Parameters

List of available options. Tables are at the bottom of the page. See Population::run() to track the simulation process. More...

Functions
clipp::group	pbf::general_options (nlohmann::json *vm)
	Options description for general purpose.
clipp::group	pbf::program_options (Parameters &params)
	Global options for simulation.
clipp::group	pbf::reproduction_options (Parameters &params)
	Options for Population::reproduce.
clipp::group	pbf::sampling_options (Parameters &params)
	Options for Population::sample.

Configurable only via JSON
See https://github.com/heavywatal/tekka/blob/master/util/parameters.json for the default values.
using	pbf::Parameters::RowMatrix = std::vector<std::vector<double>>
	Alias for readability.
std::vector< double >	pbf::Parameters::natural_mortality {}
	Array of \(M\) for quarter age: instantaneous mortality due to natural causes.
std::vector< double >	pbf::Parameters::fishing_mortality {}
	Array of \(F\) for quarter age: instantaneous mortality due to fishing activities.
std::vector< double >	pbf::Parameters::fishing_coef {}
	Array of \(e\) by year: coefficient of fishing mortality. The last element is used for the last years if its length differs from years.
std::vector< double >	pbf::Parameters::weight_for_age {}
	Weight in kg for quarter age.
std::vector< RowMatrix >	pbf::Parameters::migration_matrices {}
	Transition matrix for Population::migrate()

Global
int32_t	pbf::Parameters::seed {0}
	RNG seed. Initialized with std::random_device if 0 (default). 32-bit signed integer for R.
std::string	pbf::Parameters::outdir {}
	Output directory.
int_fast32_t	pbf::Parameters::years {80}
	Duration of simulation.
int_fast32_t	pbf::Parameters::origin {0}
	Initial number of juveniles at location 0 in season 0 in year 0. It falls back to \(\operatorname{med}(R)\) or \(K\) if 0.

Reproduction
double	pbf::Parameters::med_recruitment {0.0}
	\(\operatorname{med}(R) = \exp(\mu_{R})\) for lognormal distribution
double	pbf::Parameters::sigma_recruitment {1.0}
	\(\sigma_{R}\) for lognormal distribution
double	pbf::Parameters::carrying_capacity {2e3}
	\(K\): carrying capacity used in Population::reproduce()
double	pbf::Parameters::recruitment {2.0}
	\(r\): coefficient used in Population::reproduce()
double	pbf::Parameters::overdispersion {-1.0}
	\(k \in (0, \infty)\) for overdispersion in Population::reproduce(). Equivalent to Poisson when \(k \to \infty\) (or \(k<0\) for convience).

Sampling
int_fast32_t	pbf::Parameters::last {3}
	Sample last _ years.
std::vector< int_fast32_t >	pbf::Parameters::sample_size_adult {10, 10}
	per location
std::vector< int_fast32_t >	pbf::Parameters::sample_size_juvenile {10, 10}
	per location

Detailed Description

List of available options. Tables are at the bottom of the page. See Population::run() to track the simulation process.

The longer ones can be used as keys in JSON config file, e.g., {"years": 80} for -y,--years option.

Function Documentation

general_options()

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

inline

Options description for general purpose.

Command line option	Description
-h,--help	Print help
--version	Print version
--json	Print default values for large parameters
--default	Print default values for all parameters
-i,--infile	Config file in json format
-v,--verbose	Verbose output

program_options()

clipp::group pbf::program_options ( Parameters & params )

inline

Global options for simulation.

Command line option	Variable
--seed	Parameters::seed
-o,--outdir	Parameters::outdir
-y,--years	Parameters::years
-O,--origin	Parameters::origin

reproduction_options()

clipp::group pbf::reproduction_options ( Parameters & params )

inline

Options for Population::reproduce.

Command line option	Symbol	Variable
-R,--med_recruitment	\(\operatorname{med}(R)\)	Parameters::med_recruitment
-S,--sigma_recruitment	\(\sigma_{R}\)	Parameters::sigma_recruitment
-K,--carrying_capacity	\(K\)	Parameters::carrying_capacity
-k,--overdispersion	\(k\)	Parameters::overdispersion
-r,--recruitment	\(r\)	Parameters::recruitment

sampling_options()

clipp::group pbf::sampling_options ( Parameters & params )

inline

Options for Population::sample.

Command line option	Variable
-l,--last	Parameters::last
--sa,--sample_size_adult	Parameters::sample_size_adult
--sj,--sample_size_juvenile	Parameters::sample_size_juvenile