tekka
pbf::Parameters Struct Reference

Parameters for Population class. More...

#include <parameters.hpp>

Public Member Functions

 Parameters ()
 Constructor.
void read (std::istream &)
 Read json-only variables from stream.
std::ostream & write (std::ostream &) const
 Write json-only variables to stream.

Public Attributes

Global
int32_t seed {0}
 RNG seed. Initialized with std::random_device if 0 (default). 32-bit signed integer for R.
std::string outdir {}
 Output directory.
int_fast32_t years {80}
 Duration of simulation.
int_fast32_t 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 med_recruitment {0.0}
 \(\operatorname{med}(R) = \exp(\mu_{R})\) for lognormal distribution
double sigma_recruitment {1.0}
 \(\sigma_{R}\) for lognormal distribution
double carrying_capacity {2e3}
 \(K\): carrying capacity used in Population::reproduce()
double recruitment {2.0}
 \(r\): coefficient used in Population::reproduce()
double 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 last {3}
 Sample last _ years.
std::vector< int_fast32_t > sample_size_adult {10, 10}
 per location
std::vector< int_fast32_t > sample_size_juvenile {10, 10}
 per location

Configurable only via JSON

See https://github.com/heavywatal/tekka/blob/master/util/parameters.json for the default values.

using RowMatrix = std::vector<std::vector<double>>
 Alias for readability.
std::vector< double > natural_mortality {}
 Array of \(M\) for quarter age: instantaneous mortality due to natural causes.
std::vector< double > fishing_mortality {}
 Array of \(F\) for quarter age: instantaneous mortality due to fishing activities.
std::vector< double > 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 > weight_for_age {}
 Weight in kg for quarter age.
std::vector< RowMatrixmigration_matrices {}
 Transition matrix for Population::migrate()

Detailed Description


The documentation for this struct was generated from the following files: