# DEB-IBM for southern elephant seals

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;; ======================================== INTRODUCITON ============================================= ;; ========================== DEFINITION OF PARAMETERS AND STATE VARIABLES =========================== ;; Original model from Martin et al 2012/13 ;; Adjustments have been made to fit the model to southern elephant seal data for female seals only. ;; Values selected as per DEBtool unless otherwise specified, the definition of parameters for the ;; individuals the notation follows the DEBtool-notation as far as possible. Deviation: rates are ;; indicated with "_rate" ;; The model description and sensitivity analysis of the baseline model is published in PLoS ONE, ;; Goedegebuure et al. (2018, DOI 10.1371/journal.pone.0194950) Modelling southern elephant seals ;; Mirounga leonina using an individual-based model coupled with a dynamic energy budget. ;; For which the actual model is available from http://modelingcommons.org/browse/one_model/5348 ;; The model description and modifications from the baseline model that allow for the running ;; of the scenarios are to be published, but are as yet only available in Chapter 4 of my thesis: ;; Using the DEB-IBM to assess the drivers of the decreasing population of elephant seals at ;; Macquarie Island (submitted to external examiners May 3, 2018). ;; General model information and handbook are found at https://ccl.northwestern.edu/netlogo/docs/ ;; ========================================== MODEL START ============================================== ;; Declarations ;extensions [ ;; extensions do not work in the online version of NetLogo - thus blocked out ; profiler ;; for profiling of the model, adjusted on the interface ;] globals[ ;; set global parameters for the model my-seed model_just_started max-ticks counting ;; - - - - - - - - - - - - - - - time management ;; ---------------- to keep track of the day, month, and year in the model day-of-year day-of-month month-of-year year pups-born ;; for overall output ;; ------------------- for competition calculations population ; P competition ; Delta P carrying_capacity ; K ;; - - - - - - - - - - - - - - - stages for IBM foetus ;;0 ;; U_H < U_H^b ; not yet born pup ;;1 ;; U_H > U_H^b & U_H < U_H^x ; born and weaning juvenile ;;2 ;; U_H > U_H^x & U_H < U_H^p ; past weaning mature ;;3 ;; U_H > U_H^p ; mature ;; - - - - - - - - - - - - - - - status for IBM mother-dependent ;; 0 - foetus or pup fasting ;; 1 - resting/moulting/lactating foraging ;; 2 ;; -------------- pup mortality pup-mortality ;============================================================================================= HYPOTHESIS TESTING ;---------- K for Density dependence k1-k2 ; the difference between K1 and K2 rate-of-decline ; the number of individuals that the population declines by per year t-for-k2 ; new time to set next level of K change-time ; for periodic change in K capacity-change ; for changing K by some fraction change-factor ; 0/1 for positive or negative change in capacity ; -------------- yearling mortality percent-pup-affected ; percentage of pups affected with energy change SA_change ; --------------- fecundity percent-mum-affected fec_change fecundity_changed_now? ;---------------- climate variation climate-change clim-var ;============================================================================================= ] ;; --------------------------------------patches-own------------------------------------------------------------- ;patches-own[ ; ;; for now this isn't actually used... competition has been implemented through K1 - K2 ; X ; # / cm^2, prey density ; d_X ; change of prey density in time ;] ;; --------------------------------------------------------------------------------------------------- turtles-own[ ; is_male? ; 1 / 0 -- implement when males are included (for now running model with only females) age ; age of seals (in days) stage ; foetus, pup, juvenile or mature status ; fasting, foraging or mother-dependent ;; - - - - - - - - - - - - - - - STATE VARIABLES - - - - - - - - - - - - - - - - - - - - - - - - - - L ; cm, structural length Lmax ; cm, maximum structural length dL ; change of structural length in time U_H ; t L^2, scaled maturity dU_H ; change of scaled maturity in time U_E ; t L^2, scaled reserves dU_E ; change of scaled reserves in time e_scaled ; - , scaled reserves per unit of structure l_scaled ; - , scaled structural length U_R ; t L^2, scaled energy in reproduction buffer (not standard DEB) dU_R ; change of energy in reproduction buffer (reproduction rate) ;;- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - iv ; to include individual variability for DEB-IBM parameters on a normal distribution ; with a mean on the input paramater and a coefficent of variation equal to the cv g ; - , energy investment ratio ;; - - - - - - - - - - - - - - - FLUXES (used by several submodels) - - - - - - - - - - - - - - - - S_A ; assimilation flux S_C ; mobilisation flux ;; - - - - - - - - - - - - - - - STANDARD DEB PARAMETERS - - - - - - - - - - - - - - - - - - - - - U_H^b ; t L^2, scaled maturity at birth U_H^x ; t L^2, scaled maturity at weaning U_H^p ; t L^2, scaled maturity at puberty ;; - - - - - - - - - - - - - - - PREY DYNAMICS (only relevant if prey-dynamics not constant) f ; - , scaled functional response (food availability) (value between 0 and 1; where 1 = max feeding) ;; for now the following isn't actually used... competition has been implemented below ; K ; # / cm^2, (half) saturation coefficient ; J_XAm_rate ; # / (cm^2 t), surface-area-specific maximum ingestion rate ;; - - - - - - - - - - - - - - - AGEING -- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - r_rate ; growth rate q_accel ; - , ageing acceleration dq_accel ; change of ageing acceleration in time h_rate ; - , hazard rate dh_rate ; change of hazard rate in time ;; - - - - - - - - REPRODUCTION / MOULTING my_ID ; collect ID of self offspring_ID ; collect ID of offspring (-1 if none) mother_ID ; collect ID of mother (-1 if none) ; partner_ID ; collect ID of potential partner for mating (-1 if none) ---- as no males yet cumulative_UE ; initial cumulative energy required for allocation to pup cum_UE ; final cumulative energy required for allocation to pup ---- proportional to mother's size is_pregnant? ; 1 / 0 resting? ; 1 / 0 moulting? ; 1 / 0 haul-out? ; 1 / 0 breeding? ; 1 / 0 impregnated? ; 1 / 0 had-pup? ; 1 / 0 lactating? ; 1 / 0 tried-mating ; count for trying to get pregnant time-since-mating ; days for calculation to start conception time-since-suckling ; days for calculation to weaning days-moulting ; days for calculation of getting back to foraging days-foraging ; days for calculation for resting time (females and young ones) days-resting ; for resting calculation (females and young ones) puppy ; for plotting total-puppies ; for death output die-now ; 0 / 1 - for death in this timestep died-of-? ; 0 / 1 final-age ; recording before death final-pups ; recording before death breeding-age ; recording before death reprod-period ; recording before death fecundity ; recording before death weaning_age ; final age at weaning days-dead ; for collecting age and other final data xx ; for testing for pup-affected//mum-affected pup-affected ; 0 / 1 -- for affected with less energy intake mum-affected track-life ; for tracking life span of turtles (life table) ] ;; ========================== SETUP PROCEDURE: SETTING INITIAL CONDITIONS ============================ to setup ca set my-seed new-seed ;; to make the model reproducible but keep the seed used random ; set my-seed 1548502745 ;; manually set seed output-write word "Generated seed: " my-seed ;; print it in the output box on the interface random-seed my-seed set model_just_started true ;; for profiling reset-ticks set max-ticks max-years * 360 set carrying_capacity max-pop-1 ;------------------------------------ scenarios set k1-k2 max-pop-1 - max-pop-2 ; the difference between k1 and k2 set rate-of-decline k1-k2 / time-for-decline ; the number of individuals that the population declines by per year set percent-pup-affected 0 set fecundity_changed_now? 0 set pup-mortality 0 ;; to set for start (change in do-time-management) if (pup-mort = "minimum") [ set pup-mortality min-pup-mort ] if (pup-mort = "mean") [ set pup-mortality mean-pup-mort ] ;; mean based on McMahon et al 2000, 2003 if (pup-mort = "maximum") [ set pup-mortality max-pup-mort ] ;; - - - - - - - - - - - - - - - time management set day-of-year 1 ;; start on Jan 1 set day-of-month 1 set month-of-year 1 set year 0 ;; - - - - - - - - stages for IBM set foetus 0 ;; U_H < U_H^b set pup 1 ;; U_H > U_H^b & U_H < U_H^x set juvenile 2 ;; U_H > U_H^x & U_H < U_H^p set mature 3 ;; U_H > U_H^p ;; - - - - - - - - status for IBM set mother-dependent 0 ;; foetus/pup set fasting 1 set foraging 2 ;; - - - - - - - - - - - - - - - create seal population as on interface crt start_population ask turtles [ individual-variability ] ;; setting the initial settings of seals set climate-change 0 set clim-var 0 ; profiler:reset ;; clear the profile data end ;; ========================== SUBMODELS ============================================================== ;; -------------------------- INITIAL SETTINGS-------------------------------------------------------- to individual-variability ;; following Martin et al's model -- to apply individual variability - cv set to 0.02 ;; iv applied to DEB and IBM parameters. set iv e ^ (random-normal 0 cv) ;; calculate competition based on the current number of individuals set competition (1 - f_scaled) * ( 1 - (start_population / (2 * carrying_capacity - start_population))) ;; to set effective food availability (f) from initial food availability (f_scaled) set f (f_scaled + competition) * iv if f > 1 [set f 1] set g g_init * iv ;; set scaled maturities set U_H^b (E_H^b_init / p_am) ;* iv ;; scaled maturity at birth (cm^2 d) set U_H^x (E_H^x_init / p_am) ;* iv ;; scaled maturity at weaning (cm^2 d) set U_H^p (E_H^p_init / p_am) ;* iv ;; scaled maturity at puberty (cm^2 d) ;; set scaled length set Lmax L_w^m * shape_factor ;; max struct length ;; so that L > L_w^x and L < L_w^m (size between weaner and full adult) set L ((L_w^x + random (L_w^m - L_w^x)) * shape_factor) ;; set initial reserve ;; these initial settings are balanced out by the second generation seals set l_scaled L / Lmax ;; scaled length -- resets in calc-dL set U_E ((L ^ 3) * (l_scaled / v_rate)) ;; as e < l means starvation model is implemented and e = v_rate * U_E / L ^ 3 set U_H U_E / 2.87 ;; as U_H / U_E = 2.145 @ x, 3.585 @ p. -- not starting with pups - thus excluded from average. set e_scaled (v_rate * (U_E / (L ^ 3))) ;; resets every time step in calc-dU_E ;; sanity check if U_H < U_H^x [ set U_H U_H^x ] ;; make sure every individual to start with has enenough stored energy ;; set stages -- the model will only start with juveniles or adults (foetus/pup initiated from mother only) ifelse U_H < U_H^p [ set stage juvenile ;; 2 set age round (23 + random (1059 - 23)) set h_rate random-float 1.0e-19 set U_R U_H ] [ set stage mature ;; 3 set age round (1059 + random (5400 - 1059)) set h_rate random-float 1.0e-09 set U_R U_H ] ;; set reproduction and moutling settings -- for now no pregnancy in start of model set status foraging set my_ID who ; collect own ID set offspring_ID -1 ; collect ID of offspring (-1 when no offspring) set mother_ID -1 ; collect ID of mother (-1 when no longer relying on mother) ;; calcualtion for the cumulative energy required to produce a healthy offspring that reaches the required size at birth (L_w^b) ;; -- based on the modified calculation in comments on the DEB book (p. 38). ;; This calculation is adjusted here to suit our species by requiring only 70% ;; of the mother's UR levels for the lower limit of energy needs. (Used as the mean in simulations.) set cumulative_UE (((L_w^b * shape_factor) ^ 3) * ((f_scaled + g) / v_rate) * (1 + (3 / 4) * ((L_w^b / L_w^m) / f_scaled))) set cum_UE cumulative_UE * l_scaled * 0.2 set impregnated? 0 ; 1 / 0 conception set is_pregnant? 0 ; 1 / 0 implantation set breeding? 0 ; 1 / 0 start in september set had-pup? 0 ; 1 / 0 set moulting? 0 ; 1 / 0 once a year set lactating? 0 ; 1 / 0 after birth set resting? 0 ; 1 / 0 after foraging for extensive period set haul-out? 0 ; 1 / 0 mid winter haul out for juvenile seals set tried-mating 0 ; count for trying to mate set time-since-mating 0 ; days for calculation to start conception set time-since-suckling 0 ; days for calculation to weaning set days-moulting 0 ; days for calculation of getting back to foraging set days-foraging 0 ; days for calculation for resting time (females and young ones) set days-resting 0 ; for resting calculation (females and young ones) set puppy 0 ; for plotting set total-puppies 0 ; for death output for individuals set die-now 0 ; recording before death set died-of-? 0 set final-age 0 ; recording before death set final-pups -1 ; recording before death set breeding-age 0 ; recording before death set reprod-period 0 ; recording before death set fecundity -1 ; recording before death set weaning_age 0 ; track age at weaning set days-dead 0 ; to track dead individual parameters set xx 100 ; so that no-one starts off with being affected ;----------------------------------------- yearling mortality and fecundity scenarios set pup-affected 0 ; 0 / 1 set xx random-float 100 ; set as random value between 0 and 100 (%) if xx < percent-pup-affected [ set pup-affected 1 ] set mum-affected 0 ; 0 / 1 set xx random-float 100 if xx < percent-mum-affected [ set mum-affected 1 ] set track-life 0 ; set in time-management end ;; ========================== GO PROCEDURE: RUNNING THE MODEL ======================================== to go tick ;; start ticks at beginning of procedure so that the whole thing happens on the correct day ;; see Railsback and Grimm (2011) for more detaied information on why this should be first. ; if ((model_just_started = true) and (use_profiler? = true)) [ ; profiler:start ;; start profiling ; set model_just_started false ;; reset ; ] ;; for days of month, year etc. also adds day to the age of the turtles ;; also includes change for scenario implementations do-time-management ask turtles with [ die-now = 0 ] [ ;reset change each day set dL 0 set dU_E 0 set dU_H 0 set dU_R 0 set cum_UE cumulative_UE * l_scaled * 0.2 ] if fecundity_changed_now? = 1 [ ask turtles [ if mum-affected > 0 [ if increase? = "yes" [ set cum_UE cum_UE * (1 + fec_change) ] if increase? = "no" [ set cum_UE cum_UE * (1 - fec_change) ] ] ] ] set population (count turtles) ;with [stage > 1]) ; not mother dependent... ask turtles [ ifelse population < 1.9 * carrying_capacity [ set competition (1 - f_scaled) * ( 1 - (population / (2 * carrying_capacity - population))) set f (f_scaled + competition) * iv if climate-change = 1 [ set f f * clim-var ] ] [ set competition (1 - f_scaled) * ( 1 - (population / (carrying_capacity / 10) ) ) set f (f_scaled + competition) * iv if climate-change = 1 [ set f f * clim-var ] ] if f > 1 [ set f 1 ] ] ; if climate-change = 1 [ ; ask turtles [ ; set f (f_scaled + competition) * iv * clim-var ; if f > 1 [set f 1] ; ] ; ] ;; go through daily life of seals - only for independent seals: status = 0 for mother-dependent seals (foetus/pup) ;; U_E, U_H, and L calculations only applied to independent seals - for pups this is implemented ;; in update-offspring-energy. Individuals calculate the change in their state var based on the current conditions ask turtles with [ die-now = 0 and status > 0 ][ check-status ] ask turtles with [ die-now = 0 and status > 0 ][ check-breeding ] ask turtles with [ die-now = 0 and status > 0 ][ calc-dU_E ] ; calculate change in scaled reserve ask turtles with [die-now = 0 and status > 0] [ calc-dU_H-R ] ; calc change in scaled maturity and reproductive buffer ask turtles with [ die-now = 0 and status > 0 ][ calc-dL ] ; calculate change in structural length ;; aging is applied to all seals from the day that they were born - ageing here isn't a daily increase in age, ;; but deterioration of structure (acceleration and hazard rates) ask turtles with [ die-now = 0 and stage > 0 ][ calc-ageing ] ; apply aging to turtles ;; apply updated variables - must be implemented last as dL includes a stavation sub model which could change ;; the values in U_H, U_R and dL depending on activities. ask turtles with [ die-now = 0 and status > 0 ][ update ] ;; once adults and juveniles have updated their settings apply applicable changes to offspring ask turtles with [ die-now = 0 and is_pregnant? = 1 ][ update-offspring-energy ] ask turtles with [ die-now = 0 and stage = 1 ][ pup-feeding ] ;; apply mortality (ageing accelerations; h_rate from calc-ageing) ask turtles with [ die-now = 0 and stage > 0 ][ apply-ageing ] ;; end model if no seals or no time left. if count turtles <= 20 or ticks = max-ticks [ ; if (use_profiler? = true) [ ; profiler:stop ;; stop profiling ; print profiler:report ;; view the results ; ] if count turtles <= 20 [ print " stopped as no seals left" ] if ticks = max-ticks [ print " stopped as max time reached" ] stop ;; stop running the model ] ;; sanity check ;; to aviod completely crazy populations - stop the model when too many seals if count turtles > 50 * start_population [ ; if (use_profiler? = true) [ ; profiler:stop ;; stop profiling ; print profiler:report ;; view the results ; ] print "stopped as too many seals" stop ] ;; then the plots are updated - as when no turtles left, the plots show errors. ;;as per below ask turtles with [die-now = 1 and days-dead = 0][ set final-age age / 360 set final-pups total-puppies set reprod-period round (final-age - breeding-age) if reprod-period = 0 [ set reprod-period 1] set fecundity final-pups / round reprod-period set days-dead 1 ] ; ask turtles [if stage > 1 and f > 1 [set f 1]] do-plots ask turtles with [ die-now = 1 and days-dead > 1 ][ die ] ;; plots have been updated - so seals can now die (and be removed from the model) end ;;=================================================================================================== ;; ----------------- RESERVE DYNAMICS ---------------------------------------------------------------- ;; change in reserves: determined by the difference between assimilation (feeding; S_A) and mobilization ;; (energy use; S_C) fluxes. when food-dynamics are constant f = the value of f_scaled set in the user interface to calc-dU_E ; set f (f_scaled + competition) * iv;; competition calculated at start of timestep ; if f > 1 [set f 1] ;; cannot have access to more than 100% food set e_scaled (v_rate * (U_E / (L ^ 3))) ;; calculate the reserve energy --> usable energy saved over time, ;;this changes as U_E and L change over time (de/dt = (f-e) v_rate / L) ;; calculate S_C depending on foraging or fasting is implemented if status = foraging [ set S_C (L ^ 2 * ((g * e_scaled) / (g + e_scaled)) * (1 + ((L * k_M_rate) / v_rate ))) ] if status = fasting [ set f 0 ; fasting, thus no intake set S_C (((k_m_rate * g * kap) / v_rate) * (L ^ 3)) ] if age < 360 and status = foraging [ set xx random-float 100 if xx < 80 [ set f 0.2 * f ] ] ifelse is_pregnant? = 1 and [stage] of turtle offspring_ID = 0 ;; != nobody has been removed from here. [ set S_A (f * ((L ^ 2) + ([L ^ 2] of turtle offspring_ID))) ] ;; upregulation of intake during pregnancy [ set S_A (f * (L ^ 2)) ] if age < (age_for_pup_energy_change * 360) [ if pup-affected = 1 [ set S_A S_A * (1 - SA_change) ] ] set dU_E (S_A - S_C) end to calc-dU_H-R ;;----------------------------------------------------------- ifelse U_H > U_H^p ; ifelse stage = mature [ set dU_R ((1 - kap) * S_C - k_J_rate * U_H^p) ; adult set dU_H 0 ]; ----------------------------------------------------- [ set dU_H ((1 - kap) * S_C - k_J_rate * U_H) ; juvenile set dU_R 0 ] end ;; ----------------- DYNAMICS OF STRUCTURAL LENGTH---------------------------------------------------- ;; the following procedure calculates change in structural length, if growth is negative the individual ;; does not have enough energy to pay somatic maintenance and the starvation submodel is run where growth ;; is set to 0 and individuals divert enough energy from development (for juveniles) or reproduction ;; (for adults) to pay maintenance costs to calc-dL ;; non starvation conditions: if L < Lmax [ set dL ((1 / 3) * (((v_rate /(g * L ^ 2)) * S_C) - k_M_rate * L)) if dL < 0 [ set dL 0 ] ] ;; if scaled energy per unit of structure is less than the scaled length --> use starvation strategy set l_scaled L / Lmax ;; scaled length if e_scaled < l_scaled [ ;; modified following section 4.2.3 of DEB-IBM user manual (Martin et al) set dL 0 ;; cannot have negative growth so set growth to zero set S_C ((k_m_rate * g * kap)/ v_rate) * (L ^ 3) ;; check to see if the turtle is mature to see where remainig energy is diverted to ; ifelse U_H > U_H^p ifelse stage = mature ;--------------------------------------------------------------------------------- [ set dU_R (1 - kap) * S_C - k_J_rate * U_H^p - kap * L ^ 2 * (l_scaled - e_scaled) ;; mature (dU_R) set dU_H 0 ] [ set dU_H (1 - kap) * S_C - k_J_rate * U_H^p - kap * L ^ 2 * (l_scaled - e_scaled) ;; immature (dU_H) set dU_R 0 ] ;; adjusted reserves as S_C changed set dU_E (S_A - S_C) if e_scaled <= 0 [ type turtle who type " with stage = " type stage print " died as e < 0 " ;; sanity check if offspring_ID > -1 [ ask turtle offspring_ID [ if stage = 0 [ set die-now 1 set died-of-? 2 ] if stage = 1 [ set mother_ID -1 set stage 2 ;immediate juvenile as it needs to fend for itself set status 1 ; fasting as left on land set resting? 0 set moulting? 1 ; so that pup stays on land for ~50 days set f (f_scaled + competition) * iv if f > 1 [set f 1] ;; as offspring update happens after adults - go through this now - ;; but in this case only the check-status as energy already updated in update-offspring-energy check-status type turtle who type " juv as mum died. Age: " print [age] of turtle who ] ] ] set die-now 1 set died-of-? 1 ] ] end ;; ----------------- AGEING -------------------------------------------------------------------------- ;; the following procedure calculates the change in damage enducing compounds of an individual to calc-ageing ;; h_a not dependent on food density - thus affects the max life span. ;; s_G dependent on food density ;; h_a = max life span of ~25 years. ;; s_G from Matlab code at T, h_a manually selected based on max age. ;; calculates the rate of growth, scaled acceleration change & scaled hazard rate set r_rate (3 / L) * dL set dq_accel (((q_accel * (L ^ 3 / Lmax ^ 3) * s_G) + h_a ) * e_scaled * ((v_rate / L) - r_rate) - (r_rate * q_accel)) set dh_rate (q_accel - (r_rate * h_rate)) ; apply effects set q_accel q_accel + dq_accel set h_rate h_rate + dh_rate end to apply-ageing ;; calculate chance of death let mortality-chance random-float (mortality-float * iv) if iv < 0.95 [ set mortality-chance mortality-chance / 10] if mortality-chance < h_rate [ if offspring_ID > -1 and turtle offspring_ID != nobody [ ; print " mother died of old age" ;; sanity check ask turtle offspring_ID [ if stage = 0 [ set die-now 1 set died-of-? 2 ] if stage = 1 [ set mother_ID -1 set stage 2 ;; immediate juvenile as it needs to fend for itself set status 1 ;; fasting as left on land set resting? 0 set moulting? 1 ;; so that pup stays on land for ~50 days set f (f_scaled + competition) * iv if f > 1 [set f 1] ;; as offspring update happens after adults - go through this now - ;; but here only the check-status as energy already updated in update-offspring-energy check-status ] ] ] set die-now 1 set died-of-? 3 ] ;; apply pup mortality to pups within their first year of life ;; calculation for mortality: (1/360) * (1-0.716) = 7.89e-4 ;; based on McMahon et al 2000, 2003 for a ;; survival rate of 71.6% as pups weigh (over) the required amount if pup_mort? [ if age < 360 [ ;; yearling let chance random-float 1 if chance < pup-mortality [ if offspring_ID > -1 [ print "error - yearling has a pup?" ask turtle offspring_ID [ set die-now 1 set died-of-? 4 ] ] if mother_ID > -1 [ ;; advice mother of death of pup if applicable ask turtle mother_ID [ set offspring_ID -1 set lactating? 0 set is_pregnant? 0 set impregnated? 0 set time-since-suckling 0 ; not changing breeding or mating status as it could be that the mother has been impregnated again ] ] set die-now 1 set died-of-? 5 ] ] ] end ; ============================ UPDATE =============================================================== to update if (dU_R <= 0 and dU_H > 0) [ ;; somatic growth till age 6, start breeding at age 3 (Desprez et al 2014) if age > 360 [ ;; but should really save energy for self in first year... set dU_R (dU_H * 0.6) ; 60% to dU_R set dU_H (dU_H - dU_R) ] ] set U_E U_E + dU_E set U_H U_H + dU_H if stage = juvenile and U_H > U_H^p [ ;; if they reach puberty levels - move extras into U_R set dU_R dU_R + (U_H - U_H^p) set U_H U_H^p ] set U_R U_R + dU_R set L L + dL if (breeding-age < 1 and U_R > cum_UE) [ set breeding-age age / 360 ] if stage = 2 and age < 360 [ if U_H < 0.92 * U_H^x [ set die-now 1 set died-of-? 1 ] ] ;; kill off seals with energy levels too low if U_R < 0 or U_H < 0 or e_scaled < 0 [ if mother_ID > -1 [ print "energy levels too low to continue pregancy" ask turtle mother_ID [ set offspring_ID -1 set breeding? 0 set lactating? 0 set is_pregnant? 0 set impregnated? 0 set tried-mating 0 set time-since-mating 0 set time-since-suckling 0 ] ] if offspring_ID > -1 [ ifelse [stage] of turtle offspring_ID = 0 [ ask turtle offspring_ID [ ;; foetus set die-now 1 set died-of-? 2 ] ] [ ask turtle offspring_ID [ ;; pup set mother_ID -1 set stage 2 ;;immediate juvenile as it needs to fend for itself set status 1 ;; fasting as left on land set resting? 0 set moulting? 1 ;; so that pup stays on land for ~50 days set f (f_scaled + competition) * iv if f > 1 [set f 1] ;; as offspring update happens after adults - go through this now check-status calc-dU_E calc-dU_H-R calc-dL calc-ageing update ] ] ] set die-now 1 set died-of-? 1 ] ;; update stages (birth and weaning to juvenile to be done in different section later) if U_H >= U_H^p and stage = juvenile [ set stage mature ] end ;======================================================================================= to check-status let max-moulting-time 0 ;; max moulting time set following Carrick et al 1962 let max-resting-time 0 ;; max resting time set following Carrick et al 1962 let max-foraging-time 0 ;; max foraging time set following Carrick et al 1962 ;; setting the correct limits for each stage - applies only to juveniles and adults ;; iv (individual variability) applied to durations if stage = 2 [ ;; Carrick et al (1962) states that moulting for juveniles could be up to 4 weeks. set max-moulting-time moult-duration-juv * iv set max-resting-time resting-duration-juv * iv set max-foraging-time forage-duration-adult * iv ;; However, juveniles cannot stay out for too long in their first year, ;; and newly weaned pups need to stay on land for ~5-6 weeks (here 50 days). ;; pup resting after weaning period is included on the interface. if age < 360 [ set max-moulting-time moult-duration-pup * iv set max-foraging-time forage-duration-juv * iv ] ] ;; Female southern elephant seals come on land twice per year. Once for breeding where they come ;; on land, give birth approx. 8 days later, then have a suckling pup for 23 days after which ;; they return to the water. During this time the seals do not enter the water and loose approx. 35% ;; of their body weight over three weeks (Desprez et al 2014). The second time that the seals come on ;; land is approx. 70 days after they have returned to the water following breeding (Hindell et al 1994) ;; (98 days acording to Carrick et al 1962) for moulting. The adult female seals stay on land for ;; approx. 30 days, however, they might enter the water for a quick feed off shore (Hindell et al 1994). ;; In this model this is ignored, for simplicity. if stage = 3 [ ;; Adult moulting 30 - 50 days for females and males, respectively (Hindell et al 1994) ;; foraging 70 days after breeding season for moulting by breeding adults - (Hindell et al 1994) set max-moulting-time moult-duration-adult * iv set max-resting-time resting-duration-adult * iv set max-foraging-time forage-duration-adult * iv ] ;;========================================= FORAGING ================================================ ;;------------------------------------------------------- ;; Do this before the setting of fasting periods as otherwise they miss a day.The options for ;; counting the days that they are fasting are either time-since-breeding-start, ;; time-after-breeding-end or days-moulting. ;; Applied to either foraging or fasting status. if status = foraging [ set days-foraging days-foraging + 1 if days-foraging > max-foraging-time [ set days-foraging 0 set status fasting set resting? 1 ] ] ;;========================================== FASTING ================================================= ;; Keeping track of days out at sea, particularly for young seals. ;; If they are out for too long, they'll come back onto land for a short while to rest. ;; fasting for both moulting and resting - resting includes the period where mum gives birth to pup. ;; lactating duration dealt with in update-offspring-energy if status = fasting [ if moulting? = 1 [ ;;----------------------- moulting set days-moulting days-moulting + 1 if days-moulting > max-moulting-time [ set days-moulting 0 set moulting? 0 set resting? 0 set status foraging set days-foraging 0 ] ] if resting? = 1 [ ;;------------------------ resting set days-resting days-resting + 1 if days-resting > max-resting-time [ set days-resting 0 set resting? 0 set status foraging set days-foraging 0 ] ] if haul-out? = 1 [ ;;----------------------- mid winter haul out -- Hindell & Burton 1988 set days-resting days-resting + 1 if days-resting > (mwho-juv * iv) [ ;; as set on interface set days-resting 0 set haul-out? 0 set status foraging set days-foraging 0 ] ] ] ;; --------- implement annual moulting for females if month-of-year = 12 [ if day-of-month > 1 and day-of-month < 7 [ if age > 360 [ ;;as newly weaned pups have already moulted by now set status fasting set days-foraging 0 set moulting? 1 set days-moulting 0 ] ] ] ;; Juveniles need to have a mid-winter haul out - which is implemented here. Duration is set on the interface ;; following Carrick et al 1962. This haul out could be anywhere from April to July, but for now set for ;; only July. ;;-------------implement midwinter haulout if month-of-year = 7 [ ;; july if day-of-month > 5 and day-of-month < 15 [ if stage = 2 [ ;; juvenile if status = foraging [ ;; foraging set status fasting ;; now fasting during haul out set haul-out? 1 set resting? 0 set moulting? 0 set days-resting 0 ] ] ] ] end ;;====================================== BREEDING ================================================ to check-breeding ;; start in reverse chronological order so not everything happens in the same time step! ;; breeding is set to 1 in september - which is when the females come onto land to get impregnated. ;; This is only applied if the seal wasn't already impregnated while suckling it's previous pup. ;; As ses technically only breed every two years the breeding like this should be applied if ;; breeding is unsuccesful during weaning of previous pup. if breeding? = 1 [ if offspring_ID > -1 and turtle offspring_ID != nobody [ ;;------------------------------- if ([stage] of turtle offspring_ID = 0) and [age] of turtle offspring_ID >= breeding-duration [ give-birth set time-since-mating 0 ] ;; preparation for birth on land - 8 days prior following Carrick et al // Deprez et al? if time-since-mating = (breeding-duration + diapause - 8)[ set status fasting set resting? 1 set days-foraging 0 set days-resting 0 ] ] ;; time for pregnancy to start - foetus created following Laws 1984 in Knox 2007 if time-since-mating = diapause and is_pregnant? = 0 [ ifelse offspring_ID > -1 [ ifelse turtle offspring_ID = nobody [ set offspring_ID 0 set lactating? 0 set is_pregnant? 0 set impregnated? 0 set time-since-suckling 0 set status foraging set days-foraging 0 set puppy 0 ] [ if [age] of turtle offspring_ID > 90 [ ask turtle offspring_ID [ set f (f_scaled + competition) * iv if f > 1 [set f 1] set stage juvenile set status fasting set moulting? 1 ;; so that pup stays on land for 50 days set days-moulting 0 set mother_ID -1 ] set offspring_ID -1 set lactating? 0 set is_pregnant? 0 set impregnated? 0 set time-since-suckling 0 set status foraging set days-foraging 0 set puppy 0 ] ] ] [ do-pregnancy ] ] if impregnated? = 1 or is_pregnant? = 1[ ; add a day to the pregnancy set time-since-mating time-since-mating + 1 ] ] ;;seals not breeding yet - but it's the right time so could be: if lactating? = 0 [ ;; not lactating if impregnated? = 0 and is_pregnant? = 0 [ ;; not pregnant from this season if tried-mating = 0[ ;; hasn't tried to get pregnant yet if month-of-year = 10 [ ;; it is the right month if day-of-month < 5 [ ;; first week of the month if status = foraging [ ;; wasn't on land already set status fasting ;; adjusting settings set resting? 1 set days-foraging 0 set days-resting 0 ] ] ] ] ] ] if impregnated? = 0 and is_pregnant? = 0 and status = fasting [ ;; get pregnant if month-of-year = 10 [ if tried-mating < 7 [ get-impregnated ] ] ] ;; Included a cycle where lactating mothers breed with invisible males while they're on land with a pup. ;; Mothers come on land about 8 days before giving birth. They then give birth and stay on land for ;; 23 days with the pups while they suckle. During this time the females are getting ready for mating ;; again - and although they generally (at Macca) only breed every other year, it'd be good to get ;; this going - during that time. So after about 19 days the female can get impregnated again. ;; This leaves 4 days for trying to get pregnant - if it doesn't work, they won't breed this year. ;; Following Laws 1984, Hindell et al 1994, Hindell & Slip 1997. if lactating? = 1 [ if impregnated? = 0 and is_pregnant? = 0 [ if month-of-year = 10 [ if (time-since-suckling >= 19) [ get-impregnated ] ] ] ] if month-of-year = 9 [ ;; check month for start breeding if breeding? = 0 [ ;; check if not yet breeding if is_pregnant? = 0 and impregnated? = 0 [ set breeding? 1 ] ;; check that not already pregnant or impregnated ] ] if month-of-year = 11 and day-of-month = 1 [ ;; failed breeders - going back to foraging if breeding? = 1 [ if is_pregnant? = 0 and impregnated? = 0 [ set breeding? 0 set status foraging set resting? 0 set time-since-mating 0 set days-foraging 0 set tried-mating 0 ] ] ] end ;;================================================ to get-impregnated ;; mating success following Fedal et al 1996, Deprez et al 2014 ;; 3 yo @ 0.98, 4 yo @ 0.21, 5 yo @ 0.15, 6+ @ 0.75 ;; no breeding senecense for seals - following Hindell and Little 1988 let prob_mating_fail 0 set tried-mating tried-mating + 1 ifelse age < (6 * 360) [ ifelse age < (5 * 360) [ ifelse age < (4 * 360) [ set prob_mating_fail prob_mate_fail_3yo ] ;; < 4 yo [ set prob_mating_fail prob_mate_fail_4yo ] ;; 4-5 yo ] [ set prob_mating_fail prob_mate_fail_5yo ] ;; 5-6 yo ] [ set prob_mating_fail prob_mate_fail_6plus ] ;; > 6 yo let cum-chance random-float 1 ;; value 0 - 1 if cum-chance > prob_mating_fail [ set impregnated? 1 set time-since-mating 1 set tried-mating 0 set breeding? 1 ] end ;;================================================ to do-pregnancy set is_pregnant? 1 ;; NOTE: ;; original model for daphina spp. sets UR to zero after reproduction/hatching of offspring, ;; however, this CANNOT be done for seals as during reproductive time the seals need to fast ;; and take energy from UR to support themselves. Hence the check of UR levels before reproduction, ;; as personal survival is more important to the mothers than giving birth/producing offspring. ;; from section 7.7 in the DEB book and the associated comments we know the calculation for ;; cummulative energy invested in the pups. calculations are available for both foetal and ;; lactation periods. Thus we can make sure that a seal only goes ahead with the pregnancy if ;; they have enough energy to support the foetus through to birth. if U_R < cum_UE [ set is_pregnant? 0 set impregnated? 0 set time-since-mating 0 set status foraging set days-foraging 1 set breeding? 0 set puppy 0 ] ;; creating a new turtle/individual...... if is_pregnant? = 1 [ hatch 1 [ let hatch_ID who set mother_ID my_ID ask turtle mother_ID [ set offspring_ID hatch_ID ] ;; connect mother and young set offspring_ID -1 set my_ID who set f (f_scaled + competition) * iv if f > 1 [set f 1] set age 1 set stage foetus set status mother-dependent set-foetus-variables ] ] end ;;==================================== to give-birth set breeding? 0 set is_pregnant? 0 set impregnated? 0 set time-since-mating 0 set resting? 1 set lactating? 1 set time-since-suckling 0 set status fasting if turtle offspring_ID = nobody [ set puppy 0 set total-puppies total-puppies - 1 set resting? 0 set lactating? 0 set status foraging set breeding? 0 set pups-born pups-born - 1 ] if turtle offspring_ID != nobody [ ask turtle offspring_ID [ set h_rate random-float 1.0e-19 set stage pup set age 1 set weaning_age 0 set xx random-float 100 if xx < percent-pup-affected [ set pup-affected 1 ] ] set puppy 1 set total-puppies total-puppies + 1 set pups-born pups-born + 1 ] end ;;=============================================================================================================== to update-offspring-energy if offspring_ID > 0 [ ;; separating stages of offspring between foetus and pups if [stage] of turtle offspring_ID = foetus [ ask turtle offspring_ID [ ;; following the additonal DEB information - "Comments on DEB book" - page 152, 501 ;; adjusted the values here that aren't directly deived from Matlab - this makes a difference and allows ;; the seals grow at an accurate rate. Calculations for length following the fast foetal development should ;; be L(t) = t * v_rate / 3, but then the seals take 900-odd days till birth. Adjusting to match 217 days the ;; calculation becomes 25.85 = 217 * v_rate / 0.545 where 25.85 = L_w^b * shape-factor ;; thus: let r_B v_rate / (0.545 * Lmax) ;; adjusted growth calculation for fast foetal development - birth @ U_H^b set dL r_B * Lmax if pup-affected = 1 [ set dL dL * (1 - (SA_change / 2)) ] set L L + dL ;; The following calcualtions approximately follow the DEB book (p. 283). Reserve flux from mother ;; to foetus bypasses assimilatory system of the foetus - thus dU_E = S_A set dU_E [e_scaled] of turtle mother_ID * L ^ 2 * kap_F ;; adjusted kap_F and modified formula if pup-affected = 1 [ set dU_E dU_E * (1 - SA_change) ] set dU_H dU_E set U_E U_E + dU_E set U_H U_H + dU_H ] ;; update mother's reproduction buffer set U_R U_R - ([dU_E * kap_F] of turtle offspring_ID) ] ] end to pup-feeding ifelse mother_ID > -1 [ ;;--------------- sanity check set f f_scaled * 2 * iv ;; higher fat content in milk (16 - 55% Hindell et al 1994) set e_scaled (v_rate * (U_E / (L ^ 3))) ;; test for proportional growth of pup and energy supply by mum set S_A (f * L ^ 2) / kap_L if pup-affected = 1 [ set S_A S_A * (1 - SA_change) ] set S_C 3 * (L ^ 2 * ((g * e_scaled) / (g + e_scaled)) * (1 + ((L * k_M_rate) / v_rate ))) ;; increased the energy mobilisation of pups set dU_E (S_A - S_C) set dU_H ((1 - kap_L) * S_C - (k_J_rate * U_H)) set dL (((v_rate /(g * L ^ 2)) * S_C) - (k_M_rate * L)) ;; adjused for increase rate of growth (*3) set L L + dL set U_E U_E + dU_E set U_H U_H + dU_H set weaning_age weaning_age + 1 set l_scaled L / Lmax ask turtle mother_ID [ set U_R U_R - [ S_A * kap_L ] of turtle offspring_ID;--------see comments on DEB book (Kooijman 2010) - page 38 set time-since-suckling time-since-suckling + 1 ] ] [ ;; there's no mum -- they should go into fasting for some time before heading to the water for feeding set f (f_scaled + competition) * iv if f > 1 [set f 1] set stage juvenile set status fasting set moulting? 1 ;; so that pup stays on land for 50 days set days-moulting 0 ] if age > weaning-duration [ ask turtle mother_ID [ ;; update mother's details set offspring_ID -1 set lactating? 0 set is_pregnant? 0 set time-since-suckling 0 set status foraging set days-foraging 0 set puppy 0 ] ;; update pup details set f (f_scaled + competition) * iv if f > 1 [set f 1] ; set f 0.5 set stage juvenile set status fasting set moulting? 1 ;; so that pup stays on land for 50 days set days-moulting 0 set mother_ID -1 ] end ;;=============================================================================================================== ; -------------------------- TIME MANAGEMENT -------------------------------------------------------------------- to do-time-management ;; model works on a 360 day year, where each month has 30 days. ask turtles [ set age age + 1 ] ask turtles with [ die-now > 0 ][ set days-dead days-dead + 1 ] set day-of-year day-of-year + 1 set day-of-month day-of-month + 1 if day-of-month > 30 [ set day-of-month 1 set month-of-year month-of-year + 1 ] if month-of-year > 12 or day-of-year > 360 [ set day-of-year 1 set day-of-month 1 set month-of-year 1 set year year + 1 ask turtles with [U_H > U_H^b] [ set had-pup? 0 ] ] if ticks = (clear-plots * 360) [ clear-all-plots ] ;-------------------------------------- IMPLEMENT SCENARIOS ;--------------------------------------------------------DENSITY DEPENDENCE if food_change? [ ifelse max-pop-2 < max-pop-1 ;K2 < K1 - - population decrease [ if (ticks >= implement-change-at * 360) ;; K2 is smaller so at this time the population starts declining and (carrying_capacity > max-pop-2)[ ;; assuming (check here) that the population hasn't already reached K2 let t (ticks / 360) ;; setting t at this time if t = implement-change-at [ ;; if t (now) is when the population should start declining set carrying_capacity carrying_capacity - (rate-of-decline * period-in-K) ;; set the new K at the decline calculated for a x year period (set on interface) set t-for-k2 t + period-in-K ;; and reset the time for the next change 10 years further ] if t = t-for-k2 [ ;; if t (now) equals time for the next change set carrying_capacity carrying_capacity - (rate-of-decline * period-in-K) ;; set the new K at the decline calculated for a ten year period set t-for-k2 t + period-in-K ;; and reset the time for the next change 10 years further ] ] ] ;K2 > K1 - - population increase [ if ticks = implement-change-at * 360 [ set carrying_capacity max-pop-2 ;; as the poplation increases slowly - this can be a one off change. ] ] ] ;------------------------------------------------------------- CLIMATE VARIATION if decadal_change? [ let t (ticks / 360) if t = implement-change-at or t = t-for-K2 [ if change_freq = "ENSO" [ set change-time 7 ] if change_freq = "SAM" [ set change-time 4 ] if change_freq = "decadal" [ set change-time 10 ] if change_freq = "random" [ set change-time 15 ] set climate-change 1 set t-for-K2 t + change-time ] if climate-change = 1 [ set clim-var ((rv * (sin ((360 / change-time) * year))) + 1) ] ] ;------------------------------------------------------------- IMPLEMENT CHANGE IN PUP ENERGY INTAKE if pup_energy_change? [ let t (ticks / 360) if t = implement-change-at [ ; if percent_of_pup_change = "five" [ set percent-pup-affected 5 ] ; for 5% of pups affected ; if percent_of_pup_change = "ten" [ set percent-pup-affected 10 ] ; for 10% of pups affected if percent_of_pup_change = "twenty" [ set percent-pup-affected 20 ] ; for 20% of pups affected ; if percent_of_pup_change = "thirty" [ set percent-pup-affected 30 ] ; for 30% of pups affected ; if percent_of_pup_change = "fourty" [ set percent-pup-affected 40 ] ; for 40% of pups affected if percent_of_pup_change = "fifty" [ set percent-pup-affected 50 ] ; for 50% of pups affected ; if percent_of_pup_change = "sixty" [ set percent-pup-affected 60 ] ; for 60% of pups affected if percent_of_pup_change = "eighty" [ set percent-pup-affected 80 ] ; for 40% of pups affected ; if percent_of_energy_change = "five" [ set SA_change 0.05 ] ; for 5% less energy intake ; if percent_of_energy_change = "ten" [ set SA_change 0.10 ] ; for 10% less energy intake if percent_of_energy_change = "twenty" [ set SA_change 0.20 ] ; for 20% less energy intake ; if percent_of_energy_change = "thirty" [ set SA_change 0.30 ] ; for 30% less energy intake ; if percent_of_energy_change = "fourty" [ set SA_change 0.40 ] ; for 40% less energy intake if percent_of_energy_change = "fifty" [ set SA_change 0.50 ] ; for 50% less energy intake ; if percent_of_energy_change = "sixty" [ set SA_change 0.60 ] ; for 60% less energy intake if percent_of_energy_change = "eighty" [ set SA_change 0.80 ] ; for 80% less energy intake ] ] ;----------------------------------------------------------- IMPLEMENT CHANGE IN MUMs FECUNDITY // CUM REP THRESHOLD if mother_fecundity_change? [ let t (ticks / 360) if t = implement-change-at [ ;if percent_of_mum_change = "five" [ set percent-mum-affected 5] ;if percent_of_mum_change = "ten" [ set percent-mum-affected 10] if percent_of_mum_change = "twenty" [ set percent-mum-affected 20] if percent_of_mum_change = "fifty" [ set percent-mum-affected 50] if percent_of_mum_change = "eighty" [ set percent-mum-affected 80] ;if percent_of_mum_change = "hundred" [ set percent-mum-affected 100] ;if percent_of_fec_change = "five" [ set fec_change 0.05 ] ;if percent_of_fec_change = "ten" [ set fec_change 0.10 ] ;if percent_of_fec_change = "fifteen" [ set fec_change 0.15 ] if percent_of_fec_change = "twenty" [ set fec_change 0.20 ] if percent_of_fec_change = "fifty" [ set fec_change 0.50 ] if percent_of_fec_change = "eighty" [ set fec_change 0.80 ] set fecundity_changed_now? 1 ] ] ;; ==============================================================TRACK FOR LIFE TABLES if ticks > 56 * 360 and ticks < 57 * 360 [ ask turtles with [stage = 1 and age < 10] [set track-life 1] ] if ticks > 90 * 360 and ticks < 91 * 360 [ ask turtles with [stage = 1 and age < 10] [set track-life 1] ] end ;;=============================================================================================================== to set-foetus-variables ;; - - - - - - - - - - - - - - - STATE VARIABLES - - - - - - - - - - - - - - - - - - - - - - - - - - set L 0.0001 set dL 0 set U_H 0.0001 set dU_H 0 set U_E 0.0001 set dU_E 0 set e_scaled [e_scaled] of turtle mother_ID set l_scaled L / Lmax set U_R 0 set dU_R 0 ;;- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - set iv e ^ (random-normal 0 cv) ; set J_XAm_rate J_XAm_rate_init * iv set g g_init * iv set U_H^b (E_H^b_init / p_am) ;* iv ;; scaled maturity at birth (cm^2 d) set U_H^x (E_H^x_init / p_am) ;* iv ;; scaled maturity at weaning (cm^2 d) set U_H^p (E_H^p_init / p_am) ;* iv ;; scaled maturity at puberty (cm^2 d) ;; - - - - - - - - - - - - - - - AGEING -- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - set r_rate 0 set q_accel 0 set dq_accel 0 set h_rate 0 set dh_rate 0 ;; - - - - - - - - REPRODUCTION / MOULTING set cumulative_UE (((L_w^b * shape_factor) ^ 3) * ((f_scaled + g) / v_rate) * (1 + (3 / 4) * ((L_w^b / L_w^m) / f_scaled))) set cum_UE cumulative_UE * l_scaled * 0.2 set is_pregnant? 0 set resting? 0 set moulting? 0 set breeding? 0 set impregnated? 0 set had-pup? 0 set lactating? 0 set tried-mating 0 set time-since-mating 0 set time-since-suckling 0 set days-moulting 0 set days-foraging 0 set days-resting 0 set puppy 0 set total-puppies 0 set die-now 0 set died-of-? 0 set final-age 0 set final-pups -1 set breeding-age 0 set reprod-period 0 set fecundity -1 set weaning_age 0 set days-dead 0 set pup-affected 0 set mum-affected 0 set xx random-float 100 if xx < percent-pup-affected [ set pup-affected 1 ] set xx random-float 100 if xx < percent-mum-affected [ set mum-affected 1 ] set track-life 0 end ;;=============================================================================================================== ;; ----------------- PLOTS ---------------------------------------------------------------------------- to do-plots ;; -------------------------------------- population plotting set-current-plot "total population numbers" ;;--------------------- total numbers set-current-plot-pen "adult" plot (count turtles with [stage = 3]) set-current-plot-pen "juvenile" plot (count turtles with [stage = 2 and age > 360]) set-current-plot-pen "pup" plot (count turtles with [stage = 1]) set-current-plot-pen "embryo" plot (count turtles with [stage = 0]) set-current-plot-pen "yearling" plot (count turtles with [age < 360 and stage > 0]) set-current-plot-pen "population" plot (count turtles with [stage > 1]) set-current-plot "population dynamics" ;; ------------------------- proportion set-current-plot-pen "0.5" plot 0.5 set-current-plot-pen "adult" plot ((count turtles with [stage = 3]) / (count turtles + 0.001)) set-current-plot-pen "juvenile" plot ((count turtles with [stage = 2]) / (count turtles + 0.001)) set-current-plot-pen "pup" plot ((count turtles with [stage = 1]) / (count turtles + 0.001)) set-current-plot-pen "embryo" plot ((count turtles with [stage = 0]) / (count turtles + 0.001)) set-current-plot-pen "yearling" plot ((count turtles with [age < 360 and stage > 0]) / (count turtles + 0.001)) set-current-plot "count" ;; ---------------------- total pups and breeders set-current-plot-pen "pups" plot (sum [puppy] of turtles ) set-current-plot-pen "breeders" plot (count turtles with [U_R > cum_UE]) ; calculation for breeding energy levels set-current-plot-pen "total" plot count turtles set-current-plot-pen "K-pop" plot count turtles with [stage > 1] set-current-plot-pen "K" plot carrying_capacity set-current-plot "test pups survival" ;------------------------------------------- pup survival set-current-plot-pen "embryo" plot count turtles with [stage = 0] set-current-plot-pen "pup" plot count turtles with [stage = 1] set-current-plot-pen "yearling" plot count turtles with [stage = 2 and age < 350];-------------------------------------------------------------------- analysis set-current-plot "competition combined" set-current-plot-pen "comb" if any? turtles with [stage > 1 and age > 360 and status = 2 and f > 0][;-------------------------------------------------------------------- analysis plot mean [f] of turtles with [stage > 1 and f > 0] ] ;;; ;; ----------------------------------------------- growth actual length ;;; ;; to plot scaled length - remove "/ shape_factor" from plot and ;;; ;; add "* shape_factor" to the set levels set-current-plot "L" if any? turtles with [stage > 1][ ;; set levels set-current-plot-pen "Lmax" plot mean [Lmax / shape_factor * f_scaled] of turtles set-current-plot-pen "Lp" plot mean [L_w^p] of turtles set-current-plot-pen "Lx" plot mean [L_w^x] of turtles set-current-plot-pen "Lb" plot mean [L_w^b] of turtles ] set-current-plot-pen "mean ad" ;; adults ifelse any? turtles with [stage = 3] [ plot mean [L / shape_factor] of turtles with [stage = 3] ][ plot 0 ] set-current-plot-pen "mean juv" ;; juveniles ifelse any? turtles with [stage = 2] [ plot mean [L / shape_factor] of turtles with [stage = 2] ][ plot 0 ] set-current-plot-pen "mean pup" ;; pups ifelse any? turtles with [stage = 1] [ plot mean [L / shape_factor] of turtles with [stage = 1] ][ plot 0 ] set-current-plot-pen "mean embryo" ;; embryos ifelse any? turtles with [stage = 0] [ plot mean [L / shape_factor] of turtles with [stage = 0] ][ plot 0 ] set-current-plot-pen "min ad" ;; adults ifelse any? turtles with [stage = 3] [ plot min [L / shape_factor] of turtles with [stage = 3] ][ plot 0 ] set-current-plot-pen "min juv" ;; juveniles ifelse any? turtles with [stage = 2] [ plot min [L / shape_factor] of turtles with [stage = 2] ][ plot 0 ] set-current-plot-pen "max ad" ;; adults ifelse any? turtles with [stage = 3] [ plot max [L / shape_factor] of turtles with [stage = 3] ][ plot 0 ] set-current-plot-pen "max juv" ;; juveniles ifelse any? turtles with [stage = 2] [ plot max [L / shape_factor] of turtles with [stage = 2] ][ plot 0 ] ; ------------------------------------------- energy level plotting set-current-plot "total mean Us - adult" ;; ----------------------adult energy if any? turtles with [stage = 3][ set-current-plot-pen "0" plot 0 set-current-plot-pen "U_H^p" plot (mean [U_H^p] of turtles) set-current-plot-pen "U_H" plot (mean [U_H] of turtles with [stage = 3]) set-current-plot-pen "U_R-high" ifelse any? turtles with [stage = 3 and iv > 0.95] [ plot (mean [U_R] of turtles with [stage = 3 and iv > 0.95])][plot 0 ] set-current-plot-pen "U_R-low" ifelse any? turtles with [stage = 3 and iv < 0.95] [ plot (mean [U_R] of turtles with [stage = 3 and iv < 0.95])][plot 0 ] set-current-plot-pen "cum_UE" plot (mean [cum_UE] of turtles with [stage = 3]) ] set-current-plot "total mean Us - juv" ;; -------------------------juvenile energy if any? turtles with [stage = 2][ set-current-plot-pen "0" plot 0 set-current-plot-pen "U_H^x" plot (mean [U_H^x] of turtles) set-current-plot-pen "U_H^p" plot (mean [U_H^p] of turtles) set-current-plot-pen "U_H" plot (mean [U_H] of turtles with [stage = 2]) set-current-plot-pen "U_R-high" ifelse any? turtles with [stage = 2 and iv > 0.95] [ plot (mean [U_R] of turtles with [stage = 2 and iv > 0.95])][plot 0 ] set-current-plot-pen "U_R-low" ifelse any? turtles with [stage = 2 and iv < 0.95] [ plot (mean [U_R] of turtles with [stage = 2 and iv < 0.95])][plot 0 ] set-current-plot-pen "cum_UE" plot (mean [cum_UE] of turtles with [stage = 2]) ] set-current-plot "pregnancy ages";;-------------------------------- age at pregancy set-current-plot-pen "10y" set-plot-pen-color 127 plot 10 set-current-plot-pen "4y" plot 4 set-current-plot-pen "5y" plot 5 set-current-plot-pen "max preg" ifelse any? turtles with [stage = 3 and offspring_ID > -1] [ plot (max [age] of turtles with [stage = 3 and offspring_ID > -1] / 360) ][ plot 0 ] set-current-plot-pen "mean preg" ;;;----------------------------------------------------------------- re-written below 15/02 ifelse any? turtles with [stage = 3 and offspring_ID > -1] [ plot (mean [age] of turtles with [stage = 3 and offspring_ID > -1] / 360) ][ plot 0 ] set-current-plot-pen "min preg" ifelse any? turtles with [stage = 3 and offspring_ID > -1] [ plot (min [age] of turtles with [stage = 3 and offspring_ID > -1] / 360) ][ plot 0 ] set-current-plot-pen "mean preg" ;;;----------------------------------------------------------------- 15/02 ifelse any? turtles with [offspring_ID > -1] [ plot (mean [age] of turtles with [offspring_ID > -1] / 360) ][ plot 0 ] set-current-plot-pen "min preg" ifelse any? turtles with [offspring_ID > -1] [ plot (min [age] of turtles with [offspring_ID > -1] / 360) ][ plot 0 ] ;-------------------------------------------------------------------- analysis set-current-plot-pen "first-preg";------------------------------------------ added 15/02 ifelse any? turtles with [offspring_ID > -1 and total-puppies < 2] [ plot (mean [age] of turtles with [offspring_ID > -1 and total-puppies < 2] / 360) ][ plot 0 ] set-current-plot "fecundity" ifelse any? turtles with [fecundity > -1] [ set-current-plot-pen "max" plot max [fecundity] of turtles with [fecundity > -1];-------------------------------------------------------------------- analysis set-current-plot-pen "mean" plot mean [fecundity] of turtles with [fecundity > -1] set-current-plot-pen "min" plot min [fecundity] of turtles with [fecundity > -1] ] [ set-current-plot-pen "max" plot 0 set-current-plot-pen "mean" plot 0 set-current-plot-pen "min" plot 0 ] set-current-plot "min fecundity" if any? turtles with [fecundity > -1] [ plot min [fecundity] of turtles with [fecundity > -1]] set-current-plot "mean fecundity" if any? turtles with [fecundity > -1] [ plot mean [fecundity] of turtles with [fecundity > -1]] set-current-plot "max fecundity" if any? turtles with [fecundity > -1] [ plot max [fecundity] of turtles with [fecundity > -1]] set-current-plot "max pups over max reproductive period" ifelse any? turtles with [reprod-period > 0] [ set-current-plot-pen "pups" plot max [final-pups] of turtles with [reprod-period > 0] set-current-plot-pen "period" plot max [reprod-period] of turtles with [final-pups = max [final-pups] of turtles with [reprod-period > 0]] ] [ set-current-plot-pen "pups" plot 0 set-current-plot-pen "period" plot 0 ] set-current-plot "final pups for seals" set-current-plot-pen "default" ifelse any? turtles with [final-pups > 0] [ plot max [final-pups] of turtles with [final-pups > 0] ][plot 0] set-current-plot-pen "only breeders - max" if any? turtles with [final-pups > 0][ plot max [final-pups] of turtles with [final-pups > 0]];-------------------------------------------------------------------- analysis set-current-plot-pen "only breeders - mean" if any? turtles with [final-pups > 0][ plot mean[final-pups] of turtles with [final-pups > 0]] set-current-plot-pen "mum-aff = 1" if any? turtles with [final-pups > 0 and mum-affected = 1][ plot max [final-pups] of turtles with [final-pups > 0 and mum-affected = 1]];-------------------------------------------------------------------- analysis set-current-plot-pen "mum-aff = 0" if any? turtles with [final-pups > 0 and mum-affected = 0][ plot max [final-pups] of turtles with [final-pups > 0 and mum-affected = 0]];-------------------------------------------------------------------- analysis set-current-plot "final age" if any? turtles with [final-age > 0] [ set-current-plot-pen "default" plot mean [final-age] of turtles with [final-age > 0] set-current-plot-pen "24" plot 24 ] set-current-plot "seals older than 22 yo";;----------------------- count old seals set-current-plot-pen "count" plot count turtles with [age > (22 * 360)] set-current-plot "pup affected plot" set-current-plot-pen "default" plot ((count turtles with [pup-affected = 1 and age < (360 * 4) ]) / (count turtles with [age < (360 * 4)] + 0.001)) set-current-plot-pen "0.5" plot 0.5 set-current-plot "lifetable" set-current-plot-pen "default" ifelse any? turtles with [track-life = 1] [plot count turtles with [track-life = 1]] [plot 0] set-current-plot-pen "pen-1" ifelse any? turtles with [track-life = 1] [plot sum [puppy] of turtles with [track-life = 1]] [plot 0] ;;;;============================================================================================================================ ;;;;============================================================================================================================ ;; ;plots for tracking of individual seal - intake, storage------------------------ individual plots if (turtle track-turtle != nobody) [ set-current-plot "f of seal" set-current-plot-pen "default" plot [f] of turtle track-turtle set-current-plot-pen "1" plot 1 set-current-plot "Seal energy use" set-current-plot-pen "U_H" plot ([U_H] of turtle track-turtle) set-current-plot-pen "U_R" plot ([U_R] of turtle track-turtle) set-current-plot-pen "U_H^b" plot ([U_H^b] of turtle track-turtle) set-current-plot-pen "U_H^x" plot ([U_H^x] of turtle track-turtle) set-current-plot-pen "U_H^p" plot ([U_H^p] of turtle track-turtle) set-current-plot-pen "breeding level" plot ([cum_UE] of turtle track-turtle) set-current-plot-pen "0" plot 0 set-current-plot "seal energy intake" set-current-plot-pen "default" plot ([U_E] of turtle track-turtle) set-current-plot "seal size" plot [L / shape_factor] of turtle track-turtle set-current-plot "g and e" ;------------------------------------------- g e set-current-plot-pen "ge" plot [(g * e_scaled) / (g + e_scaled)] of turtle track-turtle set-current-plot-pen "l" plot [l_scaled] of turtle track-turtle set-current-plot-pen "e" plot [e_scaled] of turtle track-turtle set-current-plot "pregnant?" set-current-plot-pen "preg" ifelse [impregnated?] of turtle track-turtle = 1 [plot 1][plot 0] set-current-plot-pen "age" ifelse [age] of turtle track-turtle = 1 * 360 [ plot 1.5 ] [ ifelse [age] of turtle track-turtle = 2 * 360 [ plot 1.5] [ ifelse [age] of turtle track-turtle = 3 * 360 [ plot 1.5 ] [ ifelse [age] of turtle track-turtle = 4 * 360 [ plot 1.5 ] [ ifelse [age] of turtle track-turtle = 5 * 360 [ plot 1.5 ] [ ifelse [age] of turtle track-turtle = 6 * 360 [ plot 1.5] [ ifelse [age] of turtle track-turtle = 7 * 360 [ plot 1.5 ] [ ifelse [age] of turtle track-turtle = 8 * 360 [ plot 1.5 ] [ ifelse [age] of turtle track-turtle = 9 * 360 [ plot 1.5 ] [ ifelse [age] of turtle track-turtle = 10 * 360 [ plot 1.5] [ ifelse [age] of turtle track-turtle = 15 * 360 [ set-plot-pen-color 105 plot 1.5] [ plot 0] ] ] ] ] ] ] ] ] ] ] ] ; ;; ;; ;;============================================================================================================== ;; ;;================================================================================= EXTRA PLOTS================= ;;; ;;; set-current-plot "U of preg" ;;; if any? turtles with [offspring_ID > -1] ;;; [ set-current-plot-pen "0" ;;; plot 0 ;;; set-current-plot-pen "U_H^p" ;;; plot (mean [U_H^p] of turtles) ;;; set-current-plot-pen "U_H^x" ;;; plot (mean [U_H^x] of turtles) ;;; set-current-plot-pen "U_H" ;;; plot (mean [U_H] of turtles with [offspring_ID > -1]) ;;; set-current-plot-pen "U_R" ;;; plot (mean [U_R] of turtles with [offspring_ID > -1]) ;;; set-current-plot-pen "cum_UE" ;;; plot (mean [cum_UE] of turtles with [offspring_ID > -1]) ;;; ] ;; ;;; set-current-plot "dead seals" ;;; plot count turtles with [die-now = 1] ;;; ; ;; ;;; ;;; set-current-plot "breeding age" ;;; ifelse any? turtles with [breeding-age > 0] ;;; [ set-current-plot-pen "max" ;;; plot max [breeding-age] of turtles with [breeding-age > 0] ;;; set-current-plot-pen "mean" ;;; plot mean [breeding-age] of turtles with [breeding-age > 0] ;;; set-current-plot-pen "min" ;;; plot min [breeding-age] of turtles with [breeding-age > 0] ;;; ] ;;; [ set-current-plot-pen "max" plot 0 ;;; set-current-plot-pen "mean" plot 0 ;;; set-current-plot-pen "min" plot 0] ;; ;;; set-current-plot "reproductive period" ;;; ifelse any? turtles with [reprod-period > 0] ;;; [ plot max [reprod-period] of turtles with [reprod-period > 0]][plot 0] ;; ;; ;;; set-current-plot "weaning" ;;; ifelse any? turtles with [stage = 1] ;;; [ plot max [weaning_age] of turtles with [stage = 1]] ;;; [ plot 0] ;;; ;; set-current-plot "total mean Us - pup" ;; -------------------------pup energy ;; if any? turtles with [stage = 1][ ;; set-current-plot-pen "U_H^b" ;; plot (mean [U_H^b] of turtles) ;; set-current-plot-pen "U_H^x" ;; plot (mean [U_H^x] of turtles) ;; set-current-plot-pen "U_H 1" ;; plot (min [U_H] of turtles with [stage = 1]) ;; set-current-plot-pen "U_H 2" ;; plot (mean [U_H] of turtles with [stage = 1]) ;; set-current-plot-pen "U_H 3" ;; plot (max [U_H] of turtles with [stage = 1]) ;; ] ;;; ;;; set-current-plot "total mean Us - embryo" ;;--------------------- embryo enery ;;; if any? turtles with [stage = 0][ ;;; set-current-plot-pen "0" ;;; plot 0 ;;; set-current-plot-pen "U_H^b" ;;; plot (mean [U_H^b] of turtles) ;;; set-current-plot-pen "U_H^x" ;;; plot (mean [U_H^x] of turtles) ;;; set-current-plot-pen "U_H 1" ;;; plot (min [U_H] of turtles with [stage = 0]) ;;; set-current-plot-pen "U_H 2" ;;; plot (mean [U_H] of turtles with [stage = 0]) ;;; set-current-plot-pen "U_H 3" ;;; plot (max [U_H] of turtles with [stage = 0]) ;;; ;;; ] ;;; ;;; set-current-plot "Seals fasting" ;;---------------------------- total juveniles fasting ;;; set-current-plot-pen "juvenile" ;;; plot count turtles with [age > 360 and stage < 3 and status = fasting and haul-out? = 0] ;;; set-current-plot-pen "juv-mwho" ;;; plot count turtles with [age > 360 and stage < 3 and status = fasting and haul-out? = 1] ;;; set-current-plot-pen "yearling" ;;; plot count turtles with [age < 361 and status = fasting and haul-out? = 0] ;;; set-current-plot-pen "year-mwho" ;;; plot count turtles with [age < 361 and stage < 3 and status = fasting and haul-out? = 1] ;;; ;;; set-current-plot "U_R test" ;;------------------------------- reproduction buffer levels seals ;;; set-current-plot-pen "preg min" ;;; ifelse any? turtles with [is_pregnant? = 1] ;;; [ plot min [U_R] of turtles with [is_pregnant? = 1]][ plot 0 ] ;;; set-current-plot-pen "preg mean" ;;; ifelse any? turtles with [is_pregnant? = 1] ;;; [ plot mean [U_R] of turtles with [is_pregnant? = 1]][ plot 0 ] ;;;; set-current-plot-pen "preg max" ;;;; ifelse any? turtles with [is_pregnant? = 1] ;;;; [ plot max [U_R] of turtles with [is_pregnant? = 1]][ plot 0 ] ;;;; set-current-plot-pen "non-preg min" ;;;; ifelse any? turtles with [is_pregnant? = 0 and age > 4 * 360 and age < 15 * 360] ;;;; [plot min [U_R] of turtles with [is_pregnant? = 0 and age > 4 * 360 and age < 15 * 360]][plot 0] ;;;; set-current-plot-pen "non-preg mean" ;;;; ifelse any? turtles with [is_pregnant? = 0 and age > 4 * 360 and age < 15 * 360] ;;;; [plot mean [U_R] of turtles with [is_pregnant? = 0 and age > 4 * 360 and age < 15 * 360]] [plot 0] ;;;; set-current-plot-pen "non-preg max" ;;;; ifelse any? turtles with [is_pregnant? = 0 and age > 4 * 360 and age < 15 * 360] ;;;; [plot max [U_R] of turtles with [is_pregnant? = 0 and age > 4 * 360 and age < 15 * 360]][plot 0] ;;;; set-current-plot-pen "cum_UE" ;;;; plot mean [cum_UE] of turtles ;;; set-current-plot-pen "0.5 of cum_UE" ;;; plot (mean [0.5 * cum_UE] of turtles) ;; ;; ;; ;; ;; ;; ;;; set-current-plot "pup e-scaled" ;;; set-current-plot-pen "pup" ;;; ifelse any? turtles with [stage = 1] ;;; [plot mean [e_scaled] of turtles with [stage = 1]][plot 0] ;;; set-current-plot-pen "adult" ;;; ifelse any? turtles with [stage = 3] ;;; [plot mean [e_scaled] of turtles with [stage = 3]][plot 0] ;;; set-current-plot-pen "1" ;;; plot 1 ;;; ;; ;;; ;;; set-current-plot "embryo - pup L" ;;; set-current-plot-pen "embryo" ;; embryos ;;; ifelse any? turtles with [stage = 0] ;;; [ plot max [L / shape_factor] of turtles with [stage = 0] ][ plot 0 ] ;;; set-current-plot-pen "pup" ;; pups ;;; ifelse any? turtles with [stage = 1] ;;; [ plot max [L / shape_factor] of turtles with [stage = 1] ][ plot 0 ] ;;; set-current-plot-pen "1" ;;; plot mean [L_w^x] of turtles ;;; set-current-plot-pen "0" ;;; plot mean [L_w^b] of turtles ;;; ;; ;;; set-current-plot "SC_pup" ;;; set-current-plot-pen "default" ;;; ifelse any? turtles with [stage = 1] ;;; [plot mean [S_C] of turtles with [stage = 1]][plot 0] ;; ;;; ; ---------------------------------- energy level plotting ;;; ; --------------------------------------------- delta energy plotting ;;; set-current-plot "total deltas - adult" ;; adults ;;; if any? turtles with [stage = 3][ ;;; set-current-plot-pen "dU_E" ;;; plot (mean [dU_E] of turtles with [stage = 3]) ;;; set-current-plot-pen "dU_H" ;;; plot (mean [dU_H] of turtles with [stage = 3]) ;;; set-current-plot-pen "dU_R" ;;; plot (mean [dU_R] of turtles with [stage = 3]) ;;; set-current-plot-pen "0" ;;; plot 0 ;;; ] ;;; ;;; set-current-plot "total deltas - juv" ;; juveniles ;;; if any? turtles with [stage = 2][ ;;; set-current-plot-pen "dU_E" ;;; plot (mean [dU_E] of turtles with [stage = 2]) ;;; set-current-plot-pen "dU_H" ;;; plot (mean [dU_H] of turtles with [stage = 2]) ;;; set-current-plot-pen "dU_R" ;;; plot (mean [dU_R] of turtles with [stage = 2]) ;;; set-current-plot-pen "0" ;;; plot 0 ;;; ] ;;; set-current-plot "total deltas - pup" ;; pups ;;; if any? turtles with [stage = 1][ ;;;; set-current-plot-pen "dU_E" ;;;; plot (mean [dU_E] of turtles with [stage = 1]) ;;; set-current-plot-pen "dU_H" ;;; plot (mean [dU_H] of turtles with [stage = 1]) ;;; set-current-plot-pen "dU_R" ;;; plot (mean [dU_R] of turtles with [stage = 1]) ;;; set-current-plot-pen "0" ;;; plot 0 ;;; ] ;;; ;;; set-current-plot "dU_E pup" ;;; if any? turtles with [stage = 1][ ;;; set-current-plot-pen "default" ;;; plot (mean [dU_E] of turtles with [stage = 1]) ;;; ] ;;;; ;;; set-current-plot "total deltas - embryo" ;; embryos ;;; if any? turtles with [stage = 0][ ;;; set-current-plot-pen "dU_E" ;;; plot (mean [dU_E] of turtles with [stage = 0]) ;;; set-current-plot-pen "dU_H" ;;; plot (mean [dU_H] of turtles with [stage = 0]) ;;; set-current-plot-pen "dU_E w kap_F" ;;; plot (mean [dU_E * kap_F] of turtles with [stage = 0]) ;;; set-current-plot-pen "0" ;;; plot 0 ;;; ] ;; ;;; ;;----------------------------------------------- delta growth plotting ;;; set-current-plot "dL" ;-------------------------------------------- delta growth ;;; ifelse any? turtles with [stage = 3] ;; adults ;;; [ set-current-plot-pen "adult" ;;; plot (mean [dL] of turtles with [stage = 3]) ;;; ] ;;; [ set-current-plot-pen "adult" ;;; plot 0 ;;; ] ;;; ifelse any? turtles with [stage = 2] ;; juveniles ;;; [ set-current-plot-pen "juv" ;;; plot (mean [dL] of turtles with [stage = 2]) ;;; ] ;;; [ set-current-plot-pen "juv" ;;; plot 0 ;;; ] ;;;; ifelse any? turtles with [stage = 1] ;; pups ;;;; [ set-current-plot-pen "pups" ;;;; plot (mean [dL] of turtles with [stage = 1]) ;;;; ] ;;;; [ set-current-plot-pen "pups" ;;;; plot 0 ;;;; ] ;;; ;;;; set-current-plot "dL foetus + pups" ;----------------------------- delta growth foetus/pups ;;;; ifelse any? turtles with [stage = 1] ;; pups ;;;; [ set-current-plot-pen "pups" ;;;; plot (mean [dL] of turtles with [stage = 1]) ;;;; ] ;;;; [ set-current-plot-pen "pups" ;;;; plot 0 ;;;; ] ;;;; ifelse any? turtles with [stage = 0] ;; foetus ;;;; [ set-current-plot-pen "embryo" ;;;; plot (mean [dL] of turtles with [stage = 0]) ;;;; ] ;;;; [ set-current-plot-pen "embryo" ;;;; plot 0 ;;;; ] ;;; ;;; if any? turtles with [e_scaled > l_scaled][;;------------------non-starvation mode ;;;; 1) ;;; set-current-plot "normal deltas" ;--------------------------------- normal delta ;;; set-current-plot-pen "0" ;;; plot 0 ;;; set-current-plot-pen "dU_E" ;;; plot (mean [dU_E] of turtles with [e_scaled > l_scaled]) ;;; set-current-plot-pen "dU_H" ;;; plot (mean [dU_H] of turtles with [e_scaled > l_scaled]) ;;; set-current-plot-pen "dU_R" ;;; plot (mean [dU_R] of turtles with [e_scaled > l_scaled]) ;;; ;;;; 2) ;;; set-current-plot "normal Us" ;-------------------------------------- normal U ;;; set-current-plot-pen "0" ;;; plot 0 ;;; set-current-plot-pen "U_E" ;;; plot (mean [U_E] of turtles with [e_scaled > l_scaled]) ;;; set-current-plot-pen "U_H" ;;; plot (mean [U_H] of turtles with [e_scaled > l_scaled]) ;;; set-current-plot-pen "U_R" ;;; plot (mean [U_R] of turtles with [e_scaled > l_scaled]) ;;; ] ;;; ;--------------------------------- starvation condition plots ;;; if any? turtles with [e_scaled < l_scaled][ ;;;; type " count turtles with e_scaled < l_scaled " print count turtles with [e_scaled < l_scaled] ;;;; 1) ;;; set-current-plot "starvation deltas" ;------------------------------ starvation delta ;;; set-current-plot-pen "0" ;;; plot 0 ;;; set-current-plot-pen "dU_E" ;;; plot (mean [dU_E] of turtles with [e_scaled < l_scaled]) ;;; set-current-plot-pen "dU_H" ;;; plot (mean [dU_H] of turtles with [e_scaled < l_scaled]) ;;; set-current-plot-pen "dU_R" ;;; plot (mean [dU_R] of turtles with [e_scaled < l_scaled]) ;;;; 2) ;;; set-current-plot "starvation Us" ;---------------------------------- starvation Us ;;; set-current-plot-pen "0" ;;; plot 0 ;;; set-current-plot-pen "U_E" ;;; plot (mean [U_E] of turtles with [e_scaled < l_scaled]) ;;; set-current-plot-pen "U_H" ;;; plot (mean [U_H] of turtles with [e_scaled < l_scaled]) ;;; set-current-plot-pen "U_R" ;;; plot (mean [U_R] of turtles with [e_scaled < l_scaled]) ;;; ] ;; ;; ;------------------------------ general plots ;; ;;; set-current-plot "S_C" ;---------------------------------------------- SC ;;; set-current-plot-pen "0" ;;; plot 0 ;;; set-current-plot-pen "S_A" ;;; plot (mean [S_A] of turtles with [stage > 1]) ;;; set-current-plot-pen "S_C" ;;; plot (mean [S_C] of turtles with [stage > 1]) ;; ;; ;;; ;;-------------------------pregnancy/non-pregnancy U_R checks ;;; set-current-plot "U_R of pregnant seals" ;;; set-current-plot-pen "mean U_R" ;;; ifelse any? turtles with [is_pregnant? = 1] ;;; [ plot mean [U_R] of turtles with [is_pregnant? = 1]][ plot 0 ] ;;; set-current-plot-pen "min U_R" ;;; ifelse any? turtles with [is_pregnant? = 1] ;;; [ plot min [U_R] of turtles with [is_pregnant? = 1]][ plot 0 ] ;;; set-current-plot-pen "cum_UE" ;;; plot mean [cum_UE] of turtles ;;; ;;; set-current-plot "U_R of non pregnant seals" ;;; set-current-plot-pen "mean U_R" ;;; plot mean [U_R] of turtles with [is_pregnant? = 0 and age > 4 * 360 and age < 15 * 360] ;;; set-current-plot-pen "max U_R" ;;; plot max [U_R] of turtles with [is_pregnant? = 0 and age > 4 * 360 and age < 15 * 360] ;;; set-current-plot-pen "cum_UE" ;;; plot mean [cum_UE] of turtles ;; ;; ;;------------------------------------------------------- births ;;; set-current-plot "prop succesful births to breeders" ;--------------------- births of breeders ;;; set-current-plot-pen "pen-1" ;;; plot 0.25 ;;; set-current-plot-pen "pen-2" ;;; plot 0.5 ;;; set-current-plot-pen "pen-3" ;;; plot 0.75 ;;; set-current-plot-pen "pen-4" ;;; plot 1 ;;; if count turtles with [stage = 1] / (0.00000000000001 + count turtles with [U_R > cum_UE]) < 2 [ ;;; set-current-plot-pen "default" ;;; plot (count turtles with [stage = 1] / (0.00000000000001 + count turtles with [U_R > cum_UE])) ;;; ] ;;; if count turtles with [stage = 1] / (0.00000000000001 + count turtles with [U_R > cum_UE and age < (15 * 360)]) < 2 [ ;;; set-current-plot-pen "pen-5" ;;; plot (count turtles with [stage = 1] / (0.00000000000001 + count turtles with [U_R > cum_UE and age < (15 * 360)])) ;;; ] ;;; ;; set-current-plot "pop dyn" ;; ------------------------- proportion based on age ;;; set-current-plot-pen "0.5" ;;; plot 0.5 ;;; set-current-plot-pen "6+" ;;; plot ((count turtles with [stage > 1 and age > 360 * 6]) / (count turtles + 0.001)) ;;; set-current-plot-pen "pup-6" ;;; plot ((count turtles with [stage > 1 and age < 360 * 6]) / (count turtles + 0.001)) ;;; set-current-plot-pen "pup" ;;; plot ((count turtles with [stage = 1]) / (count turtles + 0.001)) ;;; set-current-plot-pen "embryo" ;;; plot ((count turtles with [stage = 0]) / (count turtles + 0.001)) ;;; ; ;; set-current-plot "fec_by_age" ;; if ticks > 50 * 360 [ ;; if any? turtles with [total-puppies > 0][ ;; ;; ifelse any? turtles with [total-puppies > 0 and age > 3 * 360 and age < 4 * 360] [ ;; set-current-plot-pen "pen-2" ;; plot mean [total-puppies / ((3 / 360) - breeding-age)] of turtles with [total-puppies > 0 and age > 3 * 360 and age < 4 * 360] ;; ][set-current-plot-pen "pen-2" plot 0] ;; ifelse any? turtles with [total-puppies > 0 and age > 4 * 360 and age < 5 * 360] [ ;; set-current-plot-pen "pen-3" ;; plot mean [total-puppies / ((4 / 360) - breeding-age)] of turtles with [total-puppies > 0 and age > 4 * 360 and age < 5 * 360] ;; ][set-current-plot-pen "pen-3" plot 0] ;; ifelse any? turtles with [total-puppies > 0 and age > 5 * 360 and age < 6 * 360] [ ;; set-current-plot-pen "pen-4" ;; plot mean [total-puppies / ((5 / 360) - breeding-age)] of turtles with [total-puppies > 0 and age > 5 * 360 and age < 6 * 360] ;; ][set-current-plot-pen "pen-4" plot 0] ;; ifelse any? turtles with [total-puppies > 0 and age < 6 * 360 and age < 7 * 360] [ ;; set-current-plot-pen "pen-5" ;; plot mean [total-puppies / ((6 / 360) - breeding-age)] of turtles with [total-puppies > 0 and age > 6 * 360 and age < 7 * 360] ;; ][set-current-plot-pen "pen-5" plot 0] ;; ifelse any? turtles with [total-puppies > 0 and age > 7 * 360 and age < 8 * 360] [ ;; set-current-plot-pen "pen-6" ;; plot mean [total-puppies / ((7 / 360) - breeding-age)] of turtles with [total-puppies > 0 and age > 7 * 360 and age < 8 * 360] ;; ][set-current-plot-pen "pen-6" plot 0] ;; ifelse any? turtles with [total-puppies > 0 and age > 8 * 360 and age < 9 * 360] [ ;; set-current-plot-pen "pen-7" ;; plot mean [total-puppies / ((8 / 360) - breeding-age)] of turtles with [total-puppies > 0 and age > 8 * 360 and age < 9 * 360] ;; ][set-current-plot-pen "pen-7" plot 0] ;; ifelse any? turtles with [total-puppies > 0 and age > 9 * 360 and age < 10 * 360] [ ;; set-current-plot-pen "pen-8" ;; plot mean [total-puppies / ((9 / 360) - breeding-age)] of turtles with [total-puppies > 0 and age > 9 * 360 and age < 10 * 360] ;; ][set-current-plot-pen "pen-8" plot 0] ;; ifelse any? turtles with [total-puppies > 0 and age > 10 * 360 and age < 11 * 360] [ ;; set-current-plot-pen "pen-9" ;; plot mean [total-puppies / ((10 / 360) - breeding-age)] of turtles with [total-puppies > 0 and age > 10 * 360 and age < 11 * 360] ;; ][set-current-plot-pen "pen-9" plot 0] ;; ifelse any? turtles with [total-puppies > 0 and age > 11 * 360] [ ;; set-current-plot-pen "pen-10" ;; plot mean [total-puppies / ((age / 360) - breeding-age)] of turtles with [total-puppies > 0 and age > 11 * 360] ;; ][set-current-plot-pen "pen-10" plot 0] ;; ;; ] ;; ] ;; ;; set-current-plot "rate_of_survival" ;; set-current-plot-pen "pen-1" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age < 1 * 360 and stage > 0] / count turtles with [die-now = 0 and age < 1 * 360 and stage > 0] ;; set-current-plot-pen "pen-2" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 1 * 360 and age < 2 * 360] / count turtles with [die-now = 0 and age > 1 * 360 and age < 2 * 360] ;; set-current-plot-pen "pen-3" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 2 * 360 and age < 3 * 360] / count turtles with [die-now = 0 and age > 2 * 360 and age < 3 * 360] ;; set-current-plot-pen "pen-4" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 3 * 360 and age < 4 * 360] / count turtles with [die-now = 0 and age > 3 * 360 and age < 4 * 360] ;; set-current-plot-pen "pen-5" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 4 * 360 and age < 5 * 360] / count turtles with [die-now = 0 and age > 4 * 360 and age < 5 * 360] ;; set-current-plot-pen "pen-6" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 5 * 360 and age < 6 * 360] / count turtles with [die-now = 0 and age > 5 * 360 and age < 6 * 360] ;; set-current-plot-pen "pen-7" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 6 * 360 and age < 7 * 360] / count turtles with [die-now = 0 and age > 6 * 360 and age < 7 * 360] ;; set-current-plot-pen "pen-8" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 7 * 360 and age < 8 * 360] / count turtles with [die-now = 0 and age > 7 * 360 and age < 8 * 360] ;; set-current-plot-pen "pen-9" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 8 * 360 and age < 9 * 360] / count turtles with [die-now = 0 and age > 8 * 360 and age < 9 * 360] ;; set-current-plot-pen "pen-10" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 19 * 360 and age < 10 * 360] / count turtles with [die-now = 0 and age > 9 * 360 and age < 10 * 360] ;; set-current-plot-pen "pen-11" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 10 * 360 and age < 11 * 360] / count turtles with [die-now = 0 and age > 10 * 360 and age < 11 * 360] ;; set-current-plot-pen "pen-12" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 11 * 360 and age < 12 * 360] / count turtles with [die-now = 0 and age > 11 * 360 and age < 12 * 360] ;; set-current-plot-pen "pen-13" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 12 * 360 and age < 13 * 360] / count turtles with [die-now = 0 and age > 12 * 360 and age < 13 * 360] ;; set-current-plot-pen "pen-14" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 13 * 360 and age < 14 * 360] / count turtles with [die-now = 0 and age > 13 * 360 and age < 14 * 360] ;; set-current-plot-pen "pen-15" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 14 * 360 and age < 15 * 360] / count turtles with [die-now = 0 and age > 14 * 360 and age < 15 * 360] ;; set-current-plot-pen "pen-16" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 15 * 360 and age < 16 * 360] / count turtles with [die-now = 0 and age > 15 * 360 and age < 16 * 360] ;; set-current-plot-pen "pen-17" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 16 * 360 and age < 17 * 360] / count turtles with [die-now = 0 and age > 16 * 360 and age < 17 * 360] ;; set-current-plot-pen "pen-18" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 17 * 360 and age < 18 * 360] / count turtles with [die-now = 0 and age > 17 * 360 and age < 18 * 360] ;; set-current-plot-pen "pen-19" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 18 * 360 and age < 19 * 360] / count turtles with [die-now = 0 and age > 18 * 360 and age < 19 * 360] ;; ;; ifelse any? turtles with [age > 19 * 360 and age < 20 * 360][ ;; set-current-plot-pen "pen-20" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 19 * 360 and age < 20 * 360] / count turtles with [die-now = 0 and age > 19 * 360 and age < 20 * 360] ;; ][set-current-plot-pen "pen-20" plot 0] ;; ifelse any? turtles with [age > 20 * 360 and age < 21 * 360][ ;; set-current-plot-pen "pen-21" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 20 * 360 and age < 21 * 360] / count turtles with [die-now = 0 and age > 20 * 360 and age < 21 * 360] ;; ][set-current-plot-pen "pen-21" plot 0] ;; ifelse any? turtles with [age > 21 * 360 and age < 22 * 360][ ;; set-current-plot-pen "pen-22" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 21 * 360 and age < 22 * 360] / count turtles with [die-now = 0 and age > 21 * 360 and age < 22 * 360] ;; ][set-current-plot-pen "pen-22" plot 0] ;; ifelse any? turtles with [age > 22 * 360 and age < 23 * 360][ ;; set-current-plot-pen "pen-23" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 22 * 360 and age < 23 * 360] / count turtles with [die-now = 0 and age > 22 * 360 and age < 23 * 360] ;; ][set-current-plot-pen "pen-23" plot 0] ;; ifelse any? turtles with [age > 23 * 360 and age < 24 * 360][ ;; set-current-plot-pen "pen-24" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 23 * 360 and age < 24 * 360] / count turtles with [die-now = 0 and age > 23 * 360 and age < 24 * 360] ;; ][set-current-plot-pen "pen-24" plot 0] ;; ifelse any? turtles with [age > 24 * 360][ ;; set-current-plot-pen "pen-25" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 24 * 360 and age < 25 * 360] / count turtles with [die-now = 0 and age > 24 * 360 and age < 25 * 360] ;; ][set-current-plot-pen "pen-25" plot 0] ;; ifelse any? turtles with [age > 25 * 360][ ;; set-current-plot-pen "pen-26" ;; plot count turtles with [die-now = 1 and days-dead = 1 and age > 25 * 360] / count turtles with [die-now = 0 and age > 25 * 360] ;; ][set-current-plot-pen "pen-26" plot 0] ; ; ; ; ;;; set-current-plot "death reason" ;;; if any? turtles with [die-now = 1 and days-dead = 1] [ ;;; set-current-plot-pen "1 - low energy" ;;; ifelse any? turtles with [die-now = 1 and days-dead = 1 and died-of-? = 1] ;;; [ plot ((count turtles with [die-now = 1 and days-dead = 1 and died-of-? = 1]) / (count turtles with [die-now = 1 and days-dead = 1 ] + 0.001))] ;;; [ plot 0 ] ;;; set-current-plot-pen "2 - foetus w mum" ;;; ifelse any? turtles with [die-now = 1 and days-dead = 1 and died-of-? = 2] ;;; [ plot ((count turtles with [die-now = 1 and days-dead = 1 and died-of-? = 2])/ (count turtles with [die-now = 1 and days-dead = 1 ] + 0.001))] ;;; [ plot 0 ] ;;; set-current-plot-pen "3 - old age" ;;; ifelse any? turtles with [die-now = 1 and days-dead = 1 and died-of-? = 3] ;;; [ plot ((count turtles with [die-now = 1 and days-dead = 1 and died-of-? = 3])/ (count turtles with [die-now = 1 and days-dead = 1 ] + 0.001))] ;;; [ plot 0 ] ;;; set-current-plot-pen "4 - error" ;;; ifelse any? turtles with [die-now = 1 and days-dead = 1 and died-of-? = 4] ;;; [ plot ((count turtles with [die-now = 1 and days-dead = 1 and died-of-? = 4])/ (count turtles with [die-now = 1 and days-dead = 1 ] + 0.001))] ;;; [ plot 0 ] ;;; set-current-plot-pen "5 - pup mort" ;;; ifelse any? turtles with [die-now = 1 and days-dead = 1 and died-of-? = 5] ;;; [ plot ((count turtles with [die-now = 1 and days-dead = 1 and died-of-? = 5])/ (count turtles with [die-now = 1 and days-dead = 1 ] + 0.001))] ;;; [ plot 0 ] ;;; ] ;; ; ;; ;;; set-current-plot "total mean Us - yearling" ;; -------------------------yearling energy ;;; if any? turtles with [stage = 2 and age < 350][ ;;; set-current-plot-pen "U_H^p" ;;; plot (mean [U_H^p] of turtles) ;;; set-current-plot-pen "U_H^x" ;;; plot (mean [U_H^x] of turtles) ;;; set-current-plot-pen "U_H^b" ;;; plot (mean [U_H^b] of turtles) ;;; set-current-plot-pen "max UH" ;;; plot (max [U_H] of turtles with [stage = 2 and age < 350]) ;;; set-current-plot-pen "mean UH" ;;; plot (mean [U_H] of turtles with [stage = 2 and age < 350]) ;;; set-current-plot-pen "min UH" ;;; plot (min [U_H] of turtles with [stage = 2 and age < 350]) ;;; ] ;; ;;set-current-plot "competition" ;; set-current-plot-pen "comb" ;; if any? turtles with [stage > 1 and age > 360 and status = 2 and f > 0][;-------------------------------------------------------------------- analysis ;; plot mean [f] of turtles with [stage > 1 and f > 0] ;; ] ;; set-current-plot-pen "max juv" ;; if any? turtles with [stage = 2 and status = 2 and f > 0 and age > 360][ ;; plot max [f] of turtles with [stage = 2 and f > 0] ; status = 2, only while foraging ;; ] ;; set-current-plot-pen "mean juv" ;; if any? turtles with [stage = 2 and status = 2 and f > 0 and age > 360][ ;; plot mean [f] of turtles with [stage = 2 and f > 0] ; status = 2, only while foraging ;; ] ;; set-current-plot-pen "min juv" ;; if any? turtles with [stage = 2 and status = 2 and f > 0 and age > 360][ ;; plot min [f] of turtles with [stage = 2 and f > 0] ; status = 2, only while foraging ;; ] ;; set-current-plot-pen "max adult" ;; if any? turtles with [stage = 3 and status = 2 and f > 0][ ;; plot max [f] of turtles with [stage = 3 and f > 0] ; status = 2, only while foraging ;; ] ;; set-current-plot-pen "mean adult" ;; if any? turtles with [stage = 3 and status = 2 and f > 0][ ;; plot mean [f] of turtles with [stage = 3 and f > 0] ; status = 2, only while foraging ;; ] ;; set-current-plot-pen "min adult" ;; if any? turtles with [stage = 3 and status = 2 and f > 0][ ;; plot min [f] of turtles with [stage = 3 and f > 0] ; status = 2, only while foraging ;; ] ; ; ;; ;;; set-current-plot "total count" ;;; set-current-plot-pen "old" ;;; plot count turtles with [stage > 1] ;;; set-current-plot-pen "young" ;;; plot count turtles with [stage = 1] ;;; ; ;; ; ; ; ;;;; ; ;; ; set-current-plot "L for export" ; if any? turtles with [stage > 1][ ;; set levels ; set-current-plot-pen "Lmax" ; plot mean [Lmax / shape_factor * f_scaled] of turtles ; set-current-plot-pen "Lp" ; plot mean [L_w^p] of turtles ; set-current-plot-pen "Lx" ; plot mean [L_w^x] of turtles ; set-current-plot-pen "Lb" ; plot mean [L_w^b] of turtles ; ] ; set-current-plot-pen "max" ; ifelse any? turtles ; [ plot (max [L / shape_factor] of turtles)][ plot 0 ] ; set-current-plot-pen "mean adult" ; ifelse any? turtles with [stage = 3] ; [ plot (mean [L / shape_factor] of turtles with [stage = 3]) ][ plot 0 ] ; set-current-plot-pen "min adult" ; ifelse any? turtles with [stage = 3] ; [ plot (min [L / shape_factor] of turtles with [stage = 3]) ][ plot 0 ] ; set-current-plot-pen "mean juv" ; ifelse any? turtles with [stage = 2] ; [ plot (mean [L / shape_factor] of turtles with [stage = 2]) ][ plot 0] ; set-current-plot-pen "min juv" ; ifelse any? turtles with [stage = 2] ; [ plot (min [L / shape_factor] of turtles with [stage = 2]) ][ plot 0 ] ; set-current-plot-pen "max pup" ; ifelse any? turtles with [stage = 2] ; [ plot (mean [L / shape_factor] of turtles with [stage = 2]) ][ plot 0] ; set-current-plot-pen "min pup" ; ifelse any? turtles with [stage = 2] ; [ plot (min [L / shape_factor] of turtles with [stage = 2]) ][ plot 0 ] ;; ;;; set-current-plot "L of embryo" ;;; if any? turtles with [stage = 0][ ;;; set-current-plot-pen "Lx" ;;; plot mean [L_w^x] of turtles ;;; set-current-plot-pen "Lb" ;;; plot mean [L_w^b] of turtles ;;; set-current-plot-pen "L 1" ;;; plot min [L / shape_factor] of turtles with [stage = 0] ;;; set-current-plot-pen "L 2" ;;; plot mean [L / shape_factor] of turtles with [stage = 0] ;;; set-current-plot-pen "L 3" ;;; plot max [L / shape_factor] of turtles with [stage = 0] ;;; ] ;; ;; ;;; ;;;;; ;;;;; ;-------------------------------------------------------------------------------- ;;;;; ;-------------------------------------------------------------------------------- ;;;;; ; ;;; ;;; ;;; ;;;; ;;---------------------------------------------------------------------------------------------------- ;;;; ;;--------------------------------------------------------------------------------------------------- ;;;;; ;;; ;---------------------------------- age plotting ;; set-current-plot "age" ;----------------------------------------------- age ;; set-current-plot-pen "max" ;;; plot (max [age] of turtles / 360) ;;; set-current-plot-pen "mean adult" ;;; ifelse any? turtles with [stage = 3] ;;; [ plot (mean [age] of turtles with [stage = 3] / 360) ][ plot 0 ];-------------------------------------------------------------------- analysis ;;; set-current-plot-pen "min adult" ;;; ifelse any? turtles with [stage = 3] ;;; [ plot (min [age] of turtles with [stage = 3] / 360) ][ plot 0 ];-------------------------------------------------------------------- analysis ;;; set-current-plot-pen "mean juv" ;;; ifelse any? turtles with [stage = 2] ;;; [ plot (mean [age] of turtles with [stage = 2] / 360) ][ plot 0] ;;; set-current-plot-pen "min juv" ;;; ifelse any? turtles with [stage = 2] ;;; [ plot (min [age] of turtles with [stage = 2] / 360) ][ plot 0 ] ;; set-current-plot-pen "max pup" ;; ifelse any? turtles with [stage = 1] ;; [ plot (mean [age] of turtles with [stage = 1] / 360) ][ plot 0] ;; set-current-plot-pen "min pup" ;; ifelse any? turtles with [stage = 1] ;; [ plot (min [age] of turtles with [stage = 1] / 360) ][ plot 0 ] ;;; set-current-plot-pen "23" ;;; plot 23 ;;; set-current-plot-pen "15" ;;; plot 15 ;;; set-current-plot-pen "7" ;;; plot 7 ;;; set-current-plot-pen "4" ;;; plot 4 ;;; set-current-plot-pen "1" ;;; plot 1 ;;; ;;;; ; ;;;; ;;;;; set-current-plot "lactating and pregnant?" ;;;;; ifelse any? turtles with [lactating? = 1 and impregnated? = 1] ;;;;; [ set-current-plot-pen "yes" ;;;;; plot 1 ;;;;; plot-pen-down ;;;;; set-plot-pen-color 127 ;;;;; set-plot-pen-mode 1 ;;;;; ] ;;;;; [ set-current-plot-pen "yes" ;;;;; plot 0.5 ;;;;; plot-pen-up ;;;;; set-plot-pen-color 7 ;;;;; ] ;;; ;;;; end

There are 2 versions of this model.

## Attached files

File | Type | Description | Last updated | |
---|---|---|---|---|

DEB-IBM for southern elephant seals .png | preview | Preview for 'DEB-IBM for southern elephant seals ' | about 5 years ago, by Merel Goedegebuure | Download |

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