Namespaces
namespace	Demo

namespace	Output

Classes
struct	AllometryParameters
	Coefficient and exponent for an allometric relationship. More...

class	ambiguous_param_type
	Exception that a parameter can be interpreted in multiple ways. More...

class	bad_array_size
	Exception that an array parameter does not have the correct length. More...

class	BreedingSeason
	Helper class for reproduction within a breeding season. More...

class	CohortPopulation
	A population of HerbivoreCohort objects. More...

class	CreateHerbivoreCohort
	Function class constructing HerbivoreCohort objects. More...

class	CreateHerbivoreCommon
	Parent class for CreateHerbivoreCohort. More...

class	Date
	Helper class to hold an absolute simulation day. More...

class	DateInterval
	Two dates framing a time interval. More...

struct	DistributeForage
	Interface for a forage distribution algorithm. More...

struct	DistributeForageEqually
	Equal forage distribution algorithm. More...

class	FatmassEnergyBudget
	A herbivore’s energy budget with fat reserves. More...

class	FeedHerbivores
	Function object to feed herbivores. More...

class	ForageBase
	Base class for herbivore forage in a habitat. More...

class	ForageValues

class	GetBackgroundMortality
	Function object to calculate constant herbivore background mortality. More...

class	GetForageDemands
	Function object to calculate forage demands for a herbivore. More...

class	GetSimpleLifespanMortality
	Function object for herbivore death after given lifespan is reached. More...

class	GetStarvationIlliusOConnor2000

class	GetStarvationMortalityThreshold
	Function object to calculate death at low body fat. More...

struct	GivenPointAllometry
	Parameters for an allometric relationship with exponent and one point. More...

class	GrassForage
	Grass forage in a habitat. More...

class	Habitat
	Abstract class of a homogenous spatial unit populated by herbivores. More...

struct	HabitatEnvironment
	Variables describing the habitat that are not forage ⇒ abiotic environment. More...

class	HabitatForage
	All values for large herbivore forage in a Habitat. More...

class	HalfMaxIntake
	Ingestion rate as Holling’s Type II functional response. More...

class	HerbivoreBase
	Abstract base class for herbivores. More...

class	HerbivoreCohort
	A herbivore cohort (age-class) More...

struct	HerbivoreInterface
	Interface for any herbivore implementation in the model. More...

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

class	InsfileReader
	Class to read parameters and HFTs from given instruction file. More...

class	invalid_option
	Exception that a string parameter does not match possible options. More...

struct	missing_group
	Exception if a group listed in `hft.groups` cannot be found. More...

struct	missing_hft_parameter
	Exception that an HFT parameter is missing in the instruction file. More...

struct	missing_parameter
	Exception that a parameter is missing in the instruction file. More...

struct	param_out_of_range
	Exception if an integer or double parameter is out of range. More...

struct	Parameters
	Parameters for the herbivory module. More...

class	PeriodAverage
	Average of a `double` value over a given time period. More...

struct	PopulationInterface
	A container of herbivore objects. More...

class	ReproductionConstMax
	Use a constant annual increase rate for herbivore reproduction. More...

class	ReproductionLinear
	Reproduction rate increases linearly with fat reserves up to maximum. More...

class	ReproductionLogistic
	Reproduction model following Illius & O’Connor (2000) More...

class	SimulateDay
	Function object to simulate one day in one habitat. More...

class	SimulationUnit
	A habitat with the herbivores that live in it. More...

struct	unknown_parameters
	Exception that parameters couldn’t be parsed in the TOML file. More...

class	World
	Central class to construct and own megafauna habitats and populations. More...

class	WorldConstructor
	Helper class of World to create various megafauna components. More...

struct	wrong_param_type
	Exception that a parameter is not of an expected data type. More...

Typedefs
typedef ForageValues< ForageValueTag::ZeroToOne >	Digestibility
	Digestibility [fraction] for different forage types. More...

typedef ForageValues< ForageValueTag::PositiveAndZero >	ForageEnergy
	Energy values [MJ] for different forage types. More...

typedef ForageValues< ForageValueTag::PositiveAndZero >	ForageEnergyContent
	Net energy content [MJ/kgDM] for different forage types. More...

typedef ForageValues< ForageValueTag::ZeroToOne >	ForageFraction
	A fraction for each forage type. More...

typedef ForageValues< ForageValueTag::PositiveAndZero >	ForageMass
	Dry matter mass values [kgDM or kgDM/km²] for different forage types. More...

typedef std::vector< std::pair< HerbivoreInterface *, ForageMass > >	ForageDistribution
	Data structure defining which herbivore gets what to eat [kgDM/km²]. More...

typedef std::list< const Habitat * >	HabitatList
	A list of Habitat pointers. More...

typedef std::vector< std::shared_ptr< const Hft > >	HftList
	List of pointers to Hft objects. More...

typedef std::vector< HerbivoreInterface * >	HerbivoreVector
	A list of herbivore interface pointers. More...

typedef std::vector< const HerbivoreInterface * >	ConstHerbivoreVector
	A list of read-only herbivore interface pointers. More...

typedef std::vector< std::shared_ptr< PopulationInterface > >	PopulationList

Enumerations
enum class	ForageType { Grass , Inedible }
	Different types of forage. More...

enum class	ForageValueTag { PositiveAndZero , ZeroToOne }
	Describes which values are allowed in Fauna::ForageValues. More...

enum class	SimMode { Lint , Simulate }
	Mode of the whole simulation program: What is it started for? More...

enum class	FurSeason { Summer , Winter }
	Selector for winter or summer pelt. More...

enum class	Sex { Female , Male }
	The sex of a herbivore. More...

enum class	ConductanceModel { BradleyDeavers1980 , CuylerOeritsland2004 }
	Selector for a function of how to calculate whole-body conductance. More...

enum class	DietComposer { PureGrazer }
	Model to define a herbivore’s diet in a multi-forage scenario. More...

enum class	DigestiveLimit { None , Allometric , FixedFraction , IlliusGordon1992 }
	Algorithm to calculate the daily digestive capacity of a herbivore. More...

enum class	ExpenditureComponent { BasalMetabolicRate , FieldMetabolicRate , Taylor1981 , Thermoregulation , Zhu2018 }
	Algorithm to calculate a herbivore’s daily energy needs. More...

enum class	ForagingLimit { GeneralFunctionalResponse , IlliusOConnor2000 }
	A factor limiting a herbivore’s daily forage harvesting. More...

enum class	NetEnergyModel { GrossEnergyFraction }
	How forage net energy content is calculated. More...

enum class	MortalityFactor { Background , Lifespan , StarvationIlliusOConnor2000 , StarvationThreshold }
	One way how a herbivore can die. More...

enum class	ReproductionModel { None , ConstantMaximum , Linear , Logistic }
	Algorithm to calculate herbivore reproduction time and success. More...

enum class	ForageDistributionAlgorithm { Equally }
	Parameter for selecting algorithm for forage distribution among herbivores. More...

enum class	HerbivoreType { Cohort }

enum class	OutputInterval { Daily , Monthly , Annual , Decadal }
	Time interval for aggregating output. More...

enum class	OutputFormat { TextTables }
	Parameter for selecting the output writer implementation. More...

Functions
double	average (const double a, const double b, const double weight_a=1.0, const double weight_b=1.0)
	Build weighted average of two numbers. More...

const std::string &	get_forage_type_name (const ForageType)
	Get a short, lowercase string identifier for a forage type. More...

ForageValues< ForageValueTag::PositiveAndZero >	foragefractions_to_foragevalues (const ForageValues< ForageValueTag::ZeroToOne > &fractions)
	Convert forage fractions (in [0,1]) into values in [0,∞]. More...

ForageFraction	foragevalues_to_foragefractions (const ForageValues< ForageValueTag::PositiveAndZero > values, const double tolerance)
	Convert forage values to fractional values. More...

ForageFraction	convert_mj_to_kg_proportionally (const ForageValues< ForageValueTag::PositiveAndZero > &mj_per_kg, const ForageValues< ForageValueTag::ZeroToOne > &mj_proportions)
	Convert forage energy to mass keeping the energy-wise proportions. More...

double	get_expenditure_taylor_1981 (const double current_bodymass, const double adult_bodymass)
	Energy expenditure [MJ/ind/day] based on cattle from Taylor et al. (1981) More...

double	get_expenditure_zhu_et_al_2018 (const double bodymass, const double ambient_temperature)
	Daily expenditure by Zhu et al (2018) [70]. More...

double	watts_to_MJ_per_day (const double W)
	Convert Watts (=J/s) to MJ/day. More...

double	get_conductance_bradley_deavers_1980 (const double bodymass)

double	get_conductance_cuyler_oeritsland_2004 (const double bodymass, const FurSeason season)
	Extrapolate conductance from reindeer fur. More...

double	get_thermoregulatory_expenditure (const double thermoneutral_rate, const double conductance, const double core_temperature, const double ambient_temperature)
	Calculate additional energy requirements to keep body temperature. More...

void	create_directories (const std::string path, const mode_t mode=0755)
	Create a folder including all its parent folders. More...

bool	directory_exists (const std::string path)
	Check whether a folder in the filesystem exists. More...

bool	file_exists (const std::string &path)
	Check whether a file in the filesystem exists. More...

void	remove_directory (const std::string &path)
	Delete a directory recursively. More...

double	get_digestive_limit_illius_gordon_1992 (const double bodymass_adult, const double bodymass, const double digestibility, const std::array< double, 3 > &ijk)
	Get digestion-limited daily grass energy intake after Illius & Gordon (1992) More...

ForageEnergyContent	get_net_energy_from_gross_energy (const ForageEnergyContent &ge_content, const Digestibility &digestibility, const double me_coefficient, const double k_maintenance)
	Get net energy content of the forage [MJ/kgDM]. More...

Overload operator * as non-member.
ForageValues< ForageValueTag::PositiveAndZero >	operator* (const double lhs, const ForageFraction &rhs)
	Multiply forage fractions with coefficient, allowing numbers >0. More...

ForageValues< ForageValueTag::PositiveAndZero >	operator* (const ForageFraction &lhs, const ForageValues< ForageValueTag::PositiveAndZero > &rhs)
	Multiply forage fractions with coefficient, allowing numbers >0. More...

ForageValues< ForageValueTag::PositiveAndZero >	operator* (const ForageValues< ForageValueTag::PositiveAndZero > &lhs, const ForageFraction &rhs)
	Multiply forage fractions with coefficient, allowing numbers >0. More...

Variables
const int	FORAGE_TYPE_COUNT = (int)ForageType::Inedible + 1
	Number of elements in ForageType. More...

const std::set< ForageType >	FORAGE_TYPES = get_all_forage_types()

Detailed Description

Namespace for the whole modular megafauna model library.

Typedef Documentation

◆ ConstHerbivoreVector

typedef std::vector<const HerbivoreInterface*> Fauna::ConstHerbivoreVector

A list of read-only herbivore interface pointers.

◆ Digestibility

typedef ForageValues<ForageValueTag::ZeroToOne> Fauna::Digestibility

Digestibility [fraction] for different forage types.

◆ ForageDistribution

typedef std::vector<std::pair<HerbivoreInterface*, ForageMass> > Fauna::ForageDistribution

Data structure defining which herbivore gets what to eat [kgDM/km²].

◆ ForageEnergy

typedef ForageValues<ForageValueTag::PositiveAndZero> Fauna::ForageEnergy

Energy values [MJ] for different forage types.

◆ ForageEnergyContent

typedef ForageValues<ForageValueTag::PositiveAndZero> Fauna::ForageEnergyContent

Net energy content [MJ/kgDM] for different forage types.

◆ ForageFraction

typedef ForageValues<ForageValueTag::ZeroToOne> Fauna::ForageFraction

A fraction for each forage type.

◆ ForageMass

typedef ForageValues<ForageValueTag::PositiveAndZero> Fauna::ForageMass

Dry matter mass values [kgDM or kgDM/km²] for different forage types.

◆ HabitatList

typedef std::list<const Habitat*> Fauna::HabitatList

A list of Habitat pointers.

◆ HerbivoreVector

typedef std::vector<HerbivoreInterface*> Fauna::HerbivoreVector

A list of herbivore interface pointers.

◆ HftList

typedef std::vector< std::shared_ptr< const Hft > > Fauna::HftList

List of pointers to Hft objects.

Using shared pointers guarantees that the Hft instances don’t get released while they may still be used.

◆ PopulationList

typedef std::vector<std::shared_ptr<PopulationInterface> > Fauna::PopulationList

Enumeration Type Documentation

◆ ConductanceModel

enum class Fauna::ConductanceModel

strong

Selector for a function of how to calculate whole-body conductance.

See also: Thermoregulation by Conductance

Enumerator

BradleyDeavers1980

Allometric formula from data by Bradley & Deavers (1980) [6].

See also: get_conductance_bradley_deavers_1980()

CuylerOeritsland2004

Allometric formula extrapolating from reindeer fur conductivity.

See also: get_conductance_cuyler_oeritsland_2004

◆ DietComposer

enum class Fauna::DietComposer

strong

Model to define a herbivore’s diet in a multi-forage scenario.

Enumerator
PureGrazer	Eat exclusively grass.

◆ DigestiveLimit

enum class Fauna::DigestiveLimit

strong

Algorithm to calculate the daily digestive capacity of a herbivore.

Enumerator
None	No digestive limit.
Allometric	Dry-matter ingestion is limited to a fraction of live herbivore body mass. The digestion-limited maximum intake, , is a fraction of body mass, , and scales allometrically with body mass in a power law relationship. Attention Too long; didn’t read: It makes sense to set the exponent of Hft::digestion_allometric to the exponent of Hft::expenditure_basal_rate minus 1. Hft::digestion_allometric defines the maximum fractional intake for adult males, $DMI_{ad}$ , as well as the exponent for the allometric scaling to other body masses. The allometric scaling relationship takes the form . Scaling maximum intake allometrically can be better than having a fixed fraction (DigestiveLimit::FixedFraction) for all animals because younger animals (and female adults) have a lower body mass and thus a higher metabolic rate per body mass. Therefore they also need a higher digestive limit. This is important so that young animals are not starving after birth because their intake is restricted. Energy expenditure must be balanced by intake. Let’s take Kleiber’s ¾ power law (Kleiber 1961[36]) as an example. Metabolic rate scales with $M^{0.75}$ , and so the metabolic rate per body mass scales with $M^{0.75}/M = M^{-0.25}$ . The forage intake per body mass must balance these expenditures. In this case it makes sense to say that the maximum relative intake ( ) also scales with $M^{-0.25}$ , which is the same as saying that the absolute intake scales with $M^{0.75}$ . In this example, the (relative) dry-matter intake (DMI) would be: $DMI(M) = DMI_{ad} * M_{ad}^{0.25} * M^{-0.25}$ For nursing newborns, the energy input comes from mother milk, but that is not considered in this model. Newborns are simulated as if they ate fresh forage directly. The very high dry-matter intake limit for newborns stands in place for the energy supply that would come from lactation. Allometric scaling of digestive limit.
FixedFraction	Dry-matter ingestion is limited to a fixed fraction of live body mass. The parameter Hft::digestion_fixed_fraction ( $f_{ad}$ ) defines the maximum daily intake in dry matter as a fraction of body mass.
IlliusGordon1992	Limit digestive limit with get_digestive_limit_illius_gordon_1992().

◆ ExpenditureComponent

enum class Fauna::ExpenditureComponent

strong

Algorithm to calculate a herbivore’s daily energy needs.

Enumerator
BasalMetabolicRate	Only the allometric basal metabolic rate. $BMR = c * M^e$ : Basal metabolic rate [MJ/ind/day]. Fasting expenditure at rest in the thermoneutral zone. : Coefficient, derived from GivenPointAllometry::value_male_adult in Hft::expenditure_basal_rate. : Current body mass [kg/ind] : Allometric exponent (AllometryParameters::exponent in member Hft::expenditure_basal_rate)
FieldMetabolicRate	Allometric basal metabolic rate with FMR constant multiplier. $FMR = f * BMR = f * c * M^e$ : Field metabolic rate [MJ/ind/day]. Total daily energy expenditure. : Constant factor to convert from BMR to FMR. Hft::expenditure_fmr_multiplier. See ExpenditureComponent::BasalMetabolicRate for the other symbols.
Taylor1981	Formula for field metabolic rate in cattle: get_expenditure_taylor_1981()
Thermoregulation	Increased expenditure in lower temperature, see Thermoregulation by Conductance.
Zhu2018	Formula for temperature-dependent field metabolic rate: get_expenditure_zhu_et_al_2018()

◆ ForageDistributionAlgorithm

enum class Fauna::ForageDistributionAlgorithm

strong

Parameter for selecting algorithm for forage distribution among herbivores.

Enumerator
Equally	Equal forage distribution: Fauna::DistributeForageEqually.

◆ ForageType

enum class Fauna::ForageType

strong

Different types of forage.

Enumerator
Grass	Forage type grass.
Inedible	Plants that are not edible for herbivores.

◆ ForageValueTag

enum class Fauna::ForageValueTag

strong

Describes which values are allowed in Fauna::ForageValues.

Enumerator
PositiveAndZero	Only values in interval [0,∞) are allowed.
ZeroToOne	Only values in interval [0,1] are allowed.

◆ ForagingLimit

enum class Fauna::ForagingLimit

strong

A factor limiting a herbivore’s daily forage harvesting.

Enumerator

GeneralFunctionalResponse

Type-II functional response applied “on top” of all other constraints.

This has no empirical basis, but serves as a way to implement an “artificial” smooth negative feedback from forage to fat mass.

Note that this model is functionally similar to ForagingLimit::IlliusOConnor2000, but Illius & O’Connor (2000) [35] use a value for Hft::foraging_half_max_intake_density that is empirical-based.

Here, it shall be explicitely stated that the half-max intake density is not based on observation, but solely used as a means to create a workable forage–intake feedback.

See also: Hft::foraging_half_max_intake_density, HalfMaxIntake

IlliusOConnor2000

Foraging is limited by a functional response towards digestion limit.

Illius & O’Connor (2000) [35] describe daily food intake rate as a Holling Type II functional response (compare HalfMaxIntake). As the maximum daily energy intake they choose the digestive capacity (compare get_digestive_limit_illius_gordon_1992()).

Like in the model of Pachzelt et al. (2013) [49], the grass forage density of the whole patch (habitat) is used (not the sward density

Note: This model for maximum foraging works only for pure grazers (⇒ DietComposer::PureGrazer). GrassForage::get_sward_density()).

See also: Hft::foraging_half_max_intake_density

◆ FurSeason

enum class Fauna::FurSeason

strong

Selector for winter or summer pelt.

Enumerator
Summer	Summer fur.
Winter	Winter fur.

◆ HerbivoreType

enum class Fauna::HerbivoreType

strong

Parameter for selecting the class implementing Fauna::HerbivoreInterface.

Enumerator
Cohort	Use class HerbivoreCohort.

◆ MortalityFactor

enum class Fauna::MortalityFactor

strong

One way how a herbivore can die.

Enumerator
Background	Independent background mortality for juveniles and adults. See also GetBackgroundMortality
Lifespan	A herbivore dies if its age exceeds Hft::life_history_lifespan. See also Fauna::GetSimpleLifespanMortality
StarvationIlliusOConnor2000	Starvation death following Illius & O’Connor (2000). See also Fauna::GetStarvationIlliusOConnor2000
StarvationThreshold	Starvation death at a minimum bodyfat threshold.

◆ NetEnergyModel

enum class Fauna::NetEnergyModel

strong

How forage net energy content is calculated.

See also: Energy Content of Forage

Enumerator
GrossEnergyFraction	Use get_net_energy_from_gross_energy().

◆ OutputFormat

enum class Fauna::OutputFormat

strong

Parameter for selecting the output writer implementation.

Enumerator
TextTables	Use class Output::TextTableWriter.

◆ OutputInterval

enum class Fauna::OutputInterval

strong

Time interval for aggregating output.

Enumerator
Daily	Don’t aggregate output over time, but write every day.
Monthly	Aggregate output for each month.
Annual	Aggregate output for each year.
Decadal	Aggregate output for 10 years intervals.

◆ ReproductionModel

enum class Fauna::ReproductionModel

strong

Algorithm to calculate herbivore reproduction time and success.

Enumerator
None	Disable reproduction all together.
ConstantMaximum	Use class ReproductionConstMax for reproduction.
Linear	Use class ReproductionLinear for reproduction.
Logistic	Use class ReproductionLogistic to calculate reproduction.

◆ Sex

enum class Fauna::Sex

strong

The sex of a herbivore.

Enumerator
Female
Male

◆ SimMode

enum class Fauna::SimMode

strong

Mode of the whole simulation program: What is it started for?

Enumerator

Lint

Only check (“lint”) the instruction file, don’t perform simulations.

See also: linter.cpp

Simulate

Default mode: We want to simulate herbivores.

Function Documentation

◆ average()

double Fauna::average	(	const double	a,
		const double	b,
		const double	weight_a = `1.0`,
		const double	weight_b = `1.0`
	)

Build weighted average of two numbers.

Exceptions

std::invalid_argument	If one weight is smaller than zero.
std::invalid_argument	If the sum of weights is zero.
std::invalid_argument	If one weight is NAN or INFINITY.

Note: NAN is checked by weight_a != weight_a, but this might not work if compiled with g++ with the option -fastmath.

◆ convert_mj_to_kg_proportionally()

ForageFraction Fauna::convert_mj_to_kg_proportionally	(	const ForageValues< ForageValueTag::PositiveAndZero > &	mj_per_kg,
		const ForageValues< ForageValueTag::ZeroToOne > &	mj_proportions
	)

Convert forage energy to mass keeping the energy-wise proportions.

Parameters

mj_per_kg	Energy content of the forage [MJ/kgDM].
mj_proportions	Energy-wise proportions [MJ/MJ]. This doesn’t need to add up to 1.0.

Returns: Mass-wise proportions [kgDM/kgDM] whose sum equals the sum of mj_proportions. When converting back from mass to energy, the proportion relative to each other will be like in mj_proportions.

◆ create_directories()

void Fauna::create_directories	(	const std::string	path,
		const mode_t	mode = `0755`
	)

Create a folder including all its parent folders.

This function works for Windows und Unix systems.

Parameters

path	The absolute or relative path to the final directory. As a file separator use backslash () on Windows and slash (/) on Linux.
mode	File permissions (only applicable to Unix filesystems.

Exceptions

std::runtime_error If an error occurred.

◆ directory_exists()

bool Fauna::directory_exists ( const std::string path )

Check whether a folder in the filesystem exists.

This function works for Windows und Unix systems.

Parameters

path	The absolute or relative path to the directory.

Returns: True if path exists, false if not.

◆ file_exists()

bool Fauna::file_exists ( const std::string & path )

Check whether a file in the filesystem exists.

This function works for Windows und Unix systems.

Parameters

path	The absolute or relative path to the file in question.

Returns: True if path exists, false if not.

◆ foragefractions_to_foragevalues()

ForageValues< ForageValueTag::PositiveAndZero > Fauna::foragefractions_to_foragevalues ( const ForageValues< ForageValueTag::ZeroToOne > & fractions )

Convert forage fractions (in [0,1]) into values in [0,∞].

Parameters

fractions A ForageValues object limited to values between zero and one.

Returns: A ForageValues object that has no upper limit for values.

◆ foragevalues_to_foragefractions()

ForageFraction Fauna::foragevalues_to_foragefractions	(	const ForageValues< ForageValueTag::PositiveAndZero >	values,
		const double	tolerance
	)

Convert forage values to fractional values.

Parameters

values	The object to convert.
tolerance	By how much a value can exceed 1.0 and still be set to 1.0. E.g. `tolerance == 0.1` means that any values from 1.0 to 1.1 will be set to 1.0.

Returns: Forage fractional values within [0,1].

Exceptions

std::invalid_argument	If one number in `values` exceeds `1.0 + tolerance`.
std::invalid_argument	If `tolerance < 0.0`.

◆ get_conductance_bradley_deavers_1980()

double Fauna::get_conductance_bradley_deavers_1980 ( const double bodymass )

inline

Get full body conductance [W/°C] after Bradley & Deavers (1980) [6] The formula is taken from Peters (1983)[53], which is based on data by Bradley & Deavers (1980).

$C = 0.224 * M^{0.574}$

230 conductance values from 192 mammal species with body weights ranging from 3.5 g to 150 kg.

Parameters

bodymass Current body weight [kg/ind].

Exceptions

std::invalid_argument If bodymass <= 0.

Returns: Full body conductance [W/°C].

◆ get_conductance_cuyler_oeritsland_2004()

double Fauna::get_conductance_cuyler_oeritsland_2004	(	const double	bodymass,
		const FurSeason	season
	)

inline

Extrapolate conductance from reindeer fur.

Cuyler & Øritsland (2004)[11] measured conductivity values of reindeer (Rangifer tarandus) pelts in calm air and dry conditions:

0.63 W/(°C*m²) in winter
2.16 W/(°C*m²) in summer

We assume a body mass of 60 kg for an adult reindeer (Soppela et al. 1986 [63]). Body surface is approximated by a formula from Hudson & White (1985) [29] as $0.09*M^{0.66}$ (in m²).

The whole-body conductance in W/°C is then:

for winter $0.63 * 0.09 * 60^{0.66} = 0.8$
for summer $2.16 * 0.09 * 60^{0.66} = 2.9$

Both Bradley & Deavers (1980)[6] and Fristoe et al. (2014)[18] suggest that the allometric exponent for body mass for whole-body conductance among mammals is about 0.57. We derive an allometric function for the conductance $C = x*M^{0.56}$ (in W/°C) that contains the value from reindeer pelts.

$x_{summer} = 2.9 * 60^{-0.56} = 0.29 \\\\ x_{winter} = 0.8 * 60^{-0.56} = 0.08$

Parameters

bodymass	Adult body mass [kg/ind].
season	Whether it’s summer or winter pelt.

Returns: Extrapolated whole-body conductance for an Arctic species [W/°C].

Exceptions

std::invalid_argument If bodymass <= 0.

◆ get_digestive_limit_illius_gordon_1992()

double Fauna::get_digestive_limit_illius_gordon_1992	(	const double	bodymass_adult,
		const double	bodymass,
		const double	digestibility,
		const std::array< double, 3 > &	ijk
	)

Get digestion-limited daily grass energy intake after Illius & Gordon (1992)

The model of digestive passage rates by Illius & Gordon (1992)[33] constrains maximum daily energy intake $I_{dig[MJ/day]}$ by gut size and retention time.

$I_{dig[MJ/day]} = i * e^{jd} * M_{ad_{[kg]}}^{(ke^d+0.73)} * u_g$

e: Euler number
d: proportional digestibility
$M_{ad}$ : Adult body mass in kg
$u_g = (M/M_{ad})^{0.75}$ is a scaling factor for gut capacity, introduced by Illius & Gordon (1999) [34]
Parameters i, j, and k are derived from regression analysis with 12 mammalian herbivores (0.05–547 kg) and are specific to hindgut fermenters and ruminants (Shipley et al. 1999)[61]. They are specified per HFT in Hft::digestion_i_g_1992_ijk

Parameters

bodymass_adult	Body mass [kg] at physical maturity.
bodymass	current body mass [kg/ind]
digestibility	proportional digestibility of the grass forage
ijk	The parameter constants i, j, k for the exponential function.

Returns: Maximum energy intake of grass [MJ/day/ind]

Exceptions

std::invalid_argument	If `bodymass_adult<=0.0`.
std::invalid_argument	If `bodymass<=0.0`
std::logic_error	If `bodymass > bodymass_adult`.

See also: DigestiveLimit::IlliusGordon1992

◆ get_expenditure_taylor_1981()

double Fauna::get_expenditure_taylor_1981	(	const double	current_bodymass,
		const double	adult_bodymass
	)

inline

Energy expenditure [MJ/ind/day] based on cattle from Taylor et al. (1981)

Taylor et al. (1981)[66] Daily energy expenditure is given by

$E [\frac{MJ}{day*ind}] = 0.4 * M * M_{ad}^{-0.27}$

where M is current body mass [kg/ind] and $M_{ad}$ is adult body mass.

Returns: energy expenditure in MJ for one herbivore individual per day [MJ/day/ind]

◆ get_expenditure_zhu_et_al_2018()

double Fauna::get_expenditure_zhu_et_al_2018	(	const double	bodymass,
		const double	ambient_temperature
	)

inline

Daily expenditure by Zhu et al (2018) [70].

$E = \frac{k_2}{e^{k_1*T}} * A^{0.75}$

: Daily energy expenditure [MJ/ind/day].
: Body mass [kg/ind].
: Constant, derived from regression analysis of data from Anderson & Jetz (2005)[1].
: Constant, calibrated to yield a range close to the values in Illius & O’Connor (2000)[35].
Parameters

bodymass Current body mass [kg/ind].

ambient_temperature Long-term mean air temperature [°C].

Returns
Daily energy expenditure per individual [MJ/ind/day].

Exceptions

std::invalid_argument If bodymass <= 0.

See also
Fauna::EC_ZHU_2018

◆ get_forage_type_name()

const std::string & Fauna::get_forage_type_name ( const ForageType ft )

Get a short, lowercase string identifier for a forage type.

The names are

unique,
lowercase,
without blank spaces or tabs, newlines etc.,
without comma oder underscore (which might be used to combine column names in the output).

◆ get_net_energy_from_gross_energy()

ForageEnergyContent Fauna::get_net_energy_from_gross_energy	(	const ForageEnergyContent &	ge_content,
		const Digestibility &	digestibility,
		const double	me_coefficient,
		const double	k_maintenance
	)

inline

Get net energy content of the forage [MJ/kgDM].

See Energy Content of Forage for a detailed description of this net energy model.

[f NE = ME * k_m = DE * ME/DE * k_m = GE * DMD * ME/DE * k_m ]f

Parameters

ge_content	Gross energy (GE), also called combustion energy, in dry matter. [MJ/kgDM]
digestibility	Proportional dry-matter digestibility (DMD).
me_coefficient	Metabolizable energy coefficient, i.e. the ratio of metabolizable energy to digestible energy, ME/DE. [fractional]
k_maintenance	Net energy coefficient (k_m) for maintenance, i.e. the proportion of metabolizable remaining energy after heat increment. [fractional]

Returns: Net energy content [MJ/kgDM].

Exceptions

std::invalid_argument If either me_coefficient or k_maintenance not in interval (0,1).

See also: Energy Content of Forage; Parameters::forage_gross_energy; Hft::digestion_me_coefficient; Hft::digestion_k_maintenance; Hft::digestion_net_energy_model; NetEnergyModel

◆ get_thermoregulatory_expenditure()

double Fauna::get_thermoregulatory_expenditure	(	const double	thermoneutral_rate,
		const double	conductance,
		const double	core_temperature,
		const double	ambient_temperature
	)

Calculate additional energy requirements to keep body temperature.

Please see Thermoregulation by Conductance for the formulas and concepts.

Parameters

thermoneutral_rate	Thermoneutral expenditure [MJ/ind/day].
conductance	Whole-body thermal conductance of the animal [W/°C].
core_temperature	Body core temperature [°C].
ambient_temperature	Ambient air temperature [°C].

Returns: Additional expenditure for thermoregulation, i.e. heat loss [MJ/ind/day].

Exceptions

std::invalid_argument If any parameter is out of range.

◆ operator*() [1/3]

ForageValues< ForageValueTag::PositiveAndZero > Fauna::operator*	(	const double	lhs,
		const ForageFraction &	rhs
	)

inline

Multiply forage fractions with coefficient, allowing numbers >0.

Note that this function takes the double value on the left side whereas the member function ForageValues<>::operator*() takes the double value as the right operand and returns a ForageValues<> object of the same template, which doesn’t allow numbers exceeding 1.0 in case of the ForageFraction (=ForageValues<ForageValueTag::ZeroToOne>) class.

◆ operator*() [2/3]

ForageValues< ForageValueTag::PositiveAndZero > Fauna::operator*	(	const ForageFraction &	lhs,
		const ForageValues< ForageValueTag::PositiveAndZero > &	rhs
	)

inline

Multiply forage fractions with coefficient, allowing numbers >0.

Note that this function takes the double value on the left side whereas the member function ForageValues<>::operator*() takes the double value as the right operand and returns a ForageValues<> object of the same template, which doesn’t allow numbers exceeding 1.0 in case of the ForageFraction (=ForageValues<ForageValueTag::ZeroToOne>) class.

◆ operator*() [3/3]

ForageValues< ForageValueTag::PositiveAndZero > Fauna::operator*	(	const ForageValues< ForageValueTag::PositiveAndZero > &	lhs,
		const ForageFraction &	rhs
	)

inline

Multiply forage fractions with coefficient, allowing numbers >0.

Note that this function takes the double value on the left side whereas the member function ForageValues<>::operator*() takes the double value as the right operand and returns a ForageValues<> object of the same template, which doesn’t allow numbers exceeding 1.0 in case of the ForageFraction (=ForageValues<ForageValueTag::ZeroToOne>) class.

◆ remove_directory()

void Fauna::remove_directory ( const std::string & path )

Delete a directory recursively.

Warning: Don’t use this function (in its current implementation) for the actual simulation code. It uses system() to call to the shell, but might fail without warning.

Parameters

path	The absolute or relative path to the directory.

Exceptions

std::invalid_argument	If `path` does not exist.
std::runtime_error	If the system shell is not available throuh `system()`.

◆ watts_to_MJ_per_day()

double Fauna::watts_to_MJ_per_day ( const double W )

inline

Convert Watts (=J/s) to MJ/day.

Variable Documentation

◆ FORAGE_TYPE_COUNT

const int Fauna::FORAGE_TYPE_COUNT = (int)ForageType::Inedible + 1

Number of elements in ForageType.

◆ FORAGE_TYPES

const std::set< ForageType > Fauna::FORAGE_TYPES = get_all_forage_types()

Set with all enum entries of ForageType except ForageType::Inedible. This set serves mainly the purpose to iterate easily over all forage types:

for (const auto& forage_type : FORAGE_TYPES) {
  \/\/Do your calculations
}

bodymass	Current body mass [kg/ind].
ambient_temperature	Long-term mean air temperature [°C].

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Detailed Description

Typedef Documentation

◆ ConstHerbivoreVector

◆ Digestibility

◆ ForageDistribution

◆ ForageEnergy

◆ ForageEnergyContent

◆ ForageFraction

◆ ForageMass

◆ HabitatList

◆ HerbivoreVector

◆ HftList

◆ PopulationList

Enumeration Type Documentation

◆ ConductanceModel

◆ DietComposer

◆ DigestiveLimit

◆ ExpenditureComponent

◆ ForageDistributionAlgorithm

◆ ForageType

◆ ForageValueTag

◆ ForagingLimit

◆ FurSeason

◆ HerbivoreType

◆ MortalityFactor

◆ NetEnergyModel

◆ OutputFormat

◆ OutputInterval

◆ ReproductionModel

◆ Sex

◆ SimMode

Function Documentation

◆ average()

◆ convert_mj_to_kg_proportionally()

◆ create_directories()

◆ directory_exists()

◆ file_exists()

◆ foragefractions_to_foragevalues()

◆ foragevalues_to_foragefractions()

◆ get_conductance_bradley_deavers_1980()

◆ get_conductance_cuyler_oeritsland_2004()

◆ get_digestive_limit_illius_gordon_1992()

◆ get_expenditure_taylor_1981()

◆ get_expenditure_zhu_et_al_2018()

◆ get_forage_type_name()

◆ get_net_energy_from_gross_energy()

◆ get_thermoregulatory_expenditure()

◆ operator*() [1/3]

◆ operator*() [2/3]

◆ operator*() [3/3]

◆ remove_directory()

◆ watts_to_MJ_per_day()

Variable Documentation

◆ FORAGE_TYPE_COUNT

◆ FORAGE_TYPES