empirical_selectivity: Empirical selectivity diagnostic

In roliveros-ramos/empirical.selectivity: Empirical selectivity fitting and diagnostics

Empirical selectivity diagnostic

Description

Function to compute the empirical selectivity diagnostic for SS outputs and methods to extract them for a particular fleet and time.

Usage

empirical_selectivity(object, ...)

## Default S3 method:
empirical_selectivity(object, thr = 1e-05, ...)

## S3 method for class 'SS_empirical_selectivity'
empirical_selectivity(object, fleet = NULL, sex = 1, by = "length", ...)

## S3 method for class 'SS_output'
empirical_selectivity(object, fleet = NULL, sex = 1, by = "length", ...)

## S3 method for class 'matrix'
empirical_selectivity(
  object,
  fleet = NULL,
  sex = 1,
  by = "length",
  years = NULL,
  bins = NULL,
  weights = NULL,
  model = NULL,
  ...
)

Arguments

object	Typically, the result of reading Stock Synthesis model outputs with SS_output.
...	Additional arguments for specific methods, see Details.
fleet	Integer, fleet number to compute the empirical selectivity.
sex	If the fleet targets a specific sex, defaults to 1.
by	Either 'length' or 'age', defaults to 'length'.

Details

This function is called on run time by SS_output, so the empirical selectivities are already computed (for length and age) in your 'rep' object. An additional call to the function can be used to extract the empirical selectivities for a particular fleet or sex.

Methods (by class)

• empirical_selectivity(default): General constructor

• empirical_selectivity(SS_empirical_selectivity): Extract from empirical_selectivity objects

• empirical_selectivity(SS_output): Extracts from SS_output object

• empirical_selectivity(matrix): Transform a matrix in a empirical_selectivity object.

Examples

## Not run: 

rep = BigEye_2020
es = empirical_selectivity(rep, fleet=2, by="length")

## End(Not run)

roliveros-ramos/empirical.selectivity documentation built on Feb. 26, 2023, 4:58 a.m.