;; finch-two-weather-patterns-0.5.nlogo ;; 08 Nov 09. Updated to reflect changes in finch-lab-0.5.nlogo: new female selectivity function. ;; 13 Mar 09. Updated to reflect changes in finch-lab-0.4.nlogo: dispersal of new finches and density dep. mortality ;; 6 Feb 09. Updated to reflect changes in finch-lab-0.3.nlogo ;; 1 Feb 09. Adding in alternating weather patterns. ;; 30 Jan 09. Added color dependent on beak length. ;; 20 Jan 09. An attempt at an EcoBeaker-type simulation ;; Based heavily on "Islands and Natural Selection" in EcoBeaker ;; Uses diploid finches ;; length genes are built by choosing the allele for each locus from the same loci on the parents two 'chromosomes' ;; loci frequently become fixed even at moderate best beak lengths. ;; timestep is one year - so finch locations are essentially territories. ;; TODO: ;; Add mutation rate ;; use reporter procedures to set finch characteristics ;; allow males to mate only once per time step (?) ;;;;;;;;;;;;;;;DECLARATIONS;;;;;;;;;;;;;; globals [ ;;loci ;; the number of loci to control beak length max-length ;; the maximum beak length min-length ;; the minimum beak length ;;female-select ;; the female selectivity (min = 0, max = ~ 5) ;;female-search ;; the female search radius the-mate ;; a turtle variable. Tracks the mate of a particular bird baseline-mort ;; the annual yearly mortality probability with no selection and no density -dependence clutch-size ;; the number young hatched by a pair in a year. speed ;; the amount by which a finch moves each year. Also controls local density dependence (not implemented) locale-size ;; the radius that defines local density dependent mortality dry-tick ;; Records the time step in which a drought is supposed to occur. drought-length-rand ;; Records a randomly chosen drought length. mating-tries ;; the number of tries that a female gets to find a mate, per time step. ] breed [finches finch] ;; so I don't have to keep calling them 'turtles' finches-own [ sex length-genes-1 length-genes-2 beak-length pmort mated] ;; mated indicates whether the bird mated or not ;;;;;;;;;;;;;;;;SETUP;;;;;;;;;;;;;;;;;; to setup clear-all setup-globals setup-patches setup-finches do-plots end to setup-globals ;;set loci 10 ;; set the number of loci to 10 (min is 1) ;;set female-select 0 ;; the female selectivity for other finches (min = 0, max = ~5) ;;set female-search 50 ;; the female search radius for mates set max-length 15 ;; the maximum beak length set min-length 5 ;; the minimum beak length set baseline-mort 0.1 set clutch-size 1 set speed 1 set locale-size 4 set dry-tick ticks + random-poisson drought-interval ;; drought-interval and drought-length set drought-length-rand random-poisson drought-length ;; are both sliders set mating-tries 10 end to setup-patches ifelse ticks >= dry-tick and ticks <= drought-length-rand + dry-tick [ ask patches [ set pcolor brown ] ] [ ask patches [ set pcolor green ] ] if ticks = dry-tick + drought-length-rand + 1 [ set dry-tick ticks + random-poisson drought-interval set drought-length-rand random-poisson drought-length ] end to setup-finches ;; create finches create-finches init-birds ;; create init-birds finches ask finches [ setxy random-xcor random-ycor ;; spread the finches around randomly set sex random 2 ;;0 is female, 1 is male set mated 0 ;;0 means hasn't mated this time step, 1 means it has. Currently doesn't change setup-genome set beak-length 0 ;; defines beak-length as a number not a list set beak-length set-beak-length (sum length-genes-1 + sum length-genes-2) set pmort set-pmort set shape "bird side" set size 2 set color set-color beak-length ] end to setup-genome ask finches [ set length-genes-1 (list ifelse-value (random-float 1 < init-long-beak-freq) [ 1 ] [ 0 ]) repeat num-loci - 1 [ set length-genes-1 fput ifelse-value (random-float 1 < init-long-beak-freq) [ 1 ] [ 0 ] length-genes-1 ] set length-genes-2 (list ifelse-value (random-float 1 < init-long-beak-freq) [ 1 ] [ 0 ]) repeat num-loci - 1 [ set length-genes-2 fput ifelse-value (random-float 1 < init-long-beak-freq) [ 1 ] [ 0 ] length-genes-2 ] ] end to-report set-beak-length [num-alleles] let length-range max-length - min-length let temp-length ((num-alleles) / ( 2 * num-loci)) * length-range + min-length report temp-length end to-report set-color [actual-length] let length-range (max-length - min-length) let mid-length length-range / 2 + min-length let color-value 45 + ((mid-length - actual-length) / length-range) * (49.8 - 40) report color-value end to-report set-pmort let best-beak-length 5 let length-selection-coef 0 if pcolor = green [ set best-beak-length wet-best-beak-length set length-selection-coef wet-selection-coef ] if pcolor = brown [ set best-beak-length dry-best-beak-length set length-selection-coef dry-selection-coef ] let temp-mort baseline-mort + (abs (beak-length - best-beak-length) * length-selection-coef) report temp-mort end ;;;;;;;;;;;;;;;;GO;;;;;;;;;;;;;;;;;; to go if ticks >= stop-time [ stop ] ;; stop-time is a slider setup-patches ;; determines whether a wet year has occurred, sets patch colors and resets wet-tick if nec. move-finches mate check-death if count finches < 2 [ do-plots stop ] tick do-plots end to move-finches ask finches [ ifelse can-move? 1 [ right random 360 forward speed ] ;; unit here corresponds to 'speed' in the ecobeaker simulation [ rt 180 ] ] end to mate ask finches [ ;; make this ask female finches only if sex = 0 [ set the-mate no-turtles choose-mate if the-mate != no-turtles [ let mamas-genes (new-genes length-genes-1 length-genes-2) let papas-genes (new-genes [length-genes-1] of the-mate [length-genes-2] of the-mate ) ;; from chosen bird hatch clutch-size [ ;; this should call a function to set up the finches. setxy random-xcor random-ycor set sex random 2 ;;0 is female, 1 is male set length-genes-1 mamas-genes set length-genes-2 papas-genes set beak-length 0 set beak-length set-beak-length (sum length-genes-1 + sum length-genes-2) set pmort set-pmort set shape "bird side" set size 2 set color set-color beak-length ] ] ] ] ;;set [mated] of finches 0 end to-report new-genes [genes-1 genes-2] let i num-loci - 1 ;; the - 1 is because list entries are indexed starting at 0. let genes (list ifelse-value(random 2 = 1) [item i genes-1] [item i genes-2]) repeat num-loci - 1[ set i i - 1 set genes fput (ifelse-value(random 2 = 1) [item i genes-1] [item i genes-2]) genes ] report genes end to choose-mate let potential-mates turtle-set finches in-radius search-rad if any? potential-mates with [ sex = 1 and mated = 0] [ set potential-mates turtle-set potential-mates with [sex = 1 and mated = 0] repeat mating-tries [ ;; give a bird a chance! let suitor one-of potential-mates let beak-diff abs ([beak-length] of self - [beak-length] of suitor) ;;show (word beak-diff "," suitor) let max-diff max-length - min-length ;; the max and min beak lengths possible let beak-diff-adj beak-diff / max-diff * 9 ;; Takes any beak difference and adjusts to a range of 0-9 ;; Calculate the probability of mating with the suitor let p-mate 1.5 / (1 + 0.5 * exp(-1 * ( -(exp(assortative) - 1) / 25) * beak-diff-adj)) ;; Decide if the beak length is acceptable to the female. if random-float 1 < p-mate [ ;; See R script to visualize set the-mate suitor ;;set [mated] of the-mate 1 ;; show the-mate stop ] ;; determine beak length ] ;; repeat loop ] ;; determine if there are any potential mates end to check-death ask finches [ let N count finches in-radius locale-size let K (carrying-capacity / count patches) * count patches in-radius locale-size let rand random-float 1 let a 10 ;; This is a constant that controls the density dependent mortality -- how close approaches 1 as N nears K let b 0.35 + log (10000 / carrying-capacity) 10 let pmort-adj (1 / (1 + exp(-(N - b * K)/(K / a))) );; Add a density dependent mortality term if (rand < pmort + pmort-adj) [ die ] ] end ;;;;;;;;;;;;;PLOTS;;;;;;;;;;;;;;;;;;; to do-plots set-current-plot "Totals" set-current-plot-pen "green" plot count finches set-current-plot "Length-hist" set-current-plot-pen "green" histogram [beak-length] of finches set-current-plot "Length-time" set-current-plot-pen "green" ifelse count finches > 0 [ plot mean [beak-length] of finches ] [ plot 0 ] set-current-plot "SD-length-time" set-current-plot-pen "sd-length" ifelse count finches > 2 [ plot standard-deviation [beak-length] of finches ] [ plot 0 ] end @#$#@#$#@ GRAPHICS-WINDOW 5 10 270 296 25 25 5.0 1 10 1 1 1 0 0 0 1 -25 25 -25 25 1 1 1 Years BUTTON 8 300 77 333 Setup setup NIL 1 T OBSERVER NIL NIL NIL NIL BUTTON 82 301 145 334 Run go T 1 T OBSERVER NIL NIL NIL NIL BUTTON 150 301 213 334 Step go NIL 1 T OBSERVER NIL NIL NIL NIL SLIDER 6 420 142 453 stop-time stop-time 0 10000 10000 10 1 yr HORIZONTAL PLOT 521 10 721 160 Totals Timestep Birds 0.0 10.0 0.0 10.0 true false PENS "default" 1.0 0 -16777216 true "green" 1.0 0 -10899396 true "brown" 1.0 0 -6459832 true SLIDER 278 172 459 205 wet-best-beak-length wet-best-beak-length 5 15 8.9 0.1 1 NIL HORIZONTAL SLIDER 277 211 432 244 dry-selection-coef dry-selection-coef 0 0.5 0.18 0.01 1 NIL HORIZONTAL SLIDER 278 18 411 51 carrying-capacity carrying-capacity 0 500 500 1 1 NIL HORIZONTAL SLIDER 7 344 166 377 init-long-beak-freq init-long-beak-freq 0 1 0.5 0.1 1 NIL HORIZONTAL PLOT 522 162 722 312 Length-hist Beak length Frequency 5.0 15.0 0.0 10.0 true false PENS "default" 1.0 0 -16777216 true "green" 1.0 1 -10899396 true "brown" 1.0 1 -6459832 true PLOT 319 368 519 518 Length-time Timesteps Mean length 0.0 10.0 0.0 15.0 true false PENS "default" 1.0 0 -16777216 true "green" 1.0 0 -10899396 true "brown" 1.0 0 -6459832 true MONITOR 588 315 647 364 Std. Dev. standard-deviation [beak-length] of finches 2 1 12 MONITOR 524 315 581 364 Mean mean [beak-length] of finches 2 1 12 SLIDER 179 379 301 412 assortative assortative 0 5 0 0.5 1 NIL HORIZONTAL SLIDER 178 416 302 449 search-rad search-rad 0 50 50 1 1 NIL HORIZONTAL SLIDER 276 249 435 282 wet-selection-coef wet-selection-coef 0 0.5 0.07 0.01 1 NIL HORIZONTAL SLIDER 277 134 458 167 dry-best-beak-length dry-best-beak-length 5 15 13 0.1 1 NIL HORIZONTAL SLIDER 180 339 301 372 num-loci num-loci 1 10 5 1 1 NIL HORIZONTAL SLIDER 277 58 423 91 drought-interval drought-interval 0 250 31 1 1 yr HORIZONTAL SLIDER 278 95 423 128 drought-length drought-length 0 50 15 1 1 yr HORIZONTAL MONITOR 432 12 516 61 drought start dry-tick 17 1 12 MONITOR 434 65 515 114 drought end dry-tick + drought-length-rand 17 1 12 SLIDER 7 380 165 413 init-birds init-birds 10 500 200 10 1 birds HORIZONTAL PLOT 525 369 725 519 SD-length-time Timesteps SD length 0.0 10.0 0.0 2.0 true false PENS "sd-length" 1.0 0 -16777216 true @#$#@#$#@ 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. 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