DEB-IBM for southern elephant seals

;; ======================================== 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