lengthen_hydra_data: lengthen hydra data for additional years

In andybeet/hydramse: Performs MSE using Hydra

Description

The Darwinian study utilizes Hydra but requires a longer period of time to run Here we extend all o fthe variables passed to Hydra to make up the additional years The first nYrs of the model run is assumed to be a period without fishing pressure followed by a period (of length hydraDataList$Nyrs) of fishing.

Usage

lengthen_hydra_data(data, nYrs)

Arguments

data	A datafile resembling hydraDataList
nYrs	The total number of years Hydra should be extended to

Value

List

Nyrs	Scalar. The Input value of nYrs
recruitmentCov	Vector. Lengthened vector for recruitment covariate. Uses mean of current values
maturityCov	Vector. Lengthened vector for maturity covariate. Uses mean of current values
growthCov	Vector. Lengthened vector for growth covariate. Uses mean of current values
observedTemperature	Matrix. Lengthened vector for observed temperature. Uses mean of current values
observedBiomass	Matrix. Lengthened vector for observed Biomass. Uses mean of current values
observedCatch	Matrix. Lengthened vector for observed Catch. Uses mean of current values
observedEffort	Matrix. Lengthened vector for observed Effort. Uses 0 for fist part of time series
redundantRecDevs	Matrix. Lengthened vector for observed Effort. Uses 0 for fist part of time series

Notes

The 8 variables that are time dependent in the model are listed above. We need to provide dummy data for the first x years during the zero fishing period where we assume the model will reach some kind of equilibrium

andybeet/hydramse documentation built on April 16, 2021, 5:23 a.m.