MLZ_data-class: MLZ_data

In quang-huynh/MLZ: Mean Length-Based Estimators of Mortality using TMB

MLZ_data

Description

An S4 class for storing data and life history parameters for a single stock. Method functions summary and plot are available for this class (see examples).

Slots

Stock

Name of stock.

Year

A vector of years to be considered in the model. Missing years are permitted.

Len_bins

A vector of midpoints of length bins for Len_matrix.

Len_matrix

A matrix of size data. The i-th row corresponds to the i-th year in MLZ_data@Year. The j-th column indexes the j-th length in MLZ_data@Len_bins.

Len_df

A data frame containing individual length observations. The first column should be the Year and the second column should be the length.

vbLinf

L-infinity from the von Bertalanffy growth function.

vbK

Parameter K from the von Bertalanffy growth function.

vbt0

Parameter t0 from the von Bertalanffy growth function.

Lc

Length of full selectivity.

M

Natural mortality rate. If specified, this is also the lower limit for Z.

lwb

Exponent b from the allometric length-weight function W = aL^b.

MeanLength

Vector of mean lengths of animals larger than Lc. The i-th entry corresponds to the i-th year in MLZ_data@Year.

ss

Vector of annual sample sizes for MeanLength. The i-th entry corresponds to the i-th year in MLZ_data@Year.

CPUE

Vector of catch-per-unit-effort data. The i-th entry corresponds to the i-th year in MLZ_data@Year.

Effort

Vector of effort data. The i-th entry corresponds to the i-th year in MLZ_data@Year.

length.units

Unit of measurement for lengths, i.e. "cm" or "mm".

Examples

data(Goosefish); Goosefish
summary(Goosefish)
plot(Goosefish)

new("MLZ_data")

quang-huynh/MLZ documentation built on Oct. 1, 2024, 4:50 a.m.