Parameters

Classes
class	pbf::IndividualJson
	Parameters for Individual class (JSON file) More...

Functions
clipp::group	pbf::program_options (nlohmann::json *vm)
	Program options.
clipp::group	pbf::reproduction_options (nlohmann::json *vm)
	Reproduction options.
std::vector< double >	pbf::IndividualJson::natural_mortality = {}
	Array of \(M\) for quarter age: instantaneous mortality due to natural causes.
std::vector< double >	pbf::IndividualJson::fishing_mortality = {}
	Array of \(F\) for quarter age: instantaneous mortality due to fishing activities.
std::vector< double >	pbf::IndividualJson::fishing_coef = {}
std::vector< double >	pbf::IndividualJson::weight_for_age = {}
	Weight in kg for quarter age.
std::vector< RowMatrix >	pbf::IndividualJson::migration_matrices = {}
	Transition matrix for migration.
const double	pbf::Population::carrying_capacity_
	\(K\): carrying capacity used in reproduce()
const double	pbf::Population::recruitment_coef_
	\(r\): coefficient used in reproduce()
const double	pbf::Population::k_nbinom_

Detailed Description

Function Documentation

program_options()

clipp::group pbf::program_options ( nlohmann::json * vm )

inline

Program options.

Command line option	Symbol
-O,--origin	-
-y,--years	-
-l,--last	-
--sa,--sample_size_adult	-
--sj,--sample_size_juvenile	-
-i,--infile	-
-o,--outdir	-

reproduction_options()

clipp::group pbf::reproduction_options ( nlohmann::json * vm )

inline

Reproduction options.

Command line option	Symbol	Variable
-r,--recruitment	\(r\)	Population::recruitment_coef_
-K,--carrying_capacity	\(K\)	Population::carrying_capacity_
-k,--overdispersion	\(k\)	Population::k_nbinom_

Variable Documentation

fishing_coef

std::vector<double> pbf::IndividualJson::fishing_coef = {}

private

Array of \(e\) by year: coefficient of fishing mortality. The last part is used for the last years if its length differs from --years option.

k_nbinom_

const double pbf::Population::k_nbinom_

private

\(k \in (0, \infty)\) for overdispersion in reproduce(). Equivalent to Poisson when \(k \to \infty\) (or \(k<0\) for convience).