# DEB-IBM for Abatus cordatus

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; the indivduals are given their own agentsets depending on lifestage, and sex for adults: breed [embryos embryo] ;; there shouldn't be any: if an embryo appears, there is an issue in the individual energetic dynamics. breed [juveniles juvenile] breed [females female] breed [males male] ;_-_-_-_-_-_-_-_-_ ; ------------------------------------------------------------------------------------------------------------------------------------------ globals[ ; global parameters: are accessible for patches and turtles, and the same for all (one change affects all) ;.....................................CALENDARS - TIMERS (from the start of the simulation)........................................................ ;repro_time ; 7 8 9 10 11 0 1 2 3 4 5 6, 7 8 .......based on reproduction timings ;GSI_time ; 5 6 7 8 9 10 11 12 1 2 3 4, 5 6 .......for accumulation or decrease of GSI ;birth_time ; 1 0 0 0 0 8 7 6 5 4 3 2, 1 0 .......only runs if triggered by reproduction, for the DEBbirth of individuals time ; 1 2 3 4 5 6 7 8 9 10 11 12, 13 14 .......no reseting: time since the start of the run ;;; ; Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep, Oct Nov.......corresponding Gregorian calendar for AH month_time ; 10 11 12 01 02 03 04 05 06 07 08 09, 10 11 .......month numeration for the Gregorian calendar year ; year count from the beginning of the run ;;; Global parameters and their dimensions: ; ...............parameters linked to temperature and resources: f ; - , scaled functional response TC ; temperature correction factor used to adapt the standard DEB parameters to species-specific site temperature ; ...............population: pop_init ; #, initial population (in a one-patch simulation configuration) prop_fem ; proportion of females on site pop_density ; indiv/m^2, current population density on site car_cap ; carrying capacity for the site density_adults ; #/m^2, density of adults on the patch density_juveniles ; #/m^2, density of juveniles on the patch surface ; number of 1m^2 patches, useful in case the model is used with a spatial component ;;;RMV? food_compet ; quantification of the scale of competition ; ...............mortality accounts: olddeath ; count of the number of death due to ageing (individual-specific) bgdeath ; count of the number of death due to background death (fixed monthly percentage of random death on the population) bgdeath_adu ; same as bgdeath but only counting the adults bgdeath_juv ; same as bgdeath but only counting the juveniles starvedeath ; count of the number of death due to starvation (individual-specific) tempdeath ; count of the number of death due to temperature (percentage of random death on the population depending on the SST) ; ............... for environmental input parameters: ;;for making the in-program LISTS (order according to the position of the column in the file): ;Temperature: timeMark ; month number on the first column of the file (0 to 71) avgTemp ; temperature value ;; average over a month for 2012-2018 from PROTEKER data avgTemp_fut ; future temperature list (new list created from present list) Tbefore ; for checking mortality: temperature of the month preceding the current tick ;Resources: infoMonth ; month number on the first column of the file (1 to 12) inputf ; f value ;; from Delille1989 inputf_fut ; future resources list (new list created from present list) ;;; Variables used only in the setup: ; ............... for calculation of the cost of an egg (specific variables used for the simulation of embryo development in calc-embryo): e_scaled_embryo ref_e_scaled U_E_embryo S_C_embryo U_H_embryo L_embryo dU_E_embryo dU_H_embryo dL_embryo lower_bound upper_bound simulation_embryo ; to count the number of loops U_E^start ; t L^2, initial embryo reserves calculated from the bisection method L_0 ; cm, initial structural volume of embryo estim_embryo ; t L^2, initial embryo reserve in the simulation ; ............... for calculation of initial parameters for each age 1 to 5yo (simulation of individual development in calc-init): simul ; to count the number of loops timestep_simul ; a different timestep is used in the setup development simulation f_simul ; constant f value for the simulation L_simul ; L, structural length used in the simulation U_E_simul U_H_simul U_H^p_simul U_R_simul h_rate_simul q_acceleration_simul dh_rate_simul dq_acceleration_simul e_scaled_simul S_C_simul S_A_simul dU_E_simul dU_H_simul dU_R_simul dL_simul age_months_simul U_E_1yo U_H_1yo U_R_1yo L_1yo h_rate_1yo q_acceleration_1yo U_E_2yo U_H_2yo U_R_2yo L_2yo h_rate_2yo q_acceleration_2yo U_E_3yo U_H_3yo U_R_3yo L_3yo h_rate_3yo q_acceleration_3yo U_E_3yo_juv U_H_3yo_juv U_R_3yo_juv L_3yo_juv h_rate_3yo_juv q_acceleration_3yo_juv U_E_4yo U_H_4yo U_R_4yo L_4yo h_rate_4yo q_acceleration_4yo U_E_5yo U_H_5yo U_R_5yo L_5yo h_rate_5yo q_acceleration_5yo ;;; other global variables (used in GO): U_E_0yo ; Reserve at birth, calculated from the bisection method (embryo simulation) L_b ; (L) structural length at birth ; ............... for plotting and data exploitation: mean values for the state variable for all turtles avg_UR_fem ; lists the mean value of females U_R for each tick min_UR_fem ; lists the min value of females U_R for each tick max_UR_fem ; lists the max value of females U_R for each tick avg_dUR_fem ; lists the mean value of females dU_R for each tick min_dUR_fem max_dUR_fem avg_dUE_fem min_dUE_fem max_dUE_fem avg_UE_fem min_UE_fem max_UE_fem avg_Lphy min_Lphy max_Lphy avg_UE_adu ; lists the mean value of adults U_E for each tick min_UE_adu max_UE_adu avg_dUE_adu min_dUE_adu max_dUE_adu avg_Lphy_adu min_Lphy_adu max_Lphy_adu avg_UE_juv ; lists the mean value of juveniles U_E for each tick min_UE_juv max_UE_juv avg_dUE_juv min_dUE_juv max_dUE_juv avg_UE ; lists the mean value of inidividuals (juveniles & all adults included) U_E for each tick min_UE max_UE avg_dUE min_dUE max_dUE avg_dL min_dL max_dL ] patches-own[ ; parameters for the environment (patch-specific): ; ............... DEB parameters for calculation of TC: T_ref ; reference temperature in Kelvin T_A ; Arrhenius temperature T ; actual temperature (in Celsius) f-scaled ; functional response f from the input file ] turtles-own[ ;variables that are turtle-only and turtle-specific: each individual has to change their own value for the variable, as changes only applies to the turtle that is asked to modify it ;;;;.....................................CALENDARS - TIMERS (from the start of the simulation)........................................................ repro_time ; 7 8 9 10 11 0 1 2 3 4 5 6, 7 8 .......based on reproduction timings GSI_time ; 5 6 7 8 9 10 11 12 1 2 3 4, 5 6 .......for accumulation or decrease of GSI ;birth_time ; 1 0 0 0 0 8 7 6 5 4 3 2, 1 0 .......only runs if triggered by reproduction, for the DEBbirth of individuals ;time ; 1 2 3 4 5 6 7 8 9 10 11 12, 13 14 .......no reseting: time since the start of the run ;;; ; Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep, Oct Nov.......corresponding Gregorian calendar for AH ;month_time ; 10 11 12 01 02 03 04 05 06 07 08 09, 10 11 .......month numeration for the Gregorian calendar ; ............... State variables (dimensions): L ; (L) 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 U_R ; (t L^2) scaled energy in reproduction buffer dU_R ; change of energy in reproduction buffer Lphy ; (L), physical length (L/del_M) age_months ; time in month from the birth of the indiv age_years ; time in years from the birht of the indiv ; ............... for ageing: q_acceleration ; (t^-2) ageing acceleration dq_acceleration ; change of ageing acceleration in time h_rate ; (t-1) specific death probability rate dh_rate ; change of hazard rate in time h_a ; (t^-2) Weibull ageing acceleration ; ............... Fluxes: S_A ; (L^2) assimilation flux (scaled) S_C ; (L^2) mobilisation flux (scaled) ; ............... Standard DEB parameters (dimensions): g ; (-) energy investment ratio v_rate ; (L/t) energy conductance kap ; (-) fraction of mobilised reserve allocated to soma kap_R ; (-) reproduction efficiency k_M_rate ; (1/t) somatic mainitenance rate coefficient k_J_rate ; (1/t) maturity mainitenance rate coefficient U_H^b ; (t L^2) scaled maturity at birth U_H^p ; (t L^2) scaled maturity at puberty scatter-multiplier ; parameter used to put a random variation in individual parameters ; ............... specific flags for dead or starving state. deceased ; flag to indicate the individual died during the tick (0/ON) deceased_old ; flag to indicate the individual died of senescence (0/ON) deceased_bg ; flag to indicate the individual died due to population bacckground mortality rate (0/ON) starvation ; flag to indicate the individual is starving (ON) or not (0) ] females-own [ ; ............... for the reproduction and laying of offsprings: reproduction ; flag switch to allow reproduction (OFF/ON) GSI ; Gonado-somatic index, needed to switch reproduction on/off GSI_init ; minimum GSI (outside of reproduction) dGSI ; delta GSI GSI_max ; GSI at the beginning of reproduction U_R_max ; U_R at the beginning of reproduction eggs ; number of eggs produced Ri ; reproductive output (for the number of juveniles born) ;.....................................CALENDARS - TIMERS (from the start of the simulation)........................................................ ;repro_time ; 7 8 9 10 11 0 1 2 3 4 5 6, 7 8 .......based on reproduction timings, backbone timer ;GSI_time ; 5 6 7 8 9 10 11 12 1 2 3 4, 5 6 .......for accumulation or decrease of GSI birth_time ; 1 0 0 0 0 8 7 6 5 4 3 2, 1 0 .......only runs if triggered by reproduction, for the DEBbirth of individuals ;time ; 1 2 3 4 5 6 7 8 9 10 11 12, 13 14 .......no reseting: time since the start of the run ;;; ; Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep, Oct Nov.......corresponding Gregorian calendar for AH ;month_time ; 10 11 12 01 02 03 04 05 06 07 08 09, 10 11 .......month numeration for the Gregorian calendar ] ; -----------------------------------------------SETUP----------------------------------------------------------------------------- ;_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-INITIALIZATION OF THE MODEL_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_- to setup clear-all ;setup the timers and calendars: set time 0 set month_time 10 set year 0 ask patches [ set T_ref 293.15 ; reference temperature for which TC = 1 set T_A 9000 ; Arrhenius temperature in tolerance range input-temperature ; get the temperature data from external file, depending on the site chosen input-resources ; procedure to get f data from external files, depending on the site chosen if projection != "present" [ ; and modify it if future scenarios are chosen for the projection future-temp future-rsces ] setup-temperature ; to get the environmental varb for the month of the setup setup-resources set pop_init 120 ; initial population for the site set car_cap 200 ; the carrying capacity of the site. set prop_fem 0.5 ; proportion of females in the pop, from Poulin1996 ] if add-my-pet? [convert-parameters] ; to use the model with another species with DEB parameters taken from the DEBtool database add-my-pet ; calcluation of initial individuals parameters: calc-embryo calc-init ; setup the pop: ask patches [ sprout pop_init [ ; each patch creates a number of individuals equal to pop_init init-birth ; and each of these individuals initialize their parameters. ] ] init-pop ; the population is divided into age classes with age-specific parameters ; setup of calendars for reproduction cycles: ask turtles [ set GSI_time 5 set repro_time 7 ] ask females [ set GSI 0.03 set birth_time 0 ] reset-ticks end ; ----------------------------------------------------------GO-------------------------------------------------------------------------------- ;_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-PROCEEDINGS OF THE MODEL_-__-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_- ;_-_-_-Each round of the model realizes the following procedures in this order and then starts again from the top: to go reset-countdeath ; reset the death counts. Disabble to obtain a cumulative death plot. update-year_timer ; timers for the month of the year are updated at the beginning for the input of environmental data ;;;Environmental settings: ask patches [ update-resources ; take the data for f and temperature for this month (calendar is the month_time calendar) update-temperature ;set f-scaled 1 ; uncomment this line and the next to run the model with DEB standard and constant values for f and T ;set T 20 if competition? [calc-compet] ; if the competition is switched on in the interface, calculate the effect of competition on f set f (f-scaled + food_compet) ; set the functional response f based on resources availability (external file) and competition if f > 1 [set f 1] ; f is 1 at maximum if f < 0 [set f 0] ; f is 0 at minimum ] ;;;Individual settings: ask turtles [ if deceased = "on" [die] ; the individuals that died during the previous timestep are removed ;(they are not removed in the previous timestep so that they appear in the plots to monitor their death, this varb was made to monitor ageing effect) convert-TC ; calculate the temperature correction and convert the parameters affected by temperature calc-dU_E ; calculate the changes in state variables that happened over the month calc-dU_H calc-dU_R calc-dL calc-ageing ; calculate the changes in ageing parameters ] update-individual ; update state variables of individuals by applying the calculated changes ask turtles [update-repro_timers] ; the timers for reproduction are updated ;;;Females settings (for reproduction): ask females [ ; mature females update-birth-timer if repro_time = 0 and reproduction = "on" [ ; if it is the timing for reproduction, and if the reproduction has been allowed by the GSI the month before, set GSI_max GSI ; set the current GSI as the GSI from which calculations will be made set eggs 27 ] calc-GSI ; in any case they calculate their GSI each month ifelse GSI >= 0.07 ; if the GSI is enough, [set reproduction "on" ; allow reproduction if repro_time = 11 [ set U_R_max U_R ; keep the last U_R before reproduction period in mind, to force the gradual decrease during reproduction set birth_time 9 ; make it known that reproduction is happening ] ] [set reproduction "off"] ; if the GSI is not higher than the required threshold, the possibility to reproduce is cancelled if (birth_time >= 6) and (birth_time <= 8) [ ; if it's one of the three reproduction month, reproduce ] ; females produce embryos (by adapting the reprobuffer) ; 5 months after conception, the juveniles are DEBborn if (birth_time <= 3) and (birth_time >= 1) [ release-offsprings ] ; let the offspring out and give it initial parameters to start dvpmt ] ;;;Population data: update-pop ; update the population by calculating the density update-time ; update the calendars and timers that haven't been updated yet tick if count turtles = 0 [ ; stop the model if all individuals died user-message ("What have you done ?! The population went extinct! (O_O') ") stop] if time = run_time * 12 [ ; stop the model after the number years indicated in the interface stop] end ; ---------------------------------------DESCRIPTION OF THE PROCEDURES--------------------------------------------------------------------------------------------------- ; ---------------------------------------Procedures for SETUP: --------------------------------------------------------------------------------------------------- ; =============== ; ====================================Input of environmental data from external file: ; =============== ;_-_-_-_-_-_-_-_-_for temperature: to input-temperature ; creating lists for each parameter if Sites = "Anse du Halage" [file-open "temp_time_monthavg_Halage.txt"] ; open the text file in the folder ;; the following is for when other sites are chosen: in that case, careful that there needs to have the appropriate resources files for the site in the folder: ;/!\for now choosing sites other than Anse du Halage, Port Couvreux or Ile Haute is not possible, the files are not available/!\/!\/!\/!\/!\/!\/!\ if Sites = "Ile Suhm" [file-open "temp_time_monthavg_Suhm.txt"] if Sites = "Port aux Français" [file-open "temp_time_monthavg_PaF.txt"] if Sites = "Ile Haute" [file-open "temp_time_monthavg_Haute.txt"] if Sites = "Fjord des Portes Noires" [file-open "temp_time_monthavg_PortesNoires.txt"] if Sites = "Port Couvreux" [file-open "temp_time_monthavg_Couvreux.txt"] set timeMark [] ; create empty list set avgTemp [] while [file-at-end? = false] [ ; concatenate the empty list and a list containing the next value in the file (the file is read from left to right, and the values taken one by one to add to the list) set timeMark sentence timeMark (list file-read) ; first list with the values for the month set avgTemp sentence avgTemp (list file-read) ; second list (parallel to the first) with the values for temp ] file-close ; created a duo of parallel lists with the timestamp and the corresponding temperature end ;_-_for the future temperature data: to future-temp ifelse future != "food only" [ ; for projections including the effect of temp changes: if projection = "RCP 2.6" [ ; depending on the chosen scenario in the interface set avgTemp_fut map [i -> i + 1.1 ] avgTemp ] ; create a new list from the current lists by adding the expected changes if projection = "RCP 8.5" [ set avgTemp_fut map [i -> i + 1.7 ] avgTemp ] ] [ ; for projections isolating the effect of food changes: if projection = "RCP 2.6" [ set avgTemp_fut avgTemp ] if projection = "RCP 8.5" [ set avgTemp_fut avgTemp ] ] end ;_-_then get the values for the month used for setup: to setup-temperature ; see 'to-report select-rsces' procedure for explanation ifelse projection = "present" [set T select-temp timeMark avgTemp 0] ; gives to T the value for temperature corresponding to the line 0 in the temp list. [set T select-temp timeMark avgTemp_fut 0] end to-report select-temp [list1 list2 timing] ; see 'to-report select-rsces' procedure for explanation: let m timing if ((timing / 72) >= 1) [ ; (if the number of ticks is higher than the number of values in the temperature list, set m (timing - (72 * floor (timing / 72))) ; get the corresponding value counting from the start of the list.) ] let Q (position m list1) report item Q list2 end ;_-_-_-_-_-_-_-_-_for resources: to input-resources if Sites = "Anse du Halage" [file-open "inputRSces_M_f_Delille.txt"] ;; the following is for when other sites are chosen: in that case, careful that there needs to have the appropriate resources files for the site in the folder: ;/!\for now the files are not available for other sites: choosing Port Couvreux of Ile Haute will use the file for Anse du Halage, while other site choices will not work at all/!\/!\/!\/!\/!\/!\/!\ if Sites = "Ile Suhm" [file-open "inputRSces_M_f_Suhm.txt"] if Sites = "Port aux Français" [file-open "inputRSces_M_f_PaF.txt"] if Sites = "Ile Haute" [file-open "inputRSces_M_f_Delille.txt"] ; [file-open "inputRSces_M_f_Haute.txt"] if the site-sepcific data is available, exchange the two commands if Sites = "Fjord des Portes Noires" [file-open "inputRSces_M_f_PortesNoires.txt"] if Sites = "Port Couvreux" [file-open "inputRSces_M_f_Delille.txt"] ; [file-open "inputRSces_M_f_Couvreux.txt"] if the site-sepcific data is available, exchange the two commands set infoMonth [] set inputf [] while [file-at-end? = false] [ set infoMonth sentence infoMonth (list file-read) set inputf sentence inputf (list file-read) ] file-close ; created a duo of parallel lists with (month) and (f) end ;_-_for future resources data: to future-rsces ifelse future != "temp only" ; for projections including the effect of food changes: [ if projection = "RCP 2.6" [ ; depending on the chosen scenario in the interface set inputf_fut map [i -> i - i * 0.1 ] inputf ] ; create new lists from the current lists by adding the expected changes if projection = "RCP 8.5" [ set inputf_fut map [i -> i - i * 0.2] inputf ] ] [ ; for projections isolating the effect of temperature changes: if projection = "RCP 2.6" [ set inputf_fut inputf ] if projection = "RCP 8.5" [ set inputf_fut inputf ] ] end ;_-_then get the values for the month used for setup: to setup-resources ; see 'to report select-rsces' procedure for explanation ifelse projection = "present" [set f-scaled select-rsces infoMonth inputf month_time ] ; get the f-scaled from the f list created in input-resources using the month list as an index. [set f-scaled select-rsces infoMonth inputf_fut month_time] end ;_-_What 'select-rsces' does: to-report select-rsces [list1 list2 timeval] ;list1 (infoMonth), list2 (inputf) and timeval (month_time) are indicators of where to take the informations let month timeval ; (month is a temporary variable existing only within the procedure) let R (position month list1) ; R temporarily marks the position of the value corresponding to month in the 'list1' (eg. it finds the value of month_time in the list infoMonth and gives to R the line number of this value in the list) report item R list2 ; gives the item with index R in list2 = gives the corresponding f value indexed at this month end ; =============== ; ====================================Parameters conversion procedures: ; =============== ;_-_-_-_-_-_-_-_-_Conversion of parameters from add-my-pet parameters (for adaptation to other species): to convert-parameters let p_am p_m * zoom / kap_init set U_H^b_init E_H^b / p_am set U_H^p_init E_H^p / p_am set k_M_rate_init p_m / E_G set g_init (E_G * v_rate_init / p_am) / kap_init end ; =============== ; =============================================Initialisation of the population: ; =============== ;_-_-_-_-_-_-_-_- Bisection method for the calculation of energy of an egg: to calc-embryo set L_0 0.00001 ; (embryos start with almost no structure) set lower_bound 0 set upper_bound 1000 ; the upper bound is given an arbitrary first value, set simulation_embryo 0 loop [ set simulation_embryo simulation_embryo + 1 ; (to keep track of the number of loops) set estim_embryo 0.5 * (lower_bound + upper_bound) set L_embryo L_0 set U_E_embryo estim_embryo set U_H_embryo 0 set e_scaled_embryo v_rate_init * (U_E_embryo / L_embryo ^ 3) set ref_e_scaled 1 while [U_H_embryo < U_H^b_init and e_scaled_embryo > ref_e_scaled] ; simulation of embryo development until DEBbirth: [ set e_scaled_embryo v_rate_init * (U_E_embryo / L_embryo ^ 3) set S_C_embryo L_embryo ^ 2 * (((g_init * e_scaled_embryo) / (g_init + e_scaled_embryo)) * (1 + ((L_embryo * k_M_rate_init) / v_rate_init))) set dU_E_embryo (-1 * S_C_embryo) ; (embryo doesn't feed and only mobilizes reserves) set dU_H_embryo ((1 - kap_init) * S_C_embryo - k_J_rate_init * U_H_embryo) set dL_embryo ((1 / 3) * (((v_rate_init / (g_init * L_embryo ^ 2)) * S_C_embryo) - k_M_rate_init * L_embryo)) set U_E_embryo U_E_embryo + dU_E_embryo set U_H_embryo U_H_embryo + dU_H_embryo set L_embryo L_embryo + dL_embryo set e_scaled_embryo v_rate_init * (U_E_embryo / L_embryo ^ 3) ] ; when the embryo reaches DEBbirth (first condition in the 'while' loop), if (e_scaled_embryo < ref_e_scaled + 0.05) and (e_scaled_embryo > ref_e_scaled - 0.05) and (U_H_embryo >= U_H^b_init) [ ; if e is around the reference, the initial reserve is set and the loop stopped: set U_E^start estim_embryo ; the cost of an egg is set. set U_E_0yo U_E_embryo ; the U_E is set for the juveniles initialization. stop] ; if the reserve is not around 1, ifelse U_H_embryo > U_H^b_init [set upper_bound estim_embryo] ; the upper or lower bound is modified accordingly for a new loop. [set lower_bound estim_embryo] if simulation_embryo > 200 ; the simulation is stopped if it an initial reserve is not found [user-message ("embryo calc did not converge") stop] ] end ;_-_-_-_-_-_-_-_-_ Calculation of individual parameters at each age: to calc-init set L_b 0.276 * del_M ; (phy length from Schatt1985) set f_simul 1 set timestep_simul 2 set simul 0 set L_simul L_b set U_E_simul U_E_0yo ; get the initial reserve from the bisection method set U_H_simul U_H^b_init set U_H^p_simul U_H^p_init set U_R_simul 0 set h_rate_simul 0 set q_acceleration_simul 0 set age_months_simul 0 loop [ ; Simulation of an individual development from birth till 5yo: set simul simul + 1 ; (to keep track of the number of loops) set e_scaled_simul (v_rate_init * (U_E_simul / L_simul ^ 3)) set S_C_simul L_simul ^ 2 * (g_init * e_scaled_simul / (g_init + e_scaled_simul)) * (1 + ((L_simul * k_M_rate_init) / v_rate_init)) set S_A_simul f_simul * L_simul ^ 2 set dU_E_simul (S_A_simul - S_C_simul) ifelse U_H_simul < U_H^p_init [set dU_H_simul ((1 - kap_init ) * S_C_simul - k_J_rate_init * U_H_simul) set dU_R_simul 0 ] [set dU_H_simul 0 set dU_R_simul (( 1 - kap_init) * S_C_simul - k_J_rate_init * U_H^p_init) ] set dL_simul ((1 / 3) * (((v_rate_init /( g_init * L_simul ^ 2 )) * S_C_simul) - k_M_rate_init * L_simul)) set dq_acceleration_simul ((q_acceleration_simul * (L_simul ^ 3 / (v_rate_init / ( g_init * k_M_rate_init)) ^ 3) * sG + h_a_init) * e_scaled_simul * ((v_rate_init / L_simul) - ((3 / L_simul) * dL_simul )) - ((3 / L_simul ) * dL_simul ) * q_acceleration_simul) set dh_rate_simul (q_acceleration_simul - ((3 / L_simul) * dL_simul ) * h_rate_simul) set U_E_simul U_E_simul + (dU_E_simul * 30.5 / timestep_simul ) set U_H_simul U_H_simul + (dU_H_simul * 30.5 / timestep_simul ) set U_R_simul U_R_simul + (dU_R_simul * 30.5 / timestep_simul ) set L_simul L_simul + (dL_simul * 30.5 / timestep_simul) set q_acceleration_simul (q_acceleration_simul + (dq_acceleration_simul * 30.5 / timestep_simul )) set h_rate_simul (h_rate_simul + (dh_rate_simul * 30.5 / timestep_simul )) set age_months_simul age_months_simul + 1 ; update the age of individuals ; get the individual parameters for each age as the loop goes: if age_months_simul = 12 [ ifelse turtles with [U_H_simul < U_H^p_init] = nobody [user-message ("no juveniles at 1 yo, calc-init failed")] [set U_E_1yo U_E_simul set U_H_1yo U_H_simul set U_R_1yo U_R_simul set L_1yo L_simul set h_rate_1yo h_rate_simul set q_acceleration_1yo q_acceleration_simul ] ] if age_months_simul = 24 [ ifelse turtles with [U_H_simul < U_H^p_init] = nobody [user-message ("no juveniles at 2 yo, calc-init failed")] [set U_E_2yo U_E_simul set U_H_2yo U_H_simul set U_R_2yo U_R_simul set L_2yo L_simul set h_rate_2yo h_rate_simul set q_acceleration_2yo q_acceleration_simul ] ] if age_months_simul = 36 [ ifelse turtles with [U_H_simul < U_H^p_init] = nobody [user-message ("no juveniles at 3 yo, calc-init failed")] [set U_E_3yo_juv U_E_simul set U_H_3yo_juv U_H_simul set U_R_3yo_juv U_R_simul set L_3yo_juv L_simul set h_rate_3yo_juv h_rate_simul set q_acceleration_3yo_juv q_acceleration_simul ] ] if age_months_simul = 36 [ ifelse turtles with [U_H_simul >= U_H^p_init] = nobody [user-message ("no adults at 3 yo, calc-init failed")] [set U_E_3yo U_E_simul set U_H_3yo U_H_simul set U_R_3yo U_R_simul set L_3yo L_simul set h_rate_3yo h_rate_simul set q_acceleration_3yo q_acceleration_simul ] ] if age_months_simul = 48 [ ifelse turtles with [U_H_simul >= U_H^p_init] = nobody [user-message ("no adults at 4 yo, calc-init failed")] [set U_E_4yo U_E_simul set U_H_4yo U_H_simul set U_R_4yo U_R_simul set L_4yo L_simul set h_rate_4yo h_rate_simul set q_acceleration_4yo q_acceleration_simul ] ] if age_months_simul = 60 [ ifelse turtles with [U_H_simul >= U_H^p_init] = nobody [user-message ("no adults at 5 yo, calc-init failed")] [set U_E_5yo U_E_simul set U_H_5yo U_H_simul set U_R_5yo U_R_simul set L_5yo L_simul set h_rate_5yo h_rate_simul set q_acceleration_5yo q_acceleration_simul ] ] ifelse age_months_simul >= 60 [stop] [if simul > 70 [print age_months_simul user-message "calc-init did not end" stop]] ] end ;_-_-_-_-_-_-_-_- Give initial parameters for newborn individuals: to init-birth ; juveniles are initialized as they just reached DEBbirth (=start feeding) set v_rate v_rate_init set kap kap_init set kap_R kap_R_init set k_M_rate k_M_rate_init set k_J_rate k_J_rate_init ;input a slight variation in parameters between individuals: set scatter-multiplier e ^ (random-normal 0 cv) ; scatter-multiplier is the exp of a number taken randomly on a normal distribution of mean 0 and sd cv(from interface) set g g_init / scatter-multiplier set U_H^b U_H^b_init / scatter-multiplier set U_H^p U_H^p_init / scatter-multiplier set U_E U_E_0yo / scatter-multiplier ; get the initial reserve from the bisection method set U_H U_H^b set U_R 0 set L L_b / scatter-multiplier set h_rate 0 set q_acceleration 0 set age_months 0 set age_years 0 set breed juveniles end ;_-_-_-_-_-_-_-_- Give initial parameters for all ages: to init-pop let nbtot count turtles ; at first, all the individuals that were created by 'sprout' are juveniles with 0yo parameters (given by init-birth procedure) ask n-of (pop_init / 6) turtles [ ; divide the initial population into 6 age-groups in a cascade-like manner and give them their parameters. ; 5 year-olds initialisation: set U_E U_E_5yo / scatter-multiplier ; parameters come from the individual development simulation calc-init, set U_H U_H_5yo / scatter-multiplier ; including a slight variation in parameters from individual to individual. set U_R U_R_5yo / scatter-multiplier set L L_5yo / scatter-multiplier set h_rate h_rate_5yo / scatter-multiplier set q_acceleration q_acceleration_5yo / scatter-multiplier set age_months 60 set age_years 5 ] let Five_yo turtles with [age_months = 60] let nb_5yo (count Five_yo) ; for age-groups above puberty, ask n-of floor (prop_fem * nb_5yo) Five_yo [set breed females] ; set the sex-ratio of the population. ask Five_yo [if breed != females [set breed males] ] ; 4 year-olds initialisation: let nb4 count turtles with [age_months < 60] ; remaining individuals which have not yet been given initial parameters ask n-of (pop_init / 6) turtles with [age_months < 60] [ set U_E U_E_4yo / scatter-multiplier set U_H U_H_4yo / scatter-multiplier set U_R U_R_4yo / scatter-multiplier set L L_4yo / scatter-multiplier set h_rate h_rate_4yo / scatter-multiplier set q_acceleration q_acceleration_4yo / scatter-multiplier set age_months 48 set age_years 4 ] let Four_yo turtles with [age_months = 48] let nb_4yo (count Four_yo) ask n-of floor (prop_fem * nb_4yo) Four_yo [set breed females] ask Four_yo [if breed != females [set breed males] ] ; 3 year-olds initialisation: let nb3 count turtles with [age_months < 48] ; remaining individuals which have not yet been given initial parameters ask n-of (pop_init / 6)turtles with [age_months < 48] [ set U_E U_E_3yo / scatter-multiplier set U_H U_H^p set U_R U_R_3yo / scatter-multiplier set L L_3yo / scatter-multiplier set h_rate h_rate_3yo / scatter-multiplier set q_acceleration q_acceleration_3yo / scatter-multiplier set age_months 36 set age_years 3 ] let Three_yo turtles with [age_months = 36] let nb_3yo (count Three_yo) ask n-of floor (prop_fem * nb_3yo) Three_yo [set breed females] ask Three_yo [if breed != females [set breed males] ] ; 2 year-olds initialisation: let nb2 count turtles with [age_months < 36] ; remaining individuals which have not yet been given initial parameters ask n-of (pop_init / 6) turtles with [age_months < 36] [ set U_E U_E_2yo / scatter-multiplier set U_H U_H_2yo / scatter-multiplier set U_R U_R_2yo / scatter-multiplier set L L_2yo / scatter-multiplier set h_rate h_rate_2yo / scatter-multiplier set q_acceleration q_acceleration_2yo / scatter-multiplier set age_months 24 set age_years 2 ] ; 1 year-olds initialisation: let nb1 count turtles with [age_months < 24] ; remaining individuals which have not yet been given initial parameters ask n-of (pop_init / 6) turtles with [age_months < 24] [ set U_E U_E_1yo / scatter-multiplier set U_H U_H_1yo / scatter-multiplier set U_R U_R_1yo / scatter-multiplier set L L_1yo / scatter-multiplier set h_rate h_rate_1yo / scatter-multiplier set q_acceleration q_acceleration_1yo / scatter-multiplier set age_months 12 set age_years 1 ] ; 0 year-olds initialisation: ; the remaining individuals keep their 0yo parameters given to them by the init-birth procedure. end ; ---------------------------------------Procedures for GO: --------------------------------------------------------------------------------------------------- ;_-_-_-_-_-_-_-_-_Resetting the death counts: to reset-countdeath set starvedeath 0 set tempdeath 0 set olddeath 0 set bgdeath_adu 0 set bgdeath_juv 0 end ; =============== ; =============================================Setting the environmental parameters up-to-date: ; =============== ;_-_-_-_-_-_-_-_-_First updating of calendar: to update-year_timer ifelse ticks = 0 [set month_time month_time] [ifelse month_time != 12 [set month_time month_time + 1] [set month_time 1]] ; resetting the month_time calendar after 12 months end ;_-_-_-_-_-_-_-_-_To get the environmental data for the month: to update-resources ; see 'to-report select-resources' procedure for explanation ifelse projection = "present" ; depending on the selected projection, take a different set of lists [set f-scaled select-rsces infoMonth inputf month_time] [set f-scaled select-rsces infoMonth inputf_fut month_time] end to update-temperature ifelse projection = "present" ; depending on the selected projection, take a different set of lists [set T select-temp timeMark avgTemp ticks] ; get the T at the corresponding time of the year, from the temp list created in input-resources using the month list as an index. [set T select-temp timeMark avgTemp_fut ticks] end ;_-_-_-_-_-_-_-_-_For the effect of competition on the f: to calc-compet calc-density ; calculate the current month's population density ifelse pop_density < 1.9 * car_cap ; this because if = 2, div by 0 error and if > 2, then the formula gives the untrue result (bigger pop less compet) [set food_compet ((1 - f-scaled) * (1 - (pop_density / (2 * car_cap - pop_density))))] [set food_compet ((1 - f-scaled) * (1 - (pop_density / (car_cap / 10))))] ;;explanation of the procedure: ;(1 - f_scaled) : compet is only effective if the food availability is less than the max. ; in which case, proportionnally to how much the f is lessened compared to max, the size of the current pop has an influence on how important the compet is: ; if the pop is below car_cap, then the food is more available for the individuals present, but if the pop is over cc, the availability of food is lessened. ; Therefore, if pop > carrying capacity, food_compet < 0 <=> f decreases ; if pop = cc, food_compet = 0 <=> f constant ; if pop < cc, food_compet > 0 <=> f increases ;Meaning, the compet is actually calculated depending on how far from the carrying capacity the pop density is, and how far from max f it is. ; the pop that isn't there times the food not available --> the less food there is and the bigger the pop, the higher the compet is. end ; =============== ; =============================================Changing individuals states and parameters: ; =============== ;_-_-_-_-_-_-_-_-_Calcualtion of the temperature correction factor: to convert-TC set TC e ^ ((T_A / T_ref) - (T_A / (T + 273.15))) ; standard DEB parameters are for 20°C while A. Cordatus lives in an average SST of 5°C, set k_M_rate k_M_rate_init * TC ; so TC corrects parameters that are time dependent set v_rate v_rate_init * TC set k_J_rate k_J_rate_init * TC set h_a h_a_init * TC ^ 2 end ;_-_-_-_-_-_-_-_-_Calculation of the changes in state variables: ;_-_change in energy contained in the reserve: to calc-dU_E if U_H < U_H^b [set f 0] ; individuals don't feed before birth set e_scaled (v_rate * (U_E / L ^ 3)) ; calculation of scaled reserve set S_C L ^ 2 * (g * e_scaled / (g + e_scaled)) * (1 + ((L * k_M_rate) / v_rate)) ; caculation of mobilisation rate (rate at which energy is leaving the reserve) set S_A f * L ^ 2 ; calculation of assimilation rate (rate at which energy is entering the reserve) set dU_E (S_A - S_C) end ;_-_change in energy contained in the maturity compartment: to calc-dU_H ifelse U_H < U_H^p ; individuals supply their maturity compartment only until puberty [set dU_H ((1 - kap ) * S_C - k_J_rate * U_H)] [set dU_H 0] ; after puberty, quantity of energy stored in the maturity compartment stays the same. end ;_-_change in energy contained in the reproduction buffer: to calc-dU_R if U_H >= U_H^p [ ; for mature individuals only. ifelse (breed = males) or (birth_time < 6) ; check if it is a male or a female outside of reproduction time, [set dU_R (( 1 - kap) * S_C - k_J_rate * U_H^p)] ; in which case the change in energy stored in repro buffer is calculated as usual. [set dU_R 0] ; for females during reproduction, repro buffer calculated in the 'reproduce' procedure. ] if U_H < U_H^p [set dU_R 0] ; for non mature individuals, no change in the repro buffer end ;_-_change in structural length: to calc-dL set dL ((1 / 3) * (((v_rate /( g * L ^ 2 )) * S_C) - k_M_rate * L)) if e_scaled < (L / (v_rate / (g * k_M_rate))) [ ; when scaled reserve density is insufficient to maintain the structural length, set starvation "on" ;(starvation flag) starve ; the individual is starving (see below for procedure). ] end ;_-_-_-_-Starvation strategy: to starve set dL 0 ; allocation of energy only for somatic maintenance ifelse U_H < U_H^p ; all other flux are stopped [set dU_H 0] [set dU_R 0] ; knowing dL = 0, the mobilisation flux is recalculated as S_C = [p_M]L^3 / {p_Am} set S_C (kap * (k_M_rate * g * L ^ 3) / v_rate) ; with [p_M] = [E_G]k_M and [E_G] = gkap{p_Am}/v set dU_E S_A - S_C ; then dU_E is recalculated and will be applied in the next procedure set e_scaled v_rate * U_E / L ^ 3 ; this new dU_E will affect e_scaled in the next tick if e_scaled <= 0 [ ; when all energy is redirected to soma maintenance, if the scaled reserve still cannot recover set starvedeath starvedeath + 1 ; (for mortality accounts) set deceased "on" ; then the individual dies (flag which will get the individual removed in the next tick). ] end ;_-_calculation of the damage due to ageing: to calc-ageing set dq_acceleration (q_acceleration * (L ^ 3 / (v_rate / ( g * k_M_rate)) ^ 3) * sG + h_a) * e_scaled * ((v_rate / L) - ((3 / L) * dL)) - ((3 / L ) * dL) * q_acceleration set dh_rate (q_acceleration - ((3 / L) * dL) * h_rate) end ;_-_-_-_-_-_-_-_-_Apply calculated changes to the individuals: to update-individual ask turtles [ set U_E U_E + (dU_E * 30.5) ; changes are based on daily calculations upscaled for a month set U_H U_H + (dU_H * 30.5) set U_R U_R + (dU_R * 30.5) set L L + (dL * 30.5) if U_H > U_H^b [ ; damage due to ageing only starts from DEBbirth set q_acceleration (q_acceleration + dq_acceleration * 30.5) set h_rate (h_rate + dh_rate * 30.5) ] if deceased != "on"[ let x random 2 let y random 1 if x = y [ ; with the current input of x = random 2 and y = random 1 (i.e. y = 0), this has 50% chance of being true if random-float 1 < ( 1 - (1 - h_rate) ^ 30.5) [ ; damage induces death in a random manner, with a higher probability as it accumulates: here the individual checks that probability set olddeath olddeath + 1 set deceased_old "on" set deceased "on" ] ] ] ] ;; setting the lifestage label of each individual: if any? juveniles with [U_H >= U_H^p] [ ; juveniles who just reached puberty this round let newadults juveniles with [U_H >= U_H^p] ; are called newadults temporarily let nb count newadults ; count how many new adults there are ask n-of (prop_fem * nb) newadults [set breed females] ; then they turn into female or male 50/50 (male priority: eg. in case of one individual, it becomes male) ask newadults [if breed != females [set breed males] ]] if any? embryos with [U_H >= U_H^b and U_H < U_H^p] [ ask embryos with [U_H >= U_H^b and U_H < U_H^p] [set breed juveniles] ; embryos turn into juveniles if they reach DEBbirth ] ask turtles with [U_H < U_H^b] [set breed embryos] ; turtles that aren't DEBborn yet are called embryos (but shouldn't appear in the model: if they do, there is an issue in the ODE) ask turtles [ ; update the age of individuals set age_months age_months + 1 set age_years age_years + (1 / 12) ] end ; =============== ; =============================================Procedures involved in reproduction: ; =============== ;_-_-_-_-_-_-_-_-_Updating of calendars/timers that are used to time reproduction events: ;_-_reproduction and GSI calendars based on reproductive cycle: to update-repro_timers ifelse ticks = 0 [set repro_time repro_time] ; at the start, keep the timing of the setup for the first round [ifelse repro_time != 11 ; for the rest of the run, the repro_time evolves [set repro_time repro_time + 1] [set repro_time 0 ] ; reset when the end of the cycle is reached ] ifelse ticks = 0 [set GSI_time GSI_time] ; at the start, keep the timing of the setup for the first round [ifelse GSI_time != 12 ; for the rest of the run, the repro_time evolves [set GSI_time GSI_time + 1] [set GSI_time 1] ; reset when the end of the cycle is reached ] end ;_-_birth and reproduction period timer: to update-birth-timer ; birth time, only for females. ifelse birth_time = 0 ; only update birth_time if it was triggered by reproduction (if not triggered, it should be 0) [set birth_time 0] [set birth_time birth_time - 1] ; this timer is a countdown end ;_-_-_-_-_-_-_-_-_Calculations of the gonado-somatic index for reproduction: to calc-GSI ifelse GSI_time < 10 ; if it is outside of the 3 month of egg-laying, calculate the GSI as usual: [set f f-scaled set GSI (TC * GSI_time * 30.5 * ((k_M_rate_init * g / f ^ 3) / (f + kap * g * y_VE)) * ((1 - kap) * f ^ 3 - k_J_rate_init * U_H^p / zoom ^ 2 / s_M ^ 3))] ; if it is in the 3 months of egg-laying, force the gradual decrease of GSI: [set GSI_init (GSI_max - GSI_max * 0.52) ; Magniez1983 females invest 52% into reproduction set dGSI ((GSI_max - GSI_init) / 3) ; change in GSI over a month set GSI (GSI - dGSI)] end ;_-_-_-_-_-_-_-_-_Reproduction event (conception of eggs): to reproduce set U_R (U_R - ((U_R_max * 0.52) / 3)) ; adapt the reproduction buffer every month of reproduction according to data in Magniez1983 end ;_-_-_-_-_-_-_-_-_How offsprings are born into the model: to release-offsprings set Ri (0.65 * eggs) ; 65% of embryos survive (Poulin 1996) until birth hatch-juveniles (Ri / 3) [ ; hatch a third of the calculated number of offsprings (1/3 per month over 3 months) init-birth ; and give them their initial parameters ] end ; =============== ; =============================================Updates: ; =============== ;_-_-_-_-_-_-_-_-_Update the state of the population: to update-pop background-mortality ; apply background mortality rates on the population ask patches [check-temperature] ; check mortality induced by critical temperature. calc-density ; calculations for the pop structure calc-pop-varb ; calculations for all individuals variables in the pop end ;_-_-_-_-_-_-_-_-_Apply background mortality: to background-mortality let juvzombies count juveniles ; temporary variable with the number of juveniles in the model ask n-of (round ((0.41 / 12) * juvzombies)) juveniles [ ; 41% of juveniles die each year if deceased != "on" [ ; check that the individual hasn't already died from another cause set bgdeath_juv bgdeath_juv + 1 ; add to the account of deaths set deceased "on" ; indicate the individual is dead ] ] let aduzombies count turtles with [U_H >= U_H^p] ; temporary variable with the number of adults in the model ask n-of (round ((0.24 / 12) * aduzombies)) turtles with [U_H >= U_H^p] [ ; 24% of adults die each year if deceased != "on" [ ; check that the individual hasn't already died from another cause set bgdeath_adu bgdeath_adu + 1 ; add to the account of deaths set deceased_bg "on" ; indicate the individual is dead of this specific cause set deceased "on" ; indicate the individual is dead ] ] end ;_-_-_-_-_-_-_-_-_Check mortality by temperature: to check-temperature ; to get the temperature from the month before on the list: ifelse projection = "present" ; for projections under current conditions [ifelse ticks = 0 [set Tbefore select-temp-before timeMark avgTemp 1] ; for setup [set Tbefore select-temp-before timeMark avgTemp ticks] ; fot the run ] ; for projections under one of the other scenarios [ifelse ticks = 0 [set Tbefore select-temp-before timeMark avgTemp_fut 1] ; for setup [set Tbefore select-temp-before timeMark avgTemp_fut ticks] ; for the run ] let zombies count turtles ; temporary variable with the number of individuals in the model ;Choice of population with: ;;; a lower proportion of individuals sensitive to high temperatures (can withstand for 1 but not 2 months): if sensitivity = "resistant" [ ifelse T >= 12 [if Tbefore >= 12 [ask turtles [set tempdeath tempdeath + 1 die]]] ; if avg temperature is >=12 for two months, 100% die [ifelse T >= 11 [if Tbefore >= 11 [ask n-of (0.30 * zombies) turtles [set tempdeath tempdeath + 1 die]]] ; if avg temperature is >=11 for two months, 30% die [ifelse T >= 9.5 [if Tbefore >= 9.5 [ask n-of (0.20 * zombies) turtles [set tempdeath tempdeath + 1 die]]] ; if avg temperature is >=11 for two months, 20% die [if T >= 8 [if Tbefore >= 8 [ask n-of (0.10 * zombies) turtles [set tempdeath tempdeath + 1 die]]]] ; if avg temperature is >=11 for two months, 10% die ] ] ] ;;; individuals not able to withstand high temperatures for 1 month: if sensitivity = "intermediate" [ ifelse T >= 12 [ask turtles [set tempdeath tempdeath + 1 die]] ; if avg temperature is >=12 for one month, 100% die [ifelse T >= 11 [ask n-of (0.30 * zombies) turtles [set tempdeath tempdeath + 1 die]] ; if avg temperature is >=12 for one month, 30% die [ifelse T >= 9.5 [ask n-of (0.20 * zombies) turtles [set tempdeath tempdeath + 1 die]] ; if avg temperature is >=12 for one month, 20% die [if T >= 8 [ask n-of (0.10 * zombies) turtles [set tempdeath tempdeath + 1 die]]]]] ; if avg temperature is >=12 for one month, 10% die ] ;;; a higher proportion of individuals sensitive to high temperatures (can withstand for 1 but not 2 months): if sensitivity = "vulnerable" [ ifelse T >= 12 [if Tbefore >= 12 [ask turtles [set tempdeath tempdeath + 1 die]]] ; if avg temperature is >=12 for two months, 100% die [ifelse T >= 11 [if Tbefore >= 11 [ask n-of (0.45 * zombies) turtles [set tempdeath tempdeath + 1 die]]] ; if avg temperature is >=11 for two months, 45% die [ifelse T >= 9.5 [if Tbefore >= 9.5 [ask n-of (0.35 * zombies) turtles [set tempdeath tempdeath + 1 die]]] ; if avg temperature is >=10 for two months, 35% die [if T >= 8 [if Tbefore >= 8 [ask n-of (0.25 * zombies) turtles [set tempdeath tempdeath + 1 die]]]] ; if avg temperature is >=9 for two months, 25% die ] ] ] end ;_-_reporting procedure to get the temperature from the month before on the list: to-report select-temp-before [list1 list2 timing] ; get the avg temp for the month before, that is at position m - 1 let m timing ; create a temporary variable m with the value of the tick let P 0 ; create a temporary variable P if ((timing / 72) >= 1) [ ; if the end of the file has been reached, set m (timing mod 72)] ; start counting from the beginning of the file to obtain the temp: ifelse m = 0 ; when it's the first line of the file, [set P (position 71 list1)] ; get the temp from the last line. [set P ((position m list1) - 1) ] ; otherwise simply get it from the line before report item P list2 ; give the corresponding temp end ;_-_-_-_-_-_-_-_-_Get the density data for the month: to calc-density let indiv count turtles with [U_H >= U_H^b] ; count the number of individuals that are DEBborn let space count patches ; count the number of 1m2 patches (here, only 1 in the current implementation) set pop_density (indiv / space) ; calculate density of total population let adu ((count females) + (count males)) set density_adults (adu / space) ; calculate density of adults only let juve count juveniles set density_juveniles (juve / space) ; calculate density of juveniles only end ;_-_-_-_-_-_-_-_-_Get the state variables data for the month: to calc-pop-varb ifelse any? females [ set avg_UR_fem mean [U_R] of females ; reproduction buffer of females set min_UR_fem min [U_R] of females set max_UR_fem max [U_R] of females set avg_dUR_fem mean [dU_R * 30.5] of females set min_dUR_fem min [dU_R * 30.5 ] of females set max_dUR_fem max [dU_R * 30.5 ] of females set avg_UE_fem mean [U_E] of females ; energy reserve of females set min_UE_fem min [U_E] of females set max_UE_fem max [U_E] of females set avg_dUE_fem mean [dU_E * 30.5] of females set min_dUE_fem min [dU_E * 30.5] of females set max_dUE_fem max [dU_E * 30.5] of females ] [ ; if there is no female, set a mock value that can be removed when processing the outputs set avg_UR_fem 500 set min_UR_fem 500 set max_UR_fem 500 set avg_dUR_fem 50 set min_dUR_fem 50 set max_dUR_fem 50 set avg_UE_fem 1500 set min_UE_fem 1500 set max_UE_fem 1500 set avg_dUE_fem 100 set min_dUE_fem 100 set max_dUE_fem 100 ] ifelse any? turtles with [U_H >= U_H^p] [ set avg_UE_adu mean [U_E] of turtles with [U_H >= U_H^p] ; energy reserve of adults only set min_UE_adu min [U_E] of turtles with [U_H >= U_H^p] set max_UE_adu max [U_E] of turtles with [U_H >= U_H^p] set avg_dUE_adu mean [dU_E * 30.5] of turtles with [U_H >= U_H^p] set min_dUE_adu min [dU_E * 30.5] of turtles with [U_H >= U_H^p] set max_dUE_adu max [dU_E * 30.5] of turtles with [U_H >= U_H^p] ask turtles [set Lphy L / del_M] ; physical length of all individuals set avg_Lphy_adu mean [Lphy] of turtles with [U_H >= U_H^p] set min_Lphy_adu min [Lphy] of turtles with [U_H >= U_H^p] set max_Lphy_adu max [Lphy] of turtles with [U_H >= U_H^p] ] [ ; if there is no adult, set a mock value that can be removed when processing the outputs afterwards set avg_UE_adu 1500 set min_UE_adu 1500 set max_UE_adu 1500 set avg_dUE_adu 100 set min_dUE_adu 100 set max_dUE_adu 100 set avg_Lphy_adu 10 set min_Lphy_adu 10 set max_Lphy_adu 10 ] ifelse any? turtles with [U_H >= U_H^b and U_H < U_H^p] [ set avg_UE_juv mean [U_E] of turtles with [U_H >= U_H^b and U_H < U_H^p] ; energy reserve of juveniles only set min_UE_juv min [U_E] of turtles with [U_H >= U_H^b and U_H < U_H^p] set max_UE_juv max [U_E] of turtles with [U_H >= U_H^b and U_H < U_H^p] set avg_dUE_juv mean [dU_E * 30.5] of turtles with [U_H >= U_H^b and U_H < U_H^p] set min_dUE_juv min [dU_E * 30.5] of turtles with [U_H >= U_H^b and U_H < U_H^p] set max_dUE_juv max [dU_E * 30.5] of turtles with [U_H >= U_H^b and U_H < U_H^p] ] [ ; if there is no juvenile, set a mock value that can be removed when processing the outputs afterwards set avg_UE_juv 1500 set min_UE_juv 1500 set max_UE_juv 1500 set avg_dUE_juv 100 set min_dUE_juv 100 set max_dUE_juv 100 ] ifelse any? turtles [ set avg_UE mean [U_E] of turtles ; energy reserve of all individuals set min_UE min [U_E] of turtles set max_UE max [U_E] of turtles set avg_dUE mean [dU_E * 30.5] of turtles set min_dUE min [dU_E * 30.5] of turtles set max_dUE max [dU_E * 30.5] of turtles set avg_dL mean [dL * 30.5] of turtles set min_dL min [dL * 30.5] of turtles set max_dL max [dL * 30.5] of turtles ask turtles [set Lphy L / del_M] ; physical length of all individuals set avg_Lphy mean [Lphy] of turtles set min_Lphy min [Lphy] of turtles set max_Lphy max [Lphy] of turtles ] [ ; if there is no individual, set a mock value that can be removed when processing the outputs afterwards set avg_UE 1500 set min_UE 1500 set max_UE 1500 set avg_dUE 100 set min_dUE 100 set max_dUE 100 set avg_dL 1 set min_dL 1 set max_dL 1 set avg_Lphy 10 set min_Lphy 10 set max_Lphy 10 ] end ;_-_-_-_-_-_-_-_-_Updating of the other timings: to update-time set time time + 1 set year year + (1 / 12) end ;;;;;;;;;;;END;;;;;;;;;;;;;;

There are 3 versions of this model.

## Attached files

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

DEB-IBM for Abatus cordatus.png | preview | Schematic representation of the model | 11 months ago, by Margot Minju Arnould-Pétré | Download |

DEB-IBM_Acordatus_info.png | png | Preview of info tab | 12 months ago, by Margot Minju Arnould-Pétré | Download |

inputRSces_M_f_Delille.txt | data | Input file for resources at Anse du Halage (necessary!) | 12 months ago, by Margot Minju Arnould-Pétré | Download |

ODD (Appendix H).pdf | ODD (+ instructions to run model) | 4 months ago, by Margot Minju Arnould-Pétré | Download | |

temp_time_monthavg_Couvreux.txt | data | Input file for temperatures at Port Couvreux (optional) | 12 months ago, by Margot Minju Arnould-Pétré | Download |

temp_time_monthavg_Halage.txt | data | Input file for temperatures at Anse du Halage (necessary!) | 12 months ago, by Margot Minju Arnould-Pétré | Download |

temp_time_monthavg_Haute.txt | data | Input file for temperatures at Ile Haute (optional) | 12 months ago, by Margot Minju Arnould-Pétré | Download |

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Margot Minju Arnould-Pétré

## How to run the model:

A few simple steps are necessary to run this model under its basic implementation (you can find the same information in the file ODD.pdf - "How to run the model + Model description"): 1/ The files for the environmental data need to exist in the same folder as where the model is stored. To do this, after downloading the model, download the data files from the ‘’Files’’ tab in the NetLogo modeling commons (http://modelingcommons.org/browse/one_model/6201#model_tabs_browse_files). For the basic implementation, the two files needed are “temp_time_monthavg_Halage.txt” for temperatures and “inputRSces_M_f_Delille.txt” for resources. Make sure the model (.nlogo) and the data (.txt) files are stored in the same folder in the computer. 2/ Once you open the model (.nlogo), the interface is generally the first thing that is visible. Navigation between the interface, the information page (this page), and the code of the model is done through the three tabs at the top of the software (‘Interface’, ‘Info’, ‘Code’). Make sure that the following elements are selected in the interface: • Sites: ‘Anse du Halage’ • projection: ‘present’ • future: ‘mixed temp & food’ • sensitivity: ‘resistant’ • competition: ’On’ • run_time: ‘210’ • cv: ‘0.1’ • add-my-pet?: ‘Off’ Also ensure that none of the green boxes (‘input paramaters’) is empty. If any of them is empty, switch the add-my-pet? button ‘On’ and fill the relevant boxes with the basic DEB parameters for A. cordatus as taken from the Add-my-Pet database (https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/entries_web/Abatus_cordatus/Abatus_cordatus_res.html): [ṗM], EHb, EHp, [EG] and Lm, which correspond to these boxes respectively: p_M, E_H^b, E_H^p, E_G, zoom. Except in the aforementioned case, do not modify any of the parameters in the green boxes placed under the line « Input parameters » on the interface. 3/ Click on the purple setup button. This initializes the model, and should barely take a second on an average computer. A sure way of knowing the model has finished setup, is color shapes appearing in the small black square that is on the bottom-right of the purple buttons. 4/ Once setup is finished, click on the purple go button. This will run the model for the simulated duration input in the run_time box (number of years). Clicking on the go button again before the end of the simulation will pause the model, clicking on it after the end of the simulation will continue the simulation without a temporal limit. The go once button will only run the model for a single loop, that is a simulation of one month. 5/ The model can be run for future projections with different combinations of food and/or temperature scenarios. For this, select in the interface the desired RCP scenario under projection and the wanted combination under future. Three types of sensitivity to high temperature are also available under sensitivity (see « Check temperature » submodel in the ODD below for a short explanation of the difference between the three types).

## Posted 9 months ago

Margot Minju Arnould-Pétré

## How to run the model

The first section of the ODD (see 'files' tab) presents step-by-step instructions on how to run the model.

## Posted 4 months ago