One herbivore functional type (i.e. one species). More...

#include <hft.h>

Public Member Functions
bool	is_valid (const Parameters &params, std::string &msg) const
	Check if all variables are okay. More...

bool	is_valid (const Parameters &params) const
	Check if all variables are okay. More...

Comparison operators
bool	operator== (const Hft &rhs) const

bool	operator!= (const Hft &rhs) const

bool	operator< (const Hft &rhs) const

Public Attributes
std::string	name = "example"
	Unique name of the herbivore type. More...

"body_fat": Body fat parameters.
double	body_fat_birth = 0.2
	Proportional fat mass at birth [kg lipids/kg empty body]. More...

double	body_fat_catabolism_efficiency = 0.8
	Efficiency for converting body fat gross energy to net energy [frac.]. More...

double	body_fat_deviation = 0.125

double	body_fat_gross_energy = 39.1
	Conversion factor from fat mass to net energy [MJ/kg]. More...

double	body_fat_maximum = 0.25
	Maximum proportional fat mass [kg lipids/kg empty body]. More...

double	body_fat_maximum_daily_gain = 0.05
	Maximum rate of fat mass gain in kg fat per kg body mass per day. More...

"body_mass": Body mass parameters.
int	body_mass_birth = 5
	Live body weight [kg] at birth for both sexes. More...

double	body_mass_empty = 0.87
	Fraction of live weight minus ingesta, blood, hair, and antlers/horns. More...

int	body_mass_female = 50
	Live body mass [kg] of an adult female individual (with average reserves). More...

int	body_mass_male = 70
	Live body mass [kg] of an adult male individual (with average reserves). More...

"breeding_season": Time period of giving birth.
int	breeding_season_length = 30
	Length of breeding season in days. More...

int	breeding_season_start = 121
	Julian day of the beginning of the breeding season (0=Jan 1st). More...

"digestion": Digestion-related parameters.
GivenPointAllometry	digestion_allometric = {-0.25, 0.05}
	Parameters for DigestiveLimit::Allometric. More...

double	digestion_digestibility_multiplier = 1.0
	Factor to change ruminant digestibility for other digestion types. More...

std::array< double, 3 >	digestion_i_g_1992_ijk = {0.034, 3.565, 0.077}
	Constants i, j, k for DigestiveLimit::IlliusGordon1992 (grass only). More...

double	digestion_fixed_fraction = 0.05

DigestiveLimit	digestion_limit = DigestiveLimit::Allometric
	Constraint for maximum daily forage intake. More...

double	digestion_me_coefficient = 0.8
	Metabolizable energy coefficient (ME/DE ratio) [fractional]. More...

double	digestion_k_fat = 0.5
	Coefficient (k_f) for converting metabolizable energy to fat mass [frac.]. More...

double	digestion_k_maintenance = 0.7
	Coefficient (k_m) for converting metabolizable to net energy (NE) [frac.]. More...

NetEnergyModel	digestion_net_energy_model
	Algorithm for forage energy content. More...

"establishment": Spawning new herbivores in empty habitats.
std::pair< int, int >	establishment_age_range = {1, 15}
	Youngest and oldest age [years] for herbivore establishment. More...

double	establishment_density = 1.0
	Total population density for establishment in one habitat [ind/km²]. More...

"expenditure": Energy expenditure parameters.
GivenPointAllometry	expenditure_basal_rate = {0.75, 7.5}
	Allometric parameters for basal metabolic rate (BMR). More...

std::set< ExpenditureComponent >	expenditure_components
	Energy expenditure components, summing up to actual expenditure. More...

double	expenditure_fmr_multiplier = 2.0
	Constant factor to convert from BMR (basal rate) to FMR (field rate). More...

"foraging": Parameters regulating food intake.
DietComposer	foraging_diet_composer = DietComposer::PureGrazer
	Model defining the herbivore’s diet composition. More...

std::set< ForagingLimit >	foraging_limits = {}
	Constraints for maximum daily forage procurement. More...

double	foraging_half_max_intake_density = 20
	Grass density [gDM/m²] where intake is half of its maximum. More...

"life_history": Life stages for herbivore individuals.
int	life_history_lifespan = 16
	Maximum age in years [1–∞). More...

int	life_history_physical_maturity_female = 3
	Age of physical maturity in years for females. More...

int	life_history_physical_maturity_male = 3
	Age of physical maturity in years for males. More...

int	life_history_sexual_maturity = 2
	Age of female sexual maturity in years. More...

"mortality": Parameters to define death of herbivores.
double	mortality_adult_rate = 0.1
	Annual background mortality rate [0.0–1.0) after first year of life. More...

std::set< MortalityFactor >	mortality_factors
	Ways how herbivores can die. More...

double	mortality_juvenile_rate = 0.3
	Annual background mortality rate [0.0–1.0) in the first year of life. More...

double	mortality_minimum_density_threshold = 0.5
	Minimum viable density of one HFT population (all cohorts) [frac.]. More...

bool	mortality_shift_body_condition_for_starvation = true
	Whether to shift mean cohort body condition on starvation mortality. More...

"reproduction": Parameters relating to annual reproduction.
double	reproduction_annual_maximum = 1.0
	Maximum annual reproduction rate for females (0.0–∞) More...

int	reproduction_gestation_length = 9
	Duration of pregnancy [number of months]. More...

std::array< double, 2 >	reproduction_logistic = {15.0, 0.3}
	Growth rate and midpoint for the logistic reproduction model. More...

ReproductionModel	reproduction_model = ReproductionModel::ConstantMaximum
	Algorithm to calculate herbivore reproduction. More...

"thermoregulation": Expenditure through heat loss.
ConductanceModel	thermoregulation_conductance
	Algorithm to calculate whole-body conductance for thermoregulation. More...

double	thermoregulation_core_temperature = 38
	Body core temperature [°C]. More...

Private Member Functions
bool	check_mortality_vs_reproduction (const Parameters &params, std::ostream &msg) const
	Check if minimum mortality exceeds maximum reproduction. More...

bool	check_intake_vs_expenditure (const Parameters &params, std::ostream &msg) const
	Check if minimum expenditure exceeds maximum energy intake. More...

Detailed Description

One herbivore functional type (i.e. one species).

Parametes are sorted alphabetically and grouped by semantic categories, which are indicated with a prefix to the member name.

The member variable names shall be spelled exactly the same as the keys in the TOML instruction file. The categories correspond to the tables in the TOML file. The prefix (separated with "_") is spelled the same as the TOML table.

The initialization values are the same as in the example file under examples/megafauna.toml. They must be valid in the context of the global parameters of the instruction file.

Member Function Documentation

◆ check_intake_vs_expenditure()

bool Hft::check_intake_vs_expenditure	(	const Parameters &	params,
		std::ostream &	msg
	)		const

private

Check if minimum expenditure exceeds maximum energy intake.

Parameters

[in]	params	The global simulation parameters.
[out]	msg	Output stream for warning or error messages for users.

Returns: true if the object has valid values

◆ check_mortality_vs_reproduction()

bool Hft::check_mortality_vs_reproduction	(	const Parameters &	params,
		std::ostream &	msg
	)		const

private

Check if minimum mortality exceeds maximum reproduction.

Parameters

[in]	params	The global simulation parameters.
[out]	msg	Output stream for warning or error messages for users.

Returns: true if the object has valid values

◆ is_valid() [1/2]

bool Hft::is_valid ( const Parameters & params ) const

Check if all variables are okay.

Parameters

[in] params The global simulation parameters.

Returns: true if the object has valid values

◆ is_valid() [2/2]

bool Hft::is_valid	(	const Parameters &	params,
		std::string &	msg
	)		const

Check if all variables are okay.

Parameters

[in]	params	The global simulation parameters.
[out]	msg	Warning or error messages for output.

Returns: true if the object has valid values

◆ operator!=()

bool Fauna::Hft::operator!= ( const Hft & rhs ) const

inline

Comparison operators are solely based on string comparison of the name.

◆ operator<()

bool Fauna::Hft::operator< ( const Hft & rhs ) const

inline

Comparison operators are solely based on string comparison of the name.

◆ operator==()

bool Fauna::Hft::operator== ( const Hft & rhs ) const

inline

Comparison operators are solely based on string comparison of the name.

Member Data Documentation

◆ body_fat_birth

double Fauna::Hft::body_fat_birth = 0.2

Proportional fat mass at birth [kg lipids/kg empty body].

This must not be greater than body_fat_maximum.

See also: body_mass_empty; Body Mass and Composition; Body Mass and Composition

◆ body_fat_catabolism_efficiency

double Fauna::Hft::body_fat_catabolism_efficiency = 0.8

Efficiency for converting body fat gross energy to net energy [frac.].

The default value is taken from Corbett et al. (1990) [10].

This value must not be higher than the fat anabolism coefficient, which is digestion_k_maintenance divided by digestion_k_fat.

See also: Fat as Energy Storage; FatmassEnergyBudget; Energy Content of Forage

◆ body_fat_deviation

double Fauna::Hft::body_fat_deviation = 0.125

Standard deviation in body condition for GetStarvationIlliusOConnor2000. Body condition is the proportion of current body fat relative to physiological maximum.

Note: For juveniles (1st year of life), body fat variation is always zero in order to avoid artificially high death rates if body fat is low at birth.

See also: Body Mass and Composition

◆ body_fat_gross_energy

double Fauna::Hft::body_fat_gross_energy = 39.1

Conversion factor from fat mass to net energy [MJ/kg].

The default value is from Blaxter (1989, p. 52)[4] :

‍For example, in sheep the enthalpy of combustion of the ether extracted (crude) fat is 39.1 kJ/g.

◆ body_fat_maximum

double Fauna::Hft::body_fat_maximum = 0.25

Maximum proportional fat mass [kg lipids/kg empty body].

This value is a fraction of empty body mass (body_mass_empty) because field data from chemical analysis of lipid content usually refer to ingesta-free carcass mass and not live weight.

See also: Body Mass and Composition

The default value is an estimate for a wild ungulate. Compare for instance Weiner (1973) [69] and Reimers et al. (1982) [55].

◆ body_fat_maximum_daily_gain

double Fauna::Hft::body_fat_maximum_daily_gain = 0.05

Maximum rate of fat mass gain in kg fat per kg body mass per day.

A value of zero indicates no limit.

◆ body_mass_birth

int Fauna::Hft::body_mass_birth = 5

Live body weight [kg] at birth for both sexes.

The birth body mass includes the body fat specified in body_fat_birth.

For simplicity’s sake, the live weight of the neonate has the same empty body fraction (body_mass_empty) as adults, even though the guts are probably not full.

See also: Body Mass and Composition

◆ body_mass_empty

double Fauna::Hft::body_mass_empty = 0.87

Fraction of live weight minus ingesta, blood, hair, and antlers/horns.

This is the fraction of the body that the body fat fraction refers to.

See also: body_fat_birth, body_fat_maximum

The default value is derived from average live body mass, M=60 kg, with the formula for ingesta weight in herbivores from Parra (1978) as cited by Clauss et al. (2005):

$0.0936 * M^{1.0768}$

◆ body_mass_female

int Fauna::Hft::body_mass_female = 50

Live body mass [kg] of an adult female individual (with average reserves).

This is the live weight of an average adult animal individual as it would be weight on a scale. It is not a particular fat nor a particular skinny individual, so the model assumes that the fat reserves are at the half of their maximum (body_fat_maximum).

See also: Body Mass and Composition

◆ body_mass_male

int Fauna::Hft::body_mass_male = 70

Live body mass [kg] of an adult male individual (with average reserves).

This is the live weight of an average adult animal individual as it would be weight on a scale. It is not a particular fat nor a particular skinny individual, so the model assumes that the fat reserves are at the half of their maximum (body_fat_maximum).

See also: /home/docs/checkouts/readthedocs.org/user_builds/modular-megafauna-model/checkouts/latest/src/Fauna/hft.h

◆ breeding_season_length

int Fauna::Hft::breeding_season_length = 30

Length of breeding season in days.

◆ breeding_season_start

int Fauna::Hft::breeding_season_start = 121

Julian day of the beginning of the breeding season (0=Jan 1st).

The instruction file parameter can also be specified as a month name. In that case the first of the month is the start of the breeding season (assuming a 365-days year).

◆ digestion_allometric

GivenPointAllometry Fauna::Hft::digestion_allometric = {-0.25, 0.05}

Parameters for DigestiveLimit::Allometric.

See documentation in DigestiveLimit::Allometric.

◆ digestion_digestibility_multiplier

double Fauna::Hft::digestion_digestibility_multiplier = 1.0

Factor to change ruminant digestibility for other digestion types.

The digestibility values in the megafauna model are assumed to be for ruminants. Other herbivores, e.g. hindgut fermenters, retain a lower fraction of the forage dry matter. The ruminant digestibility will be simply multiplied with the given factor.

◆ digestion_fixed_fraction

double Fauna::Hft::digestion_fixed_fraction = 0.05

Daily dry matter intake per kg body mass for DigestiveLimit::FixedFraction. This applies to male adults. With DigestiveLimit::FixedFraction, the fraction is scaled to animals of other (less) body mass.

◆ digestion_i_g_1992_ijk

std::array<double, 3> Fauna::Hft::digestion_i_g_1992_ijk = {0.034, 3.565, 0.077}

Constants i, j, k for DigestiveLimit::IlliusGordon1992 (grass only).

Shipley et al. (1999)[61] derived the parameters i, j, and k from regression analysis with 12 mammalian herbivores (0.05–547 kg) and are specific to hindgut fermenters and ruminants.

	Hindgut	Ruminant
i	0.108	0.034
j	3.284	3.565
k	0.080	0.077

See also: get_digestive_limit_illius_gordon_1992(); DigestiveLimit::IlliusGordon1992

◆ digestion_k_fat

double Fauna::Hft::digestion_k_fat = 0.5

Coefficient (k_f) for converting metabolizable energy to fat mass [frac.].

A number between 0 and 1 that defines how much of the metabolizable energy in forage gets converted to gross energy in body fat reserves. The energy loss is heat increment.

The default value is from Blaxter (1989, p. 259 [4]) for ox.

See also: body_fat_gross_energy; NetEnergyModel::GrossEnergyFraction; Energy Content of Forage

◆ digestion_k_maintenance

double Fauna::Hft::digestion_k_maintenance = 0.7

Coefficient (k_m) for converting metabolizable to net energy (NE) [frac.].

A number between 0 and 1 that defines how much of the metabolizable energy in forage is usable as net energy for meeting the energy needs of the metabolic rate. The energy loss is known as heat increment.

See also: NetEnergyModel::GrossEnergyFraction; Energy Content of Forage

◆ digestion_limit

DigestiveLimit Fauna::Hft::digestion_limit = DigestiveLimit::Allometric

Constraint for maximum daily forage intake.

◆ digestion_me_coefficient

double Fauna::Hft::digestion_me_coefficient = 0.8

Metabolizable energy coefficient (ME/DE ratio) [fractional].

A number between 0 and 1 defining the fraction of digestible energy (DE) that can be used by the animal’s own metabolism. The rest is lost to gas production (methane) and urine.

See also: NetEnergyModel::GrossEnergyFraction; Energy Content of Forage

◆ digestion_net_energy_model

NetEnergyModel Fauna::Hft::digestion_net_energy_model

Initial value:

=

NetEnergyModel::GrossEnergyFraction

Fauna::NetEnergyModel::GrossEnergyFraction

@ GrossEnergyFraction

Use get_net_energy_from_gross_energy().

Algorithm for forage energy content.

◆ establishment_age_range

std::pair<int, int> Fauna::Hft::establishment_age_range = {1, 15}

Youngest and oldest age [years] for herbivore establishment.

◆ establishment_density

double Fauna::Hft::establishment_density = 1.0

Total population density for establishment in one habitat [ind/km²].

◆ expenditure_basal_rate

GivenPointAllometry Fauna::Hft::expenditure_basal_rate = {0.75, 7.5}

Allometric parameters for basal metabolic rate (BMR).

GivenPointAllometry::value_male_adult is daily basal metabolic rate in MJ/day for an adult male individual (body_mass_male). The exponent (GivenPointAllometry::exponent) should match the scaling of intake so that energy input and expenditure are balanced for all possible body masses.

See also: ExpenditureComponent::BasalMetabolicRate; ExpenditureComponent::FieldMetabolicRate; DigestiveLimit::FixedFraction

◆ expenditure_components

std::set<ExpenditureComponent> Fauna::Hft::expenditure_components

Initial value:

= {

ExpenditureComponent::FieldMetabolicRate}

Fauna::ExpenditureComponent::FieldMetabolicRate

@ FieldMetabolicRate

Allometric basal metabolic rate with FMR constant multiplier.

Energy expenditure components, summing up to actual expenditure.

◆ expenditure_fmr_multiplier

double Fauna::Hft::expenditure_fmr_multiplier = 2.0

Constant factor to convert from BMR (basal rate) to FMR (field rate).

See also: ExpenditureComponent::FieldMetabolicRate; expenditure_basal_rate

◆ foraging_diet_composer

DietComposer Fauna::Hft::foraging_diet_composer = DietComposer::PureGrazer

Model defining the herbivore’s diet composition.

◆ foraging_half_max_intake_density

double Fauna::Hft::foraging_half_max_intake_density = 20

Grass density [gDM/m²] where intake is half of its maximum.

Grass (sward) density at which intake rate reaches half of its maximum (in a Holling Type II functional response). Required by specific foraging limits.

◆ foraging_limits

std::set<ForagingLimit> Fauna::Hft::foraging_limits = {}

Constraints for maximum daily forage procurement.

◆ life_history_lifespan

int Fauna::Hft::life_history_lifespan = 16

Maximum age in years [1–∞).

◆ life_history_physical_maturity_female

int Fauna::Hft::life_history_physical_maturity_female = 3

Age of physical maturity in years for females.

◆ life_history_physical_maturity_male

int Fauna::Hft::life_history_physical_maturity_male = 3

Age of physical maturity in years for males.

◆ life_history_sexual_maturity

int Fauna::Hft::life_history_sexual_maturity = 2

Age of female sexual maturity in years.

◆ mortality_adult_rate

double Fauna::Hft::mortality_adult_rate = 0.1

Annual background mortality rate [0.0–1.0) after first year of life.

◆ mortality_factors

std::set<MortalityFactor> Fauna::Hft::mortality_factors

Initial value:

= {
      MortalityFactor::Background, MortalityFactor::Lifespan,
      MortalityFactor::StarvationIlliusOConnor2000}

Ways how herbivores can die.

◆ mortality_juvenile_rate

double Fauna::Hft::mortality_juvenile_rate = 0.3

Annual background mortality rate [0.0–1.0) in the first year of life.

◆ mortality_minimum_density_threshold

double Fauna::Hft::mortality_minimum_density_threshold = 0.5

Minimum viable density of one HFT population (all cohorts) [frac.].

Given as fraction of establishment_density.

See also: Minimum Density Threshold

◆ mortality_shift_body_condition_for_starvation

bool Fauna::Hft::mortality_shift_body_condition_for_starvation = true

Whether to shift mean cohort body condition on starvation mortality.

See GetStarvationIlliusOConnor2000.

◆ name

std::string Fauna::Hft::name = "example"

Unique name of the herbivore type.

◆ reproduction_annual_maximum

double Fauna::Hft::reproduction_annual_maximum = 1.0

Maximum annual reproduction rate for females (0.0–∞)

◆ reproduction_gestation_length

int Fauna::Hft::reproduction_gestation_length = 9

Duration of pregnancy [number of months].

◆ reproduction_logistic

std::array<double, 2> Fauna::Hft::reproduction_logistic = {15.0, 0.3}

Growth rate and midpoint for the logistic reproduction model.

Growth rate (called b) must not be negative.
The midpoint (called c) must lie between 0 and 1.
See also
ReproductionLogistic

ReproductionModel::Logistic

◆ reproduction_model

ReproductionModel Fauna::Hft::reproduction_model = ReproductionModel::ConstantMaximum

Algorithm to calculate herbivore reproduction.

◆ thermoregulation_conductance

ConductanceModel Fauna::Hft::thermoregulation_conductance

Initial value:

=

ConductanceModel::BradleyDeavers1980

Fauna::ConductanceModel::BradleyDeavers1980

@ BradleyDeavers1980

Algorithm to calculate whole-body conductance for thermoregulation.

◆ thermoregulation_core_temperature

double Fauna::Hft::thermoregulation_core_temperature = 38

Body core temperature [°C].

Default is 38°C (Hudson & White, 1985[29])

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

Public Member Functions

Public Attributes

Private Member Functions

Detailed Description

Member Function Documentation

◆ check_intake_vs_expenditure()

◆ check_mortality_vs_reproduction()

◆ is_valid() [1/2]

◆ is_valid() [2/2]

◆ operator!=()

◆ operator<()

◆ operator==()

Member Data Documentation

◆ body_fat_birth

◆ body_fat_catabolism_efficiency

◆ body_fat_deviation

◆ body_fat_gross_energy

◆ body_fat_maximum

◆ body_fat_maximum_daily_gain

◆ body_mass_birth

◆ body_mass_empty

◆ body_mass_female

◆ body_mass_male

◆ breeding_season_length

◆ breeding_season_start

◆ digestion_allometric

◆ digestion_digestibility_multiplier

◆ digestion_fixed_fraction

◆ digestion_i_g_1992_ijk

◆ digestion_k_fat

◆ digestion_k_maintenance

◆ digestion_limit

◆ digestion_me_coefficient

◆ digestion_net_energy_model

◆ establishment_age_range

◆ establishment_density

◆ expenditure_basal_rate

◆ expenditure_components

◆ expenditure_fmr_multiplier

◆ foraging_diet_composer

◆ foraging_half_max_intake_density

◆ foraging_limits

◆ life_history_lifespan

◆ life_history_physical_maturity_female

◆ life_history_physical_maturity_male

◆ life_history_sexual_maturity

◆ mortality_adult_rate

◆ mortality_factors

◆ mortality_juvenile_rate

◆ mortality_minimum_density_threshold

◆ mortality_shift_body_condition_for_starvation

◆ name

◆ reproduction_annual_maximum

◆ reproduction_gestation_length

◆ reproduction_logistic

◆ reproduction_model

◆ thermoregulation_conductance

◆ thermoregulation_core_temperature