Species-class: An S4 class to represent a generic species.

Description Value Slots

Description

It holds values that are used to track the population growth (including reproduction, survival, and exploitation) of every species, and all other species objects inherit from this class. The variable names that end in 'v' are vectors; the names that end in 'mat' are matrices. The rest are scalars, except for a few that (as shown) are lists. Lists are used to hold parameters for a model. Depending on the model, those parameters may be scalars, vectors, or a combination. Holding model parameters in lists makes it easier to swap models later.

Value

Should not be instantiated; rather, instantiate the child classes.

Slots

name

character. Species name. Should match the class name.

uses_timestep

logical. Is the species tracked by timestep within a year (or just by year)?

P

numeric. Age plus-group; a scalar.

am

numeric. Age at maturity; a scalar.

maturev

numeric. Proportion mature at age; a vector.

Ninit

numeric. Numbers at age in year 1 (or timestep 1 of year 1); a vector.

Nmat

matrix. Population matrix, age x time (years, or timesteps x years).

wv

numeric. Weight at age; a vector.

Mv

numeric. Natural mortality rate (log scale) by age; a vector.

fished

logical. Is the species fished?

fishing_rule

list. Parameters for the fishing rule model; a list.

Sv

numeric. Fishing selectivity at age; a vector.

Fv

numeric. Fishing mortality rate (log scale) by time; a vector.

F_baseline

numeric. Baseline fishing mortality rate; a scalar.

gv

numeric. Proportion of F that occurs per timestep; a vector.

Cy

numeric. Catch per year; a vector.

Ct

numeric. Catch per timestep; a vector.

Zmat

matrix. Total mortality rate (log scale) by time: a vector.

R_baseyear

numeric. Recruitment in a year 1, if supplied; a scalar.

R

numeric. Recruitment by year; a vector.

lnSR_err

numeric. Stock-recruitment errors (ln scale) by time; a vector.

recruitment

list. Parameters used in recruitment model (may vary by species).

R_error

list. Parameters that control stochastic recruitment error.


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