diff --git a/inst/include/population_dynamics/population/population.hpp b/inst/include/population_dynamics/population/population.hpp index b76cf90f..bcf7a8e7 100644 --- a/inst/include/population_dynamics/population/population.hpp +++ b/inst/include/population_dynamics/population/population.hpp @@ -233,8 +233,9 @@ struct Population : public FIMSObject { 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 @@ -253,8 +254,8 @@ struct Population : public FIMSObject { * @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] * @@ -306,9 +307,10 @@ struct Population : public FIMSObject { * @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] << " " @@ -462,7 +464,8 @@ struct Population : public FIMSObject { 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])) * @@ -622,7 +625,8 @@ struct Population : public FIMSObject { 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) { diff --git a/inst/include/population_dynamics/selectivity/functors/double_logistic.hpp b/inst/include/population_dynamics/selectivity/functors/double_logistic.hpp index 635a6e99..36a4e111 100644 --- a/inst/include/population_dynamics/selectivity/functors/double_logistic.hpp +++ b/inst/include/population_dynamics/selectivity/functors/double_logistic.hpp @@ -23,14 +23,14 @@ struct DoubleLogisticSelectivity : public SelectivityBase { (x) on the ascending limb of the double logistic curve; e.g. age at which 50% of the fish are selected */ Type slope_asc; /*!() {}