LeMans_param-class {LeMaRns}

An S4 class representing the inputs of the LeMans model

Description

An S4 class representing the inputs of the LeMans model

Details

Sets the class of a LeMansParam object, which is then used to run the LeMans model.

Slots

nsc

A numeric value representing the number of length classes in the model.

nfish

A numeric value representing the number of fish species in the model.

phi_min

A numeric value representing the time step of the model.

l_bound

A numeric vector of length nsc representing the lower bounds of the length classes.

u_bound

A numeric vector of length nsc representing the upper bounds of the length classes.

mid

A numeric vector of length nfish representing the mid-point of the length classes.

species_names

A numeric or character vector of length nfish that denotes the names of the species in the model.

Linf

A numeric vector of length nfish representing the mid-point of the length classes.

W_a

A numeric vector representing the parameter a in the length-weight conversion.

W_b

A numeric vector representing the parameter b in the length-weight conversion.

k

k A numeric vector of length nfish representing the von Bertalanffy growth parameter (1/yr) for each species.

Lmat

A numeric vector of length nsc representing the length at which 50% of the individuals are mature.

mature

A matrix with dimensions nsc and nfish with elements in the range 0-1 representing the proportion of mature individuals of each species in each length class.

sc_Linf

A numeric vector of length nsc representing the length class at which each species reaches its asymptotic length.

wgt

A matrix with dimensions nsc and nfish representing the weight of each species in each length class.

phi

A matrix with dimensions nsc and nfish representing the proportion of individuals that leave each length class.

ration

A matrix with dimensions nsc and nfish representing the amount of food required for fish of a given species and length class to grow according to the von Bertalanffy growth curve in a time step.

other

A numeric value representing the amount of other food (g) available from prey that is not explicitly represented in the model.

M1

A matrix of dimensions nsc and nfish representing the natural mortality of each species for each length class.

suit_M2

A list object of length nfish. Each element in the list is an array of dimensions nsc, nsc and nfish containing a value between 0 and 1 representing prey preference and prey suitability for each species and length class.

Qs

An array of dimensions nsc, nfish and length(gear) representing the catchability of each species by each of the fishing gears.

stored_rec_funs

A list object of length rec_fun where each element includes the stock recruitment function for a given species. If an invalid recruitment function is selected, NULL is returned and a warning message is shown.

eps

A numeric value specifying a numerical offset. The default value is 1e-5.

recruit_params

A list object of length nfish specifying the parameters for the recruitment function.