Abstract base class for herbivores. More...

#include <herbivore_base.h>

Inheritance diagram for Fauna::HerbivoreBase:

Public Member Functions
virtual void	eat (const ForageMass &kg_per_km2, const Digestibility &digestibility, const ForageMass &N_kg_per_km2)
	Feed the herbivore dry matter forage. More...

virtual ForageMass	get_forage_demands (const HabitatForage &available_forage)
	Get the forage the herbivore would like to eat today. More...

virtual std::string	get_output_group () const
	The name of the HFT for aggregating output. More...

virtual double	get_kg_per_km2 () const
	Get herbivore biomass density [kg/km²]. More...

virtual const Output::HerbivoreData &	get_todays_output () const
	Read current output. More...

virtual void	simulate_day (const int day, const HabitatEnvironment &environment, double &offspring)
	Simulate daily events. More...

int	get_age_days () const
	Current age in days. More...

double	get_age_years () const
	Current age in years. More...

double	get_bodyfat () const
	Proportional body fat in empty body (fat mass/empty body mass). More...

virtual double	get_bodymass () const
	Current live weight, including fat, ingesta, blood, etc. [kg/ind]. More...

double	get_bodymass_adult () const
	Body mass at physical maturity [kg/ind]. More...

double	get_conductance () const
	Get full-body conductance [W/°C/ind]. More...

double	get_fatmass () const
	Current fat mass (pure lipids) [kg/ind]. More...

const Hft &	get_hft () const
	The herbivore functional type (HFT). More...

double	get_max_fatmass () const
	Physiological maximum of fat mass [kg/ind]. More...

double	get_structural_mass () const
	Current mass of body tissue without fat, ingesta, blood, etc. [kg/ind]. More...

int	get_today () const
	Current day of the year, as set in simulate_day(). More...

Sex	get_sex () const
	The sex of the herbivore. More...

Public Member Functions inherited from Fauna::HerbivoreInterface
virtual	~HerbivoreInterface ()=default
	Virtual destructor, which will be called by derived classes. More...

virtual void	eat (const ForageMass &kg_per_km2, const Digestibility &digestibility, const ForageMass &N_kg_per_km2=ForageMass(0))=0
	Feed the herbivore dry matter forage. More...

virtual double	get_bodymass () const =0
	Body mass of one individual [kg/ind]. More...

virtual ForageMass	get_forage_demands (const HabitatForage &available_forage)=0
	Get the forage the herbivore would like to eat today. More...

virtual std::string	get_output_group () const =0
	The name of the HFT for aggregating output. More...

virtual double	get_ind_per_km2 () const =0
	Individuals per km² More...

virtual double	get_kg_per_km2 () const =0
	Get herbivore biomass density [kg/km²]. More...

virtual const Output::HerbivoreData &	get_todays_output () const =0
	Read current output. More...

virtual bool	is_dead () const =0
	Whether the herbivore object is dead. More...

virtual void	kill ()=0
	Mark this herbivore as dead (see is_dead()). More...

virtual void	simulate_day (const int day, const HabitatEnvironment &environment, double &offspring)=0
	Simulate daily events. More...

Protected Member Functions
	HerbivoreBase (const int age_days, const double body_condition, std::shared_ptr< const Hft > hft, const Sex sex, const ForageEnergyContent &forage_gross_energy)
	Establishment constructor. More...

	HerbivoreBase (std::shared_ptr< const Hft > hft, const Sex sex, const ForageEnergyContent &forage_gross_energy)
	Birth constructor. More...

virtual	~HerbivoreBase ()=default
	Virtual destructor, which will be called by derived classes. More...

virtual void	apply_mortality (const double mortality)=0
	Apply a fractional mortality. More...

FatmassEnergyBudget &	get_energy_budget ()
	The herbivore’s energy budget object. More...

const FatmassEnergyBudget &	get_energy_budget () const
	The herbivore’s energy budget object. More...

const HabitatEnvironment &	get_environment () const
	Current abiotic conditions in the habitat. More...

Output::HerbivoreData &	get_todays_output ()
	Class-internal read/write access to current output. More...

bool	constant_members_match (const HerbivoreBase &other) const
	Check whether the constant member variables match those of another object. More...

Private Member Functions
void	apply_mortality_factors_today ()
	Calculate mortality according to user-selected mortality factors. More...

std::shared_ptr< const Hft >	check_hft_pointer (std::shared_ptr< const Hft >)
	Check whether the HFT pointer is NULL and throws an exception. More...

ForageEnergyContent	get_net_energy_content (Digestibility digestibility) const
	Get forage energy content [MJ/kgDM] using selected net energy model. More...

double	get_todays_expenditure () const
	Calculate energy expenditure as sum of given expenditure components. More...

double	get_todays_offspring_proportion () const
	Get the proportional offspring for today using selected model. More...

Private Attributes
Constants
const std::shared_ptr< const Hft >	hft

const Sex	sex

const BreedingSeason	breeding_season

const ForageEnergyContent	forage_gross_energy

State Variables
int	age_days

FatmassEnergyBudget	energy_budget

HabitatEnvironment	environment

int	today

Helper Classes
Body condition over the past x months (only females).
PeriodAverage	body_condition_gestation

Output::HerbivoreData	current_output

GetForageDemands	get_forage_demands_per_ind

Detailed Description

Abstract base class for herbivores.

Calculations are generally performed per individual.

Constructor & Destructor Documentation

◆ HerbivoreBase() [1/2]

HerbivoreBase::HerbivoreBase	(	const int	age_days,
		const double	body_condition,
		std::shared_ptr< const Hft >	hft,
		const Sex	sex,
		const ForageEnergyContent &	forage_gross_energy
	)

protected

Establishment constructor.

Parameters

age_days	age in days
body_condition	Initial fat reserve as fraction of physiological maximum [kg/kg].
hft	Herbivore functional type.
sex	The sex of the herbivore.
forage_gross_energy	The (constant) gross energy content for the forage types [MJ/kgDM]. See: Parameters::forage_gross_energy

Exceptions

std::invalid_argument If hft==NULL or age_days <= 0 or body_condition not in [0,1].

◆ HerbivoreBase() [2/2]

HerbivoreBase::HerbivoreBase	(	std::shared_ptr< const Hft >	hft,
		const Sex	sex,
		const ForageEnergyContent &	forage_gross_energy
	)

protected

Birth constructor.

Herbivores are born with Hft::body_fat_birth.

Parameters

hft	Herbivore functional type.
sex	The sex of the herbivore.
forage_gross_energy	The (constant) gross energy content for the forage types [MJ/kgDM]. See: Parameters::forage_gross_energy

Exceptions

std::invalid_argument If hft==NULL.

◆ ~HerbivoreBase()

virtual Fauna::HerbivoreBase::~HerbivoreBase ( )

protectedvirtualdefault

Virtual destructor, which will be called by derived classes.

Member Function Documentation

◆ apply_mortality()

virtual void Fauna::HerbivoreBase::apply_mortality ( const double mortality )

protectedpure virtual

Apply a fractional mortality.

Parameters

mortality Fraction of individual density/count that is dying.

Exceptions

std::invalid_argument if not 0.0≤mortality≤1.0

Implemented in Fauna::HerbivoreCohort.

◆ apply_mortality_factors_today()

void HerbivoreBase::apply_mortality_factors_today ( )

private

Calculate mortality according to user-selected mortality factors.

Calls apply_mortality(), which is implemented by child classes.

See also: Hft::mortality_factors

◆ check_hft_pointer()

std::shared_ptr< const Hft > HerbivoreBase::check_hft_pointer ( std::shared_ptr< const Hft > _hft )

private

Check whether the HFT pointer is NULL and throws an exception.

This helper function is only neededd because an exception for a NULL pointer must be thrown from the constructor. But in the initialization list there are objects that need the HFT for their own constructor. Therefore, the HFT pointer must be checked in a function first, before the HerbivoreBase constructor function body.

Exceptions

std::invalid_argument If HFT pointer is NULL.

◆ constant_members_match()

bool Fauna::HerbivoreBase::constant_members_match ( const HerbivoreBase & other ) const

inlineprotected

Check whether the constant member variables match those of another object.

◆ eat()

void HerbivoreBase::eat	(	const ForageMass &	kg_per_km2,
		const Digestibility &	digestibility,
		const ForageMass &	N_kg_per_km2
	)

virtual

Feed the herbivore dry matter forage.

Parameters

kg_per_km2	Dry matter forage mass [kgDM/km²].
N_kg_per_km2	Nitrogen in the forage [kgN/km²].
digestibility	Proportional forage digestibility.

Exceptions

std::logic_error	If `forage` exceeds intake constraints of maximal foraging and digestion.
std::logic_error	If this herbivore is dead or has no individuals.
std::invalid_argument	If `N_kg_per_km2` is larger than `kg_per_km2` for a forage type. The nitrogen mass is only a fraction of dry matter, and there cannot be more then 100% nitrogen in the forage.

Implements Fauna::HerbivoreInterface.

◆ get_age_days()

int Fauna::HerbivoreBase::get_age_days ( ) const

inline

Current age in days.

◆ get_age_years()

double Fauna::HerbivoreBase::get_age_years ( ) const

inline

Current age in years.

◆ get_bodyfat()

double HerbivoreBase::get_bodyfat ( ) const

Proportional body fat in empty body (fat mass/empty body mass).

The current body fraction, is given by the current fat mass, , and the structural mass, . Structural mass and fat mass together constitute the empty body.

$bf = \frac{FM}{SM + FM}$

See also: Body Mass and Composition

◆ get_bodymass()

double HerbivoreBase::get_bodymass ( ) const

virtual

Current live weight, including fat, ingesta, blood, etc. [kg/ind].

Current body mass, , is the sum of the empty body and the non-body parts, like ingesta, blood, etc. The empty body is given by , where is the proportion of empty body mass given by Hft::body_mass_empty.

Since the empty body consists of fat mass, , and structural mass, , we can write

$BM = SM + FM + BM * (1 - eb)$

and simplify that to:

$BM = \frac{SM + FM}{eb}$

See also: Body Mass and Composition

Implements Fauna::HerbivoreInterface.

◆ get_bodymass_adult()

double HerbivoreBase::get_bodymass_adult ( ) const

Body mass at physical maturity [kg/ind].

Hft::body_mass_female for females and Hft::body_mass_male for males.

◆ get_conductance()

double HerbivoreBase::get_conductance ( ) const

Get full-body conductance [W/°C/ind].

See also: Hft::thermoregulation_conductance

Exceptions

std::logic_error If ConductanceModel not implemented.

◆ get_energy_budget() [1/2]

FatmassEnergyBudget & Fauna::HerbivoreBase::get_energy_budget ( )

inlineprotected

The herbivore’s energy budget object.

◆ get_energy_budget() [2/2]

const FatmassEnergyBudget & Fauna::HerbivoreBase::get_energy_budget ( ) const

inlineprotected

The herbivore’s energy budget object.

◆ get_environment()

const HabitatEnvironment & Fauna::HerbivoreBase::get_environment ( ) const

inlineprotected

Current abiotic conditions in the habitat.

Exceptions

std::logic_error If simulate_day() hasn’t been called yet to set the HabitatEnvironment object.

◆ get_fatmass()

double HerbivoreBase::get_fatmass ( ) const

Current fat mass (pure lipids) [kg/ind].

See also: Body Mass and Composition

◆ get_forage_demands()

ForageMass HerbivoreBase::get_forage_demands ( const HabitatForage & available_forage )

virtual

Get the forage the herbivore would like to eat today.

Call this after simulate_day().

Note: This may be called multiple times a day in order to allow switching to another forage type!

Parameters

available_forage Available forage in the habitat [kgDM/km²].

Returns: Dry matter forage per m² that the herbivore would eat without any food competition [kgDM/km²].

Implements Fauna::HerbivoreInterface.

◆ get_hft()

const Hft & Fauna::HerbivoreBase::get_hft ( ) const

inline

The herbivore functional type (HFT).

◆ get_kg_per_km2()

double HerbivoreBase::get_kg_per_km2 ( ) const

virtual

Get herbivore biomass density [kg/km²].

Implements Fauna::HerbivoreInterface.

◆ get_max_fatmass()

double HerbivoreBase::get_max_fatmass ( ) const

Physiological maximum of fat mass [kg/ind].

The maximum fat mass, $FM_{max}$ is given by applying the fraction Hft::body_fat_maximum, $bf_{max}$ , to the empty body. The empty body mass is the sum of structural mass, , and current fat mass, which is in here the maximum $FM_{max}$ .

$\begin{eqnarray*} bf_{max} &=& \frac{FM_{max}}{SM + FM_{max}} \\ FM_{max} &=& SM * bf_{max} + FM_{max} * bf_{max} \\ FM_{max} - FM_{max} * bf_{max} &=& SM * bf_{max} \\ FM_{max} * (1 - bf_{max}) &=& SM * bf_{max} \\ FM_{max} &=& \frac{SM * bf_{max}}{1 - bf_{max}} \end{eqnarray*}$

See also: Body Mass and Composition

◆ get_net_energy_content()

ForageEnergyContent HerbivoreBase::get_net_energy_content ( Digestibility digestibility ) const

private

Get forage energy content [MJ/kgDM] using selected net energy model.

Parameters

digestibility Forage digestibility (for ruminants). This will be adjusted with Hft::digestion_digestibility_multiplier for non-ruminants.

Returns: Net energy content in MJ/kgDM.

Exceptions

std::logic_error If the net energy model is not implemented.

See also: Hft::digestion_net_energy_model; NetEnergyModel

◆ get_output_group()

std::string HerbivoreBase::get_output_group ( ) const

virtual

The name of the HFT for aggregating output.

Technically, this can be a generic identifier to aggregate output of herbivores. However, herbivores used to be aggregated only by HFT, and so this is assumed to be the HFT name until the output framework is made more flexible.

Implements Fauna::HerbivoreInterface.

◆ get_sex()

Sex Fauna::HerbivoreBase::get_sex ( ) const

inline

The sex of the herbivore.

◆ get_structural_mass()

double HerbivoreBase::get_structural_mass ( ) const

Current mass of body tissue without fat, ingesta, blood, etc. [kg/ind].

This is the body component that an ontogenetic growth curve applies to. The growth curve interpolates between the neonate structural mass and the adult structural mass.

The neonate structural mass, $SM_{birth}$ , is derived from the birth weight, $BM_{birth}$ (Hft::body_mass_birth), the body fat at birth, $bf_{birth}$ (Hft::body_fat_birth), and the empty body fraction, (Hft::body_mass_empty). The structural mass is the empty body, which is $BM_{birth}*eb$ , minus the fractional body fat $bf_{birth}$ :

$SM_{birth} = BM_{birth} * eb * (1 - bf_{birth})$

The adult structural mass, $SM_{ad}$ , is calculated in a similar way, only that the body fat fraction for the adult live weight parameter $BM_{ad}$ (Hft::body_mass_female, Hft::body_mass_male) is assumed to be half of the maximum $bf_{max}$ (Hft::body_fat_maximum):

$SM_{ad} = BM_{ad} * eb * (1 - \frac{bf_{max}}{2})$

See also: Body Mass and Composition

◆ get_today()

int HerbivoreBase::get_today ( ) const

Current day of the year, as set in simulate_day().

Exceptions

std::logic_error If current day not yet set by an initial call to simulate_day().

◆ get_todays_expenditure()

double HerbivoreBase::get_todays_expenditure ( ) const

private

Calculate energy expenditure as sum of given expenditure components.

Returns: Today’s energy needs [MJ/ind/day]

See also: Hft::expenditure_components

◆ get_todays_offspring_proportion()

double HerbivoreBase::get_todays_offspring_proportion ( ) const

private

Get the proportional offspring for today using selected model.

Reads Hft::reproduction_model and performs calculations accordingly.

Returns: Number of offspring per individual [ind/ind/day]. Zero if this herbivore is male, or has not yet reached reproductive maturity (Hft::life_history_sexual_maturity).

Exceptions

std::logic_error If Hft::reproduction_model is not implemented.

◆ get_todays_output() [1/2]

Output::HerbivoreData & Fauna::HerbivoreBase::get_todays_output ( )

inlineprotected

Class-internal read/write access to current output.

◆ get_todays_output() [2/2]

virtual const Output::HerbivoreData & Fauna::HerbivoreBase::get_todays_output ( ) const

inlinevirtual

Read current output.

Implements Fauna::HerbivoreInterface.

◆ simulate_day()

void HerbivoreBase::simulate_day	(	const int	day,
		const HabitatEnvironment &	environment,
		double &	offspring
	)

virtual

Simulate daily events.

Call this before get_forage_demands().

Parameters

[in]	day	Current day of year, 0=Jan. 1st.
[in]	environment	Current environmental conditions in the habitat.
[out]	offspring	Number of newborn today [ind/km²].

Exceptions

std::invalid_argument	If `day` not in [0,364].
std::logic_error	If this herbivore is dead.

Set current day.
Increase age.
Update records.
Update maximum fat mass and gain in Fauna::FatmassEnergyBudget.
Add new output.
Catabolize fat to compensate unmet energy needs.
Add energy needs for today.
Calculate offspring.
Apply mortality factor.

Implements Fauna::HerbivoreInterface.

Member Data Documentation

◆ age_days

int Fauna::HerbivoreBase::age_days

private

◆ body_condition_gestation

PeriodAverage Fauna::HerbivoreBase::body_condition_gestation

private

Body condition is current fat mass / max. fat mass. The record spans the lenght of a potential pregnancy, counting back from current day. This object is empty for male herbivores.

◆ breeding_season

const BreedingSeason Fauna::HerbivoreBase::breeding_season

private

◆ current_output

Output::HerbivoreData Fauna::HerbivoreBase::current_output

private

Body condition is current fat mass / max. fat mass. The record spans the lenght of a potential pregnancy, counting back from current day. This object is empty for male herbivores.

◆ energy_budget

FatmassEnergyBudget Fauna::HerbivoreBase::energy_budget

private

◆ environment

HabitatEnvironment Fauna::HerbivoreBase::environment

private

◆ forage_gross_energy

const ForageEnergyContent Fauna::HerbivoreBase::forage_gross_energy

private

◆ get_forage_demands_per_ind

GetForageDemands Fauna::HerbivoreBase::get_forage_demands_per_ind

private

Body condition is current fat mass / max. fat mass. The record spans the lenght of a potential pregnancy, counting back from current day. This object is empty for male herbivores.

◆ hft

const std::shared_ptr<const Hft> Fauna::HerbivoreBase::hft

private

◆ sex

const Sex Fauna::HerbivoreBase::sex

private

◆ today

int Fauna::HerbivoreBase::today

private

The documentation for this class was generated from the following files:

/home/docs/checkouts/readthedocs.org/user_builds/modular-megafauna-model/checkouts/latest/src/Fauna/herbivore_base.h
/home/docs/checkouts/readthedocs.org/user_builds/modular-megafauna-model/checkouts/latest/src/Fauna/herbivore_base.cpp

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ HerbivoreBase() [1/2]

◆ HerbivoreBase() [2/2]

◆ ~HerbivoreBase()

Member Function Documentation

◆ apply_mortality()

◆ apply_mortality_factors_today()

◆ check_hft_pointer()

◆ constant_members_match()

◆ eat()

◆ get_age_days()

◆ get_age_years()

◆ get_bodyfat()

◆ get_bodymass()

◆ get_bodymass_adult()

◆ get_conductance()

◆ get_energy_budget() [1/2]

◆ get_energy_budget() [2/2]

◆ get_environment()

◆ get_fatmass()

◆ get_forage_demands()

◆ get_hft()

◆ get_kg_per_km2()

◆ get_max_fatmass()

◆ get_net_energy_content()

◆ get_output_group()

◆ get_sex()

◆ get_structural_mass()

◆ get_today()

◆ get_todays_expenditure()

◆ get_todays_offspring_proportion()

◆ get_todays_output() [1/2]

◆ get_todays_output() [2/2]

◆ simulate_day()

Member Data Documentation

◆ age_days

◆ body_condition_gestation

◆ breeding_season

◆ current_output

◆ energy_budget

◆ environment

◆ forage_gross_energy

◆ get_forage_demands_per_ind

◆ hft

◆ sex

◆ today