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epiworld.hpp
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epiworld.hpp
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#include <vector>
#include <functional>
#include <memory>
#include <stdexcept>
#include <random>
#include <fstream>
#include <string>
#include <map>
#include <unordered_map>
#include <chrono>
#include <climits>
#include <cstdint>
#include <algorithm>
#include <regex>
#ifndef EPIWORLD_HPP
#define EPIWORLD_HPP
/* Versioning */
#define EPIWORLD_VERSION_MAJOR 0
#define EPIWORLD_VERSION_MINOR 4
#define EPIWORLD_VERSION_PATCH 0
static const int epiworld_version_major = EPIWORLD_VERSION_MAJOR;
static const int epiworld_version_minor = EPIWORLD_VERSION_MINOR;
static const int epiworld_version_patch = EPIWORLD_VERSION_PATCH;
namespace epiworld {
/*//////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
Start of -include/epiworld/config.hpp-
////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////*/
#ifndef EPIWORLD_CONFIG_HPP
#define EPIWORLD_CONFIG_HPP
#ifndef printf_epiworld
#define printf_epiworld fflush(stdout);printf
#endif
#ifndef EPIWORLD_MAXNEIGHBORS
#define EPIWORLD_MAXNEIGHBORS 1048576
#endif
#if defined(_OPENMP) || defined(__OPENMP)
#include <omp.h>
// #else
// #define omp_get_thread_num() 0
// #define omp_set_num_threads() 1
#endif
#ifndef epiworld_double
#define epiworld_double float
#endif
#ifndef epiworld_fast_int
#define epiworld_fast_int long long int
#endif
#ifndef epiworld_fast_uint
#define epiworld_fast_uint unsigned long long int
#endif
#define EPI_DEFAULT_TSEQ int
template<typename TSeq = EPI_DEFAULT_TSEQ>
class Model;
template<typename TSeq = EPI_DEFAULT_TSEQ>
class Agent;
template<typename TSeq = EPI_DEFAULT_TSEQ>
class PersonTools;
template<typename TSeq = EPI_DEFAULT_TSEQ>
class Virus;
template<typename TSeq = EPI_DEFAULT_TSEQ>
class Viruses;
template<typename TSeq = EPI_DEFAULT_TSEQ>
class Viruses_const;
template<typename TSeq = EPI_DEFAULT_TSEQ>
class Tool;
template<typename TSeq = EPI_DEFAULT_TSEQ>
class Tools;
template<typename TSeq = EPI_DEFAULT_TSEQ>
class Tools_const;
template<typename TSeq = EPI_DEFAULT_TSEQ>
class Entity;
template<typename TSeq = EPI_DEFAULT_TSEQ>
using VirusPtr = std::shared_ptr< Virus< TSeq > >;
template<typename TSeq = EPI_DEFAULT_TSEQ>
using ToolPtr = std::shared_ptr< Tool< TSeq > >;
template<typename TSeq = EPI_DEFAULT_TSEQ>
using ToolFun = std::function<epiworld_double(Tool<TSeq>&,Agent<TSeq>*,VirusPtr<TSeq>,Model<TSeq>*)>;
template<typename TSeq = EPI_DEFAULT_TSEQ>
using MixerFun = std::function<epiworld_double(Agent<TSeq>*,VirusPtr<TSeq>,Model<TSeq>*)>;
template<typename TSeq = EPI_DEFAULT_TSEQ>
using MutFun = std::function<bool(Agent<TSeq>*,Virus<TSeq>&,Model<TSeq>*)>;
template<typename TSeq = EPI_DEFAULT_TSEQ>
using PostRecoveryFun = std::function<void(Agent<TSeq>*,Virus<TSeq>&,Model<TSeq>*)>;
template<typename TSeq = EPI_DEFAULT_TSEQ>
using VirusFun = std::function<epiworld_double(Agent<TSeq>*,Virus<TSeq>&,Model<TSeq>*)>;
template<typename TSeq = EPI_DEFAULT_TSEQ>
using UpdateFun = std::function<void(Agent<TSeq>*,Model<TSeq>*)>;
template<typename TSeq = EPI_DEFAULT_TSEQ>
using GlobalFun = std::function<void(Model<TSeq>*)>;
template<typename TSeq>
struct Event;
template<typename TSeq = EPI_DEFAULT_TSEQ>
using EventFun = std::function<void(Event<TSeq>&,Model<TSeq>*)>;
/**
* @brief Decides how to distribute viruses at initialization
*/
template<typename TSeq = EPI_DEFAULT_TSEQ>
using VirusToAgentFun = std::function<void(Virus<TSeq>&,Model<TSeq>*)>;
/**
* @brief Decides how to distribute tools at initialization
*/
template<typename TSeq = EPI_DEFAULT_TSEQ>
using ToolToAgentFun = std::function<void(Tool<TSeq>&,Model<TSeq>*)>;
/**
* @brief Decides how to distribute entities at initialization
*/
template<typename TSeq = EPI_DEFAULT_TSEQ>
using EntityToAgentFun = std::function<void(Entity<TSeq>&,Model<TSeq>*)>;
/**
* @brief Event data for update an agent
*
* @tparam TSeq
*/
template<typename TSeq = EPI_DEFAULT_TSEQ>
struct Event {
Agent<TSeq> * agent;
VirusPtr<TSeq> virus;
ToolPtr<TSeq> tool;
Entity<TSeq> * entity;
epiworld_fast_int new_state;
epiworld_fast_int queue;
EventFun<TSeq> call;
int idx_agent;
int idx_object;
public:
/**
* @brief Construct a new Event object
*
* All the parameters are rather optional.
*
* @param agent_ Agent over who the action will happen
* @param virus_ Virus to add
* @param tool_ Tool to add
* @param virus_idx Index of virus to be removed (if needed)
* @param tool_idx Index of tool to be removed (if needed)
* @param new_state_ Next state
* @param queue_ Efect on the queue
* @param call_ The action call (if needed)
* @param idx_agent_ Location of agent in object.
* @param idx_object_ Location of object in agent.
*/
Event(
Agent<TSeq> * agent_,
VirusPtr<TSeq> virus_,
ToolPtr<TSeq> tool_,
Entity<TSeq> * entity_,
epiworld_fast_int new_state_,
epiworld_fast_int queue_,
EventFun<TSeq> call_,
int idx_agent_,
int idx_object_
) : agent(agent_), virus(virus_), tool(tool_), entity(entity_),
new_state(new_state_),
queue(queue_), call(call_), idx_agent(idx_agent_), idx_object(idx_object_) {
return;
};
};
/**
* @name Constants in epiworld
*
* @details The following are the default values some probabilities and
* rates take when no value has been specified in the model.
*/
///@{
#ifndef DEFAULT_TOOL_CONTAGION_REDUCTION
#define DEFAULT_TOOL_CONTAGION_REDUCTION 0.0
#endif
#ifndef DEFAULT_TOOL_TRANSMISSION_REDUCTION
#define DEFAULT_TOOL_TRANSMISSION_REDUCTION 0.0
#endif
#ifndef DEFAULT_TOOL_RECOVERY_ENHANCER
#define DEFAULT_TOOL_RECOVERY_ENHANCER 0.0
#endif
#ifndef DEFAULT_TOOL_DEATH_REDUCTION
#define DEFAULT_TOOL_DEATH_REDUCTION 0.0
#endif
#ifndef EPI_DEFAULT_VIRUS_PROB_INFECTION
#define EPI_DEFAULT_VIRUS_PROB_INFECTION 1.0
#endif
#ifndef EPI_DEFAULT_VIRUS_PROB_RECOVERY
#define EPI_DEFAULT_VIRUS_PROB_RECOVERY 0.1428
#endif
#ifndef EPI_DEFAULT_VIRUS_PROB_DEATH
#define EPI_DEFAULT_VIRUS_PROB_DEATH 0.0
#endif
#ifndef EPI_DEFAULT_INCUBATION_DAYS
#define EPI_DEFAULT_INCUBATION_DAYS 7.0
#endif
///@}
#ifdef EPI_DEBUG
#define EPI_DEBUG_PRINTF printf_epiworld
#define EPI_DEBUG_ERROR(etype, msg) \
(etype)("[[epi-debug]] (error) " + std::string(msg));
#define EPI_DEBUG_NOTIFY_ACTIVE() \
EPI_DEBUG_PRINTF("DEBUGGING ON (compiled with EPI_DEBUG defined)%s\n", "");
#define EPI_DEBUG_ALL_NON_NEGATIVE(vect) \
for (auto & v : vect) \
if (static_cast<double>(v) < 0.0) \
throw EPI_DEBUG_ERROR(std::logic_error, "A negative value not allowed.");
#define EPI_DEBUG_SUM_DBL(vect, num) \
double _epi_debug_sum = 0.0; \
for (auto & v : vect) \
{ \
_epi_debug_sum += static_cast<double>(v);\
if (_epi_debug_sum > static_cast<double>(num)) \
throw EPI_DEBUG_ERROR(std::logic_error, "The sum of elements not reached."); \
}
#define EPI_DEBUG_SUM_INT(vect, num) \
int _epi_debug_sum = 0; \
for (auto & v : vect) \
{ \
_epi_debug_sum += static_cast<int>(v);\
if (_epi_debug_sum > static_cast<int>(num)) \
throw EPI_DEBUG_ERROR(std::logic_error, "The sum of elements not reached."); \
}
#define EPI_DEBUG_VECTOR_MATCH_INT(a, b, c) \
if (a.size() != b.size()) {\
EPI_DEBUG_PRINTF("In '%s'", std::string(c).c_str()); \
EPI_DEBUG_PRINTF("Size of vector a: %lu\n", (a).size());\
EPI_DEBUG_PRINTF("Size of vector b: %lu\n", (b).size());\
throw EPI_DEBUG_ERROR(std::length_error, "The vectors do not match size."); \
}\
for (int _i = 0; _i < static_cast<int>(a.size()); ++_i) \
if (a[_i] != b[_i]) {\
EPI_DEBUG_PRINTF("In '%s'", std::string(c).c_str()); \
EPI_DEBUG_PRINTF("Iterating the last 5 values%s:\n", ""); \
for (int _j = std::max(0, static_cast<int>(_i) - 4); _j <= _i; ++_j) \
{ \
EPI_DEBUG_PRINTF( \
"a[%i]: %i; b[%i]: %i\n", \
_j, \
static_cast<int>(a[_j]), \
_j, static_cast<int>(b[_j])); \
} \
throw EPI_DEBUG_ERROR(std::logic_error, "The vectors do not match."); \
}
#define EPI_DEBUG_FAIL_AT_TRUE(a,b) \
if (a) \
{\
throw EPI_DEBUG_ERROR(std::logic_error, b); \
}
#define epiexception(a) std::logic_error
#else
#define EPI_DEBUG_PRINTF(fmt, ...)
#define EPI_DEBUG_ERROR(fmt, ...)
#define EPI_DEBUG_NOTIFY_ACTIVE()
#define EPI_DEBUG_ALL_NON_NEGATIVE(vect)
#define EPI_DEBUG_SUM_DBL(vect, num)
#define EPI_DEBUG_SUM_INT(vect, num)
#define EPI_DEBUG_VECTOR_MATCH_INT(a, b, c)
#define EPI_DEBUG_FAIL_AT_TRUE(a, b) \
if (a) \
return false;
#define epiexception(a) a
#endif
#if defined(EPI_DEBUG_NO_THREAD_ID) || (!defined(__OPENMP) && !defined(_OPENMP))
#define EPI_GET_THREAD_ID() 0
#else
#define EPI_GET_THREAD_ID() omp_get_thread_num()
#endif
#endif
/*//////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
End of -include/epiworld/config.hpp-
////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////*/
/*//////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
Start of -include/epiworld/epiworld-macros.hpp-
////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////*/
#ifndef EPIWORLD_MACROS_HPP
#define EPIWORLD_MACROS_HPP
/**
* @brief Helper macro to define a new tool
*
*/
#define EPI_NEW_TOOL(fname,tseq) inline epiworld_double \
(fname)(\
epiworld::Tool< tseq > & t, \
epiworld::Agent< tseq > * p, \
std::shared_ptr<epiworld::Virus< tseq >> v, \
epiworld::Model< tseq > * m\
)
/**
* @brief Create a Tool within a function
*
*/
#define EPI_NEW_TOOL_LAMBDA(funname,tseq) \
epiworld::ToolFun<tseq> funname = \
[](epiworld::Tool<tseq> & t, \
epiworld::Agent<tseq> * p, \
std::shared_ptr<epiworld::Virus<tseq>> v, \
epiworld::Model<tseq> * m) -> epiworld_double
/**
* @brief Helper macro for accessing model parameters
*
*/
#define EPI_PARAMS(i) m->operator()(i)
/**
* @brief Helper macro for defining Mutation Functions
*
*/
#define EPI_NEW_MUTFUN(funname,tseq) inline bool \
(funname)(\
epiworld::Agent<tseq> * p, \
epiworld::Virus<tseq> & v, \
epiworld::Model<tseq> * m )
#define EPI_NEW_MUTFUN_LAMBDA(funname,tseq) \
epiworld::MutFun<tseq> funname = \
[](epiworld::Agent<tseq> * p, \
epiworld::Virus<tseq> & v, \
epiworld::Model<tseq> * m) -> void
#define EPI_NEW_POSTRECOVERYFUN(funname,tseq) inline void \
(funname)( \
epiworld::Agent<tseq> * p, \
epiworld::Virus<tseq> & v, \
epiworld::Model<tseq> * m\
)
#define EPI_NEW_POSTRECOVERYFUN_LAMBDA(funname,tseq) \
epiworld::PostRecoveryFun<tseq> funname = \
[](epiworld::Agent<tseq> * p, \
epiworld::Virus<tseq> & v , \
epiworld::Model<tseq> * m) -> void
#define EPI_NEW_VIRUSFUN(funname,tseq) inline epiworld_double \
(funname)( \
epiworld::Agent<tseq> * p, \
epiworld::Virus<tseq> & v, \
epiworld::Model<tseq> * m\
)
#define EPI_NEW_VIRUSFUN_LAMBDA(funname,TSeq) \
epiworld::VirusFun<TSeq> funname = \
[](epiworld::Agent<TSeq> * p, \
epiworld::Virus<TSeq> & v, \
epiworld::Model<TSeq> * m) -> epiworld_double
#define EPI_RUNIF() m->runif()
#define EPIWORLD_RUN(a) \
if (a.get_verbose()) \
{ \
printf_epiworld("Running the model...\n");\
} \
for (epiworld_fast_uint niter = 0; niter < a.get_ndays(); ++niter)
#define EPI_TOKENPASTE(a,b) a ## b
#define MPAR(num) *(m->EPI_TOKENPASTE(p,num))
#define EPI_NEW_UPDATEFUN(funname,tseq) inline void \
(funname)(epiworld::Agent<tseq> * p, epiworld::Model<tseq> * m)
#define EPI_NEW_UPDATEFUN_LAMBDA(funname,tseq) \
epiworld::UpdateFun<tseq> funname = \
[](epiworld::Agent<tseq> * p, epiworld::Model<tseq> * m) -> void
#define EPI_NEW_GLOBALFUN(funname,tseq) inline void \
(funname)(epiworld::Model<tseq>* m)
#define EPI_NEW_GLOBALFUN_LAMBDA(funname,tseq) \
epiworld::GlobalFun<tseq> funname = \
[](epiworld::Model<tseq>* m) -> void
#define EPI_NEW_ENTITYTOAGENTFUN(funname,tseq) inline void \
(funname)(epiworld::Entity<tseq> & e, epiworld::Model<tseq> * m)
#define EPI_NEW_ENTITYTOAGENTFUN_LAMBDA(funname,tseq) \
epiworld::EntityToAgentFun<tseq> funname = \
[](epiworld::Entity<tseq> & e, epiworld::Model<tseq> * m) -> void
#endif
/*//////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
End of -include/epiworld/epiworld-macros.hpp-
////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////*/
/*//////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
Start of -include/epiworld/misc.hpp-
////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////*/
#ifndef EPIWORLD_MISC_HPP
#define EPIWORLD_MISC_HPP
template<typename TSeq>
class Model;
template<typename TSeq>
class Agent;
// Relevant for anything using vecHasher function ------------------------------
/**
* @brief Vector hasher
* @tparam T
*/
template <typename T>
struct vecHasher {
std::size_t operator()(std::vector< T > const& dat) const noexcept {
std::hash< T > hasher;
std::size_t hash = hasher(dat[0u]);
// ^ makes bitwise XOR
// 0x9e3779b9 is a 32 bit constant (comes from the golden ratio)
// << is a shift operator, something like lhs * 2^(rhs)
if (dat.size() > 1u)
for (epiworld_fast_uint i = 1u; i < dat.size(); ++i)
hash ^= hasher(dat[i]) + 0x9e3779b9 + (hash<<6) + (hash>>2);
return hash;
}
};
template<typename Ta = epiworld_double, typename Tb = epiworld_fast_uint>
using MapVec_type = std::unordered_map< std::vector< Ta >, Tb, vecHasher<Ta>>;
/**
* @name Default sequence initializers
*
* @details
* If the user does not provide a default sequence, this function is used when
* a sequence needs to be initialized. Some examples: `Agent`, `Virus`, and
* `Tool` need a default sequence.
*
* @tparam TSeq
* @return TSeq
*/
///@{
template<typename TSeq = int>
inline TSeq default_sequence(int seq_count);
// Making it 'static' so that we don't have problems when including the
// header. This is important during the linkage, e.g., in R.
// See https://en.cppreference.com/w/cpp/language/storage_duration#Linkage
// static int _n_sequences_created = 0;
template<>
inline bool default_sequence(int seq_count) {
if (seq_count == 2)
throw std::logic_error("Maximum number of sequence created.");
return seq_count++ ? false : true;
}
template<>
inline int default_sequence(int seq_count) {
return seq_count++;
}
template<>
inline epiworld_double default_sequence(int seq_count) {
return static_cast<epiworld_double>(seq_count++);
}
template<>
inline std::vector<bool> default_sequence(int seq_count) {
if (seq_count == 2)
throw std::logic_error("Maximum number of sequence created.");
return {seq_count++ ? false : true};
}
template<>
inline std::vector<int> default_sequence(int seq_count) {
return {seq_count++};
}
template<>
inline std::vector<epiworld_double> default_sequence(int seq_count) {
return {static_cast<epiworld_double>(seq_count++)};
}
///@}
/**
* @brief Check whether `a` is included in `b`
*
* @tparam Ta Type of `a`. Could be int, epiworld_double, etc.
* @param a Scalar of class `Ta`.
* @param b Vector `std::vector` of class `Ta`.
* @return `true` if `a in b`, and `false` otherwise.
*/
template<typename Ta>
inline bool IN(const Ta & a, const std::vector< Ta > & b) noexcept
{
for (const auto & i : b)
if (a == i)
return true;
return false;
}
/**
* @brief Conditional Weighted Sampling
*
* @details
* The sampling function will draw one of `{-1, 0,...,probs.size() - 1}` in a
* weighted fashion. The probabilities are drawn given that either one or none
* of the cases is drawn; in the latter returns -1.
*
* @param probs Vector of probabilities.
* @param m A `Model`. This is used to draw random uniform numbers.
* @return int If -1 then it means that none got sampled, otherwise the index
* of the entry that got drawn.
*/
template<typename TSeq, typename TDbl>
inline int roulette(
const std::vector< TDbl > & probs,
Model<TSeq> * m
)
{
// Step 1: Computing the prob on none
TDbl p_none = 1.0;
std::vector< int > certain_infection;
certain_infection.reserve(probs.size());
for (epiworld_fast_uint p = 0u; p < probs.size(); ++p)
{
p_none *= (1.0 - probs[p]);
if (probs[p] > (1 - 1e-100))
certain_infection.push_back(p);
}
TDbl r = static_cast<TDbl>(m->runif());
// If there are one or more probs that go close to 1, sample
// uniformly
if (certain_infection.size() > 0)
return certain_infection[std::floor(r * certain_infection.size())];
// Step 2: Calculating the prob of none or single
std::vector< TDbl > probs_only_p(probs.size());
TDbl p_none_or_single = p_none;
for (epiworld_fast_uint p = 0u; p < probs.size(); ++p)
{
probs_only_p[p] = probs[p] * (p_none / (1.0 - probs[p]));
p_none_or_single += probs_only_p[p];
}
// Step 3: Roulette
TDbl cumsum = p_none/p_none_or_single;
if (r < cumsum)
{
return -1;
}
for (epiworld_fast_uint p = 0u; p < probs.size(); ++p)
{
// If it yield here, then bingo, the individual will acquire the disease
cumsum += probs_only_p[p]/(p_none_or_single);
if (r < cumsum)
return static_cast<int>(p);
}
#ifdef EPI_DEBUG
printf_epiworld("[epi-debug] roulette::cumsum = %.4f\n", cumsum);
#endif
return static_cast<int>(probs.size() - 1u);
}
template<typename TSeq>
inline int roulette(std::vector< double > & probs, Model<TSeq> * m)
{
return roulette<TSeq, double>(probs, m);
}
template<typename TSeq>
inline int roulette(std::vector< float > & probs, Model<TSeq> * m)
{
return roulette<TSeq, float>(probs, m);
}
template<typename TSeq>
inline int roulette(
epiworld_fast_uint nelements,
Model<TSeq> * m
)
{
if ((nelements * 2) > m->array_double_tmp.size())
{
throw std::logic_error(
"Trying to sample from more data than there is in roulette!" +
std::to_string(nelements) + " vs " +
std::to_string(m->array_double_tmp.size())
);
}
// Step 1: Computing the prob on none
epiworld_double p_none = 1.0;
epiworld_fast_uint ncertain = 0u;
// std::vector< int > certain_infection;
for (epiworld_fast_uint p = 0u; p < nelements; ++p)
{
p_none *= (1.0 - m->array_double_tmp[p]);
if (m->array_double_tmp[p] > (1 - 1e-100))
m->array_double_tmp[nelements + ncertain++] = p;
// certain_infection.push_back(p);
}
epiworld_double r = m->runif();
// If there are one or more probs that go close to 1, sample
// uniformly
if (ncertain > 0u)
return m->array_double_tmp[nelements + std::floor(ncertain * r)]; // certain_infection[std::floor(r * certain_infection.size())];
// Step 2: Calculating the prob of none or single
// std::vector< epiworld_double > probs_only_p;
epiworld_double p_none_or_single = p_none;
for (epiworld_fast_uint p = 0u; p < nelements; ++p)
{
m->array_double_tmp[nelements + p] =
m->array_double_tmp[p] * (p_none / (1.0 - m->array_double_tmp[p]));
p_none_or_single += m->array_double_tmp[nelements + p];
}
// Step 3: Roulette
epiworld_double cumsum = p_none/p_none_or_single;
if (r < cumsum)
return -1;
for (epiworld_fast_uint p = 0u; p < nelements; ++p)
{
// If it yield here, then bingo, the individual will acquire the disease
cumsum += m->array_double_tmp[nelements + p]/(p_none_or_single);
if (r < cumsum)
return static_cast<int>(p);
}
return static_cast<int>(nelements - 1u);
}
#endif
/*//////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
End of -include/epiworld/misc.hpp-
////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////*/
/*//////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
Start of -include/epiworld/progress.hpp-
////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////*/
#ifndef EPIWORLD_PROGRESS_HPP
#define EPIWORLD_PROGRESS_HPP
#ifndef EPIWORLD_PROGRESS_BAR_WIDTH
#define EPIWORLD_PROGRESS_BAR_WIDTH 80
#endif
/**
* @brief A simple progress bar
*/
class Progress {
private:
int width; ///< Total width size (number of bars)
int n; ///< Total number of iterations
epiworld_double step_size; ///< Size of the step
int last_loc; ///< Last location of the bar
int cur_loc; ///< Last location of the bar
int i; ///< Current iteration step
public:
Progress() {};
Progress(int n_, int width_);
~Progress() {};
void start();
void next();
void end();
};
inline Progress::Progress(int n_, int width_) {
if (n_ < 0)
throw std::invalid_argument("n must be greater or equal than 0.");
if (width_ <= 0)
throw std::invalid_argument("width must be greater than 0");
width = std::max(7, width_ - 7);
n = n_;
step_size = n == 0? width : static_cast<epiworld_double>(width)/
static_cast<epiworld_double>(n);
last_loc = 0;
i = 0;
}
inline void Progress::start()
{
#ifndef EPI_DEBUG
for (int j = 0; j < (width); ++j)
{
printf_epiworld("_");
}
printf_epiworld("\n");
#endif
}
inline void Progress::next() {
if (i == 0)
start();
cur_loc = std::floor((++i) * step_size);
#ifndef EPI_DEBUG
for (int j = 0; j < (cur_loc - last_loc); ++j)
{
printf_epiworld("|");
}
#endif
if (i >= n)
end();
last_loc = cur_loc;
}
inline void Progress::end() {
#ifndef EPI_DEBUG
printf_epiworld(" done.\n");
#endif
}
#endif
/*//////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
End of -include/epiworld/progress.hpp-
////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////*/
/*//////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
Start of -include/epiworld/math/distributions.hpp-
////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////*/
#ifndef EPIWORLD_MATH_DISTRIBUTIONS_HPP
#define EPIWORLD_MATH_DISTRIBUTIONS_HPP
// Implementing the factorial function
/**
* @brief Compute the log of the factorial
*
* @param n Number
*
* @return The log of the factorial
*/
inline double log_factorial(int n)
{
if (n == 0)
return 0.0;
return std::log(static_cast<double>(n)) + log_factorial(n-1);
}
/**
* @brief Compute the Poisson probability
*
* @param k Number of events
* @param lambda Rate
* @param max_n Maximum number of events
* @param as_log Return the log of the probability
*
* @return The Poisson probability
*/
inline double dpois(
int k,
double lambda,
int max_n = 100,
bool as_log = false
)
{
if (max_n < k)
throw std::runtime_error("max_n must be greater than k");
double res = k * std::log(lambda) - lambda - log_factorial(
std::min(k, max_n)
);
return as_log ? res : std::exp(res);
}
/**
* @brief Compute the probability of the generation interval
*
* @details
* If `p_0_approx` is negative, it will be computed using the Poisson
* distribution. If `normalizing` is negative, it will be computed on the fly
*
* @param g Generation interval
* @param S Population size
* @param p_c Probability of contact
* @param p_i Probability of infection
* @param p_r Probability of recovery
* @param p_0_approx Approximation of the probability of not being infected
* @param normalizing Normalizing constant
* @param max_contacts Maximum number of contacts
* @param max_days Maximum number of days
*
* @return The probability of the generation interval
*
*/
inline double dgenint(
int g,
double S,
double p_c,
double p_i,
double p_r,
double & p_0_approx,
double & normalizing,
int max_contacts = 200,
int max_days = 200
) {
if ((g < 1) || (g > max_days))
return 0.0;
if (p_0_approx < 0.0)
{
p_0_approx = 0.0;
for (int i = 0; i < max_contacts; ++i)
{
p_0_approx += std::exp(
dpois(i, S * p_c, max_contacts, true) +
std::log(1.0 - p_i) * static_cast<double>(i)
);
}
}
double g_dbl = static_cast<double>(g);
if (normalizing < 0.0)
{
normalizing = 1.0;
double log1_p_r = std::log(1.0 - p_r);
double log_p_r = std::log(p_r);
double log_p_0_approx = std::log(p_0_approx);
for (int i = 1; i <= max_days; ++i)
{
double i_dbl = static_cast<double>(i);
normalizing -= std::exp(
log1_p_r * (i_dbl - 1.0) +
log_p_r +
log_p_0_approx * (i_dbl - 1.0)
);
}
}
return std::exp(
std::log(1 - p_r) * (g_dbl)+
std::log(p_0_approx) * (g_dbl - 1.0) +
std::log(1.0 - p_0_approx) -
std::log(normalizing)
);
}
// Mean of the generation interval
/**
* @brief Compute the mean of the generation interval
* @param S Population size.
* @param p_c Probability of contact.
* @param p_i Probability of infection.
* @param p_r Probability of recovery.
* @param max_days Maximum number of days.