initialize_N: Initialize a Species object.

In jcpayne/mice-models: Model of Intermediate Complexity for Ecosystem Assessment

Description

This function creates the population matrix, Nmat, for a Species, whose dimension is either (nAges x nYears) if use_timestep is FALSE, or (nAges x (nYears * nSteps)) if use_timestep is TRUE. It fills Nmat[,year==1], based on values in the simulationParams object. It also dimensions empty vectors that will hold the value of recruitment residuals, fishing mortality and catch (for fished species), age 1+ biomass (for prey) and proportion mature-at-age, and calculates Nm[1], and sets R[1] to zero.

Usage

initialize_N(Species, simulationParams, preynames)

Arguments

Species.	A species object.
simulationParams.	A simulationParams object that holds global values and input data.

Value

A modified Species object, with arrays initialized.

See Also

Other initialization: calibrate, distribute_byage, distribute_bytimestep, set_simParam, solve_age0_survival

Other parameter setting: get_params, get_prefs, set_simParam, set_species

jcpayne/mice-models documentation built on May 18, 2019, 10:25 p.m.