the_individual::individual_agent Type Reference

This type describes parameters of the individual agent. More...

Inheritance diagram for the_individual::individual_agent:

Collaboration diagram for the_individual::individual_agent:

Public Member Functions
procedure, public	init => individual_init_random
	Generate a random agent from the genotype. See the_individual::individual_init_random(). More...
procedure, public	create_ind => individual_create_zero
	Generate a new empty agent. See the_individual::individual_create_zero(). More...
procedure, public	dies => individual_agent_set_dead
	Set the individual to be dead. This method overrides the the_genome::individual_genome::dies() method, nullifying all reproductive and neurobiological and behavioural objects. However, this function does not deallocate the individual agent object, this may be a separate destructor function. The dies method is implemented at the following levels of the agent object hierarchy (upper overrides the lower level): More...
procedure, public	get_mortality => individual_get_risk_mortality_individual
	Get the individually-specific mortality risk for the agent. See the_individual::individual_get_risk_mortality_individual(). More...
procedure, public	fitness_calc => individual_preevol_fitness_calc
	Calculate fitness for the pre-evolution phase of the genetic algorithm. Pre-evolution is based on selection for a simple criterion without explicit reproduction etc. The criterion for selection at this phase is set by the integer the_individual::individual_agent::fitness component. See the_individual::individual_preevol_fitness_calc(). More...
Public Member Functions inherited from the_behaviour::architecture_neuro
procedure, public	init_neurobio => neurobio_init_components
	Initialise neuro-biological architecture. See the_behaviour::neurobio_init_components() for implementation. More...
Public Member Functions inherited from the_behaviour::behaviour
procedure, public	init_behaviour => behaviour_whole_agent_init
	The subroutines contained define what the agent really does, i.e. implements the actual behavioural repertoire components. More...
procedure, public	cleanup_behav_history => behaviour_cleanup_history
	Cleanup the behaviour history stack for the agent. See the_behaviour::behaviour_cleanup_history(). More...
procedure, public	deactivate => behaviour_whole_agent_deactivate
	Deactivate all behaviour units that compose the behaviour repertoire of the agent. See the_behaviour::behaviour_whole_agent_deactivate(). More...
procedure, public	behaviour_is => behaviour_get_behaviour_label_executing
	Obtain the label of the currently executing behaviour for the this agent. See the_behaviour::behaviour_get_behaviour_label_executing(). More...
procedure, public	food_item_select => behaviour_select_food_item
	Select the optimal food item among (possibly) several ones that are available in the perception object of the agent. See the_behaviour::behaviour_select_food_item(). More...
procedure, public	consp_select => behaviour_select_conspecific
	Select the optimal conspecific among (possibly) several ones that are available in the perception object of the agent. See the_behaviour::behaviour_select_conspecific(). More...
procedure, public	food_item_select_nearest => behaviour_select_food_item_nearest
	Select the nearest food item among (possibly) several ones that are available in the perception object. See the_behaviour::behaviour_select_food_item_nearest(). More...
procedure, public	consp_select_nearest => behaviour_select_conspecific_nearest
	Select the nearest conspecific among (possibly) several ones that are available in the perception object. See the_behaviour::behaviour_select_conspecific_nearest(). More...
procedure, public	do_eat_food_item => behaviour_do_eat_food_item
	Eat a food item(s) that are found in the perception object. See the_behaviour::behaviour_do_eat_food_item(). More...
procedure, public	do_reproduce => behaviour_do_reproduce
	Reproduce based on the this agent's current state. See the_behaviour::behaviour_do_reproduce(). More...
procedure, public	do_walk => behaviour_do_walk
	Perform a random Gaussian walk to a specific average distance with certain variance (set by the CV). See the_behaviour::behaviour_do_walk(). More...
procedure, public	do_freeze => behaviour_do_freeze
	Perform (execute) the the_behaviour::freeze behaviour. See the_behaviour::behaviour_do_freeze(). More...
procedure, public	do_escape => behaviour_do_escape_dart
	Perform (execute) the the_behaviour::escape_dart behaviour. See the_behaviour::behaviour_do_escape_dart(). More...
procedure, public	do_approach => behaviour_do_approach
	Approach a specific the_environment::spatial class target, i.e. execute the the_behaviour::approach behaviour. See the_behaviour::behaviour_do_approach(). More...
procedure, public	do_migrate => behaviour_do_migrate
	Perform (execute) the the_behaviour::migrate (migration) behaviour. See the_behaviour::behaviour_do_migrate(). More...
procedure, public	migrate_random => behaviour_try_migrate_random
	Perform a simplistic random migration. If the agent is within a specific distance to the target environment, it emigrates there with a specific fixed probability. See the_behaviour::behaviour_try_migrate_random(). More...
procedure, public	do_go_down => behaviour_do_go_down
	Perform (execute) the the_behaviour::go_down_depth (go down) behaviour. See the_behaviour::behaviour_do_go_down(). More...
procedure, public	do_go_up => behaviour_do_go_up
	Perform (execute) the the_behaviour::go_up_depth (go up) behaviour. See the_behaviour::behaviour_do_go_up(). More...
procedure, public	do_behave => behaviour_select_optimal
	Select and execute the optimal behaviour, i.e. the behaviour which minimizes the expected GOS arousal. See the_behaviour::behaviour_select_optimal(). More...
Public Member Functions inherited from the_neurobio::gos_global
procedure, public	init_gos => gos_init_zero_state
	Initialise GOS engine components to a zero state. See the_neurobio::gos_init_zero_state(). More...
procedure, public	dies => gos_agent_set_dead
	Set the individual to be dead. This method overrides the the_genome::individual_genome::dies() method, nullifying all reproductive and neurobiological and behavioural objects. However, this function does not deallocate the individual agent object, this may be a separate destructor function. The dies method is implemented at the following levels of the agent object hierarchy (upper overrides the lower level): More...
procedure, public	gos_find => gos_find_global_state
	Find and set the global organismic state (GOS) based on the various available motivation values. See the_neurobio::gos_find_global_state(). More...
procedure, public	gos_reset => gos_reset_motivations_non_dominant
	Reset all motivation states as NOT dominant with respect to the GOS. See the_neurobio::gos_reset_motivations_non_dominant(). More...
procedure, public	gos_label => gos_global_get_label
	Get the current global organismic state (GOS). See the_neurobio::gos_global_get_label(). More...
procedure, public	arousal => gos_get_arousal_level
	Get the overall level of arousal. Arousal is the current level of the dominant motivation that has brought about the current GOS at the previous time step. See the_neurobio::gos_get_arousal_level(). More...
procedure, public	attention_modulate => gos_attention_modulate_weights
	Modulate the attention weights to suppress all perceptions alternative to the current GOS. This is done using the attention modulation interpolation curve. See the_neurobio::gos_attention_modulate_weights(). More...
Public Member Functions inherited from the_neurobio::appraisal
procedure, public	init_appraisal => appraisal_init_zero_cleanup_all
	Initialise and cleanup all appraisal object components and sub-objects. See the_neurobio::appraisal_init_zero_cleanup_all(). More...
procedure, public	dies => appraisal_agent_set_dead
	Set the individual to be dead. This method overrides the the_genome::individual_genome::dies() method, nullifying all reproductive and neurobiological and behavioural objects. However, this function does not deallocate the individual agent object, this may be a separate destructor function. The dies method is implemented at the following levels of the agent object hierarchy (upper overrides the lower level): More...
procedure, public	motivations_percept_components => appraisal_perceptual_comps_motiv_neur_response_calculate
	Calculate perception components for each of the motivational state component. More...
procedure, public	motivations_primary_calc => appraisal_primary_motivations_calculate
	Calculate primary motivation values of the agent by summing up the perception components of each motivation state. More...
procedure, public	modulation => appraisal_motivation_modulation_non_genetic
	Calculate the final motivation values after modulation. More...
procedure, public	motivations_to_memory => appraisal_add_final_motivations_memory
	Add individual final emotional state components into the emotional memory stack. See the_neurobio::appraisal_add_final_motivations_memory(). More...
procedure, public	probability_reproduction => reproduce_do_probability_reproduction_calc
	Calculate the probability of successful reproduction for this agent in its current state. More...
procedure, public	reproduction_success => reproduction_success_stochast
	Determine a stochastic outcome of this agent reproduction. Returns TRUE if the agent has reproduced successfully. See the_neurobio::reproduction_success_stochast(). More...
Public Member Functions inherited from the_neurobio::perception
procedure, public	feel_light => light_perception_get_object
	Get light perception objects into the individual the_neurobio::perception object layer. See the_neurobio::light_perception_get_object(). More...
procedure, public	feel_depth => depth_perception_get_object
	Get depth perception objects into the individual the_neurobio::perception object layer. See the_neurobio::depth_perception_get_object(). More...
procedure, public	see_food => food_perception_get_visrange_objects
	Get available food items within the visual range of the agent, which the agent can perceive and therefore respond to. Food perception is packaged into the food perception object thisperceive_food for output. See the_neurobio::food_perception_get_visrange_objects(). More...
procedure, public	see_consp => consp_perception_get_visrange_objects
	Get available conspecific perception objects within the visual range of the agent, which the agent can perceive and therefore respond to. See the_neurobio::consp_perception_get_visrange_objects(). More...
procedure, public	see_pred => predator_perception_get_visrange_objects
	Get available predators perception objects within the visual range of the agent, which the agent can perceive and therefore respond to. See the_neurobio::predator_perception_get_visrange_objects(). More...
procedure, public	feel_stomach => stomach_perception_get_object
	Get the stomach capacity perception objects into the individual the_neurobio::perception object layer. See the_neurobio::stomach_perception_get_object(). More...
procedure, public	feel_bodymass => bodymass_perception_get_object
	Get the body mass perception objects into the individual the_neurobio::perception object layer. See the_neurobio::bodymass_perception_get_object(). More...
procedure, public	feel_energy => energy_perception_get_object
	Get the energy reserves perception objects into the individual the_neurobio::perception object layer. See the_neurobio::energy_perception_get_object(). More...
procedure, public	feel_age => age_perception_get_object
	Get the age perception objects into the individual the_neurobio::perception object layer. See the_neurobio::age_perception_get_object(). More...
procedure, public	feel_repfac => repfac_perception_get_object
	Get the reproductive factor perception objects into the individual the_neurobio::perception object layer. See the_neurobio::repfac_perception_get_object(). More...
procedure, public	predation_risk => perception_predation_risk_objective
	Calculate the risk of predation as being perceived / assessed by this agent. See the_neurobio::perception_predation_risk_objective(). More...
procedure, public	perceptions_environ => perception_objects_get_all_environmental
	A single umbrella subroutine to get all environmental perceptions: light, depth. See the_neurobio::perception_objects_get_all_environmental(). More...
procedure, public	perceptions_inner => perception_objects_get_all_inner
	A single umbrella subroutine wrapper to get all inner perceptions: stomach, body mass, energy, age. See the_neurobio::perception_objects_get_all_inner(). More...
procedure, public	perception_to_memory => perception_objects_add_memory_stack
	Add the various perception objects to the memory stack object. This procedure is called after all the perceptual components (light, depth food, conspecifics, predators, etc.) are collected (using set object-bound subroutines) into the perception bundle, so all the values are known and ready to be used. See the_neurobio::perception_objects_add_memory_stack(). More...
procedure, public	init_perception => perception_objects_init_agent
	Initialise all the perception objects for the current agent. Do not fill perception objects with the real data yet. See the_neurobio::perception_objects_init_agent(). More...
procedure, public	destroy_perception => perception_objects_destroy
	Destroy and deallocate all perception objects. See the_neurobio::perception_objects_destroy(). More...
procedure, public	has_food => food_perception_is_seeing_food
	Check if the agent sees any food items within its visual range. See the_neurobio::food_perception_is_seeing_food(). More...
procedure, public	has_consp => consp_perception_is_seeing_conspecifics
	Check if the agent sees any conspecifics within the visual range. See the_neurobio::consp_perception_is_seeing_conspecifics(). More...
procedure, public	has_pred => predator_perception_is_seeing_predators
	Check if the agent sees any predators within the visual range. See the_neurobio::predator_perception_is_seeing_predators(). More...
procedure, public	food_items_below_all => perception_food_items_below_calculate
	Calculate the number of food items in the perception object that are located below the actor agent. See the_neurobio::perception_food_items_below_calculate() More...
procedure, public	food_items_below_horiz => perception_food_items_below_horiz_calculate
	Calculate the number of food items in the perception object that are located below the actor agent within a specific vertical horizon [hz_lower,hz_upper]. The horizon limits are relative, in that they start from the depth position of the this actor agent: [z+hz_lower, z+hz_upper]. See the_neurobio::perception_food_items_below_horiz_calculate(). More...
generic, public	food_items_below => food_items_below_all, food_items_below_horiz
	A generic interface for the two functions calculating the number of food items in the perception object that are located below the actor agent. See perception::food_items_below_all(), perception::food_items_below_horiz(). More...
procedure, public	food_mass_below_all => perception_food_mass_below_calculate
	Calculate the average mass of a food item from all the items in the current perception object that are below the actor agent. See the_neurobio::perception_food_mass_below_calculate(). More...
procedure, public	food_mass_below_horiz => perception_food_mass_below_horiz_calculate
	Calculate the average mass of a food item from all the items in the current perception object that are below the actor agent within a specific vertical horizon [hz_lower,hz_upper]. The horizon limits are relative, in that they start from the depth position of the this actor agent: [z+hz_lower, z+hz_upper]. See the_neurobio::perception_food_mass_below_horiz_calculate(). More...
generic, public	food_mass_below => food_mass_below_all, food_mass_below_horiz
	A generic interface to the two functions that calculating the average mass of food items in the perception object that are located below the actor agent. See perception::food_mass_below_all(), perception::food_mass_below_horiz(). More...
procedure, public	food_items_above_all => perception_food_items_above_calculate
	Calculate the number of food items in the perception object that are located above the actor agent. See the_neurobio::perception_food_items_above_calculate() More...
procedure, public	food_items_above_horiz => perception_food_items_above_horiz_calculate
	Calculate the number of food items in the perception object that are located above the actor agent within a specific vertical horizon [hz_lower,hz_upper]. The horizon limits are relative, in that they start from the depth position of the this actor agent: [z-hz_upper, z-hz_upper]. See the_neurobio::perception_food_items_above_horiz_calculate(). More...
generic, public	food_items_above => food_items_above_all, food_items_above_horiz
	A generic interface for the two functions calculating the number of food itemsin the perception object that are located below the actor agent. See perception::food_items_above_all(), perception::food_items_above_horiz(). More...
procedure, public	food_mass_above_all => perception_food_mass_above_calculate
	Calculate the average mass of a food item from all the items in the current perception object that are above the actor agent. See the_neurobio::perception_food_mass_above_calculate(). More...
procedure, public	food_mass_above_horiz => perception_food_mass_above_horiz_calculate
	Calculate the average mass of a food item from all the items in the current perception object that are above the actor agent within a specific vertical horizon [hz_lower,hz_upper]. The horizon limits are relative, in that they start from the depth position of the this actor agent: [z-hz_upper, z-hz_upper]. See the_neurobio::perception_food_mass_above_horiz_calculate(). More...
generic, public	food_mass_above => food_mass_above_all, food_mass_above_horiz
	A generic interface to the two functions that calculating the average mass of food items in the perception object that are located above the actor agent. See perception::food_mass_above_all(), perception::food_mass_above_horiz(). More...
procedure, public	food_dist_below => perception_food_dist_below_calculate
	Calculate the average distance to all food items in the current perception object that are below the actor agent. See the_neurobio::perception_food_dist_below_calculate(). More...
procedure, public	food_dist_above => perception_food_dist_above_calculate
	Calculate the average distance to all food items in the current perception object that are above the actor agent. See the_neurobio::perception_food_dist_above_calculate(). More...
procedure, public	consp_below_all => perception_conspecifics_below_calculate
	Calculate the number of conspecifics in the perception object that are located below the actor agent. See the_neurobio::perception_conspecifics_below_calculate(). More...
procedure, public	consp_above_all => perception_conspecifics_above_calculate
	Calculate the number of conspecifics in the perception object that are located above the actor agent. See the_neurobio::perception_conspecifics_above_calculate(). More...
procedure, public	consp_below_horiz => perception_conspecifics_below_horiz_calculate
	Calculate the number of conspecifics in the perception object that are located below the actor agent within a specific vertical horizon [hz_lower,hz_upper]. See the_neurobio::perception_conspecifics_below_horiz_calculate(). More...
procedure, public	consp_above_horiz => perception_conspecifics_above_horiz_calculate
	Calculate the number of conspecifics in the perception object that are located above the actor agent within a specific vertical horizon [hz_lower,hz_upper]. See the_neurobio::perception_conspecifics_above_horiz_calculate(). More...
generic, public	consp_below => consp_below_all, consp_below_horiz
	A generic interface to the two functions that calculating the number of conspecifics in the perception object that are located below the actor agent. See perception::consp_below_all(), perception::consp_below_horiz(). More...
generic, public	consp_above => consp_above_all, consp_above_horiz
	A generic interface to the two functions that calculating the number of conspecifics in the perception object that are located above the actor agent. See perception::consp_above_all(), perception::consp_above_horiz(). More...
procedure, public	consp_dist_below => perception_consp_dist_below_calculate
	Calculate the average distance to all conspecifics in the current perception object that are below the actor agent. See the_neurobio::perception_consp_dist_below_calculate(). More...
procedure, public	consp_dist_above => perception_consp_dist_above_calculate
	Calculate the average distance to all conspecifics in the current perception object that are above the actor agent. See the_neurobio::perception_consp_dist_above_calculate(). More...
procedure, public	pred_below_all => perception_predator_below_calculate
	Calculate the number of predators in the perception object that are located below the actor agent. See the_neurobio::perception_predator_below_calculate(). More...
procedure, public	pred_above_all => perception_predator_above_calculate
	Calculate the number of predators in the perception object that are located above the actor agent. See the_neurobio::perception_predator_above_calculate(). More...
procedure, public	pred_below_horiz => perception_predator_below_horiz_calculate
	Calculate the number of predators in the perception object that are located below the actor agent within a specific vertical horizon [hz_lower,hz_upper]. See the_neurobio::perception_predator_below_horiz_calculate. More...
procedure, public	pred_above_horiz => perception_predator_above_horiz_calculate
	Calculate the number of predators in the perception object that are located above the actor agent within a specific vertical horizon [hz_lower,hz_upper]. See the_neurobio::perception_predator_above_horiz_calculate. More...
generic, public	pred_below => pred_below_all, pred_below_horiz
	A generic interface to the two functions that calculating the number of predators in the perception object that are located below the actor agent. See perception::pred_below_all(), perception::pred_below_horiz(). More...
generic, public	pred_above => pred_above_all, pred_above_horiz
	A generic interface to the two functions that calculating the number of predators in the perception object that are located above the actor agent. See perception::pred_above_all(), perception::pred_above_horiz(). More...
procedure, public	pred_dist_below => perception_predator_dist_below_calculate
	Calculate the average distance to all predators in the current perception object that are below the actor agent. See the_neurobio::perception_predator_dist_below_calculate(). More...
procedure, public	pred_dist_above => perception_predator_dist_above_calculate
	Calculate the average distance to all predators in the current perception object that are above the actor agent. See the_neurobio::perception_predator_dist_above_calculate(). More...
procedure, public	risk_pred_s => predator_capture_probability_calculate_spatobj
	Calculate the probability of attack and capture of the this agent by the predator this_predator. This probability is a function of the distance between the predator and the agent and is calculated by the predator-class-bound procedure the_environment::predator::risk_fish(). More...
procedure, public	risk_pred_p => predator_capture_probability_calculate_pred
	Calculate the probability of attack and capture of the this agent by the predator this_predator. This probability is a function of the distance between the predator and the agent and is calculated by the predator-class-bound procedure the_environment::predator::risk_fish(). More...
procedure, public	risk_pred_w => predation_capture_probability_risk_wrapper
	Calculate the overall direct predation risk for the agent, i.e. the probability of attack and capture by the nearest predator. See the_neurobio::predation_capture_probability_risk_wrapper(). More...
generic, public	risk_pred => risk_pred_s, risk_pred_p, risk_pred_w
	A single generic interface for the calculation of the probability of attack and capture of the this agent by a predator. See the_neurobio::predator_capture_probability_calculate_spatobj(), the_neurobio::predator_capture_probability_calculate_pred() and the_neurobio::predation_capture_probability_risk_wrapper(). More...
procedure, public	food_probability_capture_subjective => food_perception_probability_capture_memory_object
	Calculate the probability of capture of a subjective representation of food item based on the data from the perceptual memory stack. See the_neurobio::food_perception_probability_capture_memory_object(). More...
Public Member Functions inherited from the_body::reproduction
procedure, public	init_reproduction => reproduction_init_zero
	Init reproduction class. See the_body::reproduction_init_zero(). More...
procedure, public	is_ready_reproduce => reproduction_ready_steroid_hormones_exceed
	Determine if the agent's hormonal system is ready for reproduction See the_body::reproduction_ready_steroid_hormones_exceed(). More...
procedure, public	get_reproductions => reproduction_n_reproductions_get
	Get the number of reproductions for this agent. See the_body::reproduction_n_reproductions_get(). More...
procedure, public	reproductions_set => reproduction_n_reproductions_set
	Set the number of reproductions for the agent. See the_body::reproduction_n_reproductions_set(). More...
procedure, public	get_offspring => reproduction_n_offspring_get
	Get the number of offspring for this agent for its lifespan. See the_body::reproduction_n_offspring_get(). More...
procedure, public	offspring_set => reproduction_n_offspring_set
	Set the number of offspring this agent had during its lifespan. See the_body::reproduction_n_offspring_set(). More...
procedure, public	reproductions_increment => reproduction_n_increment
	Increment the number of reproductions and offspring for the agent. See the_body::reproduction_n_increment(). More...
procedure, public	offspring_number => reproduction_n_offspring_calc
	Calculate the number of offspring per a single reproduction. See the_body::reproduction_n_offspring_calc(). More...
procedure, public	offspring_mass => reproduction_mass_offspring_calc
	Calculate the total mass of all offspring per single reproduction. See the_body::reproduction_mass_offspring_calc(). More...
procedure, public	reproduction_cost => reproduction_cost_energy_dynamic
	Calculate the energetic cost of reproduction. More...
procedure, public	reproduction_cost_unsuccess => reproduction_cost_unsuccessful_calc
	Calculate the costs of unsuccessful reproduction. This is calculated as a fraction of the normal cost of reproduction returned by the function reproduction::reproduction_cost(). See the_body::reproduction_cost_unsuccessful_calc(). More...
Public Member Functions inherited from the_body::condition
procedure, public	init_condition => condition_init_genotype
	Initialise the individual body condition object based on the genome values. See the_body::condition_init_genotype() More...
procedure, public	mortality_birth => birth_mortality_enforce_init_fixed_debug
	This procedure enforces selective mortality of agents at birth. See the_body::birth_mortality_enforce_init_fixed_debug(). More...
procedure, public	body_history_clean => condition_clean_history
	Cleanup the history stack of the body length and mass. See the_body::condition_clean_history() More...
procedure, public	get_age => condition_age_get
	Get current age. See the_body::condition_age_get() More...
procedure, public	age_reset => condition_age_reset_zero
	Reset the age of the agent to zero. See the_body::condition_age_reset_zero(). More...
procedure, public	get_energy => condition_energy_current_get
	Get current energy reserves. See the_body::condition_energy_current_get() More...
procedure, public	get_energy_max => condition_energy_maximum_get
	Get historical maximum of energy reserves. See the_body::condition_energy_maximum_get() More...
procedure, public	get_length => condition_body_length_get
	Get current body length. See the_body::condition_body_length_get() More...
generic, public	length => get_length
	Generic interface (alias) for get_length. More...
procedure, public	get_control_unselected => condition_control_unsel_get
	Get current value of the control unselected trait. See the_body:condition_control_unsel_get:() More...
procedure, public	get_mass => condition_body_mass_get
	Get current body mass. See the_body::condition_body_mass_get() More...
generic, public	mass => get_mass
	Generic interface to get_mass. More...
procedure, public	get_energ_birth => condition_energy_birth_get
	Get historical record of energy reserves at birth. See the_body::condition_energy_birth_get(). More...
procedure, public	get_length_birth => condition_body_length_birth_get
	Get historical record of body length at birth. See the_body::condition_body_length_birth_get() More...
procedure, public	get_mass_birth => condition_body_mass_birth_get
	Get historical record of body mass at birth. See the_body::condition_body_mass_birth_get() More...
procedure, public	get_mass_max => condition_body_mass_max_get
	Get historcal maximum for body mass. See the_body::condition_body_mass_max_get() More...
procedure, public	get_smr => condition_smr_get
	Get current smr. See the_body::condition_smr_get() More...
procedure, public	get_stom_content => condition_stomach_content_get
	Get current stomach content. See the_body::condition_stomach_content_get() More...
procedure, public	age_increment => condition_age_increment
	Increment the age of the agent by one. See the_body::condition_age_increment(). More...
procedure, public	set_mass => condition_body_mass_set_update_hist
	Set body mass optionally updating the history stack. See the_body::condition_body_mass_set_update_hist() More...
procedure, public	set_length => condition_body_length_set_update_hist
	Set body length optionally updating the history stack. See the_body::condition_body_length_set_update_hist() More...
procedure, public	visibility => condition_agent_visibility_visual_range
	Calculate the visibility range of this agent. Visibility depends on the size of the agent, ambient illumination and agent contrast. Visibility is the distance from which this agent can be seen by a visual object (e.g. predator or conspecific). See the_body::condition_agent_visibility_visual_range. More...
procedure, public	food_proc_cost_v => body_mass_processing_cost_calc_v
	Calculate the basic processing cost of catching a food item with the mass food_gain. Vector-based procedure. See the_body::body_mass_processing_cost_calc_v() More...
procedure, public	food_proc_cost_o => body_mass_processing_cost_calc_o
	Calculate the basic processing cost of catching a food item with the mass food_gain. Object-based procedure. See the_body::body_mass_processing_cost_calc_o() More...
generic, public	food_process_cost => food_proc_cost_v, food_proc_cost_o
	Generic interface to the procedures calculating the basic processing cost of catching a food item. More...
procedure, public	food_fitt_v => stomach_content_food_gain_fitting_v
	Calculate the value of possible food gain as fitting into the agent's stomach (or full gain if the food item fits wholly). Vector-based. See the_body::stomach_content_food_gain_fitting_v() More...
procedure, public	food_fitt_o => stomach_content_food_gain_fitting_o
	Calculate the value of possible food gain as fitting into the agent's stomach (or full gain if the food item fits wholly). Object-based. See the_body::stomach_content_food_gain_fitting_o() More...
generic, public	food_fitting => food_fitt_v, food_fitt_o
	Generic interface to procedures that calculate the value of possible food gain as fitting into the agent's stomach (or full gain if the food item fits wholly). See the_body::stomach_content_food_gain_fitting_v() and the_body::stomach_content_food_gain_fitting_o(). More...
procedure, public	food_surpl_v => stomach_content_food_gain_non_fit_v
	Calculate extra food surplus mass non fitting into the stomach of the agent. Vector-based. See the_body::stomach_content_food_gain_non_fit_v() More...
procedure, public	food_surpl_o => stomach_content_food_gain_non_fit_o
	Calculate extra food surplus mass non fitting into the stomach of the agent. Object-based. See the_body::stomach_content_food_gain_non_fit_o() More...
generic, public	food_surplus => food_surpl_v, food_surpl_o
	Generic interface to procedures that calculate extra food surplus mass non fitting into the stomach of the agent. More...
procedure, public	mass_grow => body_mass_grow_do_calculate
	Do grow body mass based on food gain from a single food item adjusted for cost etc. See the_body::body_mass_grow_do_calculate() More...
procedure, public	stomach_increment => stomach_content_get_increment
	Do increment stomach contents with adjusted (fitted) value. See the_body::stomach_content_get_increment() More...
procedure, public	cost_factor_food_smr => body_mass_food_processing_cost_factor_smr
	The fraction of the cost of the processing of the food item(s) depending on the agent SMR. It is scaled in terms of the ratio of the food item mass to the agent mass. See the_body::body_mass_food_processing_cost_factor_smr() More...
procedure, public	cost_swim => condition_cost_swimming_burst
	The cost of swimming of a specific distance in terms of body mass loss. See the_body::condition_cost_swimming_burst() More...
procedure, public	cost_swim_std => cost_swimming_standard
	The standard cost of swimming is a diagnostic function that shows the cost, in units of the body mass, incurred if the agent passes a distance equal to commondata::lifespan units of its body length. See the_body::cost_swimming_standard(). More...
procedure, public	energy_update => condition_energy_update_after_growth
	Update the energy reserves of the agent based on its current mass and length. See the_body::condition_energy_update_after_growth() More...
procedure, public	starved_death => body_mass_is_starvation_check
	Check if the body mass is smaller than the birth body mass or structural body mass. See the_body::body_mass_is_starvation_check() More...
procedure, public	living_cost => body_mass_calculate_cost_living_step
	Calculate the cost of living for a single model step. See the_body::body_mass_calculate_cost_living_step() More...
procedure, public	subtract_living_cost => body_mass_adjust_living_cost_step
	Adjust the body mass at the end of the model step against the cost of living. See the_body::body_mass_adjust_living_cost_step() More...
procedure, public	len_incr => body_len_grow_calculate_increment_step
	Calculate body length increment. See the_body::body_len_grow_calculate_increment_step() More...
procedure, public	len_grow => body_len_grow_do_calculate_step
	Do linear growth for one model step based on the above increment function. See the_body::body_len_grow_do_calculate_step() More...
procedure, public	stomach_empify => stomach_content_mass_emptify_step
	Do digestion. Stomach contents S(t) is emptied by a constant fraction each time step. See details in the stomach_content_mass_emptify_step function call. See the_body::stomach_content_mass_emptify_step() More...
procedure, public	sex_steroids_update => sex_steroids_update_increment
	Update the level of the sex steroids. Sex steroids are incremented each time step of the model. See the_body::sex_steroids_update_increment() More...
Public Member Functions inherited from the_hormones::hormones
procedure, public	init_hormones => hormones_init_genotype
	Initialise hormone levels based on the genome value. See the_hormones::hormones_init_genotype() More...
procedure, public	hormone_history_clean => hormones_clean_history_stack
	Clean the history stack of hormones. See the_hormones::hormones_clean_history_stack() More...
procedure, public	growhorm_get => growhorm_get_level
	Get the value of thyroid. See the_hormones::growhorm_get_level() More...
procedure, public	growhorm_set => growhorm_set_level
	Set the value of thyroid. See the_hormones::growhorm_set_level() More...
procedure, public	thyroid_get => thyroid_get_level
	Get the value of thyroid. See the_hormones::thyroid_get_level() More...
procedure, public	thyroid_set => thyroid_set_level
	Set the value of thyroid. See the_hormones::thyroid_set_level() More...
procedure, public	adrenaline_get => adrenaline_get_level
	Get the value of adrenaline. See the_hormones::adrenaline_get_level() More...
procedure, public	adrenaline_set => adrenaline_set_level
	Set the value of adrenaline. See the_hormones::adrenaline_set_level() More...
procedure, public	cortisol_get => cortisol_get_level
	Get the value of cortisol. See the_hormones::cortisol_get_level() More...
procedure, public	cortisol_set => cortisol_set_level
	Set the value of cortisol. See the_hormones::cortisol_set_level() More...
procedure, public	testosterone_get => testosterone_get_level
	Get the value of testosterone. See the_hormones::testosterone_get_level() More...
procedure, public	testosterone_set => testosterone_set_level
	Set the value of testosterone. See the_hormones::testosterone_set_level() More...
procedure, public	estrogen_get => estrogen_get_level
	Get the value of estrogen. See the_hormones::estrogen_get_level() More...
procedure, public	estrogen_set => estrogen_set_level
	Set the value of estrogen. See the_hormones::estrogen_set_level() More...
procedure, public	testosterone_base_get => testosteron_baseline_get_level
	Get the value of testosterone baseline. See the_hormones::testosteron_baseline_get_level() More...
procedure, public	estrogen_base_get => estrogen_baseline_get_level
	Get the value of estrogen baseline. See the_hormones::estrogen_baseline_get_level() More...
procedure, public	reproductive_factor => hormones_reproductive_factor_calc
	Calculate the reproductive factor. Reproductive factor is defined as the current level of the_hormones::testosterone_level in males and the_hormones::estrogen_level in females. See the_hormones::hormones_reproductive_factor_calc(). More...
procedure, public	hormones_to_history => hormones_update_history
	Update the sex steroid hormones history stack from the current level See the_hormones::hormones_update_history(). More...
Public Member Functions inherited from the_genome::individual_genome
procedure, public	init_genome => genome_init_random
	Initialise the genome at random, and set sex as determined by the sex determination locus. See the_genome::genome_init_random() More...
procedure, public	create_genome => genome_create_zero
	Create a new empty genome, and set sex as determined by the sex determination locus. Genome values are from parents using inherit functions. See the_genome::genome_create_zero() More...
procedure, public	label => genome_label_set
	Label genome. If label is not provided, make a random string. More...
procedure, public	individ_label => genome_label_get
	Accessor function to get the genome label. The label is a kind of a (random) text string name of the genome and the individual agent. More...
procedure, public	sex_init => genome_sex_determine_init
	Sex has a separate status from all other genetically determined traits. It is initialised here, at the genotype level of the class hierarchy. See the_genome::genome_sex_determine_init() More...
procedure, public	is_male => genome_get_sex_is_male
	Get the logical sex ID of the genome object component. See the_genome::genome_get_sex_is_male() More...
procedure, public	is_female => genome_get_sex_is_female
	Get the logical sex ID of the genome object component. See the_genome::genome_get_sex_is_female() More...
procedure, public	label_sex => genome_get_sex_label
	Get the descriptive sex label: male or female. See the_genome::genome_get_sex_label() More...
procedure, public	trait_init => trait_init_genotype_gamma2gene
	Init a trait from the genotype, trait can be any object in any of the up level class hierarchy that is determined from the boolean genotype x phenotype matrix. See the_genome::trait_init_genotype_gamma2gene() More...
procedure, public	trait_set => trait_set_genotype_gamma2gene
	Set an individual trait of the agent that depends on the genotype. This can be any trait upwards in the class hierarchy. See the_genome::trait_set_genotype_gamma2gene() More...
generic, public	neuro_resp => trait_init, trait_set
	Generic interface to the neuronal response function. See the_genome::trait_init_genotype_gamma2gene() and the_genome::trait_set_genotype_gamma2gene(). More...
procedure, public	trait_init_linear => trait_init_linear_sum_additive_comps_2genes_r
	Init a trait from the genotype, trait can be any object in any of the up level class hierarchy that is determined from the boolean genotype x phenotype matrix. Note that this method is based on simple linear rescale rather than neuronal response. See the_genome::trait_init_linear_sum_additive_comps_2genes_r() More...
procedure, public	trait_set_linear => trait_set_linear_sum_additive_comps_2genes_r
	Set an individual trait of the agent that depends on the genotype. This can be any trait upwards in the class hierarchy. Note that this method is based on simple linear rescale rather than neuronal response. See the_genome::trait_set_linear_sum_additive_comps_2genes_r() More...
generic, public	linear_g2p => trait_init_linear, trait_set_linear
	Generic interface to the simple linear genotype to phenotype transformation functions. See the_genome::trait_init_linear_sum_additive_comps_2genes_r() and the_genome::trait_set_linear_sum_additive_comps_2genes_r(). More...
procedure, public	lives => genome_individual_set_alive
	Set the individual to be alive, normally this function is used after init or birth. See the_genome::genome_individual_set_alive() More...
procedure, public	dies => genome_individual_set_dead
	Set the individual to be dead. Note that this function does not deallocate the individual agent object, this may be a separate destructor function. The dies method is implemented at the following levels of the agent object hierarchy (upper overrides the lower level): More...
procedure, public	set_dead => genome_individual_set_dead
	Set the individual to be dead. Note that in this class this method implementation points to the same procedure as the_genome::individual_genome::dies(). However thedies` method is overriden upwards in the class hierarchy to also nullify neurobiological and behavioural objects. So this method should be only called in procedures that specifically implemented override of the dies method: More...
procedure, public	is_alive => genome_individual_check_alive
	Check if the individual is alive. See the_genome::genome_individual_check_alive() More...
procedure, public	is_dead => genome_individual_check_dead
	Check if the individual is dead (the opposite of is_alive). See the_genome::genome_individual_check_dead() More...
procedure, public	recombine_random => genome_individual_recombine_homol_full_rand_alleles
	Internal genetic recombination backend, exchange individual alleles between homologous chromosomes in mother and father genomes to form the this (offspring) genome. Fully random recombination. See the_genome::genome_individual_recombine_homol_full_rand_alleles(). More...
procedure, public	recombine_partial => genome_individual_recombine_homol_part_rand_alleles
	Internal genetic recombination backend, exchange individual alleles between homologous chromosomes in mother and father genomes to form the this (offspring) genome. Partially random recombination. See the_genome::genome_individual_recombine_homol_part_rand_alleles(). More...
procedure, public	crossover => genome_individual_crossover_homol_fix
	Internal fixed genetic crossover backend, exchange blocks of alleles between homologous chromosomes in mother and father genomes to form the this (offspring) genome. See the_genome::genome_individual_crossover_homol_fix(). More...
procedure, public	mutate => genome_mutate_wrapper
	Perform a probabilistic random mutation(s) on the individual genome. This is a high level wrapper to build mutations from various components. See the_genome::genome_mutate_wrapper(). More...
Public Member Functions inherited from the_environment::spatial_moving
procedure, public	create => spatial_moving_create_3d
	Create a new spatial moving object. Initially it has no position, all coordinate values are commondata::missing or commondata::invalid for real type coordinates. See the_environment::spatial_moving_create_3d() More...
procedure, public	position => spatial_moving_fix_position_3d_o
	Place spatial movable object into a 3D space, define the object's current coordinates, but first save previous coordinates. Object-based. See the_environment::spatial_moving_fix_position_3d_o() More...
procedure, public	repeat_position => spatial_moving_repeat_position_history_3d
	Repeat/re-save the current position into the positional history stack. See the_environment::spatial_moving_repeat_position_history_3d(). More...
procedure, public	position_v => spatial_moving_fix_position_3d_v
	Place spatial movable object into a 3D space, define the object's current coordinates, but first save previous coordinates. Vector-based. See the_environment::spatial_moving_fix_position_3d_v() More...
procedure, public	spatial_history_clean => spatial_moving_clean_hstory_3d
	Create a new empty history of positions for spatial moving object. Assign all values to the commondata::missing value code. See the_environment::spatial_moving_clean_hstory_3d() More...
procedure, public	way => spatial_moving_self_distance_3d
	Calculate the Euclidean distance between the current and previous position of a single spatial movable object. Optionally, it also calculates the total distance traversed during the from_history points from the history stack along with the distance from the current position and the last historical value. See the_environment::spatial_moving_self_distance_3d(). More...
procedure, public	go_up => spatial_moving_go_up
	The spatial moving object ascends, goes up the depth with specific fixed step size. See the_environment::spatial_moving_go_up(). More...
procedure, public	go_down => spatial_moving_go_down
	The spatial moving object decends, goes down the depth with specific fixed step size. See the_environment::spatial_moving_go_down(). More...
procedure, public	rwalk3d => spatial_moving_randomwalk_gaussian_step_3d
	Implements an optionally environment-restricted Gaussian random walk in 3D. See the_environment::spatial_moving_randomwalk_gaussian_step_3d(). More...
procedure, public	rwalk25d =>spatial_moving_randomwalk_gaussian_step_25d
	Implements an optionally environment-restricted Gaussian random walk in a "2.5 dimensions", i.e. 2D x y with separate walk parameters for the third depth dimension. See the_environment::spatial_moving_randomwalk_gaussian_step_25d(). More...
generic, public	rwalk => rwalk3d, rwalk25d
	Implements an optionally environment-restricted Gaussian random walk. Generic interface for 3D and 3.5D moves. See the_environment::spatial_moving_randomwalk_gaussian_step_3d() and the_environment::spatial_moving_randomwalk_gaussian_step_25d(). More...
procedure, public	corwalk3d => spatial_moving_corwalk_gaussian_step_3d
	Implements an optionally environment-restricted correlated directional Gaussian random walk in 3D towards (or away of) an the_environment::spatial class target object. See the_environment::spatial_moving_corwalk_gaussian_step_3d(). More...
procedure, public	corwalk25d =>spatial_moving_corwalk_gaussian_step_25d
	Implements an optionally environment-restricted correlated directional Gaussian random walk in 3D towards (or away of) an the_environment::spatial class target object. See the_environment::spatial_moving_corwalk_gaussian_step_25d(). More...
generic, public	corwalk => corwalk3d, corwalk25d
	Implements an optionally environment-restricted correlated directional Gaussian random walk. corwalk is a generic interface for 3D and "2.5"D moves. For details see the 3d version and a version with separate X,Y and depth random parameters. More...
procedure, public	dirwalk3d => spatial_moving_dirwalk_gaussian_step_3d
	Implements an optionally environment-restricted directional Gaussian random walk in 3D towards a target the_environment::spatial object. See the_environment::spatial_moving_dirwalk_gaussian_step_3d() More...
procedure, public	dirwalk25d =>spatial_moving_dirwalk_gaussian_step_25d
	Implements an optionally environment-restricted directional Gaussian random walk in "2.5"D towards a target object. i.e. 2D x y with separate walk parameters for the third depth dimension. See the_environment::spatial_moving_dirwalk_gaussian_step_25d() More...
generic, public	dirwalk => dirwalk3d, dirwalk25d
	Implements an optionally environment-restricted directional Gaussian random walk. Generic interface for 3D and "2.5"D moves. More...
Public Member Functions inherited from the_environment::spatial
procedure, public	create => spatial_create_empty
	Create an empty spatial object. More...
procedure, public	position => spatial_fix_position_3d_o
	Place spatial object into a 3D space, define the object's current coordinates. Object-based procedure. See the_environment::spatial_fix_position_3d_o() More...
procedure, public	position_v => spatial_fix_position_3d_s
	Place spatial object into a 3D space, define the object's current coordinates. Vector-based procedure. See the_environment::spatial_fix_position_3d_s() More...
procedure, public	missing => spatial_make_missing
	Assign all MISSING coordinates to the SPATIAL object. See the_environment::spatial_make_missing() More...
procedure, public	distance => spatial_distance_3d
	Calculate the Euclidean distance between two spatial objects. See the_environment::spatial_distance_3d() More...
procedure, public	distance_segment2d => geo_poly2d_dist_point_to_section
	Calculates the minimum distance from a the_environment::spatial class object to a line segment delimited by two the_environment::spatial endpoints in the 2D XY plane (the depth coordinate is ignored). See the_environment::geo_poly2d_dist_point_to_section(). More...
procedure, public	distance_segment => geo_poly3d_dist_point_to_section
	Calculates the minimum distance from a the_environment::spatial class object to a line segment delimited by two the_environment::spatial class endpoints in the 3D XY space. See the_environment::geo_poly3d_dist_point_to_section(). More...
procedure, public	way => spatial_self_distance_3d
	Calculate the Euclidean distance between the current and previous position of a single spatial object. See the_environment::spatial_self_distance_3d() More...
procedure, public	is_within => spatial_check_located_within_3d
	Function to check if this spatial object is located within an area set by an environmental object See the_environment::spatial_check_located_within_3d() More...
procedure, public	find_environment => spatial_get_environment_in_pos
	Identify in which environment from the input list this spatial agent is currently in. See the_environment::spatial_get_environment_in_pos(). More...
procedure, public	is_below => spatial_check_located_below
	Logical function to check if the argument spatial object(s) is(are) located below this spatial object. See the_environment::spatial_check_located_below() More...
procedure, public	is_above => spatial_check_located_above
	Logical function to check if the argument spatial object(s) is(are) located above this spatial object. See the_environment::spatial_check_located_above() More...
procedure, public	nearest => spatial_get_nearest_object
	Determine the nearest spatial object to this spatial object among an array of other spatial objects. See the_environment::spatial_get_nearest_object() More...
procedure, public	nearest_num => spatial_get_nearest_id
	Determine the nearest spatial object to this spatial object among an array of other spatial objects. See the_environment::spatial_get_nearest_id() More...
procedure, public	neighbours => spatial_neighbours_distances
	Calculate the distances between this spatial object and an array of its neighbours. Optionally output the distances, sorting index vector and rankings vector for each of these neighbours. Optionally do only partial indexing, up to the order rank_max for computational speed. See the_environment::spatial_neighbours_distances() More...
procedure, public	now_o => spatial_get_current_pos_3d_o
	Get the current spatial position of a SPATIAL object. Object-based. See the_environment::spatial_get_current_pos_3d_o() More...
procedure, public	now_v => spatial_get_current_pos_3d_v
	Get the current spatial position of a SPATIAL object. Vector-based. See the_environment::spatial_get_current_pos_3d_v() More...
generic, public	location => now_o, now_v
	Get the current spatial position of a SPATIAL object. Generic interface/alias. More...
generic, public	now => now_o, now_v
	Get the current spatial position of a SPATIAL object. Generic interface/alias. More...
procedure, public	xpos => spatial_get_current_pos_x_3d
	Get the current X position of a SPATIAL object. See the_environment::spatial_get_current_pos_x_3d() More...
procedure, public	ypos => spatial_get_current_pos_y_3d
	Get the current Y position of a SPATIAL object. See the_environment::spatial_get_current_pos_y_3d() More...
procedure, public	dpos => spatial_get_current_pos_d_3d
	Get the current Z (depth) position of a SPATIAL object. See the_environment::spatial_get_current_pos_d_3d() More...
procedure, public	illumination => spatial_calc_irradiance_at_depth
	Calculate the illumination (background irradiance) at the depth of the spatial object at an arbitrary time step of the model. See the_environment::spatial_calc_irradiance_at_depth() More...
procedure, public	visibility => spatial_visibility_visual_range_cm
	Calculate the visibility range of a spatial object. Wrapper to the visual_range function. This function calculates the distance from which this object can be seen by a visual object (e.g. predator or prey). See the_environment::spatial_visibility_visual_range_cm(). More...

Public Attributes
integer	fitness
	fitness is a fixed criterion for the evolution at the starting 'pre-evolution' phase of the genetic algorithm. More...
real(srp)	ind_mortality
	Individually specific mortality risk for various undefined or defined reasons, such as immune status. Note that this risk is not linked to the predation or habitat-specific factors. The latter two causes are treated separately. More...
Public Attributes inherited from the_behaviour::behaviour
type(eat_food)	eat
	Parameters that set the parameters of the behaviours and their expectancies (perceived consequences). More...
type(reproduce)	reproduce
type(walk_random)	walk_random
type(freeze)	freeze
type(escape_dart)	escape_dart
type(approach)	approach_spatial
type(approach_conspec)	approach_conspec
type(migrate)	migrate
type(go_down_depth)	depth_down
type(go_up_depth)	depth_up
type(debug_base)	debug_base
character(len=label_length)	behaviour_label
	Overall label of the behaviour being executed. It is used only for outputs. More...
character(len=label_length), dimension(history_size_behaviours)	history_behave
integer	n_eats_all_indicator
	An indicator showing the cumulative count of the_behaviour::eat_food attempts (notwithstanding successful or failures). More...
integer	n_eaten_indicator
	An indicator showing the cumulative count of the food items eaten. More...
real(srp)	mass_eaten_indicator
	An indicator showing the cumulative mass of the food items eaten. More...
Public Attributes inherited from the_neurobio::gos_global
character(len=label_length)	gos_main
	Current global organismic state (GOS). Obtained from the GOS-specific emotional state %label data component. More...
real(srp)	gos_arousal
	This is the current value of the dominant motivation. More...
integer	gos_repeated
	Integer number of the same GOS repetition, e.g. if GOS is the same the second time, gets 2 etc. Needed to asymptotically reduce GOS arousal when it is repeated, so smaller stimuli could overtake control. More...
Public Attributes inherited from the_neurobio::appraisal
type(motivation)	motivations
	The appraisal component plugs-in the different motivational/emotional objects. More...
type(memory_emotional)	memory_motivations
	The emotional state memory stack object. More...
Public Attributes inherited from the_neurobio::perception
type(percept_light)	perceive_light
type(percept_light)	perception
type(percept_light)	of
type(percept_light)	light
type(percept_depth)	perceive_depth
type(percept_depth)	perception
type(percept_depth)	of
type(percept_depth)	depth
type(percept_food)	perceive_food
type(percept_food)	perception
type(percept_food)	of
type(percept_food)	food
type(percept_conspecifics)	perceive_consp
type(percept_conspecifics)	conspecifics
type(percept_conspecifics)	perception
type(percept_predator)	perceive_predator
type(percept_predator)	perceive
type(percept_predator)	predator
type(percept_stomach)	perceive_stomach
type(percept_stomach)	perception
type(percept_stomach)	for
type(percept_stomach)	stomach
type(percept_body_mass)	perceive_body_mass
type(percept_body_mass)	perception
type(percept_body_mass)	for
type(percept_body_mass)	bodymass
type(percept_energy)	perceive_energy
type(percept_energy)	percept
type(percept_energy)	for
type(percept_energy)	energy
type(percept_age)	perceive_age
type(percept_age)	percept
type(percept_age)	of
type(percept_age)	age
type(percept_reprfact)	perceive_reprfac
type(percept_reprfact)	percept
type(percept_reprfact)	of
type(percept_reprfact)	repr
type(percept_reprfact)	factor
type(memory_perceptual)	memory_stack
type(memory_perceptual)	note
type(memory_perceptual)	memory
type(memory_perceptual)	object
Public Attributes inherited from the_body::reproduction
integer	n_reproductions
	Total number of reproductions during the lifespan. More...
integer	n_offspring
	Total number of offspring reproduced during the lifespan. More...
Public Attributes inherited from the_body::condition
integer	age
	The age of the agent in units of the integer time steps. More...
real(srp)	energy_current
	Current energy reserves, initialised non-genetically, Gaussian. More...
real(srp)	energy_maximum
	Maximum historical energy reserves. More...
real(srp)	energy_birth
	Energy reserves at birth, non-genetic, Gaussian. More...
real(srp)	body_length
	current body length, initialised non-genetically, Gaussian, will grow. More...
real(srp), dimension(history_size_agent_prop)	body_length_history
	History stack for the body length. More...
real(srp)	body_length_birth
	Body length at birth (genetically fixed), it is not used so far in the calculations but is recorded and can be output. More...
real(srp)	control_unselected
	This is a control unselected (and unused) trait that is set from the genome as normal but is not used in any calculations. It can be used as a control marker for random genetic drift. More...
real(srp)	body_mass
	Current body mass, initialised calculated from length and energy reserves. More...
real(srp), dimension(history_size_agent_prop)	body_mass_history
	History stack for body mass. More...
real(srp)	body_mass_birth
	Body mass at birth, will keep record of it. More...
real(srp)	body_mass_maximum
	Maximum historically body, will keep record of it. More...
real(srp)	smr
	Standard metabolitic rate, can change depending on hormones and psychological state (GOS)), at birth initialised from the genome. More...
real(srp)	maxstomcap = MAX_STOMACH_CAPACITY_DEF
	Maximum stomach capacity, max. fraction of body mass available for food here set from default value. But can change in future versions of the model depending on the body length and the physiological state (so specifically set for each agent rather than defined from global parameter commondata::max_stomach_capacity_def). More...
real(srp)	stomach_content_mass
	Stomach content mass. More...
Public Attributes inherited from the_hormones::hormones
real(srp)	growhorm_level
	growth hormone increases metabolic rate and growth, has costs changes/effects relatively slow and long-term. More...
real(srp)	thyroid_level
	thyroid hormone limits growth hormone, has costs changes/effects very slow, level very stable, genetically determined. More...
real(srp)	adrenaline_level
	adrenaline increases general arousal, increases escape speed/performance, primes active fear response, primes aggression, increases cognitive performance, focus attention, suppresses immune system, changes/effects relatively short-term. More...
real(srp)	cortisol_level
	cortisol (HPI axis) linked with higher stress and fear, reduces hunger, suppresses immune system, increases blood pressure, reduce cognitive performance, changes/effects long-term. More...
real(srp)	testosterone_level
	Gonadal steroids - Sex hormones of males and females. More...
real(srp)	estrogen_level
	estrogen - development of female sex characteristics, suppresses immunity, changes/effects relatively short-term. More...
real(srp)	testosterone_baseline
	The testosterone baseline genetically determined level. More...
real(srp)	estrogen_baseline
	The estrogen baseline genetically determined level. More...
real(srp), dimension(history_size_agent_prop)	testosterone_history
	History stacks for the gonadal steroids. More...
real(srp), dimension(history_size_agent_prop)	estrogen_history
Public Attributes inherited from the_genome::individual_genome
character(len=label_length)	genome_label
	label for the genome More...
integer	genome_size = N_CHROMOSOMES
	the size of the genome, i.e. N of chromosomes = N_CHROMOSOMES in this version it is constant, can implement variable genomes later. More...
type(chromosome), dimension(:,:), allocatable	chromosome
	array of chromosome objects, the two dimensions refer to (1) chromosome number in the genome and (2) the number of homologs (1:2 for diploid), so chromosome is a 2D array. More...
logical	sex_is_male
	The sex of the individual: is male = TRUE or female = FALSE this is the main sex identifier. The sex_label defined below should only be used for outputs and similar purposes. More...
character(len=label_length)	sex_label
	Verbal label for sex ("male" or "female"). More...
logical	alive
	Flag the agent is alive (TRUE) or dead (False). More...
Public Attributes inherited from the_environment::spatial_moving
type(spatial), dimension(history_size_spatial)	history
	We define prior historical values of the SPATIAL positions. More...
Public Attributes inherited from the_environment::spatial
real(srp)	x
	We define three-dimensional environment: x, y and depth. More...
real(srp)	y
real(srp)	depth

Detailed Description

This type describes parameters of the individual agent.

INDIVIDUAL_AGENT extends the neurobiological architecture type by adding the alive flag and explicit fitness. Fitness can be either set or calculated or assessed approximately. In models, it can be used in calculations or used just for data output. NOTE: procedure, final may not be implemented in all compilers. E.g. gfortran issues this error prior to 4.9: Error: Finalization at (1) is not yet implemented

Note

INDIVIDUAL_AGENT is an umbrella object for the individual

Definition at line 37 of file m_indiv.f90.

Member Function/Subroutine Documentation

init()

procedure, public the_individual::individual_agent::init

Generate a random agent from the genotype. See the_individual::individual_init_random().

Definition at line 52 of file m_indiv.f90.

create_ind()

procedure, public the_individual::individual_agent::create_ind

Generate a new empty agent. See the_individual::individual_create_zero().

Definition at line 55 of file m_indiv.f90.

dies()

procedure, public the_individual::individual_agent::dies

Set the individual to be dead. This method overrides the the_genome::individual_genome::dies() method, nullifying all reproductive and neurobiological and behavioural objects. However, this function does not deallocate the individual agent object, this may be a separate destructor function. The dies method is implemented at the following levels of the agent object hierarchy (upper overrides the lower level):

• the_genome::individual_genome::dies();
• the_neurobio::appraisal::dies();
• the_neurobio::gos_global::dies();
• the_individual::individual_agent::dies().

See the_individual::individual_agent_set_dead().

Definition at line 69 of file m_indiv.f90.

get_mortality()

procedure, public the_individual::individual_agent::get_mortality

Get the individually-specific mortality risk for the agent. See the_individual::individual_get_risk_mortality_individual().

Definition at line 72 of file m_indiv.f90.

fitness_calc()

procedure, public the_individual::individual_agent::fitness_calc

Calculate fitness for the pre-evolution phase of the genetic algorithm. Pre-evolution is based on selection for a simple criterion without explicit reproduction etc. The criterion for selection at this phase is set by the integer the_individual::individual_agent::fitness component. See the_individual::individual_preevol_fitness_calc().

Definition at line 79 of file m_indiv.f90.

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Member Data Documentation

fitness

integer the_individual::individual_agent::fitness

fitness is a fixed criterion for the evolution at the starting 'pre-evolution' phase of the genetic algorithm.

Warning

Note that fitness here is actually an "antifitness", the higher its value, the worse fitting is the agent.

Definition at line 42 of file m_indiv.f90.

ind_mortality

real(srp) the_individual::individual_agent::ind_mortality

Individually specific mortality risk for various undefined or defined reasons, such as immune status. Note that this risk is not linked to the predation or habitat-specific factors. The latter two causes are treated separately.

Definition at line 47 of file m_indiv.f90.

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The documentation for this type was generated from the following file:

• m_indiv.f90