Populations< FP, Categories > Class Template Reference

CPP API: mio::Populations< FP, Categories > Class Template Reference

CPP API

A class template for compartment populations. More...

#include <populations.h>

Inheritance diagram for mio::Populations< FP, Categories >:

Collaboration diagram for mio::Populations< FP, Categories >:

Public Types
using	Base = CustomIndexArray< UncertainValue< FP >, Categories... >

using	Index = typename Base::Index

Public Types inherited from mio::CustomIndexArray< UncertainValue< FP >, Categories... >
using	const_iterator = typename InternalArrayType::const_iterator

using	Index = ::mio::Index< Tags... >

using	InternalArrayType = Eigen::Array< Type, Eigen::Dynamic, 1 >

using	iterator = typename InternalArrayType::iterator

using	reference = Type &

using	Type = UncertainValue< FP >

using	value_type = Type

Public Member Functions
bool	apply_constraints ()
	Checks whether all compartments have non-negative values. More...

bool	check_constraints () const
	Checks whether all compartments have non-negative values and logs an error if constraint is not satisfied. More...

template<class OtherType >
requires std::convertible_to< typename Base::Type::Type, OtherType > Populations< OtherType, Categories... >	convert () const
	Convert internally stored data to OtherType and save into new Populations. More...

Eigen::VectorX< FP >	get_compartments () const
	get_compartments returns an Eigen copy of the vector of populations. More...

template<class Arr >
decltype(auto)	get_from (Arr &&y, Index const &cats) const
	get_from returns the value of a flat container at the flat index corresponding to set of enum values. More...

template<class T >
FP	get_group_total (mio::Index< T > group_idx) const
	get_group_total returns the total population of a group in one category More...

size_t	get_num_compartments () const
	get_num_compartments returns the number of compartments More...

FP	get_total () const
	get_total returns the total population of all compartments More...

	Populations (Base &&array)
	Create populations by taking ownership of a CustomIndexArray. More...

template<class... Ts>
requires std::is_constructible_v< UncertainValue< FP >, Ts... >	Populations (Index const &sizes, Ts... args)

template<class T >
void	set_difference_from_group_total (Index const &midx, FP total_group_population)
	set_difference_from_group_total sets the total population for a given group from a difference More...

void	set_difference_from_total (Index midx, FP total_population)
	set_difference_from_total takes a total population as input and sets the compartment of a given index to have the difference between the input total population and the current population in all other compartments More...

template<class T >
void	set_group_total (mio::Index< T > group_idx, FP value)
	set_group_total sets the total population for a given group More...

void	set_total (FP value)
	set_total sets the total population More...

Public Member Functions inherited from mio::CustomIndexArray< UncertainValue< FP >, Categories... >
auto &	array ()

auto const &	array () const
	array returns a reference to the internally stored flat array. More...

iterator	begin ()
	Get a start iterator for the elements. More...

const_iterator	begin () const
	Get a start iterator for the elements. More...

requires std::convertible_to< Type, OtherType > CustomIndexArray< OtherType, Tags... >	convert () const
	Convert internally stored data to OtherType and save into new CustomIndexArray. More...

	CustomIndexArray ()
	Create an empty CustomIndexArray with size 0. Use the resize member function to add entries. More...

	CustomIndexArray (Index const &dims, Iter b, Iter e)
	Initializes array with values from a range. More...

iterator	end ()
	Get an end iterator for the elements. More...

const_iterator	end () const
	Get an end iterator for the elements. More...

size_t	get_flat_index (Index const &index) const
	get_flat_index returns the flat index into the stored array, given the indices of each category More...

Ts	m_numel (product(dims))

Ts	m_y (InternalArrayType::Constant(m_numel, 1, Type{std::forward< Ts >(args)...}))

constexpr size_t	numel () const
	numel returns the number of elements More...

CustomIndexArray &	operator= (const Type &scalar)
	Assign the same value to each element of the array. More...

Type &	operator[] (Index const &index)
	returns the entry of the array given a MultiIndex More...

Type const &	operator[] (Index const &index) const
	returns the entry of the array given a flat index index More...

	requires (std::is_constructible_v< Type, Ts... >) CustomIndexArray(Index const &dims
	CustomIndexArray constructor, that initializes the array to constant instances of `CustsomIndexArray::Type`. More...

void	resize (Index new_dims)
	Resize all dimensions, invalidating entries. More...

void	resize (mio::Index< Tag > new_dim)
	Resize a single dimension, invalidating entries. More...

void	serialize (IOContext &io) const
	serialize this. More...

void	set_multiple (const std::vector< typename CustomIndexArray< UncertainValue< FP >, Tags... >::Index > &indices, const UncertainValue< FP > &value)
	Set multiple entries to the same value. More...

mio::Index< Tag >	size () const
	returns the size along the dimension provided as template parameter More...

Index	size () const
	returns the size of the array along all dimensions. More...

bool	operator== (const CustomIndexArray &other) const
	Equality comparison. More...

bool	operator!= (const CustomIndexArray &other) const
	Equality comparison. More...

Slice< Tag, iterator >	slice (Seq< size_t > idx_seq)
	Creates a slice into the multidimensional array. More...

Slice< Tag, const_iterator >	slice (Seq< size_t > idx_seq) const
	Creates a slice into the multidimensional array. More...

Slice< Tag, iterator >	slice (mio::Index< Tag > idx)
	Creates a slice into the multidimensional array. More...

Slice< Tag, const_iterator >	slice (mio::Index< Tag > idx) const
	Creates a slice into the multidimensional array. More...

requires std::is_enum_v< Tag > Slice< Tag, iterator >	slice (Tag idx)
	Creates a slice into the multidimensional array. More...

requires std::is_enum_v< Tag > Slice< Tag, const_iterator >	slice (Tag idx) const
	Creates a slice into the multidimensional array. More...

Static Public Member Functions
template<class IOContext >
static IOResult< Populations >	deserialize (IOContext &io)
	deserialize an object of this class. More...

Static Public Member Functions inherited from mio::CustomIndexArray< UncertainValue< FP >, Categories... >
static IOResult< CustomIndexArray >	deserialize (IOContext &io)
	deserialize an object of this class. More...

Additional Inherited Members
Public Attributes inherited from mio::CustomIndexArray< UncertainValue< FP >, Categories... >
Ts &&	args

Static Protected Member Functions inherited from mio::CustomIndexArray< UncertainValue< FP >, Categories... >
static IOResult< Derived >	deserialize (IOContext &io, Tag< Derived >)
	deserialize an object of a class derived from this class. More...

Detailed Description

template<typename FP, class... Categories>
class mio::Populations< FP, Categories >

A class template for compartment populations.

Populations can be split up into different Categories, e.g. by age group, yearly income group, gender etc. Compartmental models introduce the additional category of infection type. For the SEIR model these are Susceptible, Exposed, Infected and Removed. Every category is assumed to contain a finite number of groups.

This template can be instantiated given an arbitrary set of Categories. The Categories are assumed to be an enum class with a member Count refering to the number of elements in the enum.

The class created from this template contains a "flat array" of compartment populations and some functions for retrieving or setting the populations.

Member Typedef Documentation

◆ Base

template<typename FP , class... Categories>

using mio::Populations< FP, Categories >::Base = CustomIndexArray<UncertainValue<FP>, Categories...>

◆ Index

template<typename FP , class... Categories>

using mio::Populations< FP, Categories >::Index = typename Base::Index

Constructor & Destructor Documentation

◆ Populations() [1/2]

template<typename FP , class... Categories>

template<class... Ts>

requires std::is_constructible_v<UncertainValue<FP>, Ts...> mio::Populations< FP, Categories >::Populations	(	Index const &	sizes,
		Ts...	args
	)

inlineexplicit

◆ Populations() [2/2]

template<typename FP , class... Categories>

mio::Populations< FP, Categories >::Populations ( Base && array )

inlineexplicit

Create populations by taking ownership of a CustomIndexArray.

Member Function Documentation

◆ apply_constraints()

template<typename FP , class... Categories>

bool mio::Populations< FP, Categories >::apply_constraints ( )

inline

Checks whether all compartments have non-negative values.

This function can be used to prevent slighly negative function values in compartment sizes that came out due to roundoff errors if, e.g., population sizes were computed in a complex way. If negative values which are smaller than -1e-10 are found, an error is logged, otherwise, only a warning is logged.

Attention: This function should be used with care. It can not and will not set model parameters and compartments to meaningful values. In most cases it is preferable to use check_constraints, and correct values manually before proceeding with the simulation. The main usage for apply_constraints is in automated tests using random values for initialization.

Returns: Returns true if one (or more) constraint(s) were corrected, otherwise false.

◆ check_constraints()

template<typename FP , class... Categories>

bool mio::Populations< FP, Categories >::check_constraints ( ) const

inline

Checks whether all compartments have non-negative values and logs an error if constraint is not satisfied.

Returns: Returns true if one or more constraints are not satisfied, false otherwise.

◆ convert()

template<typename FP , class... Categories>

template<class OtherType >

requires std::convertible_to<typename Base::Type::Type, OtherType> Populations<OtherType, Categories...> mio::Populations< FP, Categories >::convert ( ) const

inline

Convert internally stored data to OtherType and save into new Populations.

Template Parameters

OtherType The type to convert into.

Returns: New Populations of OtherType with copy of internal data.

◆ deserialize()

template<typename FP , class... Categories>

template<class IOContext >

static IOResult<Populations> mio::Populations< FP, Categories >::deserialize ( IOContext & io )

inlinestatic

deserialize an object of this class.

See also: mio::deserialize

◆ get_compartments()

template<typename FP , class... Categories>

Eigen::VectorX<FP> mio::Populations< FP, Categories >::get_compartments ( ) const

inline

get_compartments returns an Eigen copy of the vector of populations.

This can be used as initial conditions for the ODE solver

Returns: Eigen::VectorX<FP> of populations

◆ get_from()

template<typename FP , class... Categories>

template<class Arr >

decltype(auto) mio::Populations< FP, Categories >::get_from	(	Arr &&	y,
		Index const &	cats
	)		const

inline

get_from returns the value of a flat container at the flat index corresponding to set of enum values.

It is the same as get, except that it takes the values from an outside reference flat container, rather than the initial values stored within this class

TODO: It would be better, to have CustomIndexArray be able to operate on shared data. Maybe using an Eigen::Map

Parameters

y	a reference to a flat container
cats	enum values for each category

Returns: the population of compartment

◆ get_group_total()

template<typename FP , class... Categories>

template<class T >

FP mio::Populations< FP, Categories >::get_group_total ( mio::Index< T > group_idx ) const

inline

get_group_total returns the total population of a group in one category

Parameters

T	enum class for the category
group_idx	enum value of the group

Returns: total population of the group

◆ get_num_compartments()

template<typename FP , class... Categories>

size_t mio::Populations< FP, Categories >::get_num_compartments ( ) const

inline

get_num_compartments returns the number of compartments

This corresponds to the product of the category sizes

Returns: number of compartments

◆ get_total()

template<typename FP , class... Categories>

FP mio::Populations< FP, Categories >::get_total ( ) const

inline

get_total returns the total population of all compartments

Returns: total population

◆ set_difference_from_group_total()

template<typename FP , class... Categories>

template<class T >

void mio::Populations< FP, Categories >::set_difference_from_group_total	(	Index const &	midx,
		FP	total_group_population
	)

inline

set_difference_from_group_total sets the total population for a given group from a difference

This function sets the population size

Parameters

total_population	the new value for the total population
indices	The indices of the compartment
T	The enum class of the category of the group
group_idx	The enum of the group within the category

◆ set_difference_from_total()

template<typename FP , class... Categories>

void mio::Populations< FP, Categories >::set_difference_from_total	(	Index	midx,
		FP	total_population
	)

inline

set_difference_from_total takes a total population as input and sets the compartment of a given index to have the difference between the input total population and the current population in all other compartments

Parameters

indices	the index of the compartment
total_population	the new value for the total population

◆ set_group_total()

template<typename FP , class... Categories>

template<class T >

void mio::Populations< FP, Categories >::set_group_total	(	mio::Index< T >	group_idx,
		FP	value
	)

inline

set_group_total sets the total population for a given group

This function rescales all the compartments populations proportionally. If all compartments have zero population, the total population gets distributed equally over all compartments

Parameters

T	The enum class of the category of the group
group_idx	The enum value of the group within the category
value	the new value for the total population

◆ set_total()

template<typename FP , class... Categories>

void mio::Populations< FP, Categories >::set_total ( FP value )

inline

set_total sets the total population

This function rescales all the compartments populations proportionally. If all compartments have zero population, the total population gets distributed equally over all compartments.

Parameters

value the new value for the total population

Populations&lt; FP, Categories &gt; Class Template Reference

Public Types

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

template<typename FP, class... Categories> class mio::Populations< FP, Categories >

Member Typedef Documentation

◆ Base

◆ Index

Constructor & Destructor Documentation

◆ Populations() [1/2]

◆ Populations() [2/2]

Member Function Documentation

◆ apply_constraints()

◆ check_constraints()

◆ convert()

◆ deserialize()

◆ get_compartments()

◆ get_from()

◆ get_group_total()

◆ get_num_compartments()

◆ get_total()

◆ set_difference_from_group_total()

◆ set_difference_from_total()

◆ set_group_total()

◆ set_total()

Populations< FP, Categories > Class Template Reference

template<typename FP, class... Categories>
class mio::Populations< FP, Categories >