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Correcting minor bug in dist functions and adding optional overwrite to read and add params #54

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Correcting minor bug in dist functions and adding optional overwrite to read and add params #54

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277db63
Adding negative binomial and geometric distribution rng
gvegayon Feb 20, 2025
5d3269a
Adding poisson
gvegayon Feb 20, 2025
79b8bd3
Forgot about engines
gvegayon Feb 20, 2025
17a4816
Updating the version
gvegayon Feb 20, 2025
2a6700a
Allowing to normalize or not probs
gvegayon Feb 20, 2025
e60f528
Minor fix to verision
gvegayon Feb 20, 2025
fce8670
Adding new test for random numbers
gvegayon Feb 20, 2025
1a2af8c
Test in lognormal
gvegayon Feb 20, 2025
82472d7
Test in lognormal
gvegayon Feb 20, 2025
331845c
Correcting minor bug in dist functions and adding optional overwrite …
gvegayon Feb 21, 2025
56ccc2d
Merge branch 'master' into fix-random-dist-virus-and-patch
gvegayon Feb 26, 2025
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41 changes: 28 additions & 13 deletions epiworld.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@
/* Versioning */
#define EPIWORLD_VERSION_MAJOR 0
#define EPIWORLD_VERSION_MINOR 7
#define EPIWORLD_VERSION_PATCH 0
#define EPIWORLD_VERSION_PATCH 1

static const int epiworld_version_major = EPIWORLD_VERSION_MAJOR;
static const int epiworld_version_minor = EPIWORLD_VERSION_MINOR;
Expand Down Expand Up @@ -6964,8 +6964,10 @@ class Model {
*
*/
///@{
epiworld_double add_param(epiworld_double initial_val, std::string pname);
void read_params(std::string fn);
epiworld_double add_param(
epiworld_double initial_val, std::string pname, bool overwrite = false
);
void read_params(std::string fn, bool overwrite = false);
epiworld_double get_param(epiworld_fast_uint k);
epiworld_double get_param(std::string pname);
// void set_param(size_t k, epiworld_double val);
Expand Down Expand Up @@ -9483,18 +9485,23 @@ inline void Model<TSeq>::print_state_codes() const
template<typename TSeq>
inline epiworld_double Model<TSeq>::add_param(
epiworld_double initial_value,
std::string pname
std::string pname,
bool overwrite
) {

if (parameters.find(pname) == parameters.end())
parameters[pname] = initial_value;
else if (!overwrite)
throw std::logic_error("The parameter " + pname + " already exists.");
else
parameters[pname] = initial_value;

return initial_value;

}

template<typename TSeq>
inline void Model<TSeq>::read_params(std::string fn)
inline void Model<TSeq>::read_params(std::string fn, bool overwrite)
{

std::ifstream paramsfile(fn);
Expand Down Expand Up @@ -9532,7 +9539,8 @@ inline void Model<TSeq>::read_params(std::string fn)
std::regex_replace(
match[1u].str(),
std::regex("^\\s+|\\s+$"),
"")
""),
overwrite
);

}
Expand Down Expand Up @@ -10567,15 +10575,18 @@ inline VirusToAgentFun<TSeq> distribute_virus_randomly(
idx.push_back(agent.get_id());

// Picking how many
size_t n = model->size();
int n = model->size();
int n_available = static_cast<int>(idx.size());
int n_to_sample;
if (prevalence_as_proportion)
{
n_to_sample = static_cast<int>(std::floor(prevalence * n));
n_to_sample = static_cast<int>(std::floor(
prevalence * static_cast< epiworld_double >(n)
));

if (n_to_sample == static_cast<int>(n))
n_to_sample--;
// Correcting for possible overflow
if (n_to_sample == (n + 1))
--n_to_sample;
}
else
{
Expand Down Expand Up @@ -11816,8 +11827,10 @@ inline ToolToAgentFun<TSeq> distribute_tool_randomly(
{
n_to_distribute = static_cast<int>(std::floor(prevalence * n));

if (n_to_distribute == n)
n_to_distribute--;
// Correcting for possible rounding errors
if (n_to_distribute == (n + 1))
--n_to_distribute;

}
else
{
Expand Down Expand Up @@ -12617,7 +12630,9 @@ inline EntityToAgentFun<TSeq> distribute_entity_randomly(
if (as_proportion)
{
n_to_sample = static_cast<int>(std::floor(prevalence * n));
if (n_to_sample > static_cast<int>(n))

// Correcting for possible overflow
if (n_to_sample == (static_cast<int>(n) + 1))
--n_to_sample;

} else
Expand Down
4 changes: 3 additions & 1 deletion include/epiworld/entity-distribute-meat.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,9 @@
if (as_proportion)
{
n_to_sample = static_cast<int>(std::floor(prevalence * n));
if (n_to_sample > static_cast<int>(n))

// Correcting for possible overflow
if (n_to_sample == (static_cast<int>(n) + 1))

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--n_to_sample;
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Two questions here:

  1. Why not set n_to_sample = static_cast<int>(n); instead of --n_to_sample?
  2. Is it impossible for n_to_sample to be greater than (static_cast<int>(n) + 1))? Or does it just not need to be corrected if so?


} else
Expand Down
2 changes: 1 addition & 1 deletion include/epiworld/epiworld.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@
/* Versioning */
#define EPIWORLD_VERSION_MAJOR 0
#define EPIWORLD_VERSION_MINOR 7
#define EPIWORLD_VERSION_PATCH 0
#define EPIWORLD_VERSION_PATCH 1

static const int epiworld_version_major = EPIWORLD_VERSION_MAJOR;
static const int epiworld_version_minor = EPIWORLD_VERSION_MINOR;
Expand Down
6 changes: 4 additions & 2 deletions include/epiworld/model-bones.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -607,8 +607,10 @@ class Model {
*
*/
///@{
epiworld_double add_param(epiworld_double initial_val, std::string pname);
void read_params(std::string fn);
epiworld_double add_param(
epiworld_double initial_val, std::string pname, bool overwrite = false
);
void read_params(std::string fn, bool overwrite = false);
epiworld_double get_param(epiworld_fast_uint k);
epiworld_double get_param(std::string pname);
// void set_param(size_t k, epiworld_double val);
Expand Down
12 changes: 9 additions & 3 deletions include/epiworld/model-meat.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -2035,18 +2035,23 @@
template<typename TSeq>
inline epiworld_double Model<TSeq>::add_param(
epiworld_double initial_value,
std::string pname
std::string pname,
bool overwrite
) {

if (parameters.find(pname) == parameters.end())
parameters[pname] = initial_value;
else if (!overwrite)
throw std::logic_error("The parameter " + pname + " already exists.");

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Add tests to cover this case and specific error message

else
parameters[pname] = initial_value;

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return initial_value;

}

template<typename TSeq>
inline void Model<TSeq>::read_params(std::string fn)
inline void Model<TSeq>::read_params(std::string fn, bool overwrite)
{

std::ifstream paramsfile(fn);
Expand Down Expand Up @@ -2084,7 +2089,8 @@
std::regex_replace(
match[1u].str(),
std::regex("^\\s+|\\s+$"),
"")
""),
overwrite
);

}
Expand Down
6 changes: 4 additions & 2 deletions include/epiworld/tool-distribute-meat.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -64,8 +64,10 @@
{
n_to_distribute = static_cast<int>(std::floor(prevalence * n));

if (n_to_distribute == n)
n_to_distribute--;
// Correcting for possible rounding errors
if (n_to_distribute == (n + 1))
--n_to_distribute;

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Same questions as above: why not set = n? and can n_to_distribute exceed (n+1)?


}
else
{
Expand Down
11 changes: 7 additions & 4 deletions include/epiworld/virus-distribute-meat.hpp
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Expand Up @@ -62,15 +62,18 @@
idx.push_back(agent.get_id());

// Picking how many
size_t n = model->size();
int n = model->size();
int n_available = static_cast<int>(idx.size());
int n_to_sample;
if (prevalence_as_proportion)
{
n_to_sample = static_cast<int>(std::floor(prevalence * n));
n_to_sample = static_cast<int>(std::floor(
prevalence * static_cast< epiworld_double >(n)
));

if (n_to_sample == static_cast<int>(n))
n_to_sample--;
// Correcting for possible overflow
if (n_to_sample == (n + 1))
--n_to_sample;

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Same questions as above

}
else
{
Expand Down
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