07 EffLab_V5.07 NL
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;;-----------------------------------------------------------------------------| ;; SECTION A – AUTHOR IDENTIFICATION AND CODE ABSTRACT ;;-----------------------------------------------------------------------------| ;; ;; File Name: EffLab_I_V5.06.nlogo ;; By Orrery Software ;; Dated: 2019-10-06 ;; Author contact: ;; Garvin H Boyle ;; orrery@rogers.com ;; http://orrery-software.webs.com ;; As the author, I welcome questions, discussion of issues and suggestions ;; for improvements. ;;-----------------------------------------------------------------------------| ;; This EffLab app is a laboratory in which students can study aspects ;; of the phenomenon of efficiency as described in my ;; associated diary notes. ;; In this model, nrg arrives in a steady stream from the Sun and is captured ;; in plants that produce fruit, which appears randomly in dales in the ;; forest. Nomadic seekers roaming the forest according to their own ;; heuristic strategy seek the dales currently having food, and harvest it. ;; The strategies start as ineffective bland heuristics, and evolve to be ;; much more sophisticated. In the most simple scenario, all actions are ;; instinctive. The efficiency is calculated for individual seekers, as well ;; as for the trophic level (seekers) as a whole. ;;-----------------------------------------------------------------------------| ;; SECTION B – INITIAL DECLARATIONS OF GLOBALS AND BREEDS ;;-----------------------------------------------------------------------------| ;; ;;-----------------------------------------------------------------------------| ;; This program was developed on NetLogo Version 5.0.5 ;; ;;-----------------------------------------------------------------------------| ;; code-determined global variables globals [ ;; The version should be coded in this global variable to be included in ;; output files. gs-Version ;; Note: Some global variables are declared inside of switches, sliders and ;; choosers when the interface is constructed and are not declared here. ;; For the sake of clarity and completeness, they are noted here. ;; There are several uses of global variables: ;; - Toggles (switches), and choosers which enable or disable features; ;; - Numbers (in variables or sliders) which act as parameters; ;; - Numbers (in variables) which collect data. ;; ;; Those marked as 'native Boolean' have values of true or false. ;; Those marked as 'numeric Boolean' have values of 1 or 0. ;;--------------------- ;; MODELING ENVIRONMENT ;;--------------------- ;; Assumed “Model Settings” on startup ;; horizontal wrap: on ;; vertical wrap: on ;; location of origin: centre ;; patch size: 10 pixels ;;-------------------------------------------------------------------------| ;; Implicit global variables due to model settings – patch locations ;; min-pxcor -45 ;; max-pxcor 45 ;; min-pycor -20 ;; max-pycor 20 ;; So, the arena is 41 x 91 cells. ;;---------------------------- ;; SCENARIO SELECTION CONTROLS ;;---------------------------- ;; gs-scenario ;; Chooser, string converts to a scenario number g-scenario-number ;; scenario no.; 0; interp. of gs-scenario ;; Glogal enumeration variables - There is only 1 scenario possible. ge-scenario-zero ;; scenario 0, Small Beginnings ge-scenario-one ;; scenario 1, At Carrying Capacity ;; g-seekers-at-start ;; For Scenario 0, [1,1,100,10] ;; To halt a scenario at a pre-determined tick. ;; g-halt-at-tick ;; Has it's own input box ;; Initialize the Pseudo Random Number Generator (PRNG). ;; g-use-this-seed ;; Slider [1,1,100,7] ;;----------------------------------------------- ;; BIOPHYSICAL SUB-SYSTEM CONTROLS AND PARAMETERS ;;----------------------------------------------- ;; Biophyscial life function parameters, seekers. ;; g-c2-dat-parm ;; The death age threshold ;; g-c2-det-parm ;; The death nrg threshold ;; g-c2-rat-parm ;; The reproductive age threshold ;; g-c2-ret-parm ;; The reproductive nrg threshold ;; g-c2-epm-parm ;; The nrg per move ;; g-c2-epa-parm ;; The maximum nrg an agent may hold ;; The global list of possible heading deltas for moves. gl-heading-list ;; List of heading deltas. gl-index-list ;; List of numbers 0-7 in order gl-base-factors ;; List of factors, used to mutate bases ;; Nrg control variables ;; g-nrg-per-deposit ;; Nrg deposited per Dale [1,1,100,40] ;; g-prob-of-deposit ;; Prob nrg will be deposited [0,.001,1,.05] ;; g-heuristic-delta ;; Amount added to heuristic on success [0,.001,2,1] ;; g-prob-of-mutation ;; As it says [0,.001,1,0.95] ;; g-dt-for-ind-stats ;; Delta time, used for EROI [40,40,400,200] ;; Nrg accounting variables g-nrg-in-fruit ;; Nrg held in the fruit. g-nrg-in-agents ;; Nrg held in the agents. g-nrg-in-system ;; Total nrg in the system. g-sun-takeup-actual ;; As measured ;; Global enumeration (ge-) codes for cause of death. ge-cod-none ge-cod-fission ge-cod-hunger ge-cod-oldage ;; List to hold counts of cause of death. gl-causes-of-death-per-tick gl-causes-of-death-cumulative ;;------------------------------------- ;; END OF MODEL PARAMETERS AND CONTROLS ;;------------------------------------- ;;------------------------------------- ;; DATA COLLECTION AND DISPLAY CONTROLS ;;------------------------------------- ;; The following global variables are not model controls or paramaters, ;; but, rather, are variables used to collect data about the model ;; for display in the user interface, in some fashion (monitors or plots), ;; or used to manage all of the debug routines and output. ;; Global enumeration (ge-) codes. ge-sinktype-discard ;; Discarded sunlight ge-sinktype-move-EPM ;; Seekers EPM ge-sinktype-die-DET ;; Remaining nrg of seeker on death. ge-sinktype-die-DAT ;; Remaining nrg of seeker on death. ge-sinktype-repro-RET ;; Nrg passed mother to daughter, NOT A HEAT SINK. ;; SYSTEM-WIDE AGGREGATES ;; System of nrg sinks. gl-sinks-per-tick gl-sinks-cumulative ;;---------------------------------------------------------------------------| ;; The following agent sets, counts and averages are for data collection ;; and display in monitors and plots. ;; Global counts g-no-of-patches ;; count of all patches g-no-of-dales ;; count of all dales with fruit g-no-of-empty-patches ;; count of all empty patches g-no-of-seekers ;; count of all seekers g-carrying-capacity ;; sustainable load of seekers ;; Global EROI/ETA system-wide calculations. g-sys-nrg-returned ;; Gross nrg returned (er) within delta T. g-sys-nrg-invested ;; Gross nrg invested (ei) within delta T. g-sys-nrg-benefits ;; Net nrg returned or benefits (er-ei) within delta T. gl-sys-nrg-returned ;; List of changes. gl-sys-nrg-invested ;; List of changes. g-sys-eroi ;; System-wide EROI, per tick =(I/C). g-sys-eta ;; System-wide ETA, per tick =(B/I). ;; Global lists for EROI/ETA for death by repro/hunger. g-dbr-stat-count ;; Count of agents included in lists g-dbh-stat-count ;; Count of agents included in lists g-dbo-stat-count ;; Count of agents included in lists ;; g-max-for-lte-stats ;; Maximum agents included [40,40,5000,5000] gl-lte-eroi-dbr ;; List of EROI for death by repro gl-lte-eroi-dbh ;; List of EROI for death by hunger gl-lte-eroi-dbo ;; List of EROI for death by old age gl-lte-eroi-all ;; List of EROI for death by all causes gl-lte-eta-dbr ;; List of ETA for death by repro gl-lte-eta-dbh ;; List of ETA for death by hunger gl-lte-eta-dbo ;; List of ETA for death by old age gl-lte-eta-all ;; List of ETA for death by all causes g-lte-eta-min ;; Used to set min value for histograms g-lte-eroi-max ;; Used to set max value for histograms ;; Other histogram limits g-hist-epm-max ;; Max value for EPM histogram g-hist-epm-min ;; Min value for EPM histogram g-hist-epa-max ;; Max value for EPA histogram g-hist-epa-min ;; Min value for EPA histogram ;; Averages for seekers g-ave-age ;; age of seekers g-ave-nrg ;; nrg of seekers g-ind-min-eroi ;; min eroi of individual seekers = (B/C) g-ind-ave-eroi ;; ave eroi of individual seekers = (B/C) g-ind-max-eroi ;; max eroi of individual seekers = (B/C) g-ind-min-eta ;; min eta of individual seekers = (B/I) g-ind-ave-eta ;; ave eta of individual seekers = (B/I) g-ind-max-eta ;; max eta of individual seekers = (B/I) g-ave-C1-b0 ;; c1, base character, gene-0 g-ave-C1-b1 ;; c1, base character, gene-1 g-ave-C1-b2 ;; c1, base character, gene-2 g-ave-C1-b3 ;; c1, base character, gene-3 g-ave-C1-b4 ;; c1, base character, gene-4 g-ave-C1-b5 ;; c1, base character, gene-5 g-ave-C1-b6 ;; c1, base character, gene-6 g-ave-C1-b7 ;; c1, base character, gene-7 g-ave-c1-e0 ;; c1, exponent character, gene-0 g-ave-c1-e1 ;; c1, exponent character, gene-1 g-ave-c1-e2 ;; c1, exponent character, gene-2 g-ave-c1-e3 ;; c1, exponent character, gene-3 g-ave-c1-e4 ;; c1, exponent character, gene-4 g-ave-c1-e5 ;; c1, exponent character, gene-5 g-ave-c1-e6 ;; c1, exponent character, gene-6 g-ave-c1-e7 ;; c1, exponent character, gene-7 g-ave-C1-s0 ;; c1, strength character, gene-0 g-ave-C1-s1 ;; c1, strength character, gene-1 g-ave-C1-s2 ;; c1, strength character, gene-2 g-ave-C1-s3 ;; c1, strength character, gene-3 g-ave-C1-s4 ;; c1, strength character, gene-4 g-ave-C1-s5 ;; c1, strength character, gene-5 g-ave-C1-s6 ;; c1, strength character, gene-6 g-ave-C1-s7 ;; c1, strength character, gene-7 g-ave-C1-p0 ;; c1, phenotypic character, gene-0 g-ave-C1-p1 ;; c1, phenotypic character, gene-1 g-ave-C1-p2 ;; c1, phenotypic character, gene-2 g-ave-C1-p3 ;; c1, phenotypic character, gene-3 g-ave-C1-p4 ;; c1, phenotypic character, gene-4 g-ave-C1-p5 ;; c1, phenotypic character, gene-5 g-ave-C1-p6 ;; c1, phenotypic character, gene-6 g-ave-C1-p7 ;; c1, phenotypic character, gene-7 ;; Variables used to calculate and display entropy. g-energy-entropic-index ;; Entropy associated with energy distribution. g-pheno-entropic-index ;; Entropy associated with genetic distribution. gl-ave-pheno ;; Average phenotype. ;; SWITCHES - These are declared in the switch itself, and so are ;; commented out here. They are all native Booleans, having values of ;; true or false. ;; gb-plot-data ;; Enables plotting ;; Expanding the scope of evolutionary pressures. ;; gb-mutate-epm ;; Enables mutation of EPM. ;; gb-mutate-epa ;; Enables mutation of EPA. ;; gb-include-dnd ;; Enables inclusion of D&D nrg uses. ;; D&D stands for Detrivores and Decomposers. When agents die with ;; still-useful-energy they release that energy to a sink. This ;; switch enables inclusion of that released energy in the calculation ;; of EROI and ETA. ;; Other - built-in or declared implicitly in plot interface items ;; See each plot design dialogue. ;;--------------- ;; DEBUG CONTROLS ;;--------------- gb-debug-on ;; Numeric Boolean, opens debug log file, 0 or 1. gs-debug-status ;; for monitor, '1 (On)' or '0 (Off)', ;; gs-debug-step-chooser ;; Chooser, used with gb-debug-flow-on gb-debug-flow-on ;; Numeric Boolean, in association with chooser, gs-log-file-name ;; name of the debug log file ;; opens flow to log file ] ;;------------------------------------- ;; DEFINING PATCHES AND BREEDS ;;------------------------------------- ;;-----------------------------------------------------------------------------| ;; Attributes of patches patches-own [ ;; BUILT-IN ATTRIBUTES ;; pxcor ;; min-pxcor <= pxcor < max-pxcor ;; pycor ;; min-pxcor <= pxcor < max-pxcor ;; pcolor ;; color of this patch ( 0 <= color < 140 ) ;; plabel ;; label of this patch ;; plabel-color ;; color of this patch's label ( 0 <= label-color < 140 ) ;; EffLab-DETERMINED ATTRIBUTES fruit ] ;;-----------------------------------------------------------------------------| ;; Attributes of links ;; nil ;; I don't understand links and did not use any. ;;-----------------------------------------------------------------------------| ;; Turtles and breeds breed [ seekers seeker ] ;;-----------------------------------------------------------------------------| ;; Attributes of seekers seekers-own [ ;; BUILT-IN ATTRIBUTES ;; who ;; fixed id number ;; breed ;; to which breed this turtle belongs [seeker] ;; heading ;; 0 <= heading < 360, 0 = north ;; xcor ;; min-pxcor <= xcor < max-pxcor ;; ycor ;; min-pxcor <= xcor < max-pxcor ;; size ;; size relative to a patch, default is 1 ;; shape ;; a shape chosen from the shape library ;; color ;; color of this turtle ( 0 <= color < 140 ) ;; pen-mode ;; "up" or "down" ;; pen-size ;; in pixels ;; hidden? ;; true or false ;; label ;; label of this turtle ;; label-color ;; color of this turtle's label ( 0 <= label-color < 140 ) ;; USER-DETERMINED ATTRIBUTES ;; The chromosome 1 (c1) genes are used to distinguish behaviours. c1-bases ;; c1 - list of 8 [B]ases for genes (S=B^E) c1-expos ;; c1 - list of 8 heading delta [E]xponents c1-stren ;; c1 - list of 8 [S]trengths c1-pheno ;; c1 - list of 8 [P]henotypic characters (Pi=Si/sum(Sj)) ;; The chromosome 2 (C2) genes are static in this model. DAT ;; Death Age Threshold. DET ;; Death Energy Threshold. RAT ;; Reproductive Age Threshold. RET ;; Reproductive Energy Threshold. EPM ;; Energy Per Move. EPA ;; Maximum Energy Per Agent. ;; Other variable characteristics. mas-who ;; serial number of parent agent. age ;; age of the agent in ticks nrg ;; nrg in this agent cause-of-death ;; for statistical purposes b-is-ready-to-move ;; 0 = no; 1 = ready to move b-is-ready-to-reproduce ;; mature (in age) and healthy (in nrg) b-is-ready-to-die ;; old (in age) or starved (in nrg) ;; Variables for calculating individual EROI and ETA. ind-nrg-returned ;; Numerator of EROI - an aggregate = Income of (I/C) ind-nrg-invested ;; Denominator of EROI - an aggregate = Costs of (I/C) ind-nrg-benefits ;; Numerator of ETA - an aggregate = Benefits of (B/I) ind-eroi ;; Gross nrg returned on nrg invested = (I/C) ind-eta ;; Net nrg efficiency = (B/I) l-ind-er ;; A list of delta ERs of length delta T l-ind-ei ;; A list of delta EIs of length delta T ind-eroi-tick-counter ;; For tracking time up to delta T. ;; Life-time efficiency (lte) variables. lte-er ;; Energy returned (harvested) per lifetime lte-ei ;; Energy invested (spent) per lifetime lte-eta ;; Life-time efficiency - eta lte-eroi ;; Life-time efficiency - eroi ] ;;-----------------------------------------------------------------------------| ;; SECTION C – INITIALIZATION OR SETUP PROCEDURE( S ) ;;-----------------------------------------------------------------------------| ;;-----------------------------------------------------------------------------| ;; The 'autostart' startup routine to startup ;; This routine is to be executed by the observer. ;; The manual describes this routine as follows: ;; This procedure, if it exists, will be called when a model is first loaded ;; in the NetLogo application. Startup does not run when a model is run ;; headless from the command line, or by parallel BehaviorSpace. ;; On loading the model, the debug feature is always off. set gb-debug-on 0 set gs-debug-status "0 (Off)" ;; On loading the model, the model, the choosers, switches and sliders are ;; always reset to the values that are known to work by here invoking ;; the f-reset-default-parameters routine. Only the chooser ;; for the scenario is not reset. The last saved ;; selection of scenario will therefore be persistant. This allows the ;; 'Reset Defaults' button to NOT reset the scenario number, but to reset ;; correct parameters for the scenario. f-reset-default-parameters ;; Run the setup routine to initialize other globals. setup end ;;-----------------------------------------------------------------------------| ;; Reset the default values for the interface-declared items. to f-reset-default-parameters ;; The observer executes this routine. ;; Switches, sliders and choosers implicitly declare global variables. The ;; values in these variables are parameters for the model, and many ;; combinations of those parameters are not sustainable. However, the ;; values in those user interface devices are stored with the model and ;; are persistant across a save/load action. The default values must ;; be reset on load, or available to a user as a parameter set. The ;; purpose of this routine is to store at least one viable set of ;; parameter values. ;; DO NOT re-initialize the gs-scenario chooser. The selected scenario ;; is intended to be persistent, and not subject to a default setting. ;; Initialize the Pseudo Random Number Generator (PRNG). set g-use-this-seed 7 ;; [1,1,100,7] set gb-plot-data true ;; Turn plotting on. ;;----------------------------------------------- ;; BIOPHYSICAL SUB-SYSTEM CONTROLS AND PARAMETERS ;;----------------------------------------------- ;; Slider range settings are shown as (Min,Inc,Max,Default) set g-seekers-at-start 10 ;; For Scenario 0, [1,1,100,10] set g-nrg-per-deposit 40 ;; [1,1,100,40] set g-prob-of-deposit 0.05 ;; [0,.001,1,.05] set g-prob-of-mutation 0.95 ;; [0,.001,1,0.95] set g-max-for-lte-stats 5000 ;; [40,40,5000,5000] set g-dt-for-ind-stats 200 ;; [40,40,400,200] set gb-include-dnd false ;; Detrivores and Decomposers not included. ;; Static chromosome 2 (C2) biophysical controls - borrowed from PSoup model. set g-c2-dat-parm 1600 ;; [100,10,3200,1600] set g-c2-det-parm 4 ;; [4,4,40,4] set g-c2-rat-parm 800 ;; [50,10,3200,800] set g-c2-ret-parm 1000 ;; [200,1,1600,1000] set g-c2-epm-parm 4 ;; [1,1,40,4] set g-c2-epa-parm 1600 ;; [1600,100,3000,1600] ;; Expanding the scope of evolutionary pressures. set gb-mutate-epm true ;; Enables mutation of EPM. set gb-mutate-epa true ;; Enables mutation of EPA. set gb-include-dnd false ;; Enables inclusion of D&D nrg uses. ;; End of f-reset-default-parameters end ;;-----------------------------------------------------------------------------| ;; The setup button(s) to setup ;; This routine is to be executed by the observer. ;; NOTE: The contents of switches, sliders, and choosers seem to be ;; immune to these 'clear' commands. clear-ticks clear-turtles clear-patches clear-drawing clear-all-plots clear-output ;; clear-globals ;; Suppressed to make gb-debug-on value persistent. ;; NOTE: Instead of 'clear-globals', you must ensure all globals are ;; initialized properly in 'setup'. ;; import-drawing "01-B OrrSW.jpg" ;; Set the nrg (encoded in the variable fruit) in all of the patches to zero. ask patches [ set fruit 0 set pcolor brown ] ;; The version should be coded in this global variable to be included in ;; output files. set gs-Version "EffLab_I_V1.04" ;; Debug features may be off or on depending on history. ;; - Perhaps 'setup' was called by 'to startup'. ;; - Perhaps 'setup' was called during a 'BehaviorSpace' run. ;; - Perhaps 'setup' was called by a user-pushed 'setup' button. ;; Setup needs to handle some quasi-persistant values correctly regardless of ;; the history. For gb-debug-on, in particular, I want it to be ;; persistant so I can have debug output from the 'setup' routine routed ;; to the debug log file, or to the command centre. ;; 'startup' automatically sets gb-debug-on to 0 when the application is first ;; loaded. I want to be able to (A) toggle debug on, then, (B) press ;; 'setup' and watch the debug output of the 'setup' command. The ;; gb-debug-on must be persistant through the above 'clear' commands. The ;; debug log file name and status, however, should not be persistent and ;; must be reset when setup runs, if appropriate. ifelse ( gb-debug-on = 1 ) [ ;; Debug is on due to user setting, so file name and status should be ;; reset. I do this by turning the feature off then on. ;; First toggle it off, closing any remnant log file, if needed. f-toggle-debug ;; Then toggle it back on, opening a new time-stamped log file. f-toggle-debug ] ;; else [ ;; Debug is off, possibly due to startup execution, possibly due to user ;; choice. ;; Ensure associated variables have compatible settings. set gb-debug-on 0 ;; Redundant but ensures consistency. set gs-debug-status "0 (Off)" ;; Redundant but ensures consistency. set gb-debug-flow-on 0 ;; Step-specific flow is off. file-close-all ;; Close the debug log file. set gs-log-file-name "dummyname" ] ;; Now, do the standard check that is done at the start of each debuggable ;; routine. This must follow the clear commands, which reset everything ;; except globals, switches, sliders and choosers. if( gb-debug-on = 1 ) [ ifelse( ( gs-debug-step-chooser = "all" ) or ( gs-debug-step-chooser = "setup" ) ) [ set gb-debug-flow-on 1 LOG-TO-FILE "" LOG-TO-FILE word "Do-setup: Debug on; tick = " 0 ] [ set gb-debug-flow-on 0 ] ] ;; g-use-this-seed comes from a slider, and is persistant during setup. ;; However it is NOT persistent in a 'reset-defaults' call. random-seed g-use-this-seed ;; Tells the PRNG to use this seed. ;; Establish the list of allowed headings, each 45 degrees from the last. ;; These are the possible deltas that will be added to the current heading ;; based on which of the 8 genes is expressed during a move. set gl-heading-list [ 0 45 90 135 180 225 270 315 ] set gl-index-list [ 0 1 2 3 4 5 6 7 ] ;; The factors used to mutate the base values of the genes need to be ;; calculated. let prime-list [ 7 11 13 17 ] let factor-list ( map [ 1 + ( 1 / ? ) ] prime-list ) let inverse-list ( map [ 1 - ( 1 / ? ) ] prime-list ) set gl-base-factors ( sentence factor-list inverse-list ) ;; Glogal enumeration variables - There are 2 scenarios possible. set ge-scenario-zero 0 ;; Small beginnings set ge-scenario-one 1 ;; At Carrying Capacity ;; Use the input from the chooser gs-scenario to invoke the selected scenario. f-set-scenario-number ;; For debugging the setup procedure, log the values of the globals. LOG-TO-FILE ( word " Do-set: Scenario number - " g-scenario-number ) LOG-TO-FILE ( word " Do-set: Scenario name - " gs-scenario ) LOG-TO-FILE ( word " Do-set: Random seed - " g-use-this-seed ) ;; Declare values of hidden declarations from sliders. LOG-TO-FILE ( word " Do-set: g-nrg-per-deposit - " g-nrg-per-deposit ) LOG-TO-FILE ( word " Do-set: g-prob-of-deposit - " g-prob-of-deposit ) LOG-TO-FILE ( word " Do-set: g-prob-of-mutation - " g-prob-of-mutation ) LOG-TO-FILE ( word " Do-set: g-max-for-lte-stats - " g-max-for-lte-stats ) LOG-TO-FILE ( word " Do-set: g-dt-for-ind-stats - " g-dt-for-ind-stats ) ;; Nrg accounting variables set g-nrg-in-agents 0 ;; Nrg held in the agents. set g-nrg-in-fruit 0 ;; Nrg held in the fruit. set g-nrg-in-system 0 ;; Nrg in the system. set g-sun-takeup-actual 0 ;; As measured ;; Global enumeration (ge-) codes for cause of death. set ge-cod-none 0 set ge-cod-fission 1 set ge-cod-hunger 2 set ge-cod-oldage 3 ;; List to hold counts of cause of death. set gl-causes-of-death-per-tick ( n-values 4 [0] ) set gl-causes-of-death-cumulative ( n-values 4 [0] ) ;; Global enumeration (ge-) codes for sinktype. set ge-sinktype-discard 0 ;; Discarded sunlight set ge-sinktype-move-EPM 1 ;; Seeker EPM set ge-sinktype-die-DET 2 ;; Remaining nrg of seeker on death. set ge-sinktype-die-DAT 3 ;; Remaining nrg of seeker on death. set ge-sinktype-repro-RET 4 ;; Nrg passed mother to daughter, NOT A HEAT SINK. ;; System of nrg sinks. set gl-sinks-per-tick ( n-values 5 [0] ) set gl-sinks-cumulative ( n-values 5 [0] ) ;; Global EROI system-wide calculations. set g-sys-nrg-returned 0 ;; Gross nrg returned within delta T (er). set g-sys-nrg-invested 0 ;; Gross nrg invested within delta T (ei). set g-sys-nrg-benefits 0 ;; Net nrg returned within delta T (er-ei). set gl-sys-nrg-returned [] ;; List of changes. set gl-sys-nrg-invested [] ;; List of changes. set g-sys-eroi 0 ;; System-wide EROI, per tick = (I/C). set g-sys-eta -5 ;; System-wide ETA, per tick = (B/I). ;; Global lists for EROI/ETA for death by xxx. set g-dbr-stat-count 0 ;; Count of ticks included in lists. set g-dbh-stat-count 0 ;; Count of ticks included in lists. set g-dbo-stat-count 0 ;; Count of ticks included in lists. ;; set g-max-for-lte-stats 0 ;; Maximum agents included [40,40,1000,1000] set gl-lte-eroi-dbr [] ;; List of EROI for death by repro set gl-lte-eroi-dbh [] ;; List of EROI for death by hunger set gl-lte-eroi-dbo [] ;; List of EROI for death by old age set gl-lte-eroi-all [] ;; List of EROI for death by all causes set gl-lte-eta-dbr [] ;; List of ETA for death by repro set gl-lte-eta-dbh [] ;; List of ETA for death by hunger set gl-lte-eta-dbo [] ;; List of ETA for death by old age set gl-lte-eta-all [] ;; List of ETA for death by all causes set g-lte-eta-min -1 ;; Used to set min value for histograms set g-lte-eroi-max 1 ;; Used to set max value for histograms ;; Other histogram limits set g-hist-epm-max g-c2-epm-parm + 0.1 ;; Max value for EPM histogram set g-hist-epm-min g-c2-epm-parm - 0.1 ;; Min value for EPM histogram set g-hist-epa-max g-c2-epa-parm + 1 ;; Max value for EPA histogram set g-hist-epa-min g-c2-epa-parm - 1 ;; Min value for EPA histogram ;;---------------------------------------------------------------------------| ;; The following agent sets, counts and averages are for data collection ;; and display in monitors and plots. ;; Counts set g-no-of-patches 0 ;; count of all patches set g-no-of-dales 0 ;; count of all dales with fruit set g-no-of-empty-patches 0 ;; count of all empty patches set g-no-of-seekers 0 ;; counts of all seekers set g-carrying-capacity 0 ;; sustainable load of seekers ;; Averages for seekers set g-ave-age 0 ;; age of seekers set g-ave-nrg 0 ;; nrg of seekers set g-ind-min-eroi 0 ;; min individual eroi of seekers = (I/C) set g-ind-ave-eroi 0 ;; ave individual eroi of seekers = (I/C) set g-ind-max-eroi 0 ;; max individual eroi of seekers = (I/C) set g-ind-min-eta -5 ;; min individual eta of seekers = (B/I) set g-ind-ave-eta -5 ;; ave individual eta of seekers = (B/I) set g-ind-max-eta -5 ;; max individual eta of seekers = (B/I) set g-ave-C1-b0 0 ;; c1, base character, gene-0 set g-ave-C1-b1 0 ;; c1, base character, gene-1 set g-ave-C1-b2 0 ;; c1, base character, gene-2 set g-ave-C1-b3 0 ;; c1, base character, gene-3 set g-ave-C1-b4 0 ;; c1, base character, gene-4 set g-ave-C1-b5 0 ;; c1, base character, gene-5 set g-ave-C1-b6 0 ;; c1, base character, gene-6 set g-ave-C1-b7 0 ;; c1, base character, gene-7 set g-ave-c1-e0 0 ;; c1, exponent character, gene-0 set g-ave-c1-e1 0 ;; c1, exponent character, gene-1 set g-ave-c1-e2 0 ;; c1, exponent character, gene-2 set g-ave-c1-e3 0 ;; c1, exponent character, gene-3 set g-ave-c1-e4 0 ;; c1, exponent character, gene-4 set g-ave-c1-e5 0 ;; c1, exponent character, gene-5 set g-ave-c1-e6 0 ;; c1, exponent character, gene-6 set g-ave-c1-e7 0 ;; c1, exponent character, gene-7 set g-ave-C1-s0 0 ;; c1, strength character, gene-0 set g-ave-C1-s1 0 ;; c1, strength character, gene-1 set g-ave-C1-s2 0 ;; c1, strength character, gene-2 set g-ave-C1-s3 0 ;; c1, strength character, gene-3 set g-ave-C1-s4 0 ;; c1, strength character, gene-4 set g-ave-C1-s5 0 ;; c1, strength character, gene-5 set g-ave-C1-s6 0 ;; c1, strength character, gene-6 set g-ave-C1-s7 0 ;; c1, strength character, gene-7 set g-ave-C1-p0 0 ;; c1, phenotypic character, gene-0 set g-ave-C1-p1 0 ;; c1, phenotypic character, gene-1 set g-ave-C1-p2 0 ;; c1, phenotypic character, gene-2 set g-ave-C1-p3 0 ;; c1, phenotypic character, gene-3 set g-ave-C1-p4 0 ;; c1, phenotypic character, gene-4 set g-ave-C1-p5 0 ;; c1, phenotypic character, gene-5 set g-ave-C1-p6 0 ;; c1, phenotypic character, gene-6 set g-ave-C1-p7 0 ;; c1, phenotypic character, gene-7 ;; For debugging the debug feature!!! Suppressed now. ;; show ( word "SETUP: Debug Is " gb-debug-on ) ;; show ( word "SETUP: Debug Status Is " gs-debug-status ) ;; show ( word "SETUP: Step Chooser Is " gs-debug-step-chooser ) ;; show ( word "SETUP: Flow Control Is " gb-debug-flow-on ) set-default-shape seekers "arrow" ;; pulled from shapes library ask patches [ set pcolor brown ] set g-energy-entropic-index 1 ;; Entropy associated with energy distribution. set g-pheno-entropic-index 1 ;; Entropy associated with genetic distribution. set gl-ave-pheno [ 10 10 10 10 10 10 10 10 ] ;; Average phenotype. ;; Initialize the seekers and the patches. f-initialize-seekers-and-patches reset-ticks ;; restarts tick counter, runs setup commands within plots set gb-plot-data true ;; Enables all plotting calls. ;; This call must follow 'reset-ticks' and initialization of seekers. f-update-aggregates ;; Totals and averages. ;; Clears unwanted zeros in plots. ;; clear-all-plots ;; setup-plots xxx ;; Debug controls ;; Boolean, in association with chooser, turns debug LOG-TO-FILE on/off set gb-debug-flow-on 0 ;; Input variable to set a tick for stopping. set g-halt-at-tick -1 ;; Detrivores and Decomposers not normally included in calculations of ;; EROI and ETA. set gb-include-dnd false Set g-nrg-in-fruit ( sum [fruit] of patches ) ;; ASSERT ( frb-nrg-accounts-are-all-valid ) ;; ( "Do-set: Nrg accounts invalid." ) -1 LOG-TO-FILE " Do-set: procedure completed" ;; end of to setup end ;;-----------------------------------------------------------------------------| ;; Set the scenario number using the input from the chooser. to f-set-scenario-number ;; This routine is to be executed by the observer. set g-scenario-number ge-scenario-zero ;; default if( gs-scenario = "Small Beginnings" ) [ set g-scenario-number ge-scenario-zero ] if( gs-scenario = "At Carrying Capacity" ) [ set g-scenario-number ge-scenario-one ] ;; End f-set-scenario-number end ;;-----------------------------------------------------------------------------| ;; Initialize a population of seekers. to f-initialize-seekers-and-patches ;; This routine is to be executed by the observer. set g-nrg-in-system ( 0 ) set g-no-of-patches ( count patches ) if( g-scenario-number = ge-scenario-zero ) [ f-initialize-scenario-zero ] if( g-scenario-number = ge-scenario-one ) [ f-initialize-scenario-one ] ;; Nrg accounting set g-nrg-in-agents ( sum [nrg] of seekers ) set g-nrg-in-system ( g-nrg-in-system + g-nrg-in-agents ) ;; Place more energy into patches. ask patches [ let random-number ( random-float 1 ) if( random-number < g-prob-of-deposit ) [ set fruit g-nrg-per-deposit set pcolor green ] ] set g-nrg-in-fruit ( sum [fruit] of patches ) set g-sun-takeup-actual ( g-nrg-in-fruit ) set g-carrying-capacity ( floor ( g-sun-takeup-actual / g-c2-epm-parm ) ) set g-nrg-in-system ( g-nrg-in-system + g-nrg-in-fruit ) ;; End of f-initialize-seekers-and-patches end ;;-----------------------------------------------------------------------------| ;; Calculate the strengths and phenotypic values. to f-find-strens-n-phenos ;; This routine is to be executed by a seeker. ;; It uses the second example of the map feature. ;; Examples of the map feature. ;; show (map + [1 2 3] [2 4 6]) ;; => [3 6 9] ;; show (map [?1 + ?2 = ?3] ;; [1 2 3] ;; [2 4 6] ;; [3 5 9]) ;; => [true false true] ;; Compute the strength as S=B^(G+L). set c1-stren ( map [?1 ^ ?2] c1-bases c1-expos ) ;; Compute the phenotypic character as Pi=100*(Si/sum(Sj)). set c1-pheno ( map [?1 * ?2 / ?3] ( n-values 8 [100] ) c1-stren ( n-values 8 [sum c1-stren] ) ) ;; End of f-find-strens-n-phenos end ;;-----------------------------------------------------------------------------| ;; Initialize scenario-zero. to f-initialize-scenario-zero ;; This routine is to be executed by the observer. ;; This scenario is called "Small Beginnings". The slider ;; g-seekers-at-start is used to size the initial population. By default ;; it is rather small. ;; In this scenario, we create a population of seekers which are all ;; identical except for (a) location and (b) heading. create-seekers g-seekers-at-start [ f-initialize-new-seeker ;; Set the heading as one of the 8 allowed headings. set heading ( item ( random 8 ) gl-heading-list ) set color RED set age ( random RAT ) ;; Age is random with uniform distribution. set nrg ( random RET ) ;; Nrg is random with uniform distribution. ;; All start with varied age and nrg level to reduce transient time. ;; Genetic characters. set c1-bases [ 2 2 2 2 2 2 2 2 ] ;; 8 unbiased bases set c1-expos [ 0 0 0 0 0 0 0 0 ] ;; 8 unbiased exponents ;; Calculate the strengths and phenotypic characters. f-find-strens-n-phenos LOG-TO-FILE ( word " Do-set: C1-bases - " c1-bases ) LOG-TO-FILE ( word " Do-set: c1-expos - " c1-expos ) LOG-TO-FILE ( word " Do-set: c1-stren - " c1-stren ) LOG-TO-FILE ( word " Do-set: c1-pheno - " c1-pheno ) ;; Move each agent to a random point. setxy random-xcor random-ycor ] ;; End of create. ;; End of f-initialize-scenario-zero end ;;-----------------------------------------------------------------------------| ;; Initialize a single seeker. to f-initialize-new-seeker ;; This routine is to be executed by a seeker. ;; BUILT-IN ATTRIBUTES ;; who ;; set automatically ;; heading ;; direction of motion ;; xcor ;; min-pxcor <= xcor < max-pxcor ;; ycor ;; min-pxcor <= xcor < max-pxcor ;; pen-mode ;; "up" or "down" ;; pen-size ;; in pixels ;; size ;; size relative to a patch, default is 1 ;; USER-DETERMINED ATTRIBUTES ;; These two are re-initialized specifically for some scenarios. set color RED ;; The biophysical body function genes are static in this model. ;; Load chromosome 2 with the parameters from sliders. set DAT g-c2-dat-parm set DET g-c2-det-parm set RAT g-c2-rat-parm set RET g-c2-ret-parm set EPM g-c2-epm-parm set EPA g-c2-epa-parm ;; Associated with seeker dynamics. set mas-who -1 ;; serial number of parent seeker. ;; age and nrg are set in group initialization routine. set cause-of-death ge-cod-none ;; for statistical purposes. ;; Set the logic trigger flags. set b-is-ready-to-move 1 ;; i.e. true set b-is-ready-to-reproduce 0 ;; i.e. false set b-is-ready-to-die 0 ;; i.e. false ;; Variables for calculating individual EROI and ETA. set ind-nrg-returned g-dt-for-ind-stats ;; Numerator of EROI - an aggregate set ind-nrg-invested g-dt-for-ind-stats ;; Denominator of EROI - an aggregate set ind-nrg-benefits ( ind-nrg-returned - ind-nrg-invested ) set ind-eroi 0 ;; Nrg returned on nrg invested = (I/C) set ind-eta -5 ;; individual efficiency = (B/I) set l-ind-er ( n-values g-dt-for-ind-stats [0] ) ;; Delta ERs = B of B/C set l-ind-ei ( n-values g-dt-for-ind-stats [0] ) ;; Delta EIs = C of B/C set ind-eroi-tick-counter g-dt-for-ind-stats ;; For tracking time up to delta T. ;; Life-time efficiency (lte) variables. set lte-er 0 ;; Energy returned (harvested) per lifetime set lte-ei 0 ;; Energy invested (spent) per lifetime set lte-eta -5 ;; Life-time efficiency - eta set lte-eroi 0 ;; Life-time efficiency - eroi ;; end f-initialize-new-seeker end ;;-----------------------------------------------------------------------------| ;; Initialize scenario-one. to f-initialize-scenario-one ;; This routine is to be executed by the observer. ;; This scenario is called "At Carrying Capacity". The slider ;; g-seekers-at-start is ignored. Instead, I calculate the maximum ;; carrying capacity, and start with that many seekers. ;; In this scenario, we create a population of seekers which are all ;; identical except for (a) location and (b) heading. let estimated-sunshine-takeup ( g-no-of-patches * g-nrg-per-deposit * g-prob-of-deposit ) set g-carrying-capacity ( floor ( estimated-sunshine-takeup / g-c2-epm-parm ) ) create-seekers g-carrying-capacity [ f-initialize-new-seeker ;; Set the heading as one of the 8 allowed headings. set heading ( item ( random 8 ) gl-heading-list ) set color RED set age ( random RAT ) ;; Age is random with uniform distribution. set nrg ( random RET ) ;; Nrg is random with uniform distribution. ;; All start with varied age and nrg level to reduce transient time. ;; Genetic characters. set c1-bases [ 2 2 2 2 2 2 2 2 ] ;; 8 unbiased bases set c1-expos [ 0 0 0 0 0 0 0 0 ] ;; 8 unbiased exponents ;; Calculate the strengths and phenotypic characters. f-find-strens-n-phenos LOG-TO-FILE ( word " Do-set: C1-bases - " c1-bases ) LOG-TO-FILE ( word " Do-set: c1-expos - " c1-expos ) LOG-TO-FILE ( word " Do-set: c1-stren - " c1-stren ) LOG-TO-FILE ( word " Do-set: c1-pheno - " c1-pheno ) ;; Move each agent to a random point. setxy random-xcor random-ycor ] ;; End of create. ;; End of f-initialize-scenario-one end ;;-----------------------------------------------------------------------------| ;; SECTION D – GO OR MAIN-LOOP PROCEDURE( S ) ;;-----------------------------------------------------------------------------| ;;-----------------------------------------------------------------------------| ;; The go button to go ;; This routine is to be executed by the observer. ;; Stop codes: ;; All stop decisions must be here in the 'go' procedure, as it causes an ;; exit from the current procdure only. ;; XXX Special stop code for lte statistics. ;; if( g-dbr-stat-count >= g-max-for-lte-stats ) ;; [ ;; stop ;; ] if( g-halt-at-tick = ticks ) [ set g-halt-at-tick -1 stop ] let b-should-stop-now false if( count turtles <= 0 ) [ set b-should-stop-now true ] if( b-should-stop-now = true ) [ stop ] ;; MANUAL CHANGE FOR DEBUG ;; If needed, each check for validity can be enabled between steps. ;; They have been suppressed (turned into comments) for the sake ;; of speed of execution, but can be re-enabled if a bug has ;; somehow been re-introduced. ;; A single call to the validity check has been left active inside of the ;; Do-Post-Tick step. If it flags a problem, re-activate these to ;; narrow down where the problem starts. ;; Major steps or functions, done once per tick, in order of execution. do-pre-tick ;; if( frb-agents-are-all-valid = false ) ;; [ LOG-TO-FILE ( word "Agents failed validity test: Do-pre-tick." ) ] do-energize ;; if( frb-agents-are-all-valid = false ) ;; [ LOG-TO-FILE ( word "Agents failed validity test: Do-energize." ) ] do-move ;; if( frb-agents-are-all-valid = false ) ;; [ LOG-TO-FILE ( word "Agents failed validity test: Do-move." ) ] do-feed ;; if( frb-agents-are-all-valid = false ) ;; [ LOG-TO-FILE ( word "Agents failed validity test: do-feed." ) ] do-reproduce ;; if( frb-agents-are-all-valid = false ) ;; [ LOG-TO-FILE ( word "Agents failed validity test: Do-reproduce." ) ] do-die ;; if( frb-agents-are-all-valid = false ) ;; [ LOG-TO-FILE ( word "Agents failed validity test: Do-die." ) ] do-post-tick ;; if( frb-agents-are-all-valid = false ) ;; [ LOG-TO-FILE ( word "Agents failed validity test: Do-post-tick." ) ] end ;;-----------------------------------------------------------------------------| ;; D1 - do-pre-tick procedure( s ) ;;-----------------------------------------------------------------------------| to do-pre-tick ;; This routine is to be executed by the observer. if( gb-debug-on = 1 ) [ ifelse( ( gs-debug-step-chooser = "all" ) or ( gs-debug-step-chooser = "pre-tick" ) ) [ set gb-debug-flow-on 1 LOG-TO-FILE "" LOG-TO-FILE word "Do-pre-tick: Debug on.; tick = " ticks ] [ set gb-debug-flow-on 0 ] ] ;; Enter all commands that need to be done before a tick begins. ;; Supressed. f-update-aggregates ;; Advance the tick counter by 1 tick. ifelse( gb-plot-data = true ) [ ;; Advance the ticks by one and update the plots. tick ;; 'tick' is exactly the same as 'update-plots' except that the tick counter ;; is incremented before the plot commands are executed. ] ;; else [ ;; Advance ticks by one but do not update the plots. tick-advance 1 ] ;; End else ;; Once the data is plotted, the per-tick counts can be cleared. ;; List to hold counts of cause of death. set gl-causes-of-death-per-tick ( n-values 6 [0] ) ;; Global EROI system-wide calculations. ifelse( length gl-sys-nrg-returned <= g-dt-for-ind-stats ) [ ;; Append a zero for new data. set gl-sys-nrg-returned ( lput 0 gl-sys-nrg-returned ) ;; List of changes. set gl-sys-nrg-invested ( lput 0 gl-sys-nrg-invested ) ;; List of changes. ] ;; Else [ ;; Remove old data set gl-sys-nrg-returned ( butfirst gl-sys-nrg-returned ) ;; List of changes. set gl-sys-nrg-invested ( butfirst gl-sys-nrg-invested ) ;; List of changes. ;; Append a zero for new data. set gl-sys-nrg-returned ( lput 0 gl-sys-nrg-returned ) ;; List of changes. set gl-sys-nrg-invested ( lput 0 gl-sys-nrg-invested ) ;; List of changes. ] ;; Reset the scenario number, in case the chooser has been changed. f-set-scenario-number ;; Clear the per-tick data for energy sinks. ;; This call must happen before the seeker population is stabilized. set gl-sinks-per-tick ( n-values 5 [0] ) ask seekers [ set age ( age + 1 ) ] LOG-TO-FILE ( word " Do-pre-tick: Seekers aged." ) LOG-TO-FILE ( word " Do-pre-tick: Halt at tick - " g-halt-at-tick ) LOG-TO-FILE ( word " Do-pre-tick: Current tick - " ticks ) LOG-TO-FILE " Do-pre-tick: Routine completed." ;; End of do-pre-tick end ;;-----------------------------------------------------------------------------| ;; D2 – do-energize procedure(s) ;;-----------------------------------------------------------------------------| to do-energize ;; This routine is to be executed by the observer. if( gb-debug-on = 1 ) [ ifelse( ( gs-debug-step-chooser = "all" ) or ( gs-debug-step-chooser = "energize" ) ) [ set gb-debug-flow-on 1 LOG-TO-FILE "" LOG-TO-FILE word "Do-energize: Debug on; tick = " ticks ] [ set gb-debug-flow-on 0 ] ] ;; Make a list of the patches that are without fruit (without nrg) let empty-patch-list ( patches with [fruit = 0] ) ;; Record the status of the patches, prior to energizing. set g-no-of-empty-patches ( count empty-patch-list ) set g-no-of-dales ( g-no-of-patches - g-no-of-empty-patches ) set g-sun-takeup-actual 0 ;; Use the probability of deposit to determine if fruit is added. ask empty-patch-list [ let random-number ( random-float 1 ) let threshold ( g-prob-of-deposit ) if ( random-number <= threshold ) [ set fruit ( fruit + g-nrg-per-deposit ) set pcolor green ;; Record in system nrg accounts set g-nrg-in-fruit ( g-nrg-in-fruit + g-nrg-per-deposit ) set g-sun-takeup-actual ( g-sun-takeup-actual + g-nrg-per-deposit ) ] ] ;; Estimate the carrying capacity, based on the take-up rate this tick. let mean-epm ( mean [epm] of seekers ) set g-carrying-capacity ( floor ( g-sun-takeup-actual / mean-epm ) ) set g-nrg-in-system ( g-nrg-in-system + g-sun-takeup-actual ) ;; Supressed. f-update-aggregates LOG-TO-FILE " Do-energize: procedure completed" ;; End of do-energize end ;;-----------------------------------------------------------------------------| ;; D3 – do-move procedure(s) ;;-----------------------------------------------------------------------------| to do-move ;; This routine is to be executed by the observer. if( gb-debug-on = 1 ) [ ifelse( ( gs-debug-step-chooser = "all" ) or ( gs-debug-step-chooser = "move" ) ) [ set gb-debug-flow-on 1 LOG-TO-FILE "" LOG-TO-FILE word "Do-move: Debug on; tick = " ticks ] [ set gb-debug-flow-on 0 ] ] ;; The seekers move. ask seekers [ if( b-is-ready-to-move = 1 ) [ f-seeker-moves ] ;; End if( b-is-ready-to-move = 1 ) ] ;; End ask seekers ;; Supressed. f-update-aggregates LOG-TO-FILE " Do-move: procedure completed" end ;;-----------------------------------------------------------------------------| ;; A seeker moves according to genes and heuristics. to f-seeker-moves ;; This routine is to be executed by a seeker. ;; When a seeker moves it expends energy out of its pool of nrg. ;; Determine if this seeker has sufficient nrg to move. ifelse ( nrg >= EPM ) [ ;; Establish a heading. f-seeker-sets-heading ;; Step forward forward 1 ;; Expend the nrg to the sink. f-store-data-in-sink ge-sinktype-move-EPM EPM set nrg ( nrg - EPM ) ;; Record the expenditure in the stats. set g-nrg-in-system ( g-nrg-in-system - EPM ) set g-nrg-in-agents ( g-nrg-in-agents - EPM ) ;; Record the expenditure in the EROI variables f-record-ei-for-eroi EPM set b-is-ready-to-move 1 ;; set b-is-ready-to-die 0 ] ;; Else [ ;; The seeker is marked for death, and nrg is removed. ;; It will die and be removed when do-die is executed. f-store-data-in-sink ge-sinktype-move-EPM nrg set g-nrg-in-system ( g-nrg-in-system - nrg ) set g-nrg-in-agents ( g-nrg-in-agents - nrg ) ;; Record the expenditure in the EROI variables f-record-ei-for-eroi nrg set nrg 0 set cause-of-death ge-cod-hunger set b-is-ready-to-move 0 set b-is-ready-to-die 1 ] ;; End else LOG-TO-FILE ( word " Do-move: S(heading,nrg,move-flag,die-flag) - (" heading "," floor nrg "," b-is-ready-to-move"," b-is-ready-to-die ")" ) ;; End of f-seeker-moves end ;;-----------------------------------------------------------------------------| ;; A seeker sets a heading using c1-pheno. to f-seeker-sets-heading ;; This routine is to be executed by a seeker. ;; The agent will consult its phenotypic characters, to determine the ;; best direction for the next heading. It is blind, and cannot sense ;; other agents, or patches of fruit. So the only guidance it has is ;; the genetic information received from its mother. ;; Take note of the current heading. let old-heading heading ;; DECIDE HOW MUCH TO TURN AS DELTA-HEADING. ;; Add up the indicators. let sum-of-phenos ( round ( sum c1-pheno ) ) LOG-TO-FILE ( word " Do-move: Phenos - " c1-pheno ) LOG-TO-FILE ( word " Do-move: Summed Phenos - " sum-of-phenos ) ;; Each pheno is derived from genes plus learnings. The size of ;; the pheno creates a proportional target interval in the sum. ;; Choose an interval (i.e. choose a pheno) by getting a random number. let random-number ( random-float sum-of-phenos ) LOG-TO-FILE ( word " Do-move: Random Number - " random-number ) ;; The random-number must fall between two sequential pheno aggregates. ;; E.g if the random-number is 50%, and the first two pheno numbers ;; are 13% and 25% (+=38%) then that sum is less than 50%. If the ;; next pheno is 20%, then the aggregate is 58%, which is bigger ;; than 50%. So it falls between the 2nd and 3rd aggregate of the ;; phenos. The third interval then is selected "randomly" with ;; probability determined by its relative size, among all phenos. ;; Due to zero-based indexing, the correct index is 3-1 = 2. let counter 0 let good-index -1 let this-pheno 0 let this-sum 0 let next-sum 0 while [ counter < 8 ] ;; Do not overshoot [ LOG-TO-FILE ( word " Do-move: Counter - " counter ) set this-pheno ( item counter c1-pheno ) LOG-TO-FILE ( word " Do-move: This sum - " this-sum ) LOG-TO-FILE ( word " Do-move: Pheno - " this-pheno ) set next-sum ( this-pheno + this-sum ) LOG-TO-FILE ( word " Do-move: Next sum - " next-sum ) if ( ( random-number >= this-sum ) and ( random-number < next-sum ) ) [ set good-index counter LOG-TO-FILE ( word " Do-move: Selected gene - " good-index ) ] set this-sum next-sum set counter ( counter + 1 ) ] let heading-delta ( item good-index gl-heading-list ) LOG-TO-FILE ( word " Do-move: Old heading - " heading ) ;; Set the new heading set heading ( heading + heading-delta ) LOG-TO-FILE ( word " Do-move: New heading - " heading ) ;; End of f-seeker-sets-heading end ;;-----------------------------------------------------------------------------| ;; Store data in the lists of sinks. to f-store-data-in-sink [ sinktype value ] ;; This routine is to be executed by anyone. ;; Record it in the per-tick list. let old-value ( item sinktype gl-sinks-per-tick ) let new-value ( old-value + value ) set gl-sinks-per-tick ( replace-item sinktype gl-sinks-per-tick new-value ) ;; Record it in the cumulative list. set old-value ( item sinktype gl-sinks-cumulative ) set new-value ( old-value + value ) set gl-sinks-cumulative ( replace-item sinktype gl-sinks-cumulative new-value ) ;; end of f-store-data-in-sink end ;;-----------------------------------------------------------------------------| ;; Increment the count in the lists of causes of death. to f-increment-cod-list [ breedtype codtype ] ;; This routine is to be executed by anyone. ;; Record it in the per-tick list. let old-count ( item codtype gl-causes-of-death-per-tick ) let new-count ( old-count + 1 ) set gl-causes-of-death-per-tick ( replace-item codtype gl-causes-of-death-per-tick new-count ) ;; Record it in the cumulative list. set old-count ( item codtype gl-causes-of-death-cumulative ) set new-count ( old-count + 1 ) set gl-causes-of-death-cumulative ( replace-item codtype gl-causes-of-death-cumulative new-count ) ;; End of f-increment-cod-list end ;;-----------------------------------------------------------------------------| ;; Record the 'energy invested' component of EROI calculation. to f-record-ei-for-eroi [eroi-ei] ;; This routine is to be executed by a seeker. ;; It updates both individual values, and sys-wide values. ;; There are three associated routines: ;; f-record-er-for-eroi is called by Do-feed. ;; f-record-ei-for-eroi is called by Do-Move. ;; f-record-ei-for-dnd-eroi is called by Do-Death. ;; The three routines work together to calculate individual and ;; system-wide EROI and ETA. ;; NOTE: EROI is ER/EI, that is Benefits over Costs, or (B/C). ;; ETA is (ER-EI)/ER, that is Benefits over Income, or (B/I). ;; LOG-TO-FILE ( word " Do-move: Eroi-counter - " ind-eroi-tick-counter ) ;; LOG-TO-FILE ( word " Do-move: Nrg-returned - " ind-nrg-returned ) ;; LOG-TO-FILE ( word " Do-move: Nrg-invested - " ind-nrg-invested ) ;; LOG-TO-FILE ( word " Do-move: Nrg-benefits - " ind-nrg-benefits ) ;; LOG-TO-FILE ( word " Do-move: L-ind-er - " l-ind-er ) ;; LOG-TO-FILE ( word " Do-move: L-ind-ei - " l-ind-ei ) ;; LOG-TO-FILE ( word " Do-move: Lte-er - " lte-er ) ;; LOG-TO-FILE ( word " Do-move: Lte-ei - " lte-ei ) ;; LOG-TO-FILE ( word " Do-move: Lte-eta - " lte-eta ) ;; LOG-TO-FILE ( word " Do-move: Lte-eroi - " lte-eroi ) ;; First, record it in the system-wide data. LOG-TO-FILE ( word " Do-move: g-sys-ei was - " gl-sys-nrg-invested ) let last-index ( ( length gl-sys-nrg-invested ) - 1 ) let old-value ( last gl-sys-nrg-invested ) let new-value ( old-value + eroi-ei ) set gl-sys-nrg-invested ( replace-item last-index gl-sys-nrg-invested new-value ) LOG-TO-FILE ( word " Do-move: g-sys-ei is now - " gl-sys-nrg-invested ) ;; Now record it in the individual data for this seeker. ;; Check to determine whether we are only appending data to the list, ;; or we are dropping old data and appending new data. ifelse ( ind-eroi-tick-counter < g-dt-for-ind-stats ) [ ;; Case of appending new data only. ;; Increment the counter - done only in move-related function. set ind-eroi-tick-counter ( ind-eroi-tick-counter + 1 ) ;; Append new entry to last of l-ind-ei. set l-ind-ei ( lput eroi-ei l-ind-ei ) ;; Append a place-holder zero to l-ind-er. set l-ind-er ( lput 0 l-ind-er ) ] ;; Else [ ;; Case of dropping/appending data ;; Remove oldest entry. set l-ind-ei ( butfirst l-ind-ei ) ;; Append new entry to last of l-ind-ei set l-ind-ei ( lput eroi-ei l-ind-ei ) ;; Adjust l-ind-er, removing oldest and appending a place-holder zero. ;; Remove oldest entry. set l-ind-er ( butfirst l-ind-er ) ;; Append zero to last of l-ind-er set l-ind-er ( lput 0 l-ind-er ) ] ;; End else dropping/appending ;; Life-time efficiency (lte) stats were added later. ;; Lte data is aggregated over the entire life of the seeker. set lte-ei ( lte-ei + eroi-ei ) ;; Note the added investment. ;; Re-calculate the seekers stats. set ind-nrg-invested ( sum l-ind-ei ) set ind-nrg-benefits ( ind-nrg-returned - ind-nrg-invested ) ifelse (ind-nrg-invested > 0) [ set ind-eroi ( ind-nrg-returned / ind-nrg-invested ) ] ;; (I/C) [ set ind-eroi 0 ] ;; (I/C) ifelse (ind-nrg-returned > 0) [ set ind-eta ( ind-nrg-benefits / ind-nrg-returned ) ] ;; (B/I) [ set ind-eta -5 ] ;; (B/I) ;; Re-calculate the life-time-efficiency stats ifelse (lte-ei > 0) [ set lte-eroi ( lte-er / lte-ei ) ] ;; (I/C) [ set lte-eroi 0 ] ;; (I/C) ifelse (lte-er > 0) [ set lte-eta ( ( lte-er - lte-ei ) / lte-er ) ] ;; (B/I) [ set lte-eta -5 ] ;; (B/I) ;; LOG-TO-FILE ( word " Do-move: Eroi-counter - " ind-eroi-tick-counter ) ;; LOG-TO-FILE ( word " Do-move: Nrg-returned - " ind-nrg-returned ) ;; LOG-TO-FILE ( word " Do-move: Nrg-invested - " ind-nrg-invested ) ;; LOG-TO-FILE ( word " Do-move: Nrg-benefits - " ind-nrg-benefits ) ;; LOG-TO-FILE ( word " Do-move: L-ind-er - " l-ind-er ) ;; LOG-TO-FILE ( word " Do-move: L-ind-ei - " l-ind-ei ) ;; LOG-TO-FILE ( word " Do-move: Lte-er - " lte-er ) ;; LOG-TO-FILE ( word " Do-move: Lte-ei - " lte-ei ) ;; LOG-TO-FILE ( word " Do-move: Lte-eta - " lte-eta ) ;; LOG-TO-FILE ( word " Do-move: Lte-eroi - " lte-eroi ) ;; End of f-record-ei-for-eroi end ;;-----------------------------------------------------------------------------| ;; Record the 'energy invested' component of EROI calculation. to f-record-ei-for-dnd-eroi [eroi-ei] ;; This routine is to be executed by a seeker. ;; It updates sys-wide values only, since the activity of decomposers ;; and detrivores should not affect individual statistics. ;; There are three associated routines: ;; f-record-er-for-eroi is called by Do-feed. ;; f-record-ei-for-eroi is called by Do-Move. ;; f-record-ei-for-dnd-eroi is called by Do-Death. ;; The three routines work together to calculate individual and ;; system-wide EROI and ETA. ;; NOTE: EROI is ER/EI, that is Benefits over Costs, or (B/C). ;; ETA is (ER-EI)/ER, that is Benefits over Income, or (B/I). LOG-TO-FILE ( word " Do-death: g-sys-ei was - " gl-sys-nrg-invested ) ;; First, record it in the system-wide data. let last-index ( ( length gl-sys-nrg-invested ) - 1 ) let old-value ( last gl-sys-nrg-invested ) let new-value ( old-value + eroi-ei ) set gl-sys-nrg-invested ( replace-item last-index gl-sys-nrg-invested new-value ) LOG-TO-FILE ( word " Do-death: g-sys-ei is now - " gl-sys-nrg-invested ) ;; End of f-record-ei-for-dnd-eroi end ;;-----------------------------------------------------------------------------| ;; D4 – do-feed procedure(s) ;;-----------------------------------------------------------------------------| to do-feed ;; This routine is to be executed by the observer. if( gb-debug-on = 1 ) [ ifelse( ( gs-debug-step-chooser = "all" ) or ( gs-debug-step-chooser = "feed" ) ) [ set gb-debug-flow-on 1 LOG-TO-FILE "" LOG-TO-FILE word "Do-feed: Debug on; tick = " ticks ] [ set gb-debug-flow-on 0 ] ] ;; Agents feed on fruit found in patches. ask seekers [ let this-patch patch-here ;; handle to the patch under the seeker. let nrg-available ( [fruit] of this-patch ) if ( ( nrg < ( EPA - g-nrg-per-deposit ) ) and ( nrg-available > 0 ) ) [ ;; Case of there is food to eat. ;; Seeker eats. set nrg ( nrg + nrg-available ) set g-nrg-in-agents ( g-nrg-in-agents + nrg-available ) f-record-er-for-eroi nrg-available ask this-patch [ set fruit 0 set g-nrg-in-fruit ( g-nrg-in-fruit - nrg-available ) set pcolor brown ] ] ] ;; End of ask seekers. ;; Supressed. f-update-aggregates LOG-TO-FILE " Do-feed: procedure completed" ;; End Do-feed procedure. end ;;-----------------------------------------------------------------------------| ;; Record the 'energy returned' component of EROI calculation. to f-record-er-for-eroi [eroi-er] ;; This routine is to be executed by a seeker. ;; It updates both individual values, and sys-wide values. ;; There are three associated routines: ;; f-record-er-for-eroi is called by Do-feed. ;; f-record-ei-for-eroi is called by Do-Move. ;; f-record-ei-for-dnd-eroi is called by Do-Death. ;; The three routines work together to calculate individual and ;; system-wide EROI and ETA. ;; NOTE: EROI is ER/EI, that is Benefits over Costs, or (B/C). ;; ETA is (ER-EI)/ER, that is Benefits over Income, or (B/I). ;; LOG-TO-FILE ( word " Do-feed: Eroi-counter - " ind-eroi-tick-counter ) ;; LOG-TO-FILE ( word " Do-feed: Nrg-returned - " ind-nrg-returned ) ;; LOG-TO-FILE ( word " Do-feed: Nrg-invested - " ind-nrg-invested ) ;; LOG-TO-FILE ( word " Do-feed: Nrg-benefits - " ind-nrg-benefits ) ;; LOG-TO-FILE ( word " Do-feed: L-ind-er - " l-ind-er ) ;; LOG-TO-FILE ( word " Do-feed: L-ind-ei - " l-ind-ei ) ;; LOG-TO-FILE ( word " Do-feed: Lte-er - " lte-er ) ;; LOG-TO-FILE ( word " Do-feed: Lte-ei - " lte-ei ) ;; LOG-TO-FILE ( word " Do-feed: Lte-eta - " lte-eta ) ;; LOG-TO-FILE ( word " Do-feed: Lte-eroi - " lte-eroi ) ;; First, record it in the system-wide data. ;; LOG-TO-FILE ( word " Do-feed: g-sys-er was - " gl-sys-nrg-returned ) let last-index ( ( length gl-sys-nrg-returned ) - 1 ) let old-value ( last gl-sys-nrg-returned ) let new-value ( old-value + eroi-er ) set gl-sys-nrg-returned ( replace-item last-index gl-sys-nrg-returned new-value ) ;; LOG-TO-FILE ( word " Do-feed: g-sys-er is now - " gl-sys-nrg-returned ) ;; Now, record it in the individual data. ;; DO NOT increment the counter here - done only in move-related function. ;; set ind-eroi-tick-counter ( ind-eroi-tick-counter + 1 ) ;; Remove the place-holder zero, put there in the move-related routine. set l-ind-er ( butlast l-ind-er ) ;; Append new entry to last of l-ind-er. set l-ind-er ( lput eroi-er l-ind-er ) ;; Update the life-time-efficiency (lte) stats. set lte-er ( lte-er + eroi-er ) ;; Re-calculate the seeker's stats. set ind-nrg-returned ( sum l-ind-er ) set ind-nrg-benefits ( ind-nrg-returned - ind-nrg-invested ) ifelse (ind-nrg-invested > 0) [ set ind-eroi ( ind-nrg-returned / ind-nrg-invested ) ] ;; (I/C) [ set ind-eroi 0 ] ;; (I/C) ifelse (ind-nrg-returned > 0) [ set ind-eta ( ind-nrg-benefits / ind-nrg-returned ) ] ;; (B/I) [ set ind-eta -5 ] ;; (B/I) ;; Recalculate the life-time stats. ifelse (lte-ei > 0) [ set lte-eroi ( lte-er / lte-ei ) ] [ set lte-eroi 0 ] ifelse (lte-er > 0) [ set lte-eta ( ( lte-er - lte-ei ) / lte-er ) ] [ set lte-eta -5 ] ;; LOG-TO-FILE ( word " Do-feed: Eroi-counter - " ind-eroi-tick-counter ) ;; LOG-TO-FILE ( word " Do-feed: Nrg-returned - " ind-nrg-returned ) ;; LOG-TO-FILE ( word " Do-feed: Nrg-invested - " ind-nrg-invested ) ;; LOG-TO-FILE ( word " Do-feed: Nrg-benefits - " ind-nrg-benefits ) ;; LOG-TO-FILE ( word " Do-feed: L-ind-er - " l-ind-er ) ;; LOG-TO-FILE ( word " Do-feed: L-ind-ei - " l-ind-ei ) ;; LOG-TO-FILE ( word " Do-feed: Lte-er - " lte-er ) ;; LOG-TO-FILE ( word " Do-feed: Lte-ei - " lte-ei ) ;; LOG-TO-FILE ( word " Do-feed: Lte-eta - " lte-eta ) ;; LOG-TO-FILE ( word " Do-feed: Lte-eroi - " lte-eroi ) ;; End of f-record-er-for-eroi end ;;-----------------------------------------------------------------------------| ;; D5 – do-reproduce procedure(s) ;;-----------------------------------------------------------------------------| to do-reproduce ;; This routine is to be executed by the observer. if( gb-debug-on = 1 ) [ ifelse( ( gs-debug-step-chooser = "all" ) or ( gs-debug-step-chooser = "reproduce" ) ) [ set gb-debug-flow-on 1 LOG-TO-FILE "" LOG-TO-FILE word "Do-rep: Debug on; tick = " ticks ] [ set gb-debug-flow-on 0 ] ] ask seekers [ f-set-seeker-repro-flag f-reproduce-seeker-by-fission ] ;; Supressed. f-update-aggregates LOG-TO-FILE " Do-rep: procedure completed" end ;;-----------------------------------------------------------------------------| ;; f-set-seeker-repro-flag to f-set-seeker-repro-flag ;; This routine is to be executed by a seeker. set b-is-ready-to-reproduce 1 ;; i.e. true is the default. if( nrg < RET ) [ set b-is-ready-to-reproduce 0 ] ;; i.e. false due to lack of health. if( age < RAT ) [ set b-is-ready-to-reproduce 0 ] ;; i.e. false due to lack of maturity. if( b-is-ready-to-reproduce = 1 ) [ LOG-TO-FILE ( word " Do-rep: S(age,nrg,rep-flag) - (" age "," floor nrg "," b-is-ready-to-reproduce ")" ) ] ;; End f-set-seeker-repro-flag end ;;-----------------------------------------------------------------------------| ;; A seeker reproduces via fission, one mother having two daughters. to f-reproduce-seeker-by-fission ;; This routine is to be executed by a seeker. if( b-is-ready-to-reproduce = 1 ) ;; 1 = true [ LOG-TO-FILE ( word " Do-rep: seeker Ma - " who ) ;; This mother is dying due to reproduction. Her lte-eroi and lte-eta ;; values need to be recorded in the death statistics. ;; Record the eroi and eta data of mother before reproduction by fission. if( g-dbr-stat-count >= g-max-for-lte-stats ) [ ;; Remove old data for "death by repro" (dbr). set gl-lte-eroi-dbr ( butfirst gl-lte-eroi-dbr ) set gl-lte-eta-dbr ( butfirst gl-lte-eta-dbr ) set g-dbr-stat-count ( g-dbr-stat-count - 1 ) ] set gl-lte-eroi-dbr ( lput lte-eroi gl-lte-eroi-dbr ) set gl-lte-eta-dbr ( lput lte-eta gl-lte-eta-dbr ) set g-dbr-stat-count ( g-dbr-stat-count + 1 ) set gl-lte-eroi-all ( sentence gl-lte-eroi-dbh gl-lte-eroi-dbo gl-lte-eroi-dbr ) set gl-lte-eta-all ( sentence gl-lte-eta-dbh gl-lte-eta-dbo gl-lte-eta-dbr ) ;; Let statements for fission. let mother self let mothers-who who let mothers-patch patch-here let first-share-of-nrg floor( nrg / 2 ) let second-share-of-nrg ( nrg - first-share-of-nrg ) ;; Record the nrg as passed on to daughters. f-store-data-in-sink ge-sinktype-repro-RET nrg let daughter-count 0 ask mothers-patch [ sprout-seekers 2 [ set daughter-count ( daughter-count + 1 ) LOG-TO-FILE ( word " Do-rep: seeker D" daughter-count " - " who ) f-initialize-new-seeker set color ( [color] of mother ) ;; Copy the C1 genetic/learned material. set c1-bases ( [c1-bases] of mother ) set c1-expos ( [c1-expos] of mother ) set c1-stren ( [c1-stren] of mother ) set c1-pheno ( [c1-pheno] of mother ) ;; C2 genes are static. set DAT ( [DAT] of mother ) set DET ( [DET] of mother ) set RAT ( [RAT] of mother ) set RET ( [RET] of mother ) set EPM ( [EPM] of mother ) set EPA ( [EPA] of mother ) ;; Note the mother of this daughter. set mas-who ( [who] of mother ) set age 0 ifelse ( daughter-count = 1 ) [ set nrg first-share-of-nrg ] [ set nrg second-share-of-nrg ] set cause-of-death 0 set b-is-ready-to-move 1 set b-is-ready-to-reproduce 0 set b-is-ready-to-die 0 ;; Variables for calculating individual EROI and ETA. ;; All inherited from mother. set ind-nrg-returned ( [ind-nrg-returned] of mother ) set ind-nrg-invested ( [ind-nrg-invested] of mother ) set ind-nrg-benefits ( [ind-nrg-benefits] of mother ) set ind-eroi ( [ind-eroi] of mother ) set ind-eta ( [ind-eta] of mother ) set l-ind-er ( [l-ind-er] of mother ) set l-ind-ei ( [l-ind-ei] of mother ) set ind-eroi-tick-counter ( [ind-eroi-tick-counter] of mother ) ;; Variables for calculating life-time-efficiencies EROI and ETA. set lte-ei 0 set lte-er 0 set lte-eta 0 set lte-eroi 0 f-mutate-new-seeker ] ] ;; Set the cause of death for the mother. set cause-of-death ge-cod-fission ;; The mother disappears after fission, leaving two daughters. ;; Death actually occurs in the Do-die step. ] ;; End f-reproduce-seeker-by-fission end ;;-----------------------------------------------------------------------------| ;; A new seeker mutates, changing the genetic basis of strategies. to f-mutate-new-seeker ;; This routine is to be executed by a seeker. ;; When a mutation is called for, one gene is mutated. So when one or both ;; switches are on, the probability that a C1 gene will mutate must ;; decrease. I could give each of C1, EPM and EPA equal probability of ;; occurrence. Since there are, in fact 8 C1 genes, (as opposed to 2 ;; possible C2 genes) they should get to mutate 8/10 = 80% of the time ;; or more when a mutation is called for. However, since my interest ;; is NOT on the C1 genes, a dynamic that I understand well, I want the ;; EPM and EPA to evolve more rapidly when called for. For that reason, ;; I have written the code to recognize the C1 chromosome, as a whole, ;; as having equal status as the EPM and EPA when activated. ;; Given that a mutation of some sort must hapen, the probability of ;; mutation of the various genes must be spread around appropriately. ;; The various scenarios are then: ;; -EPM=OFF; EPA=OFF; C1 gets 100%; EPM gets 0%; EPA gets 0% ;; -EPM=OFF; EPA=ON; C1 gets 50%; EPM gets 0%; EPA gets 50% ;; -EPM=ON; EPA=OFF; C1 gets 50%; EPM gets 50%; EPA gets 0% ;; -EPM=ON; EPA=ON; C1 gets 33 1/3%; EPM gets 33 1/3%; EPA gets 33 1/3% ;; This logic is rolled out over several calls to sub-routines. Note that ;; these percentages are conditional on determination that a mutation ;; must happen for this seeker daughter in this reproductive event. ;; Decide if a genetic mutation is to happen. let random-number ( random-float 1 ) let threshold ( g-prob-of-mutation ) LOG-TO-FILE ( word " Do-rep: PreMut (RN, TH) - (" random-number ", " threshold ")" ) if ( random-number <= threshold ) [ ;; I want only one gene to mutate when mutation is called for. So ;; I need some logic that responds to the toggles that control which ;; kinds of gene mutate - i.e. gb-mutate-epm and gb-mutate-epa. ifelse( ( gb-mutate-epm = false ) and ( gb-mutate-epa = false ) ) [ ;; Case of both EPM and EPA mutation is turned off. C1 gets 100%. f-mutate-c1-gene ] ;; Else [ ;; Some other case. C1 gets less than 100% probability of mutation. ;; Either a c1 gene mutates, or one of EPM or EPA (C2 genes) mutate. ;; At this point I know that at least one of EPM and EPA is to be included. ;; So, the competition is between two or three, with thresholds of 0.5 ;; or 0.33333. set threshold ( 0.3333333333333 ) ;; Default if( ( gb-mutate-epm = false ) or ( gb-mutate-epm = false ) ) [ set threshold ( 0.5 ) ] ;; Decide which type of genetic mutation is to happen. set random-number ( random-float 1 ) LOG-TO-FILE ( word " Do-rep: PreCxMut (RN, TH) - (" random-number ", " threshold ")" ) ifelse ( random-number <= threshold ) [ f-mutate-c1-gene ] [ f-mutate-c2-gene ] ] ] ;; End of f-mutate-new-seeker end ;;-----------------------------------------------------------------------------| ;; A seeker mutates a chromosome #1 (c1) gene. to f-mutate-c1-gene ;; This routine is to be executed by a seeker. ;; Case of C1 mutation to be done. LOG-TO-FILE ( word " Do-rep: PreC1Mut c1-bases - " c1-bases ) LOG-TO-FILE ( word " Do-rep: PreC1Mut c1-expos - " c1-expos ) LOG-TO-FILE ( word " Do-rep: PreC1Mut c1-stren - " c1-stren ) LOG-TO-FILE ( word " Do-rep: PreC1Mut c1-pheno - " c1-pheno ) ;; There are 8 C1 genes. Select the gene to be mutated. These genes ;; control the heuristic search strategy. let gene-to-be-mutated ( random 8 ) LOG-TO-FILE ( word " Do-rep: Target gene # - " gene-to-be-mutated ) ;; Mutate the gene base. let oldbase ( item gene-to-be-mutated c1-bases ) LOG-TO-FILE ( word " Do-rep: Old base value - " oldbase ) ;; Choose a factor for the base. let base-factor ( item (random 8) gl-base-factors ) ;; Mutate it let newbase ( oldbase * base-factor ) LOG-TO-FILE ( word " Do-rep: Factor - " base-factor ) set c1-bases ( replace-item gene-to-be-mutated c1-bases newbase ) LOG-TO-FILE ( word " Do-rep: New base value - " newbase ) ;; Mutate the gene. The gene value is an integer of either sign. let oldgene ( item gene-to-be-mutated c1-expos ) LOG-TO-FILE ( word " Do-rep: Old gene value - " oldgene ) ;; Decide whether it will increase or decrease in value. let delta ( -1 + ( 2 * ( random 2 ) ) ) ;; Either a -1 or a 1. LOG-TO-FILE ( word " Do-rep: Delta - " delta ) let newgene ( oldgene + delta ) set c1-expos ( replace-item gene-to-be-mutated c1-expos newgene ) LOG-TO-FILE ( word " Do-rep: New gene value - " newgene ) ;; Calculate the strengths and phenotypic characters. f-find-strens-n-phenos LOG-TO-FILE ( word " Do-rep: AftC1Mut c1-bases - " c1-bases ) LOG-TO-FILE ( word " Do-rep: AftC1Mut c1-expos - " c1-expos ) LOG-TO-FILE ( word " Do-rep: AftC1Mut c1-stren - " c1-stren ) LOG-TO-FILE ( word " Do-rep: AftC1Mut c1-pheno - " c1-pheno ) ;; End of f-mutate-c1-gene end ;;-----------------------------------------------------------------------------| ;; A seeker mutates a Chromosome #2 (C2) gene. to f-mutate-c2-gene ;; This routine is to be executed by a seeker. ;; To be called, at least one switch must be on. ;; One of two genes is to be mutated. Either EPM or EPA. ;; EPM is energy per move, and controls the rate of metabolic expenditure. ;; EPA is energy per agent, and controls the maximal nrg content per agent. ;; Both of these genes play a role in the throughput of energy. EPM ;; has an obvious direct role, and should have great pressure put on it. ;; EPA has an indirect role, and should have mild pressure put on it. ;; I.e. I think EPM has a strong effect on survivability, while EPA has ;; a much lesser effect. ;; Decide which genetic mutation is to happen. ;; Mutation of these genes is toggled on or off by Boolean switches. To ;; have this program called, at least one of those is on, but possibly ;; both are on. if( gb-mutate-epa = false ) [ ;; Case of EPM to be mutated. f-mutate-epm ] if( gb-mutate-epm = false ) [ ;; Case of EPA to be mutated. f-mutate-epa ] if( ( gb-mutate-epm = true ) and ( gb-mutate-epa = true ) ) [ ;; Each has a 50/50 chance. let random-number ( random-float 1 ) let threshold ( 0.50 ) LOG-TO-FILE ( word " Do-rep: PreC2Mut (RN, TH) - (" random-number ", " threshold ")" ) ifelse ( random-number <= threshold ) [ f-mutate-epm ] ;; Else [ f-mutate-epa ] ] ;; End of f-mutate-c2-gene end ;;-----------------------------------------------------------------------------| ;; The EPM C2 gene is to be mutated. to f-mutate-EPM ;; This routine is to be executed by a seeker. ;; Case of mutation of EPM. LOG-TO-FILE ( word " Do-rep: PreC2Mut EPM - " EPM ) ;; I want a variety of factors to avoid discreteness in values. ;; I want an unbiased chance of a rise or fall in value. let l-factor-list [ 1.01 1.01 1.01 1.01 1.02 1.02 1.04 0.99 0.99 0.99 0.99 0.98 0.98 0.96 ] ;; Choose a factor. let factor ( item (random 14) l-factor-list ) LOG-TO-FILE ( word " Do-rep: Factor - " factor ) ;; Mutate it set EPM ( EPM * factor ) LOG-TO-FILE ( word " Do-rep: AftC2Mut EPM - " EPM ) ;; End of f-mutate-EPM end ;;-----------------------------------------------------------------------------| ;; The EPA C2 gene is to be mutated. to f-mutate-EPA ;; This routine is to be executed by a seeker. ;; Case of mutation of EPA. LOG-TO-FILE ( word " Do-rep: PreC2Mut EPA - " EPA ) ;; I want a variety of factors to avoid discreteness in values. ;; I want an unbiased chance of a rise or fall in value. let l-factor-list [ 1.001 1.001 1.001 1.001 1.002 1.002 1.004 0.999 0.999 0.999 0.999 0.998 0.998 0.996 ] ;; Choose a factor. let factor ( item (random 14) l-factor-list ) LOG-TO-FILE ( word " Do-rep: Factor - " factor ) ;; Mutate it set EPA ( EPA * factor ) LOG-TO-FILE ( word " Do-rep: AftC2Mut EPA - " EPA ) ;; End of f-mutate-EPA end ;;-----------------------------------------------------------------------------| ;; D6 – do-die procedure(s) ;;-----------------------------------------------------------------------------| to do-die ;; This routine is to be executed by the observer. if( gb-debug-on = 1 ) [ ifelse( ( gs-debug-step-chooser = "all" ) or ( gs-debug-step-chooser = "die" ) ) [ set gb-debug-flow-on 1 LOG-TO-FILE "" LOG-TO-FILE word "Do-die: Debug on; tick = " ticks ] [ set gb-debug-flow-on 0 ] ] if( ( count seekers ) > 0 ) [ ask seekers [ f-set-seeker-death-flag f-seeker-dies ] ] ;; Supressed. f-update-aggregates LOG-TO-FILE " Do-die: procedure completed" end ;;-----------------------------------------------------------------------------| ;; f-set-seeker-death-flag to f-set-seeker-death-flag ;; This routine is to be executed by a seeker. set b-is-ready-to-die 0 ;; i.e. false, default. ;; If a cause of death has already been noted, it dies. ifelse( cause-of-death > ge-cod-none ) [ ;; A cause of death has been previously flagged. ;; This is either due to hunger (in do-move) or fission (in do-repro). ;; In both cases nrg has been stripped out already. ;; In the cases of DET and DAT, the flag is not yet set, ;; and the nrg remains. set b-is-ready-to-die 1 ] ;; Else [ ;; No cause of death has been set yet. Check basic vital signs. if( nrg <= DET ) ;; Death Energy Threshold. [ set b-is-ready-to-die 1 set cause-of-death ge-cod-hunger f-store-data-in-sink ge-sinktype-die-det nrg set g-nrg-in-system ( g-nrg-in-system - nrg ) set g-nrg-in-agents ( g-nrg-in-agents - nrg ) if( gb-include-dnd = true ) [ ;; Record the expenditure in the EROI variables f-record-ei-for-dnd-eroi nrg ] set nrg 0 ] if( age > DAT ) ;; Death Age Threshold. [ set b-is-ready-to-die 1 set cause-of-death ge-cod-oldage f-store-data-in-sink ge-sinktype-die-dat nrg set g-nrg-in-agents ( g-nrg-in-agents - nrg ) set g-nrg-in-system ( g-nrg-in-system - nrg ) if( gb-include-dnd = true ) [ ;; Record the expenditure in the EROI variables f-record-ei-for-dnd-eroi nrg ] set nrg 0 ] ] if( b-is-ready-to-die = 1 ) [ LOG-TO-FILE ( WORD " Do-die: S(age,nrg,cod) - (" age "," nrg "," cause-of-death ")" ) ] ;; End f-set-seeker-death-flag end ;;-----------------------------------------------------------------------------| ;; f-seeker-dies to f-seeker-dies ;; This routine is to be executed by a seeker. if( b-is-ready-to-die = 1 ) [ ;; Record the eroi and eta data before death by hunger. if( cause-of-death = ge-cod-hunger ) [ if( g-dbh-stat-count >= g-max-for-lte-stats ) [ ;; Remove old data for "death by hunger" (dbh). set gl-lte-eroi-dbh ( butfirst gl-lte-eroi-dbh ) set gl-lte-eta-dbh ( butfirst gl-lte-eta-dbh ) set g-dbh-stat-count ( g-dbh-stat-count - 1 ) ] set gl-lte-eroi-dbh ( lput lte-eroi gl-lte-eroi-dbh ) set gl-lte-eta-dbh ( lput lte-eta gl-lte-eta-dbh ) set g-dbh-stat-count ( g-dbh-stat-count + 1 ) set gl-lte-eroi-all ( sentence gl-lte-eroi-dbh gl-lte-eroi-dbo gl-lte-eroi-dbr ) set gl-lte-eta-all ( sentence gl-lte-eta-dbh gl-lte-eta-dbo gl-lte-eta-dbr ) ] ;; Record the lte-eroi and lte-eta data before death by old age. if( cause-of-death = ge-cod-oldage ) [ if( g-dbo-stat-count >= g-max-for-lte-stats ) [ ;; Remove old data for "death by old age" (dbo). set gl-lte-eroi-dbo ( butfirst gl-lte-eroi-dbo ) set gl-lte-eta-dbo ( butfirst gl-lte-eta-dbo ) set g-dbo-stat-count ( g-dbo-stat-count - 1 ) ] set gl-lte-eroi-dbo ( lput lte-eroi gl-lte-eroi-dbo ) set gl-lte-eta-dbo ( lput lte-eta gl-lte-eta-dbo ) set g-dbo-stat-count ( g-dbo-stat-count + 1 ) set gl-lte-eroi-all ( sentence gl-lte-eroi-dbh gl-lte-eroi-dbo gl-lte-eroi-dbr ) set gl-lte-eta-all ( sentence gl-lte-eta-dbh gl-lte-eta-dbo gl-lte-eta-dbr ) ] ;; Nrg was stripped out in do-move step. ;; However, nrg may exist for those who die of old age. f-increment-cod-list breed cause-of-death die ;; The seeker disappears from the system. ] ;; End f-seeker-dies end ;;-----------------------------------------------------------------------------| ;; D7 - do-post-tick procedure(s) ;;-----------------------------------------------------------------------------| to do-post-tick ;; This routine is to be executed by the observer. if( gb-debug-on = 1 ) [ ifelse( ( gs-debug-step-chooser = "all" ) or ( gs-debug-step-chooser = "post-tick" ) ) [ set gb-debug-flow-on 1 LOG-TO-FILE "" LOG-TO-FILE word "Do-Post-tick: Debug on; tick = " ticks ] [ set gb-debug-flow-on 0 ] ] ;; MANUAL CHANGE FOR DEBUG. ;; This is a call to a debug routine which could be suppressed if all is okay. ;; This is one of a group of such calls, most of which are between steps in ;; the 'Go' routine. They are suppressed there, but can be enabled again. ;; I have decided to leave this one active, for now. ;; It checks all agents, every tick, to ensure that all values are greater than ;; or equal to zero. if( frb-agents-are-all-valid = false ) [ LOG-TO-FILE ( word " Do-post-tick: Agents failed validity test." ) ] ;; Global EROI system-wide calculations. set g-sys-nrg-returned ( sum gl-sys-nrg-returned ) ;; Total nrg returned within delta T (er). set g-sys-nrg-invested ( sum gl-sys-nrg-invested ) ;; Total nrg invested within delta T (ei). set g-sys-nrg-benefits ( g-sys-nrg-returned - g-sys-nrg-invested ) ;; (er-ei) ifelse( g-sys-nrg-invested > 0 ) [ set g-sys-eroi ( g-sys-nrg-returned / g-sys-nrg-invested ) ] ;; (I/C) [ set g-sys-eroi 0 ] ;; (I/C) ifelse( g-sys-nrg-returned > 0 ) [ set g-sys-eta ( g-sys-nrg-benefits / g-sys-nrg-returned ) ] ;; (B/I) [ set g-sys-eta -5 ] ;; (B/I) ;; Update the aggregates for display in the monitors. f-update-aggregates display LOG-TO-FILE " Do-post-tick: procedure completed." end ;;-----------------------------------------------------------------------------| ;; SECTION E – DRAWING AND MAINTENANCE PROCEDURE(S) ;;-----------------------------------------------------------------------------| ;;-----------------------------------------------------------------------------| ;; Update the values of global aggregate numbers. to f-update-aggregates ;; This routine is to be executed by the observer. ;; Although this is a display-only routine, it may implicitly call the ;; PRNG and so may have an effect on the trajectory of the model. In a ;; standard 'go' run it is called only once per tick, before graphs are ;; updated. If you use the one-step debug buttons, it is called once ;; after each step, so debug runs that use those buttons will not ;; replicate a real run. ;;---------------------------------------------------------------------------| ;; The following agent sets, counts and averages are for data collection ;; and display in monitors and plots. ;; Counts ;; set g-no-of-patches ( count patches ) set g-no-of-seekers ( count seekers ) ;; Max value for eroi domain. let temp-list ( sentence gl-lte-eroi-dbh gl-lte-eta-dbr gl-lte-eroi-dbo) ifelse( ( length temp-list ) > 0 ) [ set g-lte-eroi-max ( max temp-list) ] ;; else [ set g-lte-eroi-max ( 0 ) ] ;; Min value for eta domain. set temp-list ( sentence gl-lte-eta-dbh gl-lte-eta-dbr gl-lte-eta-dbo) ifelse( ( length temp-list ) > 0 ) [ set g-lte-eta-min ( min temp-list ) ] ;; else [ set g-lte-eta-min ( 0 ) ] ;; Other histogram limits set g-hist-epm-max ( ( ceiling ( ( .1 + max [epm] of seekers ) * 10 ) ) / 10 ) set g-hist-epm-min ( ( floor ( ( -.1 + min [epm] of seekers ) * 10 ) ) / 10 ) set g-hist-epa-max ( ceiling ( 1 + max [epa] of seekers ) ) set g-hist-epa-min ( floor ( -1 + min [epa] of seekers ) ) ;; Averages - seekers ifelse( 0 = ( count seekers ) ) [ set g-ave-age 0 ;; age of seekers set g-ave-nrg 0 ;; nrg of seekers set g-ind-min-eroi 0 ;; eroi of seekers set g-ind-ave-eroi 0 ;; eroi of seekers set g-ind-max-eroi 0 ;; eroi of seekers set g-ind-min-eta 0 ;; eta of seekers set g-ind-ave-eta 0 ;; eta of seekers set g-ind-max-eta 0 ;; eta of seekers set g-ave-C1-b0 0 ;; c1, base character, gene-0 set g-ave-C1-b1 0 ;; c1, base character, gene-1 set g-ave-C1-b2 0 ;; c1, base character, gene-2 set g-ave-C1-b3 0 ;; c1, base character, gene-3 set g-ave-C1-b4 0 ;; c1, base character, gene-4 set g-ave-C1-b5 0 ;; c1, base character, gene-5 set g-ave-C1-b6 0 ;; c1, base character, gene-6 set g-ave-C1-b7 0 ;; c1, base character, gene-7 set g-ave-c1-e0 0 ;; c1, exponent character, gene-0 set g-ave-c1-e1 0 ;; c1, exponent character, gene-1 set g-ave-c1-e2 0 ;; c1, exponent character, gene-2 set g-ave-c1-e3 0 ;; c1, exponent character, gene-3 set g-ave-c1-e4 0 ;; c1, exponent character, gene-4 set g-ave-c1-e5 0 ;; c1, exponent character, gene-5 set g-ave-c1-e6 0 ;; c1, exponent character, gene-6 set g-ave-c1-e7 0 ;; c1, exponent character, gene-7 set g-ave-C1-s0 0 ;; c1, strength character, gene-0 set g-ave-C1-s1 0 ;; c1, strength character, gene-1 set g-ave-C1-s2 0 ;; c1, strength character, gene-2 set g-ave-C1-s3 0 ;; c1, strength character, gene-3 set g-ave-C1-s4 0 ;; c1, strength character, gene-4 set g-ave-C1-s5 0 ;; c1, strength character, gene-5 set g-ave-C1-s6 0 ;; c1, strength character, gene-6 set g-ave-C1-s7 0 ;; c1, strength character, gene-7 set g-ave-C1-p0 0 ;; c1, phenotypic character, gene-0 set g-ave-C1-p1 0 ;; c1, phenotypic character, gene-1 set g-ave-C1-p2 0 ;; c1, phenotypic character, gene-2 set g-ave-C1-p3 0 ;; c1, phenotypic character, gene-3 set g-ave-C1-p4 0 ;; c1, phenotypic character, gene-4 set g-ave-C1-p5 0 ;; c1, phenotypic character, gene-5 set g-ave-C1-p6 0 ;; c1, phenotypic character, gene-6 set g-ave-C1-p7 0 ;; c1, phenotypic character, gene-7 ] ;; Else [ set g-ave-age ( mean [age] of seekers ) set g-ave-nrg ( mean [nrg] of seekers ) set g-ind-min-eroi ( min [ind-eroi] of seekers ) set g-ind-ave-eroi ( mean [ind-eroi] of seekers ) set g-ind-max-eroi ( max [ind-eroi] of seekers ) set g-ind-min-eta ( min [ind-eta] of seekers ) set g-ind-ave-eta ( mean [ind-eta] of seekers ) set g-ind-max-eta ( max [ind-eta] of seekers ) set g-ave-C1-b0 ( f-compute-C1-bases-average 0 ) set g-ave-C1-b1 ( f-compute-C1-bases-average 1 ) set g-ave-C1-b2 ( f-compute-C1-bases-average 2 ) set g-ave-C1-b3 ( f-compute-C1-bases-average 3 ) set g-ave-C1-b4 ( f-compute-C1-bases-average 4 ) set g-ave-C1-b5 ( f-compute-C1-bases-average 5 ) set g-ave-C1-b6 ( f-compute-C1-bases-average 6 ) set g-ave-C1-b7 ( f-compute-C1-bases-average 7 ) set g-ave-c1-e0 ( f-compute-c1-expos-average 0 ) set g-ave-c1-e1 ( f-compute-c1-expos-average 1 ) set g-ave-c1-e2 ( f-compute-c1-expos-average 2 ) set g-ave-c1-e3 ( f-compute-c1-expos-average 3 ) set g-ave-c1-e4 ( f-compute-c1-expos-average 4 ) set g-ave-c1-e5 ( f-compute-c1-expos-average 5 ) set g-ave-c1-e6 ( f-compute-c1-expos-average 6 ) set g-ave-c1-e7 ( f-compute-c1-expos-average 7 ) set g-ave-C1-s0 ( f-compute-c1-stren-average 0 ) set g-ave-C1-s1 ( f-compute-c1-stren-average 1 ) set g-ave-C1-s2 ( f-compute-c1-stren-average 2 ) set g-ave-C1-s3 ( f-compute-c1-stren-average 3 ) set g-ave-C1-s4 ( f-compute-c1-stren-average 4 ) set g-ave-C1-s5 ( f-compute-c1-stren-average 5 ) set g-ave-C1-s6 ( f-compute-c1-stren-average 6 ) set g-ave-C1-s7 ( f-compute-c1-stren-average 7 ) set g-ave-C1-p0 ( f-compute-c1-pheno-average 0 ) set g-ave-C1-p1 ( f-compute-c1-pheno-average 1 ) set g-ave-C1-p2 ( f-compute-c1-pheno-average 2 ) set g-ave-C1-p3 ( f-compute-c1-pheno-average 3 ) set g-ave-C1-p4 ( f-compute-c1-pheno-average 4 ) set g-ave-C1-p5 ( f-compute-c1-pheno-average 5 ) set g-ave-C1-p6 ( f-compute-c1-pheno-average 6 ) set g-ave-C1-p7 ( f-compute-c1-pheno-average 7 ) ] ;; End else ;; Calculate the entropic index of the energy distribution. set g-energy-entropic-index ( fr-get-energy-entropic-index ( [nrg] of seekers ) ) print "" ;; Calculate the entropic index of the phenotype probability distribution. let l-pheno-partition ( fr-make-pheno-partition ) set g-pheno-entropic-index ( fr-calc-pheno-entropic-index l-pheno-partition ) ;; This log entry may come from any step during debug operations. LOG-TO-FILE " Do-update: All aggregates updated." ;; End of f-update-aggregates end ;;-----------------------------------------------------------------------------| ;; Clear the Life-Time Efficiency (LTE) data. to f-clear-lte-data ;; This routine is to be executed by the observer. ;; Global lists for EROI/ETA for death by repro/hunger. set g-dbr-stat-count 0 ;; Count of ticks included in lists. set g-dbh-stat-count 0 ;; Count of ticks included in lists. set g-dbo-stat-count 0 ;; Count of ticks included in lists. ;; set g-max-for-lte-stats 0 ;; Maximum agents included [40,40,1000,1000] set gl-lte-eroi-dbr [] ;; List of EROI for death by repro set gl-lte-eroi-dbh [] ;; List of EROI for death by hunger set gl-lte-eroi-dbo [] ;; List of EROI for death by old age set gl-lte-eroi-all [] ;; List of EROI for death by all causes set gl-lte-eta-dbr [] ;; List of ETA for death by repro set gl-lte-eta-dbh [] ;; List of ETA for death by hunger set gl-lte-eta-dbo [] ;; List of ETA for death by old age set gl-lte-eta-all [] ;; List of ETA for death by all causes set g-lte-eroi-max 1 ;; Used to set max value for histograms ;; End of f-clear-lte-data end ;;-----------------------------------------------------------------------------| ;; Compute an average for C1-bases, by preferred gene type. to-report f-compute-C1-bases-average [ gene-to-check ] ;; This routine is to be executed by the observer. let count-of-seekers ( count seekers ) let appropriate-sum ( sum ( [item gene-to-check c1-bases] of seekers ) ) let answer 0 if ( count-of-seekers > 0 ) [ set answer ( appropriate-sum / count-of-seekers ) ] ;; LOG-TO-FILE ( word " Do-update: g# - " gene-to-check ", ave [B] - " answer ) report answer ;; End of f-compute-C1-bases-average end ;;-----------------------------------------------------------------------------| ;; Compute an average for c1-expos, by preferred gene type. to-report f-compute-c1-expos-average [ gene-to-check ] ;; This routine is to be executed by the observer. let count-of-seekers ( count seekers ) let appropriate-sum ( sum ( [item gene-to-check c1-expos] of seekers ) ) let answer 0 if ( count-of-seekers > 0 ) [ set answer ( appropriate-sum / count-of-seekers ) ] ;; LOG-TO-FILE ( word " Do-update: g# - " gene-to-check ", ave [E] - " answer ) report answer ;; End of f-compute-c1-expos-average end ;;-----------------------------------------------------------------------------| ;; Compute an average for c1-stren, by preferred gene type. to-report f-compute-c1-stren-average [ gene-to-check ] ;; This routine is to be executed by the observer. let count-of-seekers ( count seekers ) let appropriate-sum ( sum ( [item gene-to-check c1-stren] of seekers ) ) let answer 0 if ( count-of-seekers > 0 ) [ set answer ( appropriate-sum / count-of-seekers ) ] ;; LOG-TO-FILE ( word " Do-update: g# - " gene-to-check ", ave [S] - " answer ) report answer ;; End of f-compute-c1-stren-average end ;;-----------------------------------------------------------------------------| ;; Compute an average for c1-pheno, by preferred gene type. to-report f-compute-c1-pheno-average [ gene-to-check ] ;; This routine is to be executed by the observer. let count-of-seekers ( count seekers ) let appropriate-sum ( sum ( [item gene-to-check c1-pheno] of seekers ) ) let answer 0 if ( count-of-seekers > 0 ) [ set answer ( appropriate-sum / count-of-seekers ) ] ;; LOG-TO-FILE ( word " Do-update: g# - " gene-to-check ", ave [P] - " answer ) report answer ;; End of f-compute-c1-pheno-average end ;;-------------------------- ;; DATA CAPTURE TO CSV FILES ;;-------------------------- ;;-----------------------------------------------------------------------------| ;; Record the data is several selected plots to CSV files to f-record-selected-plots ;; This routine is to be executed by the observer. ;; The template for the export command is: ;; export-plot plotname filename ;; Get a common timestamp for all plots. let timestamp fr-get-time-stamp ;; Plot 01 let plotname "[B]ase Values By Gene #" let plot-filename ( word timestamp "_Sc" g-scenario-number "_Se" g-use-this-seed "_Pl01_BVBG.CSV" ) export-plot plotname plot-filename ;; Plot 02 set plotname "[E]xponent Values By Gene #" set plot-filename ( word timestamp "_Sc" g-scenario-number "_Se" g-use-this-seed "_Pl02_EVBG.CSV" ) export-plot plotname plot-filename ;; Plot 03 set plotname "[S]trengths By Gene #" set plot-filename ( word timestamp "_Sc" g-scenario-number "_Se" g-use-this-seed "_Pl03_SVBG.CSV" ) export-plot plotname plot-filename ;; Plot 04 set plotname "[P]henotype Values By Gene #" set plot-filename ( word timestamp "_Sc" g-scenario-number "_Se" g-use-this-seed "_Pl04_PVBG.CSV" ) export-plot plotname plot-filename ;; End f-record-selected-plots end ;;-----------------------------------------------------------------------------| ;; Construct a time stamp for a file name for data in CSV format. to-report fr-get-time-stamp ;; This routine is to be executed by the observer. ;; ;; Date-string format "01:19:36.685 PM 19-Sep-2002" let date-string date-and-time let time-stamp "" ;; Append the year as yy. set time-stamp word time-stamp ( substring date-string 25 27 ) ;; Append the month as Mmm. set time-stamp word time-stamp fr-convert-mmm-mm ( substring date-string 19 22 ) ;; Append the day as dd. set time-stamp word time-stamp ( substring date-string 16 18 ) ;; Append a dash. set time-stamp word time-stamp "_" ;; Append the hour as hh. set time-stamp word time-stamp fr-convert1224 ( substring date-string 0 2 ) ( substring date-string 13 15 ) ;; Append the minute as mm. set time-stamp word time-stamp ( substring date-string 3 5 ) ;; Append the second as ss. set time-stamp word time-stamp ( substring date-string 6 8 ) report time-stamp ;; End fr-get-time-stamp end ;;-----------------------------------------------------------------------------| ;; DEBUG AND DEBUG LOG FILE MANAGEMENT FUNCTIONS ;;-----------------------------------------------------------------------------| ;;-----------------------------------------------------------------------------| ;; Open a log file for debug output. to f-open-log-file ;; This routine is to be executed by the observer. ;; Ensure previous log file is closed. if ( is-string? gs-log-file-name ) [ if ( file-exists? gs-log-file-name ) [ file-close-all ] ] ;; Date-string format "01:19:36.685 PM 19-Sep-2002" let date-string date-and-time set gs-log-file-name "EffLab_I_Log_" ;; Append the year as yy. set gs-log-file-name word gs-log-file-name ( substring date-string 25 27 ) ;; Append the month as Mmm. set gs-log-file-name word gs-log-file-name fr-convert-mmm-mm ( substring date-string 19 22 ) ;; Append the day as dd. set gs-log-file-name word gs-log-file-name ( substring date-string 16 18 ) ;; Append a dash. set gs-log-file-name word gs-log-file-name "_" ;; Append the hour as hh. set gs-log-file-name word gs-log-file-name fr-convert1224 ( substring date-string 0 2 ) ( substring date-string 13 15 ) ;; Append the minute as mm. set gs-log-file-name word gs-log-file-name ( substring date-string 3 5 ) ;; Append the second as ss. set gs-log-file-name word gs-log-file-name ( substring date-string 6 8 ) ;; Append the .txt extension. set gs-log-file-name word gs-log-file-name ".txt" file-open gs-log-file-name file-show "Log File for a EffLab (NetLogo) Model." file-show word "File Name: " gs-log-file-name file-show word "File opened at:" date-and-time file-show "" ;; Send a message directly to the command centre. ifelse ( file-exists? gs-log-file-name ) [ show word gs-log-file-name " opened." ] [ show word gs-log-file-name " not opened." ] end ;;-----------------------------------------------------------------------------| ;; Convert month in text form to digital form. to-report fr-convert-mmm-mm [ mmm ] ;; This routine is to be executed by the observer. ;; It converts a string in the form mmm ( alpha text ) to the form mm ( digit-text ). let mm "00" if( mmm = "Jan" ) [ set mm "01" ] if( mmm = "Feb" ) [ set mm "02" ] if( mmm = "Mar" ) [ set mm "03" ] if( mmm = "Apr" ) [ set mm "04" ] if( mmm = "May" ) [ set mm "05" ] if( mmm = "Jun" ) [ set mm "06" ] if( mmm = "Jul" ) [ set mm "07" ] if( mmm = "Aug" ) [ set mm "08" ] if( mmm = "SeP" ) [ set mm "09" ] if( mmm = "Oct" ) [ set mm "10" ] if( mmm = "Nov" ) [ set mm "11" ] if( mmm = "Dec" ) [ set mm "12" ] report mm end ;;-----------------------------------------------------------------------------| ;; Convert hour in 12 format to 24 hour format. to-report fr-convert1224 [ hh ampm ] ;; This routine is to be executed by the observer. ;; It converts a string in 12 hour format to 24 hour format. let hour read-from-string hh if( ampm = "PM" ) [ set hour ( hour + 12 ) ] let dd ( word "00" hour ) let d2 last dd set dd but-last dd let d1 last dd set dd ( word d1 d2 ) report dd end ;;-----------------------------------------------------------------------------| ;; Close a log file for debug output. to f-close-log-file ;; This routine is to be executed by the observer. let b-filename-exists 0 if ( is-string? gs-log-file-name ) [ if ( file-exists? gs-log-file-name ) [ set b-filename-exists 1 ] ] ifelse( b-filename-exists = 1 ) [ ;; Ensure the file is selected. file-open gs-log-file-name ;; Stanp it. LOG-TO-FILE word "File closed at: " date-and-time ;; Flush the buffers. file-flush ;; Close it. file-close-all ;; Note sent to command centre. show word gs-log-file-name " closed." ;; Revert to dummy name. set gs-log-file-name "dummyname" ] [ if( gs-log-file-name = "dummyname" ) [ show "No log file is open. Cannot close it." ] ] end ;;-----------------------------------------------------------------------------| ;; Select an already opened log file. to f-select-log-file ;; This routine is to be executed by the observer. ifelse ( file-exists? gs-log-file-name ) [ ;; Ensure the file is selected. file-open gs-log-file-name ;; Ensure it is open for writing. LOG-TO-FILE "" LOG-TO-FILE "SELECTED" ] [ show word gs-log-file-name " is not open. Cannot select it." ] end ;;-----------------------------------------------------------------------------| ;; Change the debug mode from on to off, or vice versa. to f-toggle-debug ;; This routine is to be executed by the observer, and is activated by a ;; button. ifelse( gb-debug-on = 1 ) [ ;; Debug is On, turn it Off. ;; Close the file before turning debug logging off. f-close-log-file set gs-debug-status "0 (Off)" ;; This appears in the monitor. set gb-debug-on 0 ;; But this controls the debug feature. ] [ ;; Debug is Off, turn it On. set gs-debug-status "1 (On)" ;; This appears in the monitor. set gb-debug-on 1 ;; But this controls the debug feature. ;; The switches, if needed, are reset manually by the user. ;; Open the log file after turning debug logging on. f-open-log-file ] end ;;-----------------------------------------------------------------------------| ;; 'Show' a string in a debug log. to LOG-TO-FILE [ log-this-string ] ;; This routine may be executed by observer or seeker. ;; It should be invoked as a debug routine only, and would not be used for ;; normal output. It sends output to the debug log file, or, optionally, ;; also to the command centre. ;; gb-debug-on is a global Boolean and has value 1 (true) or 0 (false). if( gb-debug-on = 1 ) [ ;; gb-debug-flow-on is declared as a global Boolean variable, and its value ;; is 0 ( false ) or 1 ( true ) and is set on or off at the beginning of each ;; function ( each do-step ). It is controlled by the chooser that selects 'all' ;; or a specific do-function. ;; ;; When it is 'on' you can assume the debug log file exists and is open for ;; write. if( gb-debug-flow-on = 1 ) [ file-show log-this-string show log-this-string ] ] end ;;-----------------------------------------------------------------------------| ;; This replicates the effect of an 'ASSERTION' in C++ to ASSERT [ error-test error-string error-who ] ;; This routine can be run by observer or seeker. if( error-test = false ) [ show ( word error-test " " error-string " " error-who ) ;; Cause a run-time error and display a message. error ( word "Agent: " error-who " - " error-string ) ] end ;;-----------------------------------------------------------------------------| ;; Check whether the nrg accounts are all valid. to-report frb-nrg-accounts-are-all-valid ;; This routine can be run by the observer. let b-accounts-are-all-valid 1 if( gb-debug-on = 1 ) [ ;; Do the check only if debug is on. let temp-nrg-in-seekers ( sum [nrg] of seekers ) let temp-nrg-in-fruit ( sum [fruit] of patches ) let temp-total-nrg ( temp-nrg-in-seekers + temp-nrg-in-fruit ) if (temp-nrg-in-fruit != g-nrg-in-fruit ) [ set b-accounts-are-all-valid 0 LOG-TO-FILE ( word "F-nrg-check: SB:" temp-nrg-in-fruit ", IS:" g-nrg-in-fruit ) ] if (temp-nrg-in-seekers != g-nrg-in-agents ) [ set b-accounts-are-all-valid 0 LOG-TO-FILE ( word "S-nrg-check: SB:" temp-nrg-in-seekers ", IS:" g-nrg-in-agents ) ] if (temp-total-nrg != g-nrg-in-system ) [ set b-accounts-are-all-valid 0 LOG-TO-FILE ( word "T-nrg-check: SB:" temp-total-nrg ", IS:" g-nrg-in-system ) ] ] report b-accounts-are-all-valid ;; End of frb-nrg-accounts-are-all-valid end ;;-----------------------------------------------------------------------------| ;; Check whether the agents are all valid. to-report frb-agents-are-all-valid ;; This routine can be run by the observer. let b-agents-are-all-valid true if( gb-debug-on = 1 ) [ ;; Do the check only if debug is on. ;; Check the seekers. ask seekers [ if( frb-seeker-is-valid = false ) [ set b-agents-are-all-valid false ] ] ] report b-agents-are-all-valid ;; End of frb-agents-are-all-valid end ;;-----------------------------------------------------------------------------| ;; Check whether a seeker is valid. to-report frb-seeker-is-valid ;; This routine can be run by a seeker. let b-seeker-is-valid true report b-seeker-is-valid ;; End of frb-seeker-is-valid end ;;---------------------------------------------------------------------|-------| ;; Partitions in ABMs. Entropic index in ABMs. GammaLn() function in ABMs. ;;---------------------------------------------------------------------|-------| ;; ;; REFERENCES: The diary notes including (or more recent versions): ;; A. 150527 PPR - Definition of Ei R17.PDF ;; B. 190927 NTF Shannon Vs Boltzmann R4.PDF ;; C. 180214 NTF Entropy and Units of Measure R5.PDF ;; D. 180822 NTF FactLn() and GammaLn() R3.PDF ;; E. 190927 NTF Entropy in a Histogram R4.PDF ;; ;; NOTE: These routines create a partition (i.e. a histogram) independent of ;; the capabilities of the plot controls in the interface tab. ;;---------------------------------------------------------------------|-------| to-report fr-get-energy-entropic-index [ l-data-input ] ;; This routine is to be executed by the observer. ;; show "----------" ;; show "fr-get-energy-entropic-index" let l-energy-partition ( fr-make-energy-partition l-data-input ) ;; show ( word "fr-nrg-ei: l-energy-partition - " l-energy-partition ) let nrg-ei ( fr-calc-energy-entropic-index l-energy-partition ) ;; show ( word "nrg-ei: " nrg-ei ) report nrg-ei ;; End of fr-get-energy-entropic-index end ;;---------------------------------------------------------------------|-------| to-report fr-make-energy-partition [ l-data-input ] ;; This routine is to be executed by the observer. ;; show "----------" ;; show "fr-make-energy-partition" ;; show ( word "l-data-input:" l-data-input ) ;; It creates binned data (a partition) that can be used to plot a histogram. ;; A typical call might look like this: ;; set l-energy-partition ;; ( fr-make-energy-partition ( [energy] in seekers ) ) ;; reports [ l-partition ] ;; Allocate memory. let a-no-of-agents length l-data-input let k-no-of-bins ( floor ( sqrt a-no-of-agents ) ) let ave-data ( mean l-data-input ) let min-data ( ( min l-data-input ) - 0.001 ) let max-data ( ( max l-data-input ) + 0.001 ) let bin-delta 0 ;; show ( word "fmep: ave-data(1): " ave-data ) ;; show ( word "fmep: min-data(1): " min-data ) ;; show ( word "fmep: max-data(1): " max-data ) ;; show ( word "fmep: bin-delta(1): " bin-delta ) ;; show "" ifelse ( ( max-data - min-data ) < k-no-of-bins ) [ ;; Case of all data-points being the same. set min-data ( ave-data - ( k-no-of-bins / 2 ) ) set max-data ( ave-data + ( k-no-of-bins / 2 ) ) set bin-delta ( ( max-data - min-data ) / k-no-of-bins ) ;; show ( word "fmep: min-data(2): " min-data ) ;; show ( word "fmep: max-data(2): " max-data ) ;; show ( word "fmep: bin-delta(2): " bin-delta ) ] ;; Else [ set bin-delta ( ( max-data - min-data ) / k-no-of-bins ) ] ;; Initialize the output histogram with zeros. let l-partition ( n-values k-no-of-bins [0] ) ;; show ( word "fmep: l-partition: " l-partition ) let counter 0 let data-point 0 let bin-no 0 let agents-in-bin 0 let limit ( ( length l-data-input ) - 1 ) ;; show ( word "fmep: limit: " limit ) while [counter <= limit ] [ ;; show ( word "fmep: counter(3): " counter ) set data-point ( item counter l-data-input ) ;; We need to convert this data point into a bin-number for the partition. set bin-no ( ( ( data-point - min-data ) / bin-delta ) ) ;; show ( word "fmep: bin-no(3): " bin-no ) set bin-no ( floor ( ( data-point - min-data ) / bin-delta ) ) ;; show ( word "fmep: bin-no(3): " bin-no ) ;; bin-no is a whole number which determines which bin the agent is counted in. ;; show ( word "fmep: data-point(3): " data-point ) ;; show ( word "fmep: min-data(3): " min-data ) ;; show ( word "fmep: bin-delta(3): " bin-delta ) set agents-in-bin ( item bin-no l-partition ) set agents-in-bin ( agents-in-bin + 1 ) set l-partition ( replace-item bin-no l-partition agents-in-bin ) set counter ( counter + 1 ) ] report l-partition ;; End fr-make-energy-partition. end ;;---------------------------------------------------------------------|-------| to-report fr-calc-energy-entropic-index [ l-partition ] ;; This routine can be called by any agent. ;; show "----------" ;; show "fr-calc-energy-entropic-index" ;; It uses the formula that was developed in a series of diary notes ;; that investigated the most effective formula for calculating ;; entropy in an agent-based model such as "Model I" of EiLab. ;; I hypothesize that it is equally valid in most agent-based models, but ;; that hypothesis needs to be expored and examined and tested. ;; THIS IS AN EXAMPLE OF AN AS-YET UNEXAMINED USAGE. ;; ;; REFERENCES: The diary notes including (or more recent versions): ;; A. 150527 PPR - Definition of Ei R17.PDF ;; B. 190927 NTF Shannon Vs Boltzmann R4.PDF ;; C. 180214 NTF Entropy and Units of Measure R5.PDF ;; D. 180822 NTF FactLn() and GammaLn() R3.PDF ;; E. 190927 NTF Entropy in a Histogram R4.PDF ;; ;; The formula used is equation 30 in the Ref E document. ;; It can be written like this: ;; I = (GammaLn(A+1) - Sum(GammaLn(ai+1))) / (A*Ln(K)) ;; where: ;; K is the number of bins in a histogram of some conserved quantity. ;; A is the number of agents in the model. ;; ai is the count of agents in bin i of the histogram. ;; The expected input is a partition constructed from a list of energy values. ;; The sum of all elements of all bins equals the number of agents. let a-no-of-agents ( sum l-partition ) let k-no-of-bins ( length l-partition ) ;; Note that GammaLn( ) is not native to NetLogo. A version is implemented ;; below. ;; show ( word "l-partition: " l-partition ) let entropic-index fr-gammaln ( 1 + a-no-of-agents ) foreach l-partition [ set entropic-index ( entropic-index - fr-gammaln ( 1 + ? ) ) ] let alpha ( a-no-of-agents / k-no-of-bins ) let boltzmann-max ( fr-gammaln ( 1 + a-no-of-agents ) ) set boltzmann-max ( boltzmann-max - ( k-no-of-bins * fr-gammaln ( alpha + 1 ) ) ) set entropic-index ( entropic-index / boltzmann-max ) report entropic-index ;; End of fr-calc-entropic-index. end ;;---------------------------------------------------------------------|-------| to-report fr-make-pheno-partition ;; This routine is to be executed by the observer. ;; show "----------" ;; show "fr-make-pheno-partition" ;; It creates binned data (a partition) that can be used to plot a histogram. ;; A typical call might look like this: ;; set l-pheno-partition ( fr-make-pheno-partition ) ;; reports [ l-partition ] ;; Allocate memory. let a-no-of-agents count turtles let k-no-of-bins 8 let new-value 0 let l-pheno-list 0 ;; Initialize the output histogram with zeros. let l-partition ( n-values k-no-of-bins [0] ) ;; show ( word "fmpp: l-partition: " l-partition ) ;; One-by-one, calculate the average phenotype value, and insert. let counter 0 let limit ( length l-partition ) while [ counter < limit ] [ set l-pheno-list ( [ item counter c1-pheno ] of seekers ) ;; show ( word "fmpp: l-pheno-list: " l-pheno-list ) set new-value ( mean l-pheno-list ) ;; show ( word "fmpp: new-value: " new-value ) set l-partition ( replace-item counter l-partition new-value ) ;; show ( word "fmpp: l-partition:" l-partition ) set counter ( counter + 1 ) ] ;; show ( word "fmpp: l-partition: " l-partition ) set gl-ave-pheno l-partition report l-partition ;; End fr-make-pheno-partition. end ;;---------------------------------------------------------------------|-------| to-report fr-calc-pheno-entropic-index [ l-partition ] ;; This routine can be called by any agent. ;; show "----------" ;; show "fr-calc-pheno-entropic-index" ;; It uses the formula that was developed in a series of diary notes ;; that investigated the most effective formula for calculating ;; entropy in an agent-based model such as "Model I" of EiLab. ;; I hypothesize that it is equally valid in most agent-based models, but ;; that hypothesis needs to be expored and examined and tested. ;; THIS IS AN EXAMPLE OF AN AS-YET UNEXAMINED USAGE. ;; ;; REFERENCES: The diary notes including (or more recent versions): ;; A. 150527 PPR - Definition of Ei R17.PDF ;; B. 190927 NTF Shannon Vs Boltzmann R4.PDF ;; C. 180214 NTF Entropy and Units of Measure R5.PDF ;; D. 180822 NTF FactLn() and GammaLn() R3.PDF ;; E. 190927 NTF Entropy in a Histogram R4.PDF ;; ;; The formula used is equation 30 in the Ref E document. ;; It can be written like this: ;; I = (GammaLn(A+1) - Sum(GammaLn(ai+1))) / (A*Ln(K)) ;; where: ;; K is the number of bins in a histogram of some conserved quantity. ;; A is the number of agents in the model. ;; ai is the count of agents in bin i of the histogram. ;; The expected input is a partition constructed from a list of energy values. ;; The sum of all elements of all bins equals the number of agents. let a-total ( sum l-partition ) let k-no-of-bins ( length l-partition ) ;; Note that GammaLn( ) is not native to NetLogo. A version is implemented ;; below. ;; show ( word "frcpei: l-partition: " l-partition ) let entropic-index fr-gammaln ( 1 + a-total ) foreach l-partition [ set entropic-index ( entropic-index - fr-gammaln ( 1 + ? ) ) ] let alpha ( a-total / k-no-of-bins ) let boltzmann-max ( fr-gammaln ( 1 + a-total ) ) set boltzmann-max ( boltzmann-max - ( k-no-of-bins * fr-gammaln ( alpha + 1 ) ) ) set entropic-index ( entropic-index / boltzmann-max ) report entropic-index ;; End of fr-calc-pheno-entropic-index. end ;;---------------------------------------------------------------------|-------| to-report fr-gammaln [ input-value ] ;; This routine can be called by any agent. ;; It reproduces a routine found on page 207 of this book: ;; Press, Teukolsky, Vetterling and Flanery (1986) "Numerical Recipes in ;; Fortran", Cambridge, pp 206-209. ;; It uses Lanczos' approximation of the Ln(Gamma(x)) function. ;; Note that, when input-value is an integer, GammaLn(x+1) approximates Ln(x!). ;; When x = 160, the error seems to be about 1 in a billion. That's pretty good. ;; This follows the Fortran code rather closely here. let x input-value let y x let tmp ( x + 5.5 ) ;; Note that here I use ln( ) instead of log( ) as shown in the text. ;; The same problem comes up down below also. With ln() it seems ;; to work correctly. set tmp ( ( ( x + 0.5 ) * ( ln tmp ) ) - tmp ) let ser 1.000000000190015 ;; Next, I have unscrolled the six iterations of the loop. ;; cof(6) is now six different parameters. ;; Iteration 1 set y ( y + 1 ) set ser ( ser + ( 76.18009172947146 / y ) ) ;; Iteration 2 set y ( y + 1 ) set ser ( ser + ( -86.50532032941677 / y ) ) ;; Iteration 3 set y ( y + 1 ) set ser ( ser + ( 24.01409824083091 / y ) ) ;; Iteration 4 set y ( y + 1 ) set ser ( ser + ( -1.231739572450155 / y ) ) ;; Iteration 5 set y ( y + 1 ) set ser ( ser + ( 0.001208650973866179 / y ) ) ;; Iteration 6 set y ( y + 1 ) set ser ( ser + ( -0.000005395239384953 / y ) ) ;; Now, I follow the Fortran code closely again. let stp 2.5066282746310005 ;; Note that here I use ln( ) instead of log( ) as shown in the text. let gammaln ( tmp + ( ln ( stp * ser / x ) ) ) report precision gammaln 15 ;; End of fr-gammaln. end ;;---------------------------------------------------------------------|-------| to-report fr-factorial [ input-value ] ;; This routine can be called by any agent. ;; It uses recursion to calculate n!. let n input-value ifelse ( n > 0 ) [ report n * fr-factorial ( n - 1 ) ] [ report 1 ] ;; End of fr-factorial. end ;;---------------------------------------------------------------------|-------| to-report fr-factorialln [ input-value ] ;; This routine can be called by any agent. ;; It uses the recursive function to calculate n!, then takes the logarithm. let n input-value let factorialln fr-factorial n report precision ( ln factorialln ) 15 ;; End of fr-factorialln. end
There is only one version of this model, created about 5 years ago by Garvin Boyle.
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07 EffLab_V5.07 NL.png | preview | Preview for '07 EffLab_V5.07 NL' | about 5 years ago, by Garvin Boyle | Download |
151224 NTF ICBT and PowEff R8.pdf | Brute-force Examination of All Possible Ways to Combine Income, Costs and Benefits | about 5 years ago, by Garvin Boyle | Download | |
170430 NTF On Efficiency and Energy Grade R6.pdf | Background File. | about 5 years ago, by Garvin Boyle | Download | |
170514 NTF On Efficiencies R3.pdf | Background File. | about 5 years ago, by Garvin Boyle | Download | |
170518 NTF On Efficiency and Growth R3.pdf | Background File. | about 5 years ago, by Garvin Boyle | Download | |
190207 NTF Goldilocks Hypothesis R1.pdf | Background File. | about 5 years ago, by Garvin Boyle | Download | |
190506 NTF Telecon - On Conservation in EffLab R1.pdf | Record of a telephone conversation about EffLab. | about 5 years ago, by Garvin Boyle | Download | |
190927 NTF Entropy in a Histogram R4.pdf | Background information about entropy in ABMs. | about 5 years ago, by Garvin Boyle | Download | |
191007 NTF EffLab V5.07 User Doc R2.pdf | High Level Design Document / User Document. | about 5 years ago, by Garvin Boyle | Download | |
Boyle_ISBPE_2017 Modeling EROI R9.pptx | powerpoint | Presentation made at ISBPE conference in 2017. | about 5 years ago, by Garvin Boyle | Download |
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