high-res-ndvi? true
while [ year != 1000 ] [
go
]
scenario-var-reset
;; run scenario and collect results for 100 years.
while [ year != 100 ] [
go
]
] ;; end control with hunters if
if scenario = "control-no-hunters-hi" [
;; make sure variable settings are appropriately set.
set use-hunters? false
set hunter-mutate? false
set hunter-recombine? false
set hunter-training? false
set use-high-res-ndvi? true
;; evolve agents for 1000 years.
while [ year != 1000 ] [
go
]
scenario-var-reset
;; run scenario and collect results for 100 years.
while [ year != 100 ] [
go
]
] ;; end control no hunters if
if scenario = "obd-w-hunters-hi" [
set deflect-pipeline? true
set deflect-oil? true
set deflect-roads? true
set use-high-res-ndvi? true
while [ year != 1000 ] [
go
]
scenario-var-reset
while [ year != 100 ] [
go
]
] ;; end obd w hunters if
if scenario = "obd-no-hunters-hi" [
set deflect-pipeline? true
set deflect-oil? true
set deflect-roads? true
set use-hunters? false
set hunter-mutate? false
set hunter-recombine? false
set hunter-training? false
set use-high-res-ndvi? true
while [ year != 1000 ]
[
go
]
scenario-var-reset
while [ year != 100 ]
[
go
]
] ;; end obd-no-hunters if
if scenario = "veg-later-shift-w-hunters-hi" [
;; add in matrix shift...
set use-high-res-ndvi? true
set-later-shifted-ndvi-data-list
while [ year != 1000 ] [
go
]
scenario-var-reset
while [ year != 100 ] [
go
]
] ;; end veg-shift-w-hunters if
if scenario = "veg-later-shift-no-hunters-hi" [
;; add in matrix shift...
set use-high-res-ndvi? true
set use-hunters? false
set hunter-mutate? false
set hunter-recombine? false
set hunter-training? false
set-later-shifted-ndvi-data-list
while [ year != 1000 ] [
go
]
scenario-var-reset
while [ year != 100 ] [
go
]
] ;; end veg-shift-no-hunters if
if scenario = "veg-early-shift-w-hunters-hi" [
;; add in matrix shift...
set use-high-res-ndvi? true
set-early-shifted-ndvi-data-list
while [ year != 1000 ] [
go
]
scenario-var-reset
while [ year != 100 ] [
go
]
] ;; end veg-shift-w-hunters if
if scenario = "veg-early-shift-no-hunters-hi" [
;; add in matrix shift...
set use-high-res-ndvi? true
set use-hunters? false
set hunter-mutate? false
set hunter-recombine? false
set hunter-training? false
set-early-shifted-ndvi-data-list
while [ year != 1000 ] [
go
]
scenario-var-reset
while [ year != 100 ] [
go
]
] ;; end veg-shift-no-hunters if
if scenario = "caribou-evolution-hi" [
set use-high-res-ndvi? true
set calibrateCaribouVar? true
set randomCaribouVarStart? true
set import-caribou-var? false
set is-random? true
set Nuiqsut? false
set CD5? false
while [ year <= 2500 ] [ go ] ;; user will have to use space bar interrupt in file to stop evolution before end point.
] ;; end caribou-evolution if
if scenario = "hunter-evolution-hi" [
set use-high-res-ndvi? true
set random-hunter-fcm? true
while [ year <= 1 ] [ go ] ;; user will have to use space bar interrupt in file to stop evolution before end point.
] ;; end hunter-evolution if
;combined scenarios
if scenario = "combined-early-ndvi-w-hunters-hi" [
set deflect-pipeline? true
set deflect-oil? true
set deflect-roads? true
set-early-shifted-ndvi-data-list
set use-high-res-ndvi? true
set use-hunters? true
while [ year != 1000 ] [
go
]