the_body::condition Type Reference

CONDITION defines the physical condition of the agent More...

Inheritance diagram for the_body::condition:

Collaboration diagram for the_body::condition:

Public Member Functions
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	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

CONDITION defines the physical condition of the agent

Definition at line 29 of file m_body.f90.

Member Function/Subroutine Documentation

init_condition()

procedure, public the_body::condition::init_condition

Initialise the individual body condition object based on the genome values. See the_body::condition_init_genotype()

Definition at line 79 of file m_body.f90.

mortality_birth()

procedure, public the_body::condition::mortality_birth

This procedure enforces selective mortality of agents at birth. See the_body::birth_mortality_enforce_init_fixed_debug().

Definition at line 82 of file m_body.f90.

body_history_clean()

procedure, public the_body::condition::body_history_clean

Cleanup the history stack of the body length and mass. See the_body::condition_clean_history()

Definition at line 86 of file m_body.f90.

get_age()

procedure, public the_body::condition::get_age

Get current age. See the_body::condition_age_get()

Definition at line 90 of file m_body.f90.

age_reset()

procedure, public the_body::condition::age_reset

Reset the age of the agent to zero. See the_body::condition_age_reset_zero().

Definition at line 93 of file m_body.f90.

get_energy()

procedure, public the_body::condition::get_energy

Get current energy reserves. See the_body::condition_energy_current_get()

Definition at line 96 of file m_body.f90.

get_energy_max()

procedure, public the_body::condition::get_energy_max

Get historical maximum of energy reserves. See the_body::condition_energy_maximum_get()

Definition at line 99 of file m_body.f90.

get_length()

procedure, public the_body::condition::get_length

Get current body length. See the_body::condition_body_length_get()

Definition at line 102 of file m_body.f90.

length()

generic, public the_body::condition::length

Generic interface (alias) for get_length.

Definition at line 104 of file m_body.f90.

get_control_unselected()

procedure, public the_body::condition::get_control_unselected

Get current value of the control unselected trait. See the_body:condition_control_unsel_get:()

Definition at line 107 of file m_body.f90.

get_mass()

procedure, public the_body::condition::get_mass

Get current body mass. See the_body::condition_body_mass_get()

Definition at line 110 of file m_body.f90.

mass()

generic, public the_body::condition::mass

Generic interface to get_mass.

Definition at line 112 of file m_body.f90.

get_energ_birth()

procedure, public the_body::condition::get_energ_birth

Get historical record of energy reserves at birth. See the_body::condition_energy_birth_get().

Definition at line 115 of file m_body.f90.

get_length_birth()

procedure, public the_body::condition::get_length_birth

Get historical record of body length at birth. See the_body::condition_body_length_birth_get()

Definition at line 118 of file m_body.f90.

get_mass_birth()

procedure, public the_body::condition::get_mass_birth

Get historical record of body mass at birth. See the_body::condition_body_mass_birth_get()

Definition at line 121 of file m_body.f90.

get_mass_max()

procedure, public the_body::condition::get_mass_max

Get historcal maximum for body mass. See the_body::condition_body_mass_max_get()

Definition at line 124 of file m_body.f90.

get_smr()

procedure, public the_body::condition::get_smr

Get current smr. See the_body::condition_smr_get()

Definition at line 127 of file m_body.f90.

get_stom_content()

procedure, public the_body::condition::get_stom_content

Get current stomach content. See the_body::condition_stomach_content_get()

Definition at line 130 of file m_body.f90.

age_increment()

procedure, public the_body::condition::age_increment

Increment the age of the agent by one. See the_body::condition_age_increment().

Definition at line 134 of file m_body.f90.

set_mass()

procedure, public the_body::condition::set_mass

Set body mass optionally updating the history stack. See the_body::condition_body_mass_set_update_hist()

Definition at line 137 of file m_body.f90.

set_length()

procedure, public the_body::condition::set_length

Set body length optionally updating the history stack. See the_body::condition_body_length_set_update_hist()

Definition at line 140 of file m_body.f90.

visibility()

procedure, public the_body::condition::visibility

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.

Definition at line 146 of file m_body.f90.

food_proc_cost_v()

procedure, public the_body::condition::food_proc_cost_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()

Definition at line 153 of file m_body.f90.

food_proc_cost_o()

procedure, public the_body::condition::food_proc_cost_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()

Definition at line 157 of file m_body.f90.

food_process_cost()

generic, public the_body::condition::food_process_cost

Generic interface to the procedures calculating the basic processing cost of catching a food item.

Definition at line 160 of file m_body.f90.

food_fitt_v()

procedure, public the_body::condition::food_fitt_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()

Definition at line 166 of file m_body.f90.

food_fitt_o()

procedure, public the_body::condition::food_fitt_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()

Definition at line 170 of file m_body.f90.

food_fitting()

generic, public the_body::condition::food_fitting

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().

Definition at line 176 of file m_body.f90.

food_surpl_v()

procedure, public the_body::condition::food_surpl_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()

Definition at line 181 of file m_body.f90.

food_surpl_o()

procedure, public the_body::condition::food_surpl_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()

Definition at line 185 of file m_body.f90.

food_surplus()

generic, public the_body::condition::food_surplus

Generic interface to procedures that calculate extra food surplus mass non fitting into the stomach of the agent.

Definition at line 188 of file m_body.f90.

mass_grow()

procedure, public the_body::condition::mass_grow

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()

Definition at line 193 of file m_body.f90.

stomach_increment()

procedure, public the_body::condition::stomach_increment

Do increment stomach contents with adjusted (fitted) value. See the_body::stomach_content_get_increment()

Definition at line 196 of file m_body.f90.

cost_factor_food_smr()

procedure, public the_body::condition::cost_factor_food_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()

Definition at line 202 of file m_body.f90.

cost_swim()

procedure, public the_body::condition::cost_swim

The cost of swimming of a specific distance in terms of body mass loss. See the_body::condition_cost_swimming_burst()

Definition at line 206 of file m_body.f90.

cost_swim_std()

procedure, public the_body::condition::cost_swim_std

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().

Definition at line 211 of file m_body.f90.

energy_update()

procedure, public the_body::condition::energy_update

Update the energy reserves of the agent based on its current mass and length. See the_body::condition_energy_update_after_growth()

Definition at line 216 of file m_body.f90.

starved_death()

procedure, public the_body::condition::starved_death

Check if the body mass is smaller than the birth body mass or structural body mass. See the_body::body_mass_is_starvation_check()

Definition at line 220 of file m_body.f90.

living_cost()

procedure, public the_body::condition::living_cost

Calculate the cost of living for a single model step. See the_body::body_mass_calculate_cost_living_step()

Definition at line 227 of file m_body.f90.

subtract_living_cost()

procedure, public the_body::condition::subtract_living_cost

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()

Definition at line 231 of file m_body.f90.

len_incr()

procedure, public the_body::condition::len_incr

Calculate body length increment. See the_body::body_len_grow_calculate_increment_step()

Definition at line 234 of file m_body.f90.

len_grow()

procedure, public the_body::condition::len_grow

Do linear growth for one model step based on the above increment function. See the_body::body_len_grow_do_calculate_step()

Definition at line 238 of file m_body.f90.

stomach_empify()

procedure, public the_body::condition::stomach_empify

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()

Definition at line 243 of file m_body.f90.

sex_steroids_update()

procedure, public the_body::condition::sex_steroids_update

Update the level of the sex steroids. Sex steroids are incremented each time step of the model. See the_body::sex_steroids_update_increment()

Definition at line 247 of file m_body.f90.

Member Data Documentation

age

integer the_body::condition::age

The age of the agent in units of the integer time steps.

Definition at line 31 of file m_body.f90.

energy_current

real(srp) the_body::condition::energy_current

Current energy reserves, initialised non-genetically, Gaussian.

Definition at line 33 of file m_body.f90.

energy_maximum

real(srp) the_body::condition::energy_maximum

Maximum historical energy reserves.

Definition at line 35 of file m_body.f90.

energy_birth

real(srp) the_body::condition::energy_birth

Energy reserves at birth, non-genetic, Gaussian.

Definition at line 37 of file m_body.f90.

body_length

real(srp) the_body::condition::body_length

current body length, initialised non-genetically, Gaussian, will grow.

Definition at line 39 of file m_body.f90.

body_length_history

real(srp), dimension(history_size_agent_prop) the_body::condition::body_length_history

History stack for the body length.

Definition at line 41 of file m_body.f90.

body_length_birth

real(srp) the_body::condition::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.

Definition at line 44 of file m_body.f90.

control_unselected

real(srp) the_body::condition::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.

Definition at line 48 of file m_body.f90.

body_mass

real(srp) the_body::condition::body_mass

Current body mass, initialised calculated from length and energy reserves.

Definition at line 51 of file m_body.f90.

body_mass_history

real(srp), dimension(history_size_agent_prop) the_body::condition::body_mass_history

History stack for body mass.

Definition at line 53 of file m_body.f90.

body_mass_birth

real(srp) the_body::condition::body_mass_birth

Body mass at birth, will keep record of it.

Definition at line 55 of file m_body.f90.

body_mass_maximum

real(srp) the_body::condition::body_mass_maximum

Maximum historically body, will keep record of it.

Definition at line 57 of file m_body.f90.

smr

real(srp) the_body::condition::smr

Standard metabolitic rate, can change depending on hormones and psychological state (GOS)), at birth initialised from the genome.

Note

SMR is not used in this version.

Definition at line 61 of file m_body.f90.

maxstomcap

real(srp) the_body::condition::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).

Note

In the old model the stomach content cannot surpass maxstomcap=15% of agent's body mass.

Definition at line 69 of file m_body.f90.

stomach_content_mass

real(srp) the_body::condition::stomach_content_mass

Stomach content mass.

Definition at line 71 of file m_body.f90.

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

• m_body.f90