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fix: refactor parameter constructor #455

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merged 2 commits into from
Sep 21, 2023
Merged

fix: refactor parameter constructor #455

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ae43558
fix: refactor parameter constructor
Bai-Li-NOAA Aug 22, 2023
3035bd4
refactor: update members in the Parameter class
Bai-Li-NOAA Sep 13, 2023
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10 changes: 5 additions & 5 deletions inst/include/interface/rcpp/rcpp_interface.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -174,11 +174,11 @@ RCPP_MODULE(fims) {
.constructor()
.constructor<double>()
.constructor<Parameter>()
.field("value", &Parameter::value)
.field("min", &Parameter::min)
.field("max", &Parameter::max)
.field("is_random_effect", &Parameter::is_random_effect)
.field("estimated", &Parameter::estimated);
.field("value", &Parameter::value_m)
.field("min", &Parameter::min_m)
.field("max", &Parameter::max_m)
.field("is_random_effect", &Parameter::is_random_effect_m)
.field("estimated", &Parameter::estimated_m);

Rcpp::class_<BevertonHoltRecruitmentInterface>("BevertonHoltRecruitment")
.constructor()
Expand Down
16 changes: 8 additions & 8 deletions inst/include/interface/rcpp/rcpp_objects/rcpp_fleet.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -115,8 +115,8 @@ class FleetInterface : public FIMSRcppInterfaceBase {
f0->observed_index_data_id = this->observed_index_data_id;
f0->selectivity_id = this->selectivity_id;

f0->log_obs_error = this->log_obs_error.value;
if (this->log_obs_error.estimated) {
f0->log_obs_error = this->log_obs_error.value_m;
if (this->log_obs_error.estimated_m) {
d0->RegisterParameter(f0->log_obs_error);
}
f0->log_q = this->log_q;
Expand Down Expand Up @@ -158,8 +158,8 @@ class FleetInterface : public FIMSRcppInterfaceBase {
f1->index_likelihood_id = this->index_likelihood_id;
f1->observed_agecomp_data_id = this->observed_agecomp_data_id;
f1->observed_index_data_id = this->observed_index_data_id;
f1->log_obs_error = this->log_obs_error.value;
if (this->log_obs_error.estimated) {
f1->log_obs_error = this->log_obs_error.value_m;
if (this->log_obs_error.estimated_m) {
d1->RegisterParameter(f1->log_obs_error);
}
f1->selectivity_id = this->selectivity_id;
Expand Down Expand Up @@ -203,8 +203,8 @@ class FleetInterface : public FIMSRcppInterfaceBase {
f2->index_likelihood_id = this->index_likelihood_id;
f2->observed_agecomp_data_id = this->observed_agecomp_data_id;
f2->observed_index_data_id = this->observed_index_data_id;
f2->log_obs_error = this->log_obs_error.value;
if (this->log_obs_error.estimated) {
f2->log_obs_error = this->log_obs_error.value_m;
if (this->log_obs_error.estimated_m) {
d2->RegisterParameter(f2->log_obs_error);
}
f2->selectivity_id = this->selectivity_id;
Expand Down Expand Up @@ -248,8 +248,8 @@ class FleetInterface : public FIMSRcppInterfaceBase {
f3->observed_agecomp_data_id = this->observed_agecomp_data_id;
f3->observed_index_data_id = this->observed_index_data_id;
f3->selectivity_id = this->selectivity_id;
f3->log_obs_error = this->log_obs_error.value;
if (this->log_obs_error.estimated) {
f3->log_obs_error = this->log_obs_error.value_m;
if (this->log_obs_error.estimated_m) {
d3->RegisterParameter(f3->log_obs_error);
}
f3->log_q = this->log_q;
Expand Down
16 changes: 8 additions & 8 deletions inst/include/interface/rcpp/rcpp_objects/rcpp_interface_base.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -25,34 +25,34 @@
*/
class Parameter {
public:
double value; /**< initial value of the parameter*/
double min =
double value_m; /**< initial value of the parameter*/
double min_m =
std::numeric_limits<double>::min(); /**< min value of the parameter*/
double max =
double max_m =
std::numeric_limits<double>::max(); /**< max value of the parameter*/
bool is_random_effect = false; /**< Is the parameter a random effect
bool is_random_effect_m = false; /**< Is the parameter a random effect
parameter? Default value is false.*/
bool estimated =
bool estimated_m =
false; /**< Is the parameter estimated? Default value is false.*/

/**
* @brief Constructor for initializing Parameter.
* @details Inputs include value, min, max, estimated.
*/
Parameter(double value, double min, double max, bool estimated)
: value(value), min(min), max(max), estimated(estimated) {}
: value_m(value), min_m(min), max_m(max), estimated_m(estimated) {}

/**
* @brief Constructor for initializing Parameter.
* @details Inputs include value.
*/
Parameter(double value) { this->value = value; }
Parameter(double value) { value_m = value; }

/**
* @brief Constructor for initializing Parameter.
* @details Set value to 0 when there is no input value.
*/
Parameter() { this->value = 0; }
Parameter() { value_m = 0; }
};

/**
Expand Down
52 changes: 26 additions & 26 deletions inst/include/interface/rcpp/rcpp_objects/rcpp_maturity.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -74,8 +74,8 @@ class LogisticMaturityInterface : public MaturityInterfaceBase {
virtual double evaluate(double x) {
fims::LogisticMaturity<double> LogisticMat;

LogisticMat.median = this->median.value;
LogisticMat.slope = this->slope.value;
LogisticMat.median = this->median.value_m;
LogisticMat.slope = this->slope.value_m;
return LogisticMat.evaluate(x);
}

Expand All @@ -90,17 +90,17 @@ class LogisticMaturityInterface : public MaturityInterfaceBase {

// set relative info
lm0->id = this->id;
lm0->median = this->median.value;
if (this->median.estimated) {
if (this->median.is_random_effect) {
lm0->median = this->median.value_m;
if (this->median.estimated_m) {
if (this->median.is_random_effect_m) {
d0->RegisterRandomEffect(lm0->median);
} else {
d0->RegisterParameter(lm0->median);
}
}
lm0->slope = this->slope.value;
if (this->slope.estimated) {
if (this->slope.is_random_effect) {
lm0->slope = this->slope.value_m;
if (this->slope.estimated_m) {
if (this->slope.is_random_effect_m) {
d0->RegisterRandomEffect(lm0->slope);
} else {
d0->RegisterParameter(lm0->slope);
Expand All @@ -118,17 +118,17 @@ class LogisticMaturityInterface : public MaturityInterfaceBase {

// set relative info
lm1->id = this->id;
lm1->median = this->median.value;
if (this->median.estimated) {
if (this->median.is_random_effect) {
lm1->median = this->median.value_m;
if (this->median.estimated_m) {
if (this->median.is_random_effect_m) {
d1->RegisterRandomEffect(lm1->median);
} else {
d1->RegisterParameter(lm1->median);
}
}
lm1->slope = this->slope.value;
if (this->slope.estimated) {
if (this->slope.is_random_effect) {
lm1->slope = this->slope.value_m;
if (this->slope.estimated_m) {
if (this->slope.is_random_effect_m) {
d1->RegisterRandomEffect(lm1->slope);
} else {
d1->RegisterParameter(lm1->slope);
Expand All @@ -146,17 +146,17 @@ class LogisticMaturityInterface : public MaturityInterfaceBase {

// set relative info
lm2->id = this->id;
lm2->median = this->median.value;
if (this->median.estimated) {
if (this->median.is_random_effect) {
lm2->median = this->median.value_m;
if (this->median.estimated_m) {
if (this->median.is_random_effect_m) {
d2->RegisterRandomEffect(lm2->median);
} else {
d2->RegisterParameter(lm2->median);
}
}
lm2->slope = this->slope.value;
if (this->slope.estimated) {
if (this->slope.is_random_effect) {
lm2->slope = this->slope.value_m;
if (this->slope.estimated_m) {
if (this->slope.is_random_effect_m) {
d2->RegisterRandomEffect(lm2->slope);
} else {
d2->RegisterParameter(lm2->slope);
Expand All @@ -174,17 +174,17 @@ class LogisticMaturityInterface : public MaturityInterfaceBase {

// set relative info
lm3->id = this->id;
lm3->median = this->median.value;
if (this->median.estimated) {
if (this->median.is_random_effect) {
lm3->median = this->median.value_m;
if (this->median.estimated_m) {
if (this->median.is_random_effect_m) {
d3->RegisterRandomEffect(lm3->median);
} else {
d3->RegisterParameter(lm3->median);
}
}
lm3->slope = this->slope.value;
if (this->slope.estimated) {
if (this->slope.is_random_effect) {
lm3->slope = this->slope.value_m;
if (this->slope.estimated_m) {
if (this->slope.is_random_effect_m) {
d3->RegisterRandomEffect(lm3->slope);
} else {
d3->RegisterParameter(lm3->slope);
Expand Down
80 changes: 40 additions & 40 deletions inst/include/interface/rcpp/rcpp_objects/rcpp_recruitment.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -83,22 +83,22 @@ class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {
virtual double evaluate(double spawners, double ssbzero) {
fims::SRBevertonHolt<double> BevHolt;

BevHolt.logit_steep = this->logit_steep.value;
if (this->logit_steep.value == 1.0) {
BevHolt.logit_steep = this->logit_steep.value_m;
if (this->logit_steep.value_m == 1.0) {
warning(
"Steepness is subject to a logit transformation, so its value is "
"0.7848469. Fixing it at 1.0 is not currently possible.");
}

BevHolt.log_rzero = this->log_rzero.value;
BevHolt.log_rzero = this->log_rzero.value_m;

return BevHolt.evaluate(spawners, ssbzero);
}

virtual double evaluate_nll() {
fims::SRBevertonHolt<double> NLL;

NLL.log_sigma_recruit = this->log_sigma_recruit.value;
NLL.log_sigma_recruit = this->log_sigma_recruit.value_m;
NLL.recruit_deviations.resize(deviations.size()); // Vector from TMB
for (int i = 0; i < deviations.size(); i++) {
NLL.recruit_deviations[i] = deviations[i];
Expand All @@ -121,25 +121,25 @@ class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {

// set relative info
b0->id = this->id;
b0->logit_steep = this->logit_steep.value;
if (this->logit_steep.estimated) {
if (this->logit_steep.is_random_effect) {
b0->logit_steep = this->logit_steep.value_m;
if (this->logit_steep.estimated_m) {
if (this->logit_steep.is_random_effect_m) {
d0->RegisterRandomEffect(b0->logit_steep);
} else {
d0->RegisterParameter(b0->logit_steep);
}
}
b0->log_rzero = this->log_rzero.value;
if (this->log_rzero.estimated) {
if (this->log_rzero.is_random_effect) {
b0->log_rzero = this->log_rzero.value_m;
if (this->log_rzero.estimated_m) {
if (this->log_rzero.is_random_effect_m) {
d0->RegisterRandomEffect(b0->log_rzero);
} else {
d0->RegisterParameter(b0->log_rzero);
}
}
b0->log_sigma_recruit = this->log_sigma_recruit.value;
if (this->log_sigma_recruit.estimated) {
if (this->log_sigma_recruit.is_random_effect) {
b0->log_sigma_recruit = this->log_sigma_recruit.value_m;
if (this->log_sigma_recruit.estimated_m) {
if (this->log_sigma_recruit.is_random_effect_m) {
d0->RegisterRandomEffect(b0->log_sigma_recruit);
} else {
d0->RegisterParameter(b0->log_sigma_recruit);
Expand Down Expand Up @@ -170,25 +170,25 @@ class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {

// set relative info
b1->id = this->id;
b1->logit_steep = this->logit_steep.value;
if (this->logit_steep.estimated) {
if (this->logit_steep.is_random_effect) {
b1->logit_steep = this->logit_steep.value_m;
if (this->logit_steep.estimated_m) {
if (this->logit_steep.is_random_effect_m) {
d1->RegisterRandomEffect(b1->logit_steep);
} else {
d1->RegisterParameter(b1->logit_steep);
}
}
b1->log_rzero = this->log_rzero.value;
if (this->log_rzero.estimated) {
if (this->log_rzero.is_random_effect) {
b1->log_rzero = this->log_rzero.value_m;
if (this->log_rzero.estimated_m) {
if (this->log_rzero.is_random_effect_m) {
d1->RegisterRandomEffect(b1->log_rzero);
} else {
d1->RegisterParameter(b1->log_rzero);
}
}
b1->log_sigma_recruit = this->log_sigma_recruit.value;
if (this->log_sigma_recruit.estimated) {
if (this->log_sigma_recruit.is_random_effect) {
b1->log_sigma_recruit = this->log_sigma_recruit.value_m;
if (this->log_sigma_recruit.estimated_m) {
if (this->log_sigma_recruit.is_random_effect_m) {
d1->RegisterRandomEffect(b1->log_sigma_recruit);
} else {
d1->RegisterParameter(b1->log_sigma_recruit);
Expand Down Expand Up @@ -219,25 +219,25 @@ class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {

// set relative info
b2->id = this->id;
b2->logit_steep = this->logit_steep.value;
if (this->logit_steep.estimated) {
if (this->logit_steep.is_random_effect) {
b2->logit_steep = this->logit_steep.value_m;
if (this->logit_steep.estimated_m) {
if (this->logit_steep.is_random_effect_m) {
d2->RegisterRandomEffect(b2->logit_steep);
} else {
d2->RegisterParameter(b2->logit_steep);
}
}
b2->log_rzero = this->log_rzero.value;
if (this->log_rzero.estimated) {
if (this->log_rzero.is_random_effect) {
b2->log_rzero = this->log_rzero.value_m;
if (this->log_rzero.estimated_m) {
if (this->log_rzero.is_random_effect_m) {
d2->RegisterRandomEffect(b2->log_rzero);
} else {
d2->RegisterParameter(b2->log_rzero);
}
}
b2->log_sigma_recruit = this->log_sigma_recruit.value;
if (this->log_sigma_recruit.estimated) {
if (this->log_sigma_recruit.is_random_effect) {
b2->log_sigma_recruit = this->log_sigma_recruit.value_m;
if (this->log_sigma_recruit.estimated_m) {
if (this->log_sigma_recruit.is_random_effect_m) {
d2->RegisterRandomEffect(b2->log_sigma_recruit);
} else {
d2->RegisterParameter(b2->log_sigma_recruit);
Expand Down Expand Up @@ -268,25 +268,25 @@ class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {

// set relative info
b3->id = this->id;
b3->logit_steep = this->logit_steep.value;
if (this->logit_steep.estimated) {
if (this->logit_steep.is_random_effect) {
b3->logit_steep = this->logit_steep.value_m;
if (this->logit_steep.estimated_m) {
if (this->logit_steep.is_random_effect_m) {
d3->RegisterRandomEffect(b3->logit_steep);
} else {
d3->RegisterParameter(b3->logit_steep);
}
}
b3->log_rzero = this->log_rzero.value;
if (this->log_rzero.estimated) {
if (this->log_rzero.is_random_effect) {
b3->log_rzero = this->log_rzero.value_m;
if (this->log_rzero.estimated_m) {
if (this->log_rzero.is_random_effect_m) {
d3->RegisterRandomEffect(b3->log_rzero);
} else {
d3->RegisterParameter(b3->log_rzero);
}
}
b3->log_sigma_recruit = this->log_sigma_recruit.value;
if (this->log_sigma_recruit.estimated) {
if (this->log_sigma_recruit.is_random_effect) {
b3->log_sigma_recruit = this->log_sigma_recruit.value_m;
if (this->log_sigma_recruit.estimated_m) {
if (this->log_sigma_recruit.is_random_effect_m) {
d3->RegisterRandomEffect(b3->log_sigma_recruit);
} else {
d3->RegisterParameter(b3->log_sigma_recruit);
Expand Down
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