Classes
class	AbstractTreatment
	Abstract interface for treatment classes. More...

class	BaseTreatment
	Base treatment class. More...

class	CauchyKernel
	Dispersal kernel for cauchy distribution class utilized by RadialKernel and DeterministicKernel. More...

class	Config

class	Date
	Representation and manipulation of a date for the simulation. More...

class	DeterministicDispersalKernel
	Dispersal kernel for deterministic spread to cell with highest probability of spread. More...

class	DeterministicNeighborDispersalKernel
	Dispersal kernel for deterministic spread to a next cell. More...

class	ExponentialKernel
	Dispersal kernel for exponential distribution class utilized by RadialKernel and DeterministicKernel. More...

class	ExponentialPowerKernel
	Dispersal kernel for exponential power distribution class utilized by RadialKernel and DeterministicKernel. More...

class	GammaKernel
	Dispersal kernel for gamma distribution class utilized by RadialKernel and DeterministicKernel. More...

class	HyperbolicSecantKernel
	Dispersal kernel for hyperbolic secant class utilized by RadialKernel and DeterministicKernel. More...

class	LogisticKernel
	Dispersal kernel for logistic distribution class utilized by RadialKernel and DeterministicKernel. More...

class	LogNormalKernel
	Dispersal kernel for log normal distribution class utilized by RadialKernel and DeterministicKernel. More...

class	Model

class	NaturalAnthropogenicDispersalKernel
	Dispersal kernel template for natural and anthropogenic distance dispersal. More...

class	Network
	Network structure and algorithms. More...

class	NetworkDispersalKernel
	Dispersal kernel for dispersal over a network. More...

class	NormalKernel
	Dispersal kernel for normal distribution class utilized by RadialKernel and DeterministicKernel. More...

class	PesticideTreatment
	Pesticide treatment class. More...

class	PowerLawKernel
	Dispersal kernel for power law distribution class utilized by RadialKernel and DeterministicKernel. More...

class	QuarantineEscape
	Class storing and computing quarantine escap metrics for one simulation. More...

class	RadialDispersalKernel
	Dispersal kernel providing all the radial kernels. More...

class	Raster
	Representation of a raster image. More...

class	Scheduler

class	Season
	Holds beginning and end of a season and decides what is in season. More...

class	SimpleTreatment
	Simple treatment class. More...

class	Simulation
	The main class to control the spread simulation. More...

class	SpreadRate
	Class storing and computing step spread rate for one simulation. More...

class	Step
	Representation and manipulation of a date for the simulation. More...

class	SwitchDispersalKernel
	Dispersal kernel providing all the radial kernels. More...

class	Treatments
	Treatments class manages all treatments. More...

class	UniformDispersalKernel
	Dispersal kernel for random uniform dispersal over the whole landscape. More...

class	VonMisesDistribution
	Von Mises Distribution (Circular data distribution) More...

class	WeibullKernel
	Dispersal kernel for weibull distribution class utilized by RadialKernel and DeterministicKernel. More...

Typedefs
template<typename IntegerRaster , typename RasterIndex >
using	DispersalKernel = NaturalAnthropogenicDispersalKernel< SwitchDispersalKernel< IntegerRaster, RasterIndex >, SwitchDispersalKernel< IntegerRaster, RasterIndex > >
	Dispersal kernel supporting all available kernels for natural and anthropogenic distance spread. More...

typedef std::tuple< double, Direction >	DistDir

typedef std::tuple< bool, DistDir >	EscapeDistDir

typedef std::vector< EscapeDistDir >	EscapeDistDirs

Enumerations
enum	DispersalKernelType { DispersalKernelType::Cauchy, DispersalKernelType::Exponential, DispersalKernelType::Uniform, DispersalKernelType::DeterministicNeighbor, DispersalKernelType::PowerLaw, DispersalKernelType::HyperbolicSecant, DispersalKernelType::Gamma, DispersalKernelType::ExponentialPower, DispersalKernelType::Weibull, DispersalKernelType::Normal, DispersalKernelType::LogNormal, DispersalKernelType::Logistic, DispersalKernelType::Network, DispersalKernelType::None }
	Type of dispersal kernel. More...

enum	StepUnit { StepUnit::Day, StepUnit::Week, StepUnit::Month }
	Enum for step unit. More...

enum	ModelType { ModelType::SusceptibleInfected, ModelType::SusceptibleExposedInfected }
	The type of a epidemiological model (SI or SEI) More...

enum	TreatmentApplication { TreatmentApplication::Ratio, TreatmentApplication::AllInfectedInCell }
	The enum to decide how treatment is applied. More...

Functions
std::ostream &	operator<< (std::ostream &os, const Date &d)

bool	operator> (const Date &d1, const Date &d2)

bool	operator<= (const Date &d1, const Date &d2)

bool	operator< (const Date &d1, const Date &d2)

bool	operator>= (const Date &d1, const Date &d2)

bool	operator== (const Date &d1, const Date &d2)

bool	operator!= (const Date &d1, const Date &d2)

DispersalKernelType	kernel_type_from_string (const std::string &text)
	Get a corresponding enum value for a string which is a kernel name. More...

DispersalKernelType	kernel_type_from_string (const char *text)
	Overload which allows to pass C-style string which is nullptr (NULL) More...

std::ostream &	operator<< (std::ostream &os, const Direction &obj)

template<typename IntegerRaster >
double	quarantine_escape_probability (const std::vector< QuarantineEscape< IntegerRaster >> escape_infos, unsigned step)
	Reports probability of escaping quarantine based on multiple runs for certain step. More...

template<typename IntegerRaster >
std::vector< DistDir >	distance_direction_to_quarantine (const std::vector< QuarantineEscape< IntegerRaster >> escape_infos, unsigned step)
	Reports minimum distances to quarantine boundary (bbox) and associated distances for each run for certain step. More...

template<typename IntegerRaster >
std::string	write_quarantine_escape (const std::vector< QuarantineEscape< IntegerRaster >> escape_infos, unsigned num_steps)
	Writes quarantine escape summary for all steps into a string. More...

Direction	direction_from_string (const std::string &text)
	Get a corresponding enum value for a string which direction. More...

Direction	direction_from_string (const char *text)
	Overload which allows to pass C-style string which is nullptr (NULL) More...

template<class InputIt1 , class InputIt2 , class BinaryOperation >
BinaryOperation	for_each_zip (InputIt1 first1, InputIt1 last1, InputIt2 first2, BinaryOperation f)
	Iterate over two ranges and apply a binary function which modifies the first parameter. More...

template<typename LeftNumber , typename RightNumber , typename ResultNumber = typename std::common_type<LeftNumber, RightNumber>::type>
Raster< ResultNumber >	operator+ (const Raster< LeftNumber > &lhs, const Raster< RightNumber > &rhs)

template<typename LeftNumber , typename RightNumber , typename ResultNumber = typename std::common_type<LeftNumber, RightNumber>::type>
Raster< ResultNumber >	operator- (const Raster< LeftNumber > &lhs, const Raster< RightNumber > &rhs)

template<typename LeftNumber , typename RightNumber , typename ResultNumber = typename std::common_type<LeftNumber, RightNumber>::type>
Raster< ResultNumber >	operator* (const Raster< LeftNumber > &lhs, const Raster< RightNumber > &rhs)

template<typename LeftNumber , typename RightNumber , typename ResultNumber = typename std::common_type<LeftNumber, RightNumber>::type>
Raster< ResultNumber >	operator/ (const Raster< LeftNumber > &lhs, const Raster< RightNumber > &rhs)

std::ostream &	operator<< (std::ostream &os, const Step &step)

StepUnit	step_unit_enum_from_string (const std::string &text)
	Get step enum from string. More...

unsigned	simulation_step_to_action_step (const std::vector< bool > &action_schedule, unsigned step)
	Converts simulation step to step of actions. More...

unsigned	get_number_of_scheduled_actions (const std::vector< bool > &action_schedule)
	Returns how many actions are scheduled. More...

std::vector< bool >	schedule_from_string (const Scheduler &scheduler, const std::string &frequency, unsigned n=0)
	Get output (export) schedule based on frequency string ("year", "month", "week", "day", "every_n_steps", "final_step"). More...

template<typename Container >
void	rotate_left_by_one (Container &container)
	Rotate elements in a container to the left by one. More...

template<typename Generator >
std::vector< int >	draw_n_from_v (std::vector< int > v, unsigned n, Generator &generator)
	Draws n elements from a vector. More...

ModelType	model_type_from_string (const std::string &text)
	Get a corresponding enum value for a string which is a model type name. More...

ModelType	model_type_from_string (const char *text)
	Overload which allows to pass C-style string which is nullptr (NULL) More...

template<typename Raster >
BBoxFloat	average_spread_rate (const std::vector< SpreadRate< Raster >> &rates, unsigned step)
	Computes average spread rate in n, s, e, w directions from vector of spread rates. More...

template<typename IntegerRaster >
unsigned	sum_of_infected (const IntegerRaster &infected, const std::vector< std::vector< int >> &suitable_cells)
	Computes sum of infected hosts from all cells of a raster. More...

template<typename IntegerRaster >
double	area_of_infected (const IntegerRaster &infected, double ew_res, double ns_res, const std::vector< std::vector< int >> &suitable_cells)
	Computes infected area as number of cell > 0 times cell size. More...

TreatmentApplication	treatment_app_enum_from_string (const std::string &text)
	Get treatment application enum from string. More...

Typedef Documentation

◆ DispersalKernel

template<typename IntegerRaster , typename RasterIndex >

using pops::DispersalKernel = typedef NaturalAnthropogenicDispersalKernel< SwitchDispersalKernel<IntegerRaster, RasterIndex>, SwitchDispersalKernel<IntegerRaster, RasterIndex> >

Dispersal kernel supporting all available kernels for natural and anthropogenic distance spread.

This is a typedef defining the main disperal kernel class in the PoPS library. When you are using the library, this is default choice.

The choices which are allowed by this class are:

                    kernel type
                   /           \
                  /             \
             natural        anthropogenic
            /   |   \          /   |   \
       radial uniform ...   radial uniform ...
       /  | \_____                 |
      /   |       \                |
cauchy exponential ...            ...

The ellipses represent whatever the SwitchDispersalKernel and RadialDispersalKernel classes support.

See NaturalAnthropogenicDispersalKernel and SwitchDispersalKernel for further documentation.

Definition at line 81 of file kernel.hpp.

◆ DistDir

typedef std::tuple<double, Direction> pops::DistDir

Definition at line 37 of file quarantine.hpp.

◆ EscapeDistDir

typedef std::tuple<bool, DistDir> pops::EscapeDistDir

Definition at line 38 of file quarantine.hpp.

◆ EscapeDistDirs

typedef std::vector<EscapeDistDir> pops::EscapeDistDirs

Definition at line 39 of file quarantine.hpp.

Enumeration Type Documentation

◆ DispersalKernelType

enum pops::DispersalKernelType

strong

Type of dispersal kernel.

This contains all kernels supported by the PoPS library and it may be further used by the various classes which support more than one kernel type.

None is to represent no spread in the given context, e.g., no long distance spread.

Enumerator
Cauchy	Cauchy dispersal kernel.
Exponential	Exponential dispersal kernel.
Uniform	Random uniform dispersal kernel.
DeterministicNeighbor	Deterministic immediate neighbor dispersal kernel.
PowerLaw	Power law dispersal kernel.
HyperbolicSecant	Hyperbolic secant dispersal kernel.
Gamma	Gamma dispersal kernel.
ExponentialPower	Exponential power dispersal kernel.
Weibull	Weibull dispersal kernel.
Normal	Normal dispersal kernel.
LogNormal	Log-normal dispersal kernel.
Logistic	Logistic dispersal kernel.
Network	Network spread.
None	No dispersal kernel (no spread)

Definition at line 53 of file kernel_types.hpp.

◆ ModelType

enum pops::ModelType

strong

The type of a epidemiological model (SI or SEI)

Enumerator
SusceptibleInfected	SI (susceptible - infected)
SusceptibleExposedInfected	SEI (susceptible - exposed - infected)

Definition at line 60 of file simulation.hpp.

◆ StepUnit

enum pops::StepUnit

strong

Enum for step unit.

Enumerator
Day
Week
Month

Definition at line 66 of file scheduling.hpp.

◆ TreatmentApplication

enum pops::TreatmentApplication

strong

The enum to decide how treatment is applied.

Enumerator
Ratio	A ratio is applied to all treated rasters.
AllInfectedInCell	All infected individuals are removed, rest by ratio.

Definition at line 36 of file treatments.hpp.

Function Documentation

◆ area_of_infected()

template<typename IntegerRaster >

double pops::area_of_infected	(	const IntegerRaster &	infected,
		double	ew_res,
		double	ns_res,
		const std::vector< std::vector< int >> &	suitable_cells
	)

Computes infected area as number of cell > 0 times cell size.

Definition at line 42 of file statistics.hpp.

◆ average_spread_rate()

template<typename Raster >

BBoxFloat pops::average_spread_rate	(	const std::vector< SpreadRate< Raster >> &	rates,
		unsigned	step
	)

Computes average spread rate in n, s, e, w directions from vector of spread rates.

Checks if any rate is nan to not include it in the average.

Definition at line 193 of file spread_rate.hpp.

◆ direction_from_string() [1/2]

Direction pops::direction_from_string ( const char * text )

inline

Overload which allows to pass C-style string which is nullptr (NULL)

Definition at line 77 of file radial_kernel.hpp.

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◆ direction_from_string() [2/2]

Direction pops::direction_from_string ( const std::string & text )

inline

Get a corresponding enum value for a string which direction.

Throws an std::invalid_argument exception if the values was not found or is not supported (which is the same thing).

Definition at line 51 of file radial_kernel.hpp.

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◆ distance_direction_to_quarantine()

template<typename IntegerRaster >

std::vector<DistDir> pops::distance_direction_to_quarantine	(	const std::vector< QuarantineEscape< IntegerRaster >>	escape_infos,
		unsigned	step
	)

Reports minimum distances to quarantine boundary (bbox) and associated distances for each run for certain step.

If in certain runs infection escaped, it reports nan for distance and None for direction.

Definition at line 256 of file quarantine.hpp.

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◆ draw_n_from_v()

template<typename Generator >

std::vector<int> pops::draw_n_from_v	(	std::vector< int >	v,
		unsigned	n,
		Generator &	generator
	)

Draws n elements from a vector.

Expects n to be equal or less than v.size().

Definition at line 48 of file simulation.hpp.

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◆ for_each_zip()

template<class InputIt1 , class InputIt2 , class BinaryOperation >

BinaryOperation pops::for_each_zip	(	InputIt1	first1,
		InputIt1	last1,
		InputIt2	first2,
		BinaryOperation	f
	)

Iterate over two ranges and apply a binary function which modifies the first parameter.

Definition at line 35 of file raster.hpp.

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◆ get_number_of_scheduled_actions()

unsigned pops::get_number_of_scheduled_actions ( const std::vector< bool > & action_schedule )

Returns how many actions are scheduled.

action_schedule: [F, T, F, F, F, T, F] -> 2

Definition at line 390 of file scheduling.hpp.

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◆ kernel_type_from_string() [1/2]

DispersalKernelType pops::kernel_type_from_string ( const char * text )

inline

Overload which allows to pass C-style string which is nullptr (NULL)

Definition at line 128 of file kernel_types.hpp.

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◆ kernel_type_from_string() [2/2]

DispersalKernelType pops::kernel_type_from_string ( const std::string & text )

inline

Get a corresponding enum value for a string which is a kernel name.

Throws an std::invalid_argument exception if the values was not found or is not supported (which is the same thing).

Definition at line 76 of file kernel_types.hpp.

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◆ model_type_from_string() [1/2]

ModelType pops::model_type_from_string ( const char * text )

inline

Overload which allows to pass C-style string which is nullptr (NULL)

See also: model_type_from_string(const std::string& text)

Definition at line 92 of file simulation.hpp.

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◆ model_type_from_string() [2/2]

ModelType pops::model_type_from_string ( const std::string & text )

inline

Get a corresponding enum value for a string which is a model type name.

Throws an std::invalid_argument exception if the value was not found or is not supported (which is the same thing).

Definition at line 71 of file simulation.hpp.

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◆ operator!=()

bool pops::operator!=	(	const Date &	d1,
		const Date &	d2
	)

Definition at line 272 of file date.hpp.

◆ operator*()

template<typename LeftNumber , typename RightNumber , typename ResultNumber = typename std::common_type<LeftNumber, RightNumber>::type>

Raster<ResultNumber> pops::operator*	(	const Raster< LeftNumber > &	lhs,
		const Raster< RightNumber > &	rhs
	)

Definition at line 574 of file raster.hpp.

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◆ operator+()

template<typename LeftNumber , typename RightNumber , typename ResultNumber = typename std::common_type<LeftNumber, RightNumber>::type>

Raster<ResultNumber> pops::operator+	(	const Raster< LeftNumber > &	lhs,
		const Raster< RightNumber > &	rhs
	)

Definition at line 530 of file raster.hpp.

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◆ operator-()

template<typename LeftNumber , typename RightNumber , typename ResultNumber = typename std::common_type<LeftNumber, RightNumber>::type>

Raster<ResultNumber> pops::operator-	(	const Raster< LeftNumber > &	lhs,
		const Raster< RightNumber > &	rhs
	)

Definition at line 552 of file raster.hpp.

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◆ operator/()

template<typename LeftNumber , typename RightNumber , typename ResultNumber = typename std::common_type<LeftNumber, RightNumber>::type>

Raster<ResultNumber> pops::operator/	(	const Raster< LeftNumber > &	lhs,
		const Raster< RightNumber > &	rhs
	)

Definition at line 596 of file raster.hpp.

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◆ operator<()

bool pops::operator<	(	const Date &	d1,
		const Date &	d2
	)

Definition at line 240 of file date.hpp.

◆ operator<<() [1/3]

std::ostream& pops::operator<<	(	std::ostream &	os,
		const Date &	d
	)

Definition at line 109 of file date.hpp.

◆ operator<<() [2/3]

std::ostream& pops::operator<<	(	std::ostream &	os,
		const Direction &	obj
	)

Definition at line 31 of file quarantine.hpp.

◆ operator<<() [3/3]

std::ostream& pops::operator<<	(	std::ostream &	os,
		const Step &	step
	)

Definition at line 57 of file scheduling.hpp.

◆ operator<=()

bool pops::operator<=	(	const Date &	d1,
		const Date &	d2
	)

Definition at line 235 of file date.hpp.

◆ operator==()

bool pops::operator==	(	const Date &	d1,
		const Date &	d2
	)

Definition at line 265 of file date.hpp.

◆ operator>()

bool pops::operator>	(	const Date &	d1,
		const Date &	d2
	)

Definition at line 215 of file date.hpp.

◆ operator>=()

bool pops::operator>=	(	const Date &	d1,
		const Date &	d2
	)

Definition at line 260 of file date.hpp.

◆ quarantine_escape_probability()

template<typename IntegerRaster >

double pops::quarantine_escape_probability	(	const std::vector< QuarantineEscape< IntegerRaster >>	escape_infos,
		unsigned	step
	)

Reports probability of escaping quarantine based on multiple runs for certain step.

1 means 100% probability of escaping.

Definition at line 236 of file quarantine.hpp.

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◆ rotate_left_by_one()

template<typename Container >

void pops::rotate_left_by_one ( Container & container )

Rotate elements in a container to the left by one.

Rotates (moves) elements in a container to the left (anticlockwise) by one. The second element is moved to the front and the first element is moved to the back.

Definition at line 40 of file simulation.hpp.

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◆ schedule_from_string()

std::vector<bool> pops::schedule_from_string	(	const Scheduler &	scheduler,
		const std::string &	frequency,
		unsigned	n = `0`
	)

inline

Get output (export) schedule based on frequency string ("year", "month", "week", "day", "every_n_steps", "final_step").

If frequency is "every_n_steps", then output is scheduled every n steps of the simulation.

Throws an std::invalid_argument exception if the value is not supported or the output frequency is not compatible with simulation step (e.g., frequency is weekly, but simulation runs every 2 weeks). If frequency is empty string, empty output schedule is returned.

Definition at line 406 of file scheduling.hpp.

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◆ simulation_step_to_action_step()

unsigned pops::simulation_step_to_action_step	(	const std::vector< bool > &	action_schedule,
		unsigned	step
	)

Converts simulation step to step of actions.

This is useful for getting the right index of lethal temperature file.

schedule: [F, T, F, F, F, T, F] step: 1 -> returns 0 step: 5 -> returns 1

Result for input step any other then 1 and 5 in this case returns valid number but has no particular meaning.

Definition at line 373 of file scheduling.hpp.

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◆ step_unit_enum_from_string()

StepUnit pops::step_unit_enum_from_string ( const std::string & text )

inline

Get step enum from string.

Throws an std::invalid_argument exception if the value is not supported.

Definition at line 79 of file scheduling.hpp.

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◆ sum_of_infected()

template<typename IntegerRaster >

unsigned pops::sum_of_infected	(	const IntegerRaster &	infected,
		const std::vector< std::vector< int >> &	suitable_cells
	)

Computes sum of infected hosts from all cells of a raster.

Definition at line 26 of file statistics.hpp.

◆ treatment_app_enum_from_string()

TreatmentApplication pops::treatment_app_enum_from_string ( const std::string & text )

inline

Get treatment application enum from string.

Throws an std::invalid_argument exception if the value is not supported.

Definition at line 48 of file treatments.hpp.

◆ write_quarantine_escape()

template<typename IntegerRaster >

std::string pops::write_quarantine_escape	(	const std::vector< QuarantineEscape< IntegerRaster >>	escape_infos,
		unsigned	num_steps
	)

Writes quarantine escape summary for all steps into a string.

Uses CSV fomat with commas (step, probability of escape, distance, direction as azimuth from runs). E.g. "0,0.4,1000,0,2000,90,1500,0" If escaped in particular run, there is empty value for that distance and direction (...,1000,0,,,2000,90,...).

Definition at line 278 of file quarantine.hpp.

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Classes

Typedefs

Enumerations

Functions

Typedef Documentation

◆ DispersalKernel

◆ DistDir

◆ EscapeDistDir

◆ EscapeDistDirs

Enumeration Type Documentation

◆ DispersalKernelType

◆ ModelType

◆ StepUnit

◆ TreatmentApplication

Function Documentation

◆ area_of_infected()

◆ average_spread_rate()

◆ direction_from_string() [1/2]

◆ direction_from_string() [2/2]

◆ distance_direction_to_quarantine()

◆ draw_n_from_v()

◆ for_each_zip()

◆ get_number_of_scheduled_actions()

◆ kernel_type_from_string() [1/2]

◆ kernel_type_from_string() [2/2]

◆ model_type_from_string() [1/2]

◆ model_type_from_string() [2/2]

◆ operator!=()

◆ operator*()

◆ operator+()

◆ operator-()

◆ operator/()

◆ operator<()

◆ operator<<() [1/3]

◆ operator<<() [2/3]

◆ operator<<() [3/3]

◆ operator<=()

◆ operator==()

◆ operator>()

◆ operator>=()

◆ quarantine_escape_probability()

◆ rotate_left_by_one()

◆ schedule_from_string()

◆ simulation_step_to_action_step()

◆ step_unit_enum_from_string()

◆ sum_of_infected()

◆ treatment_app_enum_from_string()

◆ write_quarantine_escape()