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Adding option for row/col major in DEFM
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@gvegayon
gvegayon committed Sep 19, 2023
1 parent 24d8e8a commit dd48fa3
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Showing 5 changed files with 106 additions and 81 deletions.
85 changes: 48 additions & 37 deletions defm.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1220,34 +1220,32 @@ inline void rules_dont_become_zero(
class DEFM : public DEFMModel {
private:

// std::shared_ptr< std::mt19937 > rengine = nullptr;
// std::shared_ptr< DEFMModel > model = nullptr;

/**
* @brief Model data
*/
///@{
int * Y = nullptr; ///< Outcome variable
int * ID = nullptr; ///< Individual ids
double * X = nullptr; ///< Covariates
int * Y = nullptr; ///< Outcome variable
int * ID = nullptr; ///< Individual ids
double * X = nullptr; ///< Covariates
bool column_major = true; ///< Whether the data is column major or not

// In case we need a copy of the data
std::shared_ptr<std::vector< int >> Y_shared; ///< Outcome variable
std::shared_ptr<std::vector< int >> ID_shared; ///< Individual ids
std::shared_ptr<std::vector< double >> X_shared;///< Covariates
std::shared_ptr<std::vector< int >> Y_shared; ///< Outcome variable
std::shared_ptr<std::vector< int >> ID_shared; ///< Individual ids
std::shared_ptr<std::vector< double >> X_shared; ///< Covariates

size_t N; ///< Number of agents/individuals
size_t ID_length; ///< Length of the vector IDs
size_t Y_ncol; ///< Number of columns in the response
size_t Y_length; ///< Length of the vector Y
size_t X_ncol; ///< Number of columns in the features
size_t X_length; ///< Length of the vector X
size_t M_order; ///< Markov order of the model

std::vector< std::string > Y_names;
std::vector< std::string > X_names;
std::vector< size_t > start_end;
std::vector< size_t > model_ord;
size_t N; ///< Number of agents/individuals
size_t ID_length; ///< Length of the vector IDs
size_t Y_ncol; ///< Number of columns in the response
size_t Y_length; ///< Length of the vector Y
size_t X_ncol; ///< Number of columns in the features
size_t X_length; ///< Length of the vector X
size_t M_order; ///< Markov order of the model

std::vector< std::string > Y_names; ///< Names of the response variables
std::vector< std::string > X_names; ///< Names of the covariates
std::vector< size_t > start_end; ///< Start and end of each observation
std::vector< size_t > model_ord; ///< Order of the model
///@}

public:
Expand All @@ -1260,22 +1258,10 @@ class DEFM : public DEFMModel {
size_t y_ncol,
size_t x_ncol,
size_t m_order,
bool copy_data = true
bool copy_data = true,
bool column_major = true
);

// ~DEFM() {

// if (n_owners-- == 1)
// {
// delete[] Y;
// delete[] ID;
// delete[] X;
// }

// DEFMModel::~Model();

// };

DEFMModel & get_model() {
return *this;
};
Expand Down Expand Up @@ -1450,7 +1436,8 @@ inline DEFM::DEFM(
size_t y_ncol,
size_t x_ncol,
size_t m_order,
bool copy_data
bool copy_data,
bool column_major
) {

// Pointers
Expand Down Expand Up @@ -1557,6 +1544,24 @@ inline void DEFM::init()
// Adding the rule
rules_markov_fixed(this->get_rules(), M_order);

// Element access will be contingent on the column major
std::function<size_t(size_t,size_t,size_t,size_t)> element_access;

if (this->column_major)
{

element_access = [](size_t i, size_t j, size_t nrow, size_t) -> size_t {
return i + j * nrow;
};

} else {

element_access = [](size_t i, size_t j, size_t, size_t ncol) -> size_t {
return j + i * ncol;
};

}

// Creating the arrays
for (size_t i = 0u; i < N; ++i)
{
Expand All @@ -1581,7 +1586,13 @@ inline void DEFM::init()
// Filling-out the array
for (size_t k = 0u; k < Y_ncol; ++k)
for (size_t o = 0u; o < (M_order + 1u); ++o)
array(o, k) = *(Y + k * ID_length + start_i + n_proc + o);
// array(o, k) = *(Y + k * ID_length + start_i + n_proc + o);
array(o, k) = *(Y + element_access(
start_i + n_proc + o, // Row
k, // Column
ID_length, // N_row
Y_ncol // N_col
));

// Adding to the model
model_ord.push_back( this->add_array(array, true) );
Expand Down
56 changes: 21 additions & 35 deletions include/barry/models/defm/defm-bones.hpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,34 +4,32 @@
class DEFM : public DEFMModel {
private:

// std::shared_ptr< std::mt19937 > rengine = nullptr;
// std::shared_ptr< DEFMModel > model = nullptr;

/**
* @brief Model data
*/
///@{
int * Y = nullptr; ///< Outcome variable
int * ID = nullptr; ///< Individual ids
double * X = nullptr; ///< Covariates
int * Y = nullptr; ///< Outcome variable
int * ID = nullptr; ///< Individual ids
double * X = nullptr; ///< Covariates
bool column_major = true; ///< Whether the data is column major or not

// In case we need a copy of the data
std::shared_ptr<std::vector< int >> Y_shared; ///< Outcome variable
std::shared_ptr<std::vector< int >> ID_shared; ///< Individual ids
std::shared_ptr<std::vector< double >> X_shared;///< Covariates
std::shared_ptr<std::vector< int >> Y_shared; ///< Outcome variable
std::shared_ptr<std::vector< int >> ID_shared; ///< Individual ids
std::shared_ptr<std::vector< double >> X_shared; ///< Covariates

size_t N; ///< Number of agents/individuals
size_t ID_length; ///< Length of the vector IDs
size_t Y_ncol; ///< Number of columns in the response
size_t Y_length; ///< Length of the vector Y
size_t X_ncol; ///< Number of columns in the features
size_t X_length; ///< Length of the vector X
size_t M_order; ///< Markov order of the model

std::vector< std::string > Y_names;
std::vector< std::string > X_names;
std::vector< size_t > start_end;
std::vector< size_t > model_ord;
size_t N; ///< Number of agents/individuals
size_t ID_length; ///< Length of the vector IDs
size_t Y_ncol; ///< Number of columns in the response
size_t Y_length; ///< Length of the vector Y
size_t X_ncol; ///< Number of columns in the features
size_t X_length; ///< Length of the vector X
size_t M_order; ///< Markov order of the model

std::vector< std::string > Y_names; ///< Names of the response variables
std::vector< std::string > X_names; ///< Names of the covariates
std::vector< size_t > start_end; ///< Start and end of each observation
std::vector< size_t > model_ord; ///< Order of the model
///@}

public:
Expand All @@ -44,22 +42,10 @@ class DEFM : public DEFMModel {
size_t y_ncol,
size_t x_ncol,
size_t m_order,
bool copy_data = true
bool copy_data = true,
bool column_major = true
);

// ~DEFM() {

// if (n_owners-- == 1)
// {
// delete[] Y;
// delete[] ID;
// delete[] X;
// }

// DEFMModel::~Model();

// };

DEFMModel & get_model() {
return *this;
};
Expand Down
29 changes: 27 additions & 2 deletions include/barry/models/defm/defm-meat.hpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -109,7 +109,8 @@ inline DEFM::DEFM(
size_t y_ncol,
size_t x_ncol,
size_t m_order,
bool copy_data
bool copy_data,
bool column_major
) {

// Pointers
Expand Down Expand Up @@ -216,6 +217,24 @@ inline void DEFM::init()
// Adding the rule
rules_markov_fixed(this->get_rules(), M_order);

// Element access will be contingent on the column major
std::function<size_t(size_t,size_t,size_t,size_t)> element_access;

if (this->column_major)
{

element_access = [](size_t i, size_t j, size_t nrow, size_t) -> size_t {
return i + j * nrow;
};

} else {

element_access = [](size_t i, size_t j, size_t, size_t ncol) -> size_t {
return j + i * ncol;
};

}

// Creating the arrays
for (size_t i = 0u; i < N; ++i)
{
Expand All @@ -240,7 +259,13 @@ inline void DEFM::init()
// Filling-out the array
for (size_t k = 0u; k < Y_ncol; ++k)
for (size_t o = 0u; o < (M_order + 1u); ++o)
array(o, k) = *(Y + k * ID_length + start_i + n_proc + o);
// array(o, k) = *(Y + k * ID_length + start_i + n_proc + o);
array(o, k) = *(Y + element_access(
start_i + n_proc + o, // Row
k, // Column
ID_length, // N_row
Y_ncol // N_col
));

// Adding to the model
model_ord.push_back( this->add_array(array, true) );
Expand Down
14 changes: 8 additions & 6 deletions tests/16-defm-counts-with-formulas.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,13 +29,13 @@ BARRY_TEST_CASE("DEFM motif formula", "[DEFM motif formula]") {
std::vector< bool > sign_2 = {true, true, true, false};
std::vector< bool > sign_3 = {true};

defmcounters::defm_motif_parser("{y1, y3}", res_locations1a, res_sign1a, 1, 4);
defmcounters::defm_motif_parser("{y1_0, y3} > {y1_1, 0y3_1}", res_locations2a, res_sign2a, 1, 4);
defmcounters::defm_motif_parser("{y1}", res_locations3a, res_sign3a, 1, 4);
defm::defm_motif_parser("{y1, y3}", res_locations1a, res_sign1a, 1, 4);
defm::defm_motif_parser("{y1_0, y3} > {y1_1, 0y3_1}", res_locations2a, res_sign2a, 1, 4);
defm::defm_motif_parser("{y1}", res_locations3a, res_sign3a, 1, 4);

defmcounters::defm_motif_parser("{y1_1, y3}", res_locations1b, res_sign1b, 1, 4);
defmcounters::defm_motif_parser("{y1_0, y3_0} > {y1, 0y3_1}", res_locations2b, res_sign2b, 1, 4);
defmcounters::defm_motif_parser("{y1_1}", res_locations3b, res_sign3b, 1, 4);
defm::defm_motif_parser("{y1_1, y3}", res_locations1b, res_sign1b, 1, 4);
defm::defm_motif_parser("{y1_0, y3_0} > {y1, 0y3_1}", res_locations2b, res_sign2b, 1, 4);
defm::defm_motif_parser("{y1_1}", res_locations3b, res_sign3b, 1, 4);


#ifdef CATCH_CONFIG_MAIN
Expand Down Expand Up @@ -70,6 +70,8 @@ BARRY_TEST_CASE("DEFM motif formula", "[DEFM motif formula]") {
#endif


#ifndef CATCH_CONFIG_MAIN
return 0;
#endif

}
3 changes: 2 additions & 1 deletion tests/main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -24,4 +24,5 @@
#include "10-geese-predict.cpp" // This is not working yet
#include "11-phylo-counts.cpp"
#include "14-variable-transformation.cpp"
#include "15-defm-counts.cpp"
#include "15-defm-counts.cpp"
#include "16-defm-counts-with-formulas.cpp"

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