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format C++ code with clang format #490

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Oct 24, 2023
Merged

format C++ code with clang format #490

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22 changes: 13 additions & 9 deletions inst/include/population_dynamics/population/population.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -233,8 +233,9 @@ struct Population : public FIMSObject<Type> {
inline void CalculateNumbersAA(size_t i_age_year, size_t i_agem1_yearm1,
size_t age) {
// using Z from previous age/year
this->numbers_at_age[i_age_year] = this->numbers_at_age[i_agem1_yearm1] *
(fims::exp(-this->mortality_Z[i_agem1_yearm1]));
this->numbers_at_age[i_age_year] =
this->numbers_at_age[i_agem1_yearm1] *
(fims::exp(-this->mortality_Z[i_agem1_yearm1]));
FIMS_LOG << " z at i_agem1_yearm1 = " << i_agem1_yearm1 << " is "
<< this->mortality_Z[i_agem1_yearm1] << std::endl;
// Plus group calculation
Expand All @@ -253,8 +254,8 @@ struct Population : public FIMSObject<Type> {
* @param i_agem1_yearm1 dimension folded index for age-1 and year-1
* @param age age index
*/
inline void CalculateUnfishedNumbersAA(size_t i_age_year, size_t i_agem1_yearm1,
size_t age) {
inline void CalculateUnfishedNumbersAA(size_t i_age_year,
size_t i_agem1_yearm1, size_t age) {
// using M from previous age/year
this->unfished_numbers_at_age[i_age_year] =
this->unfished_numbers_at_age[i_agem1_yearm1] *
Expand Down Expand Up @@ -306,9 +307,10 @@ struct Population : public FIMSObject<Type> {
* @param age the age who's biomass is being added into total spawning biomass
*/
void CalculateSpawningBiomass(size_t i_age_year, size_t year, size_t age) {
this->spawning_biomass[year] +=
this->proportion_female * this->numbers_at_age[i_age_year] *
this->proportion_mature_at_age[i_age_year] * growth->evaluate(ages[age]);
this->spawning_biomass[year] += this->proportion_female *
this->numbers_at_age[i_age_year] *
this->proportion_mature_at_age[i_age_year] *
growth->evaluate(ages[age]);
FIMS_LOG << " proportion female " << this->proportion_female << " "
<< " mature age " << age << " is "
<< this->proportion_mature_at_age[i_age_year] << " "
Expand Down Expand Up @@ -462,7 +464,8 @@ struct Population : public FIMSObject<Type> {
if (this->fleets[fleet_]->is_survey == false) {
catch_ = (this->fleets[fleet_]->Fmort[year] *
this->fleets[fleet_]->selectivity->evaluate(ages[age])) /
this->mortality_Z[i_age_year] * this->numbers_at_age[i_age_year] *
this->mortality_Z[i_age_year] *
this->numbers_at_age[i_age_year] *
(1 - fims::exp(-(this->mortality_Z[i_age_year])));
} else {
catch_ = (this->fleets[fleet_]->selectivity->evaluate(ages[age])) *
Expand Down Expand Up @@ -622,7 +625,8 @@ struct Population : public FIMSObject<Type> {
Expected recruitment in year 0 is numbers at age 0 in year 0.
*/

this->expected_recruitment[i_age_year] = this->numbers_at_age[i_age_year];
this->expected_recruitment[i_age_year] =
this->numbers_at_age[i_age_year];

} else {
if (a == 0) {
Expand Down
8 changes: 4 additions & 4 deletions inst/include/population_dynamics/selectivity/functors/double_logistic.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -23,14 +23,14 @@ struct DoubleLogisticSelectivity : public SelectivityBase<Type> {
(x) on the ascending limb of the double logistic curve; e.g. age
at which 50% of the fish are selected */
Type slope_asc; /*!<scalar multiplier of difference between quantity of
interest value (x) and median on the ascending limb of the double
logistic curve*/
interest value (x) and median on the ascending limb of the
double logistic curve*/
Type median_desc; /*!< 50% quantile of the value of the quantity of interest
(x) on the descending limb of the double logistic curve; e.g.
age at which 50% of the fish are selected */
Type slope_desc; /*!<scalar multiplier of difference between quantity of
interest value (x) and median on the descending limb of the double
logistic curve */
interest value (x) and median on the descending limb of the
double logistic curve */

DoubleLogisticSelectivity() : SelectivityBase<Type>() {}

Expand Down
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