Defines an umbrella class for the complete fish organism An outline of the ::fish class inheritance is presented below. More...
Public Member Functions | |
| procedure, public | activity_baseline => fish_activity_baseline_component |
| Calculate the baseline locomotor activity of the fish, it is fixed to the values of commondata::global_baseline_activity_day and commondata::global_baseline_activity_night for day and night respectively See the_fish::fish_activity_baseline_component(). More... | |
| procedure, public | activity_appetite => fish_activity_appetite_factor |
| procedure, public | amr => fish_amr_locomotion_energy_cost |
| Calculate AMR, see the_fish::fish_amr_locomotion_energy_cost() More... | |
| procedure, public | energy_update => fish_energy_balance_update |
| Calculate and update the current energy balance of the fish. See the_fish::fish_energy_balance_update() More... | |
| procedure, public | uptake_energy => fish_energy_consumption_step |
| Calculate energy energy expenditures and O2 uptake See the_fish::fish_energy_consumption_step() and the_fish::fish_oxygen_consumption_step()) More... | |
| procedure, public | uptake_o2 => fish_oxygen_consumption_step |
| Calculate osygen consumption (l) of the fish depending on temperature (O2 = O2_SMR + O2_AMR + O2_SDA) See the_fish::fish_oxygen_consumption_step() More... | |
| procedure, public | sda_fact => fish_energy_sda_factor |
| Calculate the scaling factor for SDA (specific dynamic action) that depends on the absorption rate. See the_fish::fish_energy_sda_factor() More... | |
| procedure, public | ue_ze => fish_energy_branchial_step |
| Calculate bronchial and urine energy see the_fish::fish_energy_branchial_step() More... | |
| procedure, public | appetite_energy =>fish_appetite_factor_energy_balance |
| Calculate appetite factor that depends on the energy balance See the_fish::fish_appetite_factor_energy_balance() More... | |
| procedure, public | appetite => fish_appetite_probability_ingestion |
| Calculate the overall appetite of the fish, which defines the probability to ingest any food item. See the_fish::fish_appetite_probability_ingestion(). More... | |
| procedure, public | decide_eat => fish_decide_eat_food_item_ptr |
| Making decision to eat a single food item that is available. See the_fish::fish_decide_eat_food_item_ptr(). More... | |
| procedure, public | do_ingest => fish_ingest_food_item |
| The fish does eat a single food item. See the_fish::fish_ingest_food_item(). More... | |
| procedure, public | do_grow => fish_grow_increment_energy |
| Grow the fish body mass: increment mass based on energy See the_fish::fish_grow_increment_energy() More... | |
 Public Member Functions inherited from the_fish::midgut | |
| procedure, public | mg_init => fish_midgut_init |
| Initialise an empty fish stomach object. See the_fish::fish_midgut_init(). More... | |
| procedure, public | mg_step => fish_midgut_update_from_stomach |
| Update the time the food item spent in the midgut of the fish. See the_fish::fish_midgut_update_from_stomach(). More... | |
| procedure, public | history_update => fish_midgut_history_update |
| Calculate the cumulative history of absorption in midgut See the_fish::fish_midgut_history_update() More... | |
| procedure, public | mg_food_mass => fish_midgut_total_mass_food |
| Calculate the total mass of food in the fish midgut. See the_fish::fish_midgut_total_mass_food(). More... | |
| procedure, public | add_midgut =>fish_midgut_shift_items_after_new_ingest |
| Shift food items in the midgut after a new food item is ingested and therefore food items are shifted in stomach adding the new item. See the_fish::fish_midgut_shift_items_after_new_ingest(). More... | |
| procedure, public | appetite_midgut => fish_appetite_factor_midgut |
| Calculate the fish appetite factor based on relative midgut fullness. See the_fish::fish_appetite_factor_midgut(). More... | |
| procedure, public | absorption_rate => fish_midgut_absorption_rate |
| Calculate instantaneous absorption rate. See the_fish::fish_midgut_absorption_rate(). More... | |
| procedure, public | absorption_factor => fish_midgut_absorption_factor |
| Appetite factor multiplier based on the total absorption rate. See the_fish::fish_midgut_absorption_factor(). More... | |
| procedure, public | absorp_last_i => midgut_absorp_history_last_past_idx |
| Determine the index of the latest absorption item in the history stack array. Note that in most cases the function should return commondata::history_size as the history stack is filled with previous values. See the_fish::midgut_absorp_history_last_past_idx() More... | |
| procedure, public | evacuated_step =>fish_midgut_total_mass_evacuated_step |
| Calculate the total mass of food evacuated from the midgut see the_fish::fish_midgut_total_mass_evacuated_step() More... | |
| procedure, public | evacuated_n => fish_midgut_n_evacuated_step |
| Calculate the number of the total mass of food evacuated from the midgut after full absorption and evacuation delay (see commondata:global_maximum_duration_midgut_min) that occurs at one time step. See the_fish::fish_midgut_n_evacuated_step() More... | |
| Public Member Functions inherited from the_fish::stomach | |
| procedure, public | st_init => fish_stomach_init |
| Initialise an empty fish stomach object. See the_fish::fish_stomach_init(). More... | |
| procedure, public | st_step => fish_stomach_update_step |
| Update one time step (s) in the fish stomach life cycle. See the_fish::fish_stomach_update_step(). More... | |
| procedure, public | st_food_mass => fish_stomach_total_mass_food |
| Calculate total mass of food in the fish stomach. the_fish::fish_stomach_total_mass_food(). More... | |
| procedure, public | appetite_stomach => fish_appetite_factor_stomach |
| Calculate the fish appetite factor based on relative stomach fullness. the_fish::fish_appetite_factor_stomach(). More... | |
| procedure, public | emptying => fish_stomach_emptying_time |
| Object-oriented frontend for stomach_emptying_time(): Calculate the stomach emptying time for a fish with specific body mass at a specific temperature. Calculation is based on spline interpolation of experimental data. See the_fish::fish_stomach_emptying_time(). More... | |
| Public Member Functions inherited from the_fish::fish_skel | |
| procedure, public | new => fish_init_new_zero |
| Initialise an empty fish base. See the fish::fish_init_new_zero(). More... | |
| procedure, public | smr => fish_smr_temp_bodymass_evan1990_scalar |
| Calculate SMR, see the_fish::fish_skel::smr() and the_fish::smr(). More... | |
| procedure, public | body_energy => fish_whole_body_energy_trout |
| Calculate whole body energy of the fish, see the_fish::fish_whole_body_energy_trout() More... | |
| procedure, public | mass => fish_body_mass_current_get |
| Get the current body mass of the fish, note that this function is a shortcut to obtain the last body mass from the history array (the_fish::fish_skel::history::body_mass_current). See the_fish::fish_body_mass_current_get(). More... | |
Additional Inherited Members | |
| Public Attributes inherited from the_fish::midgut | |
| real(srp) | mass_midgut |
| Total mass capacity of the fish midgut. More... | |
| integer | n_food_items_midgut |
| Number of food items within the midgut of the fish. More... | |
| type(food_item_eaten_mg), dimension(max_food_items_index) | food_items_midgut |
| An array of ::food_item_eaten objects representing food items in the midgut. More... | |
| Public Attributes inherited from the_fish::stomach | |
| real(srp) | mass_stomach |
| Total mass capacity of fish stomach. More... | |
| integer | n_food_items_stomach |
| Number of food items within the stomach of the fish. More... | |
| type(food_item_eaten), dimension(max_food_items_index) | food_items_stomach |
| An array of ::food_item_eaten objects representing food items in the stomach. More... | |
| Public Attributes inherited from the_fish::fish_skel | |
| integer | idnum |
| ID number of the fish. More... | |
| type(history_array_fish) | history |
| A limited history of past indicators (of size ::history_array_fish) More... | |
| real(srp) | body_mass0 |
| Body mass of the fish, g. More... | |
Detailed Description
Defines an umbrella class for the complete fish organism An outline of the ::fish class inheritance is presented below.
Definition at line 249 of file m_fish.f90.
Member Function/Subroutine Documentation
◆ activity_baseline()
| procedure, public the_fish::fish::activity_baseline |
Calculate the baseline locomotor activity of the fish, it is fixed to the values of commondata::global_baseline_activity_day and commondata::global_baseline_activity_night for day and night respectively See the_fish::fish_activity_baseline_component().
Definition at line 256 of file m_fish.f90.
◆ activity_appetite()
| procedure, public the_fish::fish::activity_appetite |
Definition at line 258 of file m_fish.f90.
◆ amr()
| procedure, public the_fish::fish::amr |
Calculate AMR, see the_fish::fish_amr_locomotion_energy_cost()
Definition at line 261 of file m_fish.f90.
◆ energy_update()
| procedure, public the_fish::fish::energy_update |
Calculate and update the current energy balance of the fish. See the_fish::fish_energy_balance_update()
Definition at line 264 of file m_fish.f90.
◆ uptake_energy()
| procedure, public the_fish::fish::uptake_energy |
Calculate energy energy expenditures and O2 uptake See the_fish::fish_energy_consumption_step() and the_fish::fish_oxygen_consumption_step())
Definition at line 268 of file m_fish.f90.
◆ uptake_o2()
| procedure, public the_fish::fish::uptake_o2 |
Calculate osygen consumption (l) of the fish depending on temperature (O2 = O2_SMR + O2_AMR + O2_SDA) See the_fish::fish_oxygen_consumption_step()
Definition at line 272 of file m_fish.f90.
◆ sda_fact()
| procedure, public the_fish::fish::sda_fact |
Calculate the scaling factor for SDA (specific dynamic action) that depends on the absorption rate. See the_fish::fish_energy_sda_factor()
Definition at line 275 of file m_fish.f90.
◆ ue_ze()
| procedure, public the_fish::fish::ue_ze |
Calculate bronchial and urine energy see the_fish::fish_energy_branchial_step()
Definition at line 278 of file m_fish.f90.
◆ appetite_energy()
| procedure, public the_fish::fish::appetite_energy |
Calculate appetite factor that depends on the energy balance See the_fish::fish_appetite_factor_energy_balance()
Definition at line 281 of file m_fish.f90.
◆ appetite()
| procedure, public the_fish::fish::appetite |
Calculate the overall appetite of the fish, which defines the probability to ingest any food item. See the_fish::fish_appetite_probability_ingestion().
Definition at line 285 of file m_fish.f90.
◆ decide_eat()
| procedure, public the_fish::fish::decide_eat |
Making decision to eat a single food item that is available. See the_fish::fish_decide_eat_food_item_ptr().
- Warning
- This method must be applied to the top-level object hierarchy.
Definition at line 290 of file m_fish.f90.
◆ do_ingest()
| procedure, public the_fish::fish::do_ingest |
The fish does eat a single food item. See the_fish::fish_ingest_food_item().
Definition at line 293 of file m_fish.f90.
◆ do_grow()
| procedure, public the_fish::fish::do_grow |
Grow the fish body mass: increment mass based on energy See the_fish::fish_grow_increment_energy()
Definition at line 296 of file m_fish.f90.
The documentation for this type was generated from the following file:
