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The AHA Model
Revision: 12809
Reference implementation 04 (HEDG02_04)
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The AHA Model
Revision: 12809
Reference implementation 04 (HEDG02_04)
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This type describes parameters of the individual agent's genome The genome is an array of allocatable the_genome::chromosome objects, different kinds of agents may have different genomes with different number of chromosomes. See "the genome structure" for as general description and "genome" for details. More...
Public Member Functions | |
| 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 | |
| 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 |
This type describes parameters of the individual agent's genome The genome is an array of allocatable the_genome::chromosome objects, different kinds of agents may have different genomes with different number of chromosomes. See "the genome structure" for as general description and "genome" for details.
Definition at line 160 of file m_genome.f90.
| procedure, public the_genome::individual_genome::init_genome |
Initialise the genome at random, and set sex as determined by the sex determination locus. See the_genome::genome_init_random()
Definition at line 182 of file m_genome.f90.
| procedure, public the_genome::individual_genome::create_genome |
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()
Definition at line 187 of file m_genome.f90.
| procedure, public the_genome::individual_genome::label |
Label genome. If label is not provided, make a random string.
SPATIAL_MOVING. See the_genome::genome_label_set() Definition at line 192 of file m_genome.f90.
| procedure, public the_genome::individual_genome::individ_label |
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.
the_genome::genome_label_get() Definition at line 198 of file m_genome.f90.
| procedure, public the_genome::individual_genome::sex_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()
Definition at line 203 of file m_genome.f90.
| procedure, public the_genome::individual_genome::is_male |
Get the logical sex ID of the genome object component. See the_genome::genome_get_sex_is_male()
Definition at line 206 of file m_genome.f90.
| procedure, public the_genome::individual_genome::is_female |
Get the logical sex ID of the genome object component. See the_genome::genome_get_sex_is_female()
Definition at line 209 of file m_genome.f90.
| procedure, public the_genome::individual_genome::label_sex |
Get the descriptive sex label: male or female. See the_genome::genome_get_sex_label()
Definition at line 212 of file m_genome.f90.
| procedure, public the_genome::individual_genome::trait_init |
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()
Definition at line 218 of file m_genome.f90.
| procedure, public the_genome::individual_genome::trait_set |
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()
Definition at line 222 of file m_genome.f90.
| generic, public the_genome::individual_genome::neuro_resp |
Generic interface to the neuronal response function. See the_genome::trait_init_genotype_gamma2gene() and the_genome::trait_set_genotype_gamma2gene().
Definition at line 226 of file m_genome.f90.
| procedure, public the_genome::individual_genome::trait_init_linear |
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()
Definition at line 233 of file m_genome.f90.
| procedure, public the_genome::individual_genome::trait_set_linear |
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()
Definition at line 240 of file m_genome.f90.
| generic, public the_genome::individual_genome::linear_g2p |
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().
Definition at line 246 of file m_genome.f90.
| procedure, public the_genome::individual_genome::lives |
Set the individual to be alive, normally this function is used after init or birth. See the_genome::genome_individual_set_alive()
Definition at line 251 of file m_genome.f90.
| procedure, public the_genome::individual_genome::dies |
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):
See the_genome::genome_individual_set_dead()
Definition at line 263 of file m_genome.f90.
| procedure, public the_genome::individual_genome::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:
See the_genome::genome_individual_set_dead()
Definition at line 275 of file m_genome.f90.
| procedure, public the_genome::individual_genome::is_alive |
Check if the individual is alive. See the_genome::genome_individual_check_alive()
Definition at line 278 of file m_genome.f90.
| procedure, public the_genome::individual_genome::is_dead |
Check if the individual is dead (the opposite of is_alive). See the_genome::genome_individual_check_dead()
Definition at line 281 of file m_genome.f90.
| procedure, public the_genome::individual_genome::recombine_random |
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().
Definition at line 287 of file m_genome.f90.
| procedure, public the_genome::individual_genome::recombine_partial |
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().
Definition at line 293 of file m_genome.f90.
| procedure, public the_genome::individual_genome::crossover |
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().
Definition at line 299 of file m_genome.f90.
| procedure, public the_genome::individual_genome::mutate |
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().
Definition at line 305 of file m_genome.f90.
| character(len=label_length) the_genome::individual_genome::genome_label |
label for the genome
Definition at line 162 of file m_genome.f90.
| integer the_genome::individual_genome::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.
Definition at line 165 of file m_genome.f90.
| type(chromosome), dimension(:,:), allocatable the_genome::individual_genome::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.
Definition at line 169 of file m_genome.f90.
| logical the_genome::individual_genome::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.
Definition at line 173 of file m_genome.f90.
| character(len=label_length) the_genome::individual_genome::sex_label |
Verbal label for sex ("male" or "female").
Definition at line 175 of file m_genome.f90.
| logical the_genome::individual_genome::alive |
Flag the agent is alive (TRUE) or dead (False).
Definition at line 177 of file m_genome.f90.
1.9.1